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A fermentation in which microorganisms convert sugars to acetoin and 2,3-butanediol neutral end products through the butanediol pathway.

An autotrophic carbon-fixation pathway in which two molecules of bicarbonate are fixed via 3-hydroxypropionate and converted to glyoxylate and pyruvate. It is characteristic of the filamentous anoxygenic phototroph Chloroflexus aurantiacus.

An autotrophic carbon-fixation pathway that fixes two molecules of bicarbonate per turn via 3-hydroxypropionate and 4-hydroxybutyrate intermediates. It operates in aerobic and microaerophilic Crenarchaeota such as Sulfolobus and Metallosphaera.

A phage defense system in which an organism possesses a 6A-MBL locus that can protect bacteria from bacteriophage infection.

An abortive infection system in which an organism possesses a single-component Abi-like locus represented by the DefenseFinder Abi2 model namespace and mandatory Abi2__Abi_2/PF07751 profile.

An abortive infection system in which an organism possesses an AbiA-family locus whose copy number or expression modulates Lactococcus lactis resistance to multiple phages and that DefenseFinder represents with AbiA_large or AbiA_small model subrules.

An abortive infection system in which an organism possesses an abi-alpha-family locus represented by the DefenseFinder AbiAlpha__AbiAlpha profile and exemplified by the Enterococcus faecalis V583 prophage 6 abi-alpha determinant, whose encoded DUF4393/PF14337-family activity perturbs the Idefix lytic cycle and causes premature lysis of infected Enterococcus faecalis.

An abortive infection system in which an organism possesses an abiB-family locus represented by the DefenseFinder AbiB__AbiB profile and exemplified by the Lactococcus lactis IL1403 determinant whose AbiB activity blocks sensitive bIL170 phage growth and promotes rapid degradation of sensitive phage transcripts after infection.

An abortive infection system in which an organism possesses an abiC-family locus represented by the DefenseFinder AbiC__AbiC profile and exemplified by the Lactococcus lactis subsp. lactis ME2 pTN20 determinant whose abiC structural gene confers Prf abortive resistance to small isometric-headed phage p2, reducing plaquing, plaque size, and burst size while killing most infected Prf-positive cells.

An abortive infection system in which an organism possesses an abiD-family locus represented by the DefenseFinder AbiD__AbiD profile and exemplified by the Lactococcus lactis subsp. lactis KR5 pBF61 determinant whose abiD open reading frame confers an abortive phage infection phenotype with reduced plating efficiency, plaque size, and c2 phage burst size.

An abortive infection system in which an organism possesses an abiE bicistronic locus whose AbiEii DUF1814-family bacteriostatic toxin and AbiEi COG5340-family antitoxin constitute a non-interacting type IV toxin-antitoxin module that supports phage resistance.

An abortive infection system in which an organism possesses a pNP40-derived abiF locus whose single complete open reading frame encodes a phage-insensitivity determinant that inhibits bacteriophage phi 712 DNA replication.

An abortive infection system in which an organism possesses a two-gene abiG locus with abiGi and abiGii open reading frames, exemplified by the Lactococcus lactis subsp. cremoris UC653 plasmid pCI750 locus that restricts lactococcal phages without blocking phage DNA replication and is represented by the DefenseFinder AbiG__AbiGi and AbiG__AbiGii profiles.

An abortive infection system in which an organism possesses an abiH-family locus represented by the DefenseFinder AbiH__AbiH profile and exemplified by the Lactococcus lactis S94 abiH gene that encodes lactococcal phage abortive-infection resistance.

An abortive infection system in which an organism possesses an abiI-family locus represented by the DefenseFinder AbiI__AbiI profile and exemplified by the Lactococcus lactis M138 pND852 locus whose single abiI open reading frame restricts lactococcal phage propagation by an abortive-infection mechanism.

An abortive infection system in which an organism possesses an AbiJ-family locus represented by the DefenseFinder AbiJ model namespace and mandatory AbiJ__AbiJ profile.

An abortive infection system in which an organism possesses an abiK locus encoding a reverse-transcriptase-related polymerase that uses conserved RT motifs for phage resistance and restricts 936/P335 lactococcal phage propagation.

An abortive infection system in which an organism possesses a two-component AbiL-family locus represented by DefenseFinder as mandatory AbiL__AbiLi and AbiL__AbiLii profiles.

An abortive infection system in which an organism possesses a single-component AbiN-family locus represented by DefenseFinder as a mandatory AbiN__AbiN profile.

An abortive infection system in which an organism possesses a single-component AbiO-family locus represented by DefenseFinder as a mandatory AbiO__AbiO profile.

An abortive infection system in which an organism possesses a single-component AbiP2-family reverse-transcriptase-like locus represented by DefenseFinder as a mandatory AbiP2__AbiP2 profile.

An abortive infection system in which an organism possesses an AbiQ type III toxin-antitoxin locus whose protein endoribonuclease and cognate RNA antitoxin module alter early phage mRNA profiles and restrict phage propagation after adsorption.

An abortive infection system in which an organism possesses a multicomponent AbiR determinant represented by the DefenseFinder AbiR__AbiRa, AbiR__AbiRb, and AbiR__AbiRc profiles and capable of restricting lactococcal phage propagation by an early abortive-infection mechanism that impedes phage DNA replication, as exemplified by the two pKR223 loci from Lactococcus lactis subsp. lactis KR2 separated by the LlaKR2I restriction-modification genes.

An abortive infection system in which an organism possesses the two-gene pED1 abiT locus whose constitutively cotranscribed abiTi and abiTii genes encode an AbiTi-AbiTii phage-resistance module that acts late in the 936/P335 lactococcal phage lytic cycle.

An abortive infection system in which an organism possesses an abiU-family locus represented by the DefenseFinder AbiU__AbiU profile and exemplified by the Lactococcus lactis LL51-1 AbiU determinant, whose abiU1 open reading frame is responsible for phage resistance, whose abiU2 region may downregulate 936/P335 resistance, and whose activity reduces c2, 936, and P335 lactococcal phage plaquing while delaying transcription of phages 712 and c2.

An abortive infection system in which an organism possesses an abiV locus whose encoded AbiV protein can restrict 936-like or c2-like lactococcal phages by interacting with phage-encoded SaV and inhibiting phage protein translation.

An abortive infection system in which an organism possesses an abiZ locus encoding a membrane-associated lactococcal phage-resistance determinant that accelerates infected-cell lysis through AbiZ-enhanced holin/lysin activity and restricts P335 phage propagation.

A genomics trait describing possession of a bacteriophage abortive-infection defense system in which phage infection activates a host-encoded growth-arrest or cell-death program that prevents completion of phage replication and protects nearby bacterial cells.

An OBJECT_PROPERTY relating an organism to a chemical entity that the organism intracellularly accumulates above environmental concentration.

A methanogenesis in which acetate is split into methane and carbon dioxide.

A metabolism that produces acetate as the primary end product through the reduction of carbon dioxide or other carbon compounds using the Wood-Ljungdahl pathway, typically performed by acetogenic bacteria under anaerobic conditions.

A fermentation in which solventogenic bacteria convert organic carbon sources to organic acids and then reassimilate those acids to produce acetone, butanol, and ethanol solvents.

A physiological enzyme-activity phenotype in which a cell produces active acid phosphatase enzymes that dephosphorylate phosphate-containing compounds under acidic conditions.

A pH growth preference in which an organism grows optimally at pH values below 5.

A pH growth preference characterized by the ability to tolerate acidic environments (typically pH below 5.5) while maintaining optimal growth near neutral pH.

A phage defense system in which an organism possesses a two-component Aditi locus represented by DitA and DitB profiles that can protect bacteria from bacteriophage infection.

An oxygen preference in which growth occurs in the presence of molecular oxygen (O₂), typically using O₂ as the terminal electron acceptor.

A photoheterotrophy in which aerobic heterotrophic bacteria use bacteriochlorophyll-containing reaction centers to harvest light as auxiliary energy while requiring organic carbon substrates for growth.

A respiration in which molecular oxygen serves as the terminal electron acceptor in the electron transport chain, generating ATP through oxidative phosphorylation with water as the final product.

A motile phenotype in which active locomotion is directionally biased along an oxygen concentration gradient toward preferred oxygen conditions.

An oxygen preference that does not use O₂ for growth but tolerates its presence.

A phenotype in which polarized growth is directionally biased in response to a spatial oxygen concentration gradient.

An autophagy phenotype in which a microbial cell selectively degrades protein aggregates through macroautophagic delivery to lysosomal or vacuolar compartments.

A morphology trait in which a filamentous cyanobacterium differentiates enlarged, thick-coated, spore-like dormant cells called akinetes that can germinate into vegetative cells.

A physiological enzyme-activity phenotype in which a cell exhibits alanine arylamidase/alanyl aminopeptidase activity, releasing N-terminal residues from peptide, amide, or arylamide substrates with preference for alanine.

A physiological enzyme-activity phenotype in which a cell produces active alkaline phosphatase enzymes that dephosphorylate phosphate-containing compounds.

A pH growth preference in which an organism grows optimally at pH values above 9.

A pH growth preference in which an organism can tolerate alkaline pH but grows optimally at neutral pH.

A physiological enzyme-activity phenotype in which a cell exhibits chymotrypsin-like serine endopeptidase activity, preferentially cleaving peptide bonds on the carboxyl side of tyrosine, tryptophan, phenylalanine, or leucine residues.

A physiological enzyme-activity phenotype in which a cell produces active alpha-fucosidase enzymes that hydrolyze alpha-L-fucosides to L-fucose and an alcohol.

A physiological enzyme-activity phenotype in which a cell produces active alpha-galactosidase enzymes that hydrolyze alpha-1,6-linked galactose residues in oligosaccharides and polymeric galactomannans.

A physiological enzyme-activity phenotype in which a cell produces active alpha-glucosidase enzymes that hydrolyze alpha-glucosidic bonds in alpha-D-glucosides.

A physiological enzyme-activity phenotype in which a cell produces active alpha-mannosidase enzymes that hydrolyze terminal, non-reducing alpha-D-mannose residues in alpha-D-mannosides.

A phage defense system in which an organism possesses a five-gene Ambrosia locus encoding AbrR, AbrA, AbrB, AbrC, and AbrD components that can limit siphophage and myophage propagation.

A flagellar arrangement with flagella (single filaments or tufts) at both poles of the cell.

A physiological enzyme-activity phenotype in which a cell produces active amylolytic enzymes that hydrolyze starch.

An oxygen preference in which growth occurs in the absence of molecular oxygen (O₂).

An anaerobic nitrogen metabolism in which ammonium is oxidized with nitrite as the electron acceptor to form dinitrogen.

A metabolism in which methane is oxidized under anoxic conditions, classically coupled to sulfate reduction and mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria. It is a major sink for methane in marine sediments.

A respiration in which an organism uses electron acceptors other than oxygen for energy production.

A pathogen that infects organisms in the kingdom Metazoa.

A sexual-reproduction phenotype in which the fusing gametes belong to two types that differ in size, with smaller male and larger female gametes.

A phototrophic metabolism that uses light energy with a single photosystem and bacteriochlorophyll, using electron donors other than water (e.g. H2S, H2, Fe(II), organics) and therefore not evolving oxygen. Characteristic of purple and green sulfur bacteria, Chloroflexi, and heliobacteria.

A physiological capacity to grow in the presence of antibiotic concentrations that inhibit susceptible cells, mediated by efflux, target modification, drug inactivation, or reduced permeability.

A phage defense system in which an organism possesses a single-component ApeA locus represented by the DefenseFinder Gao_Ape__ApeA profile, encoding an oligomeric HEPN-domain antiviral ribonuclease whose activation can cleave RNA substrates to restrict bacteriophage infection.

A genomics trait describing possession of an ApsAB anti-plasmid defense locus encoding the nuclease/helicase ApsA and Argonaute-like ApsB proteins that can destabilize high- and low-copy-number plasmids.

A physiological enzyme-activity phenotype in which a cell exhibits arginine arylamidase/arginyl aminopeptidase activity, releasing N-terminal arginine or lysine residues from peptides or hydrolyzing arginine and lysine arylamides.

A physiological pathway-activity phenotype in which a cell converts L-arginine through the arginine deiminase pathway to generate ATP.

A phage defense system in which an organism possesses an Aristaios locus that can restrict bacteriophage infection.

A phage defense system in which an organism possesses an ARMADA YprA-like-helicase locus whose Type I and Type II operons share BrxHII-like and PglX-like components with DISARM Class I systems and whose experimentally tested Type II forms protect against a broad range of phages.

A metabolism in which an organism catabolizes an aromatic compound, whether or not that compound is a hydrocarbon.

A hydrocarbon degradation in which the substrate carries at least one aromatic ring.

An anaerobic respiration in which an organism uses arsenate as the terminal electron acceptor and reduces it to arsenite for energy conservation.

A metalloid tolerance in which an organism grows in the presence of elevated arsenic (arsenite/arsenate) concentrations, typically via the ars operon, whose ArsB pump extrudes arsenite from the cytoplasm.

A metabolism in which an organism enzymatically oxidizes arsenite to arsenate as an energy-generating electron donor or detoxification substrate.

An OBJECT_PROPERTY relating an organism to a chemical entity that the organism takes up and incorporates into cellular biomass.

A phage defense system in which an organism possesses an Audmula locus that can restrict bacteriophage infection.

A sexual-reproduction phenotype in which two meiotically derived gametic nuclei formed within one unpaired, undivided cell fuse with each other, without fusion of separate gametes.

A reproductive phenotype in which the reduction of reproductive nuclear ploidy is prevented or compensated and progeny derive their reproductive nuclei solely from products of one meiotically dividing cell or their descendants.

An autophagy phenotype in which a microbial cell degrades intracellular glycogen by delivering it to lysosomal or vacuolar compartments.

A physiological phenotype in which a microbial cell degrades intracellular material, including its own constituents or intracellular non-self cargo, by delivering that material to lysosomal or vacuolar compartments.

A trophic type in which an organism produces organic compounds from inorganic carbon sources (primarily carbon dioxide or bicarbonate) using energy from light (photoautotrophy) or from the oxidation of inorganic compounds (chemoautotrophy).

A phage defense system in which an organism possesses a locus encoding a STAND-superfamily antiviral ATPase/NTPase that functions as a modular Avs receptor-effector, recognizes conserved bacteriophage proteins, and activates subtype-specific antiphage outputs to inhibit bacteriophage replication.

An AVAST system in which an organism possesses a genome-encoded subtype I locus represented by DefenseFinder with Avs1A, Avs1B, and Avs1C profiles.

An AVAST system in which an organism possesses a genome-encoded subtype II locus represented by DefenseFinder with an Avs2A profile.

An AVAST system in which an organism possesses a genome-encoded subtype III locus represented by DefenseFinder with Avs3A and Avs3B profiles.

An AVAST system in which an organism possesses a genome-encoded subtype IV locus represented by DefenseFinder with an Avs4A profile.

An AVAST system in which an organism possesses a genome-encoded subtype V locus represented by DefenseFinder with an Avs5A profile.

A motility where the flagellum filament of an organism is located in the periplasm and does not extend past the cell envelope.

A phage defense system in which an organism possesses an Azaca locus represented by ZacA, ZacB, and ZacC profiles that can protect bacteria from bacteriophage infection.

A cell shape characterized by an elongated, rod cylindrical morphology with relatively parallel sides and rounded ends.

A predatory bacterial phenotype in which cells kill susceptible conspecific cells and obtain nutrients from the killed cells.

A physiological trait in which bacteria produce bacteriocins, ribosomally synthesized antimicrobial peptides or proteins that kill or inhibit other bacteria.

A phage defense system in which an organism possesses a Belenos locus represented by a VCA0457 profile that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a Belisama locus represented by a VCA0458 profile that can protect bacteria from bacteriophage infection.

A physiological enzyme-activity phenotype in which a cell produces active beta-galactosidase enzymes that hydrolyze lactose into glucose and galactose.

A physiological enzyme-activity phenotype in which a cell produces active beta-glucosidase enzymes that hydrolyze beta-D-glucosidic bonds in beta-D-glucosides.

A physiological enzyme-activity phenotype in which a cell produces active beta-glucuronidase enzymes that hydrolyze beta-D-glucuronosides to D-glucuronate and an alcohol.

A physiological enzyme-activity phenotype in which a cell produces active beta-N-acetylhexosaminidase enzymes that hydrolyze terminal, non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.

A phage defense system in which an organism possesses a Bil bacterial ubiquitin-like conjugation locus that can covalently attach a ubiquitin-like protein to the bacteriophage central tail fibre and impair phage infectivity.

An ecological lifestyle in which cells form surface-attached, matrix-enclosed multicellular communities (biofilms) held together by extracellular polymeric substances — a widespread mode of microbial life.

A execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.

A physiological capability to emit visible light through a luciferase-catalyzed reaction, frequently regulated by quorum sensing in marine bacteria such as Aliivibrio and Photobacterium.

A metabolism in which an organism secretes enzymes to depolymerize recalcitrant biopolymers (such as cellulose, hemicellulose, chitin, and lignin) into assimilable units for growth.

A quality that categorizes biological agents according to their hazard level and required containment measures.

A biosafety level that poses minimal potential hazard to laboratory workers and the environment, requiring only standard microbiological practices.

A biosafety level that poses moderate risk and is associated with human diseases present in the community.

A biosafety level that can cause serious or potentially lethal disease through inhalation or other routes, requiring specialized containment facilities with controlled access, directional airflow, and strict safety protocols.

A biosafety level that poses extreme risk of life-threatening disease through aerosol transmission with no available treatment.

A biosafety level that is proposed as a classification beyond BSL-4 for hypothetical biological agents requiring enhanced containment.

A fungal mating phenotype in which compatibility between partners is governed by a single segregating mating-type factor.

A pigmentation phenotype in which microbial colonies or cells appear black or very dark due to accumulation of dark pigments such as melanins.

A phage defense system in which an organism possesses a Borvo locus represented by BovA profiles that can protect bacteria from bacteriophage infection.

A cell shape in which an organism forms lateral branches from filamentous or hyphal cells.

A phage defense system in which an organism possesses a gcu113/Brc113 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a gcu142/Brc142 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a gcu167/Brc167 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a gcu217/Brc217 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a gcu22/Brc22 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a gcu23/Brc23 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a gcu233/Brc233 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a gcu24/Brc24 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a Brc59 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a gcu76/Brc76 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A phage defense system in which an organism possesses a gcuWGS21/BrcWGS21 bacteriophage-resistance integron cassette that supports growth during bacteriophage challenge.

A genomics trait describing possession of a bacteriophage exclusion defense system that uses host DNA methylation to discriminate self from non-self and inhibit phage DNA replication.

A phage defense system in which an organism possesses a brig1-family locus whose encoded DNA glycosylase can excise alpha-glucosyl-hydroxymethylcytosine nucleobases from T-even bacteriophage DNA, generate abasic sites, and inhibit viral DNA replication.

A phage defense system in which an organism possesses a Brigantia locus represented by a VCA0419 profile that can protect bacteria from bacteriophage infection.

A pigmentation phenotype in which microbial colonies or cells appear brown due to accumulation of brown pigments such as pyomelanin or other melanins.

An abortive infection system in which an organism possesses a BstA-family phage-defense locus whose encoded BstA protein can suppress lytic phage DNA replication and whose cognate anti-BstA aba element can self-immunize the encoding prophage from BstA activity.

An OBJECT_PROPERTY relating an organism to a chemical substrate from which the organism produces an acidic metabolite, lowering medium pH.

An OBJECT_PROPERTY relating an organism to a chemical substrate from which the organism produces an alkaline metabolite, raising medium pH.

An OBJECT_PROPERTY relating an organism to a chemical substrate from which the organism produces a gaseous metabolite (e.g. CO2, H2, N2, H2S, CH4).

A phage defense system in which an organism possesses a two-component Bunzi locus represented by BnzA and BnzB profiles that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a Butters gp30-gp31 locus that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a Butters gp57r locus that can protect bacteria from bacteriophage infection.

A fermentation in which anaerobic bacteria convert organic substrates to butyrate as a major reduced end product while conserving energy by substrate-level phosphorylation or ion-gradient generation.

A metabolism in which electrons are transferred over centimeter-scale distances through multicellular filaments.

A metal tolerance in which an organism grows in the presence of elevated cadmium (Cd2+) concentrations, typically via cation-efflux resistance systems such as the czc determinant.

An autotrophic carbon-fixation pathway (the reductive pentose phosphate cycle) that fixes CO2 using ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). It is the most widespread CO2-fixation pathway, used by plants, algae, cyanobacteria, and many proteobacteria.

A general OBJECT_PROPERTY relating an organism to a biological process or metabolic capability the organism is capable of. Intended use is predicate + class composition at assertion time, with a METPO biological-process (or GO biological-process) class as the object.

A phenotype describing an organism that requires elevated concentrations of carbon dioxide for growth.

A phage defense system in which an organism possesses a fused CapRel toxin-antitoxin locus encoding an N-terminal toxSAS toxin domain and a C-terminal antitoxin sensor domain that together can restrict bacteriophage propagation.

A morphology trait in which the cell is surrounded by a well-organized layer of polysaccharide (or rarely polypeptide) external to the cell envelope, mediating adhesion, desiccation resistance, and immune evasion.

A metabolic process in which an organism assimilates inorganic carbon (CO2 or bicarbonate) into organic compounds (autotrophy). Six distinct natural autotrophic carbon-fixation pathways are currently recognized.

A trophic type in which an organism derives energy from the oxidation of carbon monoxide.

A physiological enzyme-activity phenotype in which a cell produces active carboxylesterase enzymes that hydrolyze carboxylic esters to alcohols and carboxylates.

A bacterial microcompartment — a polyhedral protein-shelled organelle that encapsulates RuBisCO and carbonic anhydrase to concentrate CO2 for carbon fixation in cyanobacteria and many chemoautotrophs.

A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_Endonuclease subtype locus represented by the CARD_NLR__Endonuclease mandatory rule profile.

A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_GasderMIN subtype locus represented by the CARD_NLR_GasderMIN rule row requiring the GasderMIN__bGSDM profile.

A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_Phospho subtype locus represented by the CARD_NLR__Trypsin_Phospho mandatory rule profile.

A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_Subtilase subtype locus represented by the CARD_NLR_Subtilase rule row requiring the CARD_NLR__Subtilase_long_new profile.

A phage defense system in which an organism possesses a CARD-NLR locus represented by the DefenseFinder CARD_NLR model namespace, coupling bacterial CARD-like detector components and NLR-like profiles to subtype-specific GasderMIN, endonuclease, Trypsin_Phospho, or Subtilase effector profiles that can promote cell death after phage recognition.

A CARD-NLR system in which an organism possesses a genome-encoded DefenseFinder CARD_NLR_like subtype locus represented by the CARD_NLR_like rule row requiring two matches from the CARD_NLR__Endonuclease, CARD_NLR__Phospho_Trypsin, CARD_NLR__Subtilase_long_new, and CARD_NLR__Trypsin_Phospho effector-profile set and four genes overall after considering CARD_NLR__CARD_Protease, CARD_NLR__NLR_new, and CARD_NLR__Trypsin accessory profiles.

A pigmentation phenotype caused by microbial production and accumulation of carotenoid pigments.

A physiological enzyme-activity phenotype in which a cell produces active caseinase proteases that hydrolyze casein.

A physiological enzyme-activity phenotype in which a cell produces catalase, which decomposes hydrogen peroxide into water and oxygen; it is the basis of the diagnostic catalase test.

Test-outcome phenotype where the catalase test yields a negative result (no bubbling on H2O2). The underlying enzyme-organism relation should additionally be asserted via <organism> METPO:2000303 'does not show activity of' GO:0004096 'catalase activity'.

A biochemical test that detects catalase enzyme activity by exposing cells to hydrogen peroxide and observing for visible bubbling. The test outcome (positive or negative) is captured by its child classes; this class itself does not assert that the organism has catalase activity.

A genomics trait describing possession of a cyclic-oligonucleotide-based antiphage signaling locus in which an oligonucleotide cyclase produces cyclic oligonucleotide signals during phage infection that activate an effector to inhibit bacteriophage replication.

A phenotype that inheres in a cell by virtue of its longer dimension when viewed on a plane.

A cell-length phenotype in which the longer cell dimension exceeds approximately 3 micrometers.

A cell-length phenotype in which the longer cell dimension lies approximately between 2 and 3 micrometers.

A cell-length phenotype in which the longer cell dimension lies approximately between 1.3 and 2 micrometers.

A cell-length phenotype in which the longer cell dimension is at most approximately 1.3 micrometers.

A phenotype that describes the characteristic three-dimensional morphological form of a microbial cell, determined by cell wall structure, cytoskeletal elements, and environmental factors.

A phenotype that inheres in a cell by virtue of its shorter dimension when viewed on a plane.

A cell-width phenotype in which the shorter cell dimension exceeds approximately 0.9 micrometers.

A cell-width phenotype in which the shorter cell dimension lies approximately between 0.65 and 0.9 micrometers.

A cell-width phenotype in which the shorter cell dimension lies approximately between 0.5 and 0.65 micrometers.

A cell-width phenotype in which the shorter cell dimension is at most approximately 0.5 micrometers.

A physiology trait in which intracellular gas vesicles reduce a microbial cell's effective density enough to provide buoyancy and vertical positioning in the water column.

A biopolymer-degradation metabolism in which an organism hydrolyzes cellulose to cellodextrins and glucose using cellulase systems, sometimes organized into cellulosomes.

A phage defense system in which an organism possesses a Ceres locus that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a Cernunnos locus represented by a VCA0410 profile that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a Charlie gp32 locus that can protect bacteria from bacteriophage infection.

A material entity that is a physical entity of interest in chemistry, including molecular entities, parts thereof, and chemical substances. Used as the range class for the majority of METPO chemical-use OBJECT_PROPERTYs (uses_as_carbon_source, uses_as_electron_donor, ferments, oxidizes, etc.) so that organism-to-chemical assertions resolve to a curated chemical class.

A trophic type in which an organism uses chemical oxidation of inorganic compounds as the energy source and carbon dioxide as the primary carbon source for biosynthesis.

A trophic type in which an organism obtains energy from oxidation of inorganic compounds and carbon from carbon dioxide.

A trophic type in which an organism obtains both energy and carbon from organic compounds.

A motile phenotype in which swimming speed changes in response to chemical concentration, without requiring directional bias along a chemical gradient.

A trophic type in which an organism obtains energy from oxidation of inorganic compounds (lithotrophy) and carbon from carbon dioxide.

A trophic type characterized by the use of inorganic chemical compounds as electron donors for energy generation while utilizing organic compounds as the primary carbon source.

A trophic type characterized by the use of inorganic chemical compounds as electron donors and carbon dioxide as the primary carbon source for energy generation and biosynthesis.

A trophic type in which an organism obtains both energy and carbon from organic compounds through oxidation.

A trophic type in which an organism obtains energy through chemical oxidation of organic compounds that also serve as the carbon source for biosynthesis.

A behavioral physiology in which cells bias their movement toward attractants or away from repellents by modulating flagellar motor switching in response to chemical gradients.

A trophic type in which an organism obtains energy from chemical oxidation of either inorganic or organic compounds.

A phenotype in which polarized growth is directionally biased in response to a spatial chemical gradient.

A biopolymer-degradation metabolism in which an organism hydrolyzes chitin to N-acetylglucosamine oligomers and monomers using secreted chitinases.

An anaerobic respiration in which an organism uses chlorate as the terminal electron acceptor and reduces it to chloride for energy conservation.

A colony shape that has a regular round outline.

A fermentation in which citrate is the primary fermentable substrate.

A phage defense system in which an organism possesses a Clover anti-phage system whose CloA deoxynucleoside triphosphohydrolase dynamically responds to an activating phage cue and to a CloB-produced inhibitory p3diT nucleotide signal to coordinate nucleotide-pool disruption during antiviral immunity.

An abortive infection system in which an organism possesses a cmdTAC toxin-antitoxin-chaperone locus whose CmdC chaperone senses viral capsid proteins and whose CmdA antitoxin degradation liberates the CmdT ADP-ribosyltransferase to modify messenger RNA, arrest translation, and inhibit bacteriophage replication.

A physiological enzyme-activity phenotype in which a cell produces coagulase factors that activate prothrombin and convert fibrinogen to fibrin, clotting blood plasma.

Test-outcome phenotype where the coagulase test yields a negative result. The underlying enzyme-organism relation should additionally be asserted via <organism> METPO:2000303 'does not show activity of' <coagulase enzyme term> once a sufficiently specific enzyme term is selected.

Test-outcome phenotype where the coagulase test yields a positive result (plasma clotting). The underlying enzyme-organism relation should additionally be asserted via <organism> METPO:2000302 'shows activity of' <coagulase enzyme term> once a sufficiently specific enzyme term is selected (no GO/EC term currently exists at the bacteriological coagulase test granularity).

A metal tolerance in which an organism grows in the presence of elevated cobalt (Co2+) concentrations, typically via cation-efflux resistance systems such as the czc and cnr determinants.

A cell shape intermediate between spherical cocci and elongated bacilli, typically appearing as short or plump rods.

A cell shape in which an organism has a spherical or nearly spherical morphology, with roughly equal dimensions in all directions.

A phage defense system in which an organism possesses a CoCoNuT locus from a coiled-coil nuclease tandem branch of McrBC Type IV restriction systems whose domain and genomic-context architecture predict RNA targeting and, in many CoCoNuTs, DNA targeting via McrC nuclease homologs.

A genome-sequence property describing non-uniform usage of synonymous codons across a genome, shaped by mutational bias and translational selection and correlated with gene expression level.

A stress response in which a rapid temperature downshift induces nucleic-acid-binding cold-shock proteins and RNA-remodeling functions that preserve gene expression at low temperature.

A phenotype characterized by macroscopic colony characteristics such as shape, margin, elevation, surface, colour, and size.

A colony morphology characterized by the overall macroscopic colony outline as observed on solid medium.

A symbiosis in which the microorganism benefits from the association (e.g. resources, shelter, transport) while the host's fitness remains essentially unaffected.

An OBJECT_PROPERTY relating an organism to a chemical that the organism sequesters into a specific subcellular compartment or specialised organelle.

A nitrification metabolism in which a single organism oxidizes ammonia via nitrite to nitrate.

A physiological phenotype in which microbial cells exchange outer-membrane lipids and proteins with other cells through direct intercellular contact.

A nutrient adaptation in which an organism thrives in environments with high nutrient concentrations, typically exhibiting rapid growth rates and utilizing diverse carbon sources.

A metal tolerance in which an organism grows in the presence of elevated copper (Cu2+/Cu+) concentrations, typically via the cue, cus, pco, and cop systems and ATPase-driven cytoplasmic copper efflux.

A pigmentation phenotype in which colony or cell coloration is a pale, off-white or cream hue, typically reflecting low-density carotenoid or other light-absorbing pigments.

A cell shape in which an organism has a curved crescent-like morphology with a concave inner side and a convex outer side.

A genomics trait describing possession of a CRISPR-Cas adaptive immune system that records fragments of invading nucleic acids in CRISPR arrays and uses Cas proteins to recognize and cleave matching sequences.

A phage defense system in which an organism possesses a Crouga antiviral locus that is encoded by P4-like phage satellites and can protect bacteria from bacteriophage infection.

A cell shape in which an organism has a bent or curved cell body rather than a straight rod or sphere.

A physiological enzyme-activity phenotype in which a cell produces active cystine arylamidase enzymes that hydrolyze cystine arylamide substrates.

A sexual-reproduction phenotype in which a paired cell self-fertilizes by fusion of its own gametic nuclei without exchanging gametic nuclei with its partner.

A phage defense system in which an organism possesses a Dag-family DNA-glycosylase system whose Dag1 or Dag2 effectors selectively target phages carrying modified guanine bases.

A phage defense system in which an organism possesses a Damona locus represented by a VCA0399 profile that can protect bacteria from bacteriophage infection.

A metabolism in which an organism oxidizes molecular hydrogen as an electron donor for energy conservation independently of light.

A sulfur oxidation in which an organism oxidizes a reduced inorganic sulfur compound as an electron donor for energy conservation independently of light.

A phage defense system in which activated DARNA cleaves a subset of host tRNAs and thereby inhibits phage propagation after activation by single-stranded DNA presented by phage SSB.

A phage defense system in which an organism possesses a DarTG toxin-antitoxin locus whose DarT toxin can be released during bacteriophage infection to ADP-ribosylate viral DNA, block phage genome replication, and prevent production of mature virions.

A phage defense system in which an organism possesses a two-component Dazbog locus encoding DzbA and DzbB components that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a dCTPdeaminase locus that converts dCTP into deoxy-uracil nucleotides during phage infection, depletes dCTP from the nucleotide pool, and halts phage replication by starving the phage of an essential DNA building block.

A genomics trait describing possession of a DdmDE anti-plasmid defense locus encoding the DNA-guided prokaryotic Argonaute DdmE and the helicase-nuclease DdmD, whose DNA recognition and handoff trigger processive plasmid destruction.

An OBJECT_PROPERTY relating an organism to a chemical substrate that the organism enzymatically breaks down.

A phenotype characterized by the difference between maximum and minimum values of a growth parameter.

An anaerobic respiratory metabolism in which nitrate is reduced stepwise to gaseous dinitrogen via nitrite, nitric oxide, and nitrous oxide, removing fixed nitrogen from the system as gas.

An environmental tolerance in which an organism survives extreme water loss and resumes growth after rehydration (anhydrobiosis), protecting cellular macromolecules during drying.

A phage defense system in which an organism possesses a Detocs locus represented in DefenseFinder by DtcA and DtcB profiles plus optional DtcC-family profiles, with an ATP nucleosidase output that can degrade ATP and dATP upon phage infection and halt phage propagation.

A phage defense system in which an organism possesses a dGTPase locus that degrades dGTP into phosphate-free deoxy-guanosine during phage infection, depletes dGTP from the nucleotide pool, and halts phage replication by starving the phage of an essential DNA building block.

An autotrophic carbon-fixation pathway that fixes one molecule of CO2 and one of bicarbonate per turn via a dicarboxylate stage and a 4-hydroxybutyrate stage. It operates in anaerobic and microaerophilic Crenarchaeota such as Ignicoccus and Thermoproteales.

An anaerobic respiration in which an organism uses dimethyl sulfoxide as the terminal electron acceptor for energy conservation.

A phage defense system in which an organism possesses a three-gene Dionysus locus encoding DinA, DinB, and DinC components that can block jumbo-phage infection.

A cell shape in which spherical cells remain attached in pairs following cell division, forming characteristic doublets.

A genomics trait describing possession of a Defense Island System Associated with Restriction-Modification locus that uses methyltransferase-associated self/non-self discrimination and DrmAB activation to inhibit bacteriophage DNA replication.

A DISARM system in which an organism possesses a genome-encoded DefenseFinder DISARM_1 subtype locus represented by DISARM_1__drmD, DISARM_1__drmMI, DISARM__drmA, DISARM__drmB, and DISARM__drmC rule profiles.

A DISARM system in which an organism possesses a genome-encoded DefenseFinder DISARM_2 subtype locus represented by DISARM_2__drmE, DISARM_2__drmMII, DISARM__drmA, DISARM__drmB, and DISARM__drmC rule profiles.

A cell shape in which an organism is flat and circular.

An OBJECT_PROPERTY relating an organism to a chemical substrate that the organism simultaneously oxidises and reduces (disproportionation), yielding both higher- and lower-oxidation-state products.

A metabolism in which a single substrate simultaneously undergoes both oxidation and reduction reactions, with part of the substrate serving as the electron donor and another part serving as the electron acceptor.

An anaerobic respiratory metabolism in which an organism conserves energy for growth by coupling the oxidation of organic matter or hydrogen to the reduction of Fe(III) as a terminal electron acceptor. Characteristic of Geobacter and Shewanella, often via extracellular electron transfer.

An anaerobic respiratory metabolism in which an organism conserves energy by reducing Mn(IV) oxides to soluble Mn(II) as a terminal electron acceptor while oxidizing organic matter or hydrogen.

An anaerobic respiratory metabolism in which an organism conserves energy for growth by coupling the oxidation of organic matter or hydrogen to the reduction of a metal (e.g. Fe(III), Mn(IV)) as a terminal electron acceptor.

An anaerobic respiratory metabolism in which nitrate is reduced via nitrite to ammonium (rather than to N2), conserving fixed nitrogen within the ecosystem. It is favored over denitrification under nitrate-limited, high-electron-donor conditions.

An anaerobic respiratory metabolism in which an organism uses sulfate as the terminal electron acceptor, reducing it to hydrogen sulfide while oxidizing organic matter or hydrogen for energy.

A phage defense system in which an organism possesses a Divona locus represented by a VCA0374 profile that can protect bacteria from bacteriophage infection.

A physiological enzyme-activity phenotype in which a cell produces active DNase enzymes that hydrolyze DNA.

A phosphorothioate defense system in which an organism possesses a Dnd restriction-modification locus that pairs a Dnd-family DNA phosphorothioation module with a DndFGH restriction module to nick invading DNA that lacks phosphorothioate modification.

A phosphorothioate defense system in which an organism possesses a DndCDEA-PbeABCD locus that pairs DndCDEA-mediated host-DNA phosphorothioation with PbeABCD-dependent targeting of non-phosphorothioated viral DNA to inhibit viral DNA replication.

A phage defense system in which an organism possesses a two-component Dodola locus represented by DolA and DolB profiles that can protect bacteria from bacteriophage infection.

An OBJECT_PROPERTY asserting that an organism does NOT intracellularly accumulate a given chemical entity above environmental concentration. Negation companion of the positive 'accumulates' predicate. The intended use is predicate + class composition at assertion time, e.g. `<organism> <this property> <CHEBI class>`.

An OBJECT_PROPERTY asserting that an organism does NOT take up and incorporate a given chemical entity into cellular biomass. Negation companion of the positive 'assimilates' predicate.

An OBJECT_PROPERTY asserting that an organism does NOT produce an acidic metabolite from a given chemical substrate (no medium acidification observed). Negation companion of 'builds acid from'.

An OBJECT_PROPERTY asserting that an organism does NOT produce an alkaline metabolite from a given chemical substrate (no medium alkalinisation observed). Negation companion of 'builds base from'.

An OBJECT_PROPERTY asserting that an organism does NOT produce a gaseous metabolite from a given chemical substrate. Negation companion of 'builds gas from'.

An OBJECT_PROPERTY asserting that an organism does NOT sequester a given chemical into a specific subcellular compartment. Negation companion of 'compartmentalizes'.

An OBJECT_PROPERTY asserting that an organism does NOT enzymatically break down a given chemical substrate. Negation companion of 'degrades'.

An OBJECT_PROPERTY asserting that an organism does NOT carry out a disproportionation reaction on a given chemical substrate. Negation companion of 'disproportionates'.

An OBJECT_PROPERTY asserting that an organism does NOT export a given chemical from the cytoplasm. Negation companion of 'exports'.

An OBJECT_PROPERTY asserting that an organism does NOT ferment a given chemical substrate. Negation companion of 'ferments'.

An OBJECT_PROPERTY asserting that an organism does NOT hydrolyse a given chemical substrate. Negation companion of 'hydrolyzes'.

An OBJECT_PROPERTY asserting that an organism does NOT import a given chemical from the extracellular environment. Negation companion of 'imports'.

An OBJECT_PROPERTY asserting that an organism does NOT oxidise a given chemical substrate. Negation companion of 'oxidizes'.

An OBJECT_PROPERTY asserting that an organism does NOT produce a given chemical as a metabolic product. Negation companion of 'produces'.

An OBJECT_PROPERTY asserting that an organism does NOT reduce a given chemical substrate. Negation companion of 'reduces'.

An OBJECT_PROPERTY asserting that an organism does NOT sequester or chelate a given chemical. Negation companion of 'sequesters'.

An OBJECT_PROPERTY asserting that an organism does NOT show the catalytic activity of a given enzyme (material entity) class. Negation companion of 'shows activity of'. Intended use is predicate + class composition at assertion time with a METPO enzyme class (METPO:1000527 or its subclass) as the object.

An OBJECT_PROPERTY asserting that an organism does NOT transport a given chemical across its membranes. Negation companion of 'transports'.

An OBJECT_PROPERTY asserting that an organism does *not* use a given chemical entity as a source of carbon for biosynthesis. The intended use is predicate + class composition at assertion time, e.g. `<organism> METPO:2000031 CHEBI:17234` ("organism does not use glucose as carbon source"). Negation companion to METPO:2000006.

An OBJECT_PROPERTY asserting that an organism does *not* use a given chemical entity as a terminal electron acceptor in respiration. The intended use is predicate + class composition at assertion time, e.g. `<organism> METPO:X CHEBI:17632` ("organism does not use nitrate as electron acceptor"). Negation companion to METPO:2000008.

An OBJECT_PROPERTY asserting that an organism does *not* use a given chemical entity as an electron donor. The intended use is predicate + class composition at assertion time, e.g. `<organism> METPO:X CHEBI:18276` ("organism does not use H2 as electron donor"). Negation companion to METPO:2000009.

An OBJECT_PROPERTY asserting that an organism does NOT use a given chemical as a source of energy for metabolism. Negation companion of 'uses as energy source'.

An OBJECT_PROPERTY asserting that an organism does NOT use a given chemical as a source of nitrogen for biosynthesis. Negation companion of 'uses as nitrogen source'.

An OBJECT_PROPERTY asserting that an organism does NOT use a given chemical as a source of sulfur for biosynthesis. Negation companion of 'uses as sulfur source'.

An OBJECT_PROPERTY asserting that an organism does NOT catabolise a given substrate under aerobic conditions. Negation companion of 'uses for aerobic catabolization'.

An OBJECT_PROPERTY asserting that an organism does NOT grow under aerobic conditions using a given chemical. Negation companion of 'uses for aerobic growth'.

An OBJECT_PROPERTY asserting that an organism does NOT catabolise a given substrate under anaerobic conditions. Negation companion of 'uses for anaerobic catabolization'.

An OBJECT_PROPERTY asserting that an organism does NOT grow under anaerobic conditions using a given chemical. Negation companion of 'uses for anaerobic growth'.

An OBJECT_PROPERTY asserting that an organism does NOT grow under anaerobic conditions without illumination using a given chemical. Negation companion of 'uses for anaerobic growth in the dark'.

An OBJECT_PROPERTY asserting that an organism does NOT grow under anaerobic conditions with illumination using a given chemical. Negation companion of 'uses for anaerobic growth with light'.

An OBJECT_PROPERTY asserting that an organism does NOT grow on a given chemical. Negation companion of 'uses for growth'.

An OBJECT_PROPERTY asserting that an organism does NOT use a given chemical in respiratory metabolism. Negation companion of 'uses for respiration'.

Catch-all negation OBJECT_PROPERTY asserting that an organism does NOT use a given chemical in any way not covered by the more specific predicates. Negation companion of 'uses in other way'.

A reversible physiological state of greatly reduced metabolic activity that allows a cell to survive unfavorable conditions and later resuscitate, generating a microbial seed bank.

A phage defense system in which an organism possesses a Dpd genomic island whose dpdA-K genes install 7-deazaguanine derivatives into DNA and are modeled by DefenseFinder as a multi-profile Dpd system.

A phage defense system in which an organism possesses a defense-associated reverse transcriptase locus whose RT-domain component or components can confer bacteriophage defense and are modeled by DefenseFinder as DRT subtypes.

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT_1 subtype locus represented by the mandatory DRT_1__drt1a and DRT_1__drt1b profiles.

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT_2 subtype locus represented by the DRT_2__drt2 profile.

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT_3 subtype locus represented by the mandatory DRT_3__drt3a and DRT_3__drt3b profiles.

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT_4 subtype locus represented by the DRT_4__drt4 profile.

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT_5 subtype locus represented by the DRT_5__drt5 profile.

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT6 subtype locus represented by the DRT6__DRT6 profile.

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT7 subtype locus represented by the DRT7__DRT7 or DRT7__DRT7_small profiles.

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT8 subtype locus represented by a mandatory DRT8__DRT8 profile, optionally accompanied by the DRT8__DRT8b accessory profile.

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT9 subtype locus represented by a mandatory DRT9__DRT9 profile.

A Druantia system in which an organism possesses a genome-encoded DefenseFinder Druantia_III subtype locus represented by the Druantia_III rule row requiring both the Druantia_III__DruH and Druantia__DruE_1 profiles.

A phage defense system in which an organism possesses a Druantia locus encoding a conserved DruE-family core and subtype-specific partner proteins.

A Druantia system in which an organism possesses a locus encoding DruE together with DruB, DruC and DruD, with or without DruA.

A Druantia system in which an organism possesses a locus encoding DruE together with DruM, DruF and DruG.

A Druantia system in which an organism possesses a locus encoding DruE and DruF together with DruL, without the type-II DruM and DruG components.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 1 locus cataloged as working transcriptional unit D390 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 10 locus cataloged as working transcriptional unit ZAPB and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 11 locus cataloged as working transcriptional unit IMPD and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 12 locus cataloged as working transcriptional unit PD3A and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses a genome-encoded DefensePredictor-discovered system 13 locus represented in the pinned DefenseFinder model inventory by DS-13A and DS-13B custom HMM profiles.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 14 locus cataloged as working transcriptional unit RMOR and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the three-gene DefensePredictor-discovered system 15 locus cataloged as working transcriptional unit AAA1 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 16 locus cataloged as working transcriptional unit PLIK and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 17 locus cataloged as working transcriptional unit NUCS and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 18 locus cataloged as working transcriptional unit 6602 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 19 locus cataloged as working transcriptional unit PDP4 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the three-gene DefensePredictor-discovered system 2 locus cataloged as working transcriptional unit DISA and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 20 locus cataloged as working transcriptional unit PDX1 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the three-gene DefensePredictor-discovered system 21 locus cataloged as working transcriptional unit TOXO and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 22 locus cataloged as working transcriptional unit MVB1 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 23 locus cataloged as working transcriptional unit E2DP and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 24 locus cataloged as working transcriptional unit RED2 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses a genome-encoded DefensePredictor-discovered system 25 locus represented in the pinned DefenseFinder model inventory by DS-25A and DS-25B custom HMM profiles.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 26 locus cataloged as working transcriptional unit NERD and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 27 locus cataloged as working transcriptional unit SMEK and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 28 locus cataloged as working transcriptional unit ANEX and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 29 locus cataloged as working transcriptional unit HEP3 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the one-gene DefensePredictor-discovered system 3 locus cataloged as working transcriptional unit PIN8 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the four-gene DefensePredictor-discovered system 30 locus cataloged as working transcriptional unit ABC3 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 31 locus cataloged as working transcriptional unit RED7 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 32 locus cataloged as working transcriptional unit NADR and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 33 locus cataloged as working transcriptional unit GNAT and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 34 locus cataloged as working transcriptional unit CITO and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 35 locus cataloged as working transcriptional unit RED5 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses a genome-encoded DefensePredictor-discovered system 36 locus represented in the pinned DefenseFinder model inventory by the DS-36 custom HMM profile.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 37 locus cataloged as working transcriptional unit SC24 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 38 locus cataloged as working transcriptional unit HEP2 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 39 locus cataloged as working transcriptional unit AAA5 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the five-gene DefensePredictor-discovered system 4 locus cataloged as working transcriptional unit NTTI and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 40 locus cataloged as working transcriptional unit D295 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 41 locus cataloged as working transcriptional unit AAA2 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the three-gene DefensePredictor-discovered system 42 locus cataloged as working transcriptional unit PRO1 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 43 locus cataloged as working transcriptional unit D668 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses a genome-encoded DefensePredictor-discovered system 44 locus represented in the pinned DefenseFinder model inventory by the DS-44 custom HMM profile.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 45 locus cataloged as working transcriptional unit 2971 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DS-46 locus cataloged as working transcriptional unit RMRT and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 5 locus cataloged as working transcriptional unit PN12 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 6 locus cataloged with working_id HIPA and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 7 locus cataloged with working_id SVIR and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 8 locus cataloged with working_id MNAC and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 9 locus cataloged with working_id MHAD and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

A phage defense system in which an organism possesses a defense-associated sirtuin locus whose SIR2-domain effector can deplete NAD+ during bacteriophage defense and is modeled by DefenseFinder as Dsr subtypes.

A phage defense system in which an organism possesses a genome-encoded, DUF262-associated prokaryotic Schlafen nuclease locus.

A cell shape in which an organism consists of two rounded cell bodies connected by a narrower central isthmus, often resulting from incomplete or snapping cell division.

A motile phenotype in which active migration is directionally biased in response to a spatial gradient in substrate stiffness.

A type IV modification-dependent restriction system in which an organism possesses an EcoKMcrA mcrA locus encoding a methylcytosine- and hydroxymethylcytosine-dependent restriction endonuclease whose nuclease active site is required for efficient restriction of DNA modified in the correct sequence context.

A metabolism in which electrons are transferred from an electron donor to an electron acceptor.

A phage defense system in which an organism possesses an Eleos locus represented by LeoA, LeoB, LeoBC, and LeoC profiles that can protect bacteria from bacteriophage infection.

A cell shape in which an organism has an oval or ellipse morphology, elongated along one axis with rounded ends, intermediate between spherical and rod-shaped.

A physiological phenotype in which a microbial cell takes up extracellular material or plasma-membrane components into intracellular membrane-bound compartments by remodeling and internalizing its plasma membrane.

A host-associated trait in which a microbe resides within living internal plant tissues without causing apparent disease in the host.

A symbiosis in which the microorganism lives inside the cells or tissues of its host. Obligate intracellular endosymbionts (e.g. of insects) frequently undergo extreme genome reduction.

A phage defense system in which an organism possesses an ENDPaCF1 Type IIS restriction endonuclease-like locus with an inactive Endonuclease III sensing domain that can recognize diverse DNA hypermodifications and protect bacteria from hypermodified phages.

A motile phenotype in which directional locomotion is regulated by sensing changes in the electron transport system associated with cellular energy generation.

A biological macromolecule (typically a protein, occasionally a catalytic RNA) that catalyses a specific biochemical reaction. This class is the material-entity sense of "enzyme" (the molecule itself), matching METPO:1000527's placement as a subclass of METPO:1000186 (material entity). Used as the range class for METPO enzyme-related OBJECT_PROPERTYs (shows_activity_of, enzyme_activity_analyzed, does_not_show_activity_of).

An OBJECT_PROPERTY relating an organism to an enzyme (material entity) whose catalytic activity has been experimentally assayed for that organism. Intended use is predicate + class composition at assertion time with a METPO enzyme class (METPO:1000527 or its subclass) as the object.

A phenotype characterized by a microbe that lives on the external surface of a host organism or substrate, as distinct from endosymbionts (which live inside the host); captures host-association mode, not specific host taxonomy.

A host-associated trait in which a microbe resides on living aerial plant surfaces.

A phage defense system in which an organism possesses an Epona locus represented by a VCA0366 profile that can protect bacteria from bacteriophage infection.

An autophagy phenotype in which a microbial cell selectively degrades portions of its endoplasmic reticulum by delivering them to lysosomal or vacuolar compartments.

A phage defense system in which an organism possesses an Erebus locus that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses an Esos locus represented by a VCA0450 profile that can protect bacteria from bacteriophage infection.

A fermentation in which pyruvate is decarboxylated to acetaldehyde (releasing CO2) and then reduced by NADH to ethanol, regenerating NAD+ for glycolysis. Characteristic of yeasts and the bacterium Zymomonas mobilis.

A halophily preference in which an organism can tolerate a wide range of salinity conditions.

A physiological phenotype in which a microbial cell releases material from an intracellular membrane-bounded compartment to the cell exterior through a fusion pore between the compartment membrane and the plasma membrane.

An OBJECT_PROPERTY relating an organism to a chemical that the organism exports from the cytoplasm to the periplasm or extracellular environment.

A physiological phenotype in which microbial cells give rise to closed, cell-derived lipid-membrane vesicles in the extracellular space.

A temperature preference that grows optimally at temperatures above 90°C.

A halophily preference in which an organism requires very high salt concentrations (typically 15-30% NaCl or higher) for optimal growth and cannot grow at salt concentrations below approximately 12%.

An oxygen preference that describes a microorganism that can grow with or without molecular oxygen.

A temperature preference characterized by the ability to grow at low temperatures (typically below 20 degrees C) while maintaining optimal growth at moderate temperatures.

A pH growth preference characterized by optimal growth in acidic environments (pH below 5.5) with the capacity to also grow at near-neutral pH values.

An oxygen preference in which growth can occur without oxygen but is capable of aerobic growth.

A pH growth preference in which an organism can grow at alkaline pH but does not require it.

An oxygen preference in which growth can occur with or without molecular oxygen (O₂).

A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors.

A fermentation in which an organism disposes of excess reducing equivalents by producing molecular hydrogen (H2), typically via hydrogenases acting on reduced ferredoxin or formate.

An OBJECT_PROPERTY relating an organism to a chemical substrate that the organism ferments — using organic compounds as both electron donors and acceptors with substrate-level phosphorylation for ATP.

A morphology trait in which a bacterial cell forms membrane-bound ferrosome organelles that store intracellular iron as non-crystalline iron phosphate biomineral.

A cell shape in which an organism grows as elongated filamentous cells or hypha-like structures.

A colony shape that has a thread-like or filamentous outline.

A morphology trait describing the number and spatial distribution of flagella on a cell (the flagellation pattern), e.g. monotrichous, lophotrichous, amphitrichous, or peritrichous.

A motile in which an organism possesses flagella for locomotion.

A cell shape in which an organism has a bulbous body with a narrower neck-like extension at one pole.

A phage defense system in which an organism possesses a two-component Fliodhais locus that can reduce Lactococcus bacteriophage c2 plaque development.

A habitat association in which an organism lives independently in the environment, not obligately associated with a host.

A colony shape that has a raised opaque centre and a translucent peripheral zone, resembling a fried egg.

A phage defense system in which an organism possesses an FS_GIY_YIG locus represented by DefenseFinder as a single-profile model requiring FS_GIY_YIG__GIY_YIG.

A phage defense system in which an organism possesses an FS_HEPN_TM locus represented by DefenseFinder as a two-profile model requiring FS_HEPN_TM__HEPN and FS_HEPN_TM__TM.

A phage defense system in which an organism possesses an FS_HP locus represented by DefenseFinder as a single-profile model requiring FS_HP__HP.

A phage defense system in which an organism possesses an FS_HP_SDH_sah locus represented by DefenseFinder as a two-profile model requiring FS_HP_SDH_sah__HP and FS_HP_SDH_sah__SDH_sah.

A phage defense system in which an organism possesses an FS_HsdR_like locus represented by DefenseFinder as a two-gene model drawing from custom FS_HsdR_like__DUF6731, FS_HsdR_like__HP, and FS_HsdR_like__HdrR profiles.

A phage defense system in which an organism possesses an FS_Sma locus represented by DefenseFinder as a single-profile model requiring FS_Sma__Sma.

An anaerobic respiration in which an organism uses fumarate as the terminal electron acceptor and reduces it to succinate for energy conservation.

A cell shape that is wide in the middle and tapers at both ends.

A genomics trait describing possession of a Gabija antiphage defense locus whose GajA and GajB proteins assemble into a complex that inhibits bacteriophage replication.

A motile phenotype in which an organism biases its active movement in response to an electric field.

A phenotype in which growth is directionally oriented or reoriented in response to an electric field.

A physiological enzyme-activity phenotype in which a cell exhibits gamma-glutamyltransferase/glutathione-hydrolase activity, processing glutathione, glutathione-S-conjugates, or other N-terminal L-gamma-glutamyl substrates through a gamma-glutamyl-enzyme intermediate.

A phage defense system in which an organism possesses a Gao_Her locus represented by DefenseFinder as either a Gao_Her_DUF or Gao_Her_SIR two-profile subsystem.

A phage defense system in which an organism possesses a Gao_Her_DUF locus represented by DefenseFinder as a two-profile model requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF.

A phage defense system in which an organism possesses a Gao_Her_SIR locus represented by DefenseFinder as a two-profile model requiring Gao_Her_SIR__HerA_SIR2 and Gao_Her_SIR__SIR2.

A phage defense system in which an organism possesses a Gao_Hhe locus represented by DefenseFinder as a single-profile model requiring Gao_Hhe__HheA.

A phage defense system in which an organism possesses a Gao_Iet locus represented by DefenseFinder as a two-profile model requiring Gao_Iet__IetA and Gao_Iet__IetS.

A phage defense system in which an organism possesses a Gao_Mza locus represented by DefenseFinder as a five-profile model requiring Gao_Mza__MzaA, Gao_Mza__MzaB, Gao_Mza__MzaC, Gao_Mza__MzaD, and Gao_Mza__MzaE.

A phage defense system in which an organism possesses a Gao_Ppl locus represented by DefenseFinder as a single-profile model requiring Gao_Ppl__PplA.

A phage defense system in which an organism possesses a Gao_Qat locus represented by DefenseFinder as a four-profile model requiring Gao_Qat__QatA, Gao_Qat__QatB, Gao_Qat__QatC, and Gao_Qat__QatD.

A phage defense system in which an organism possesses a Gao_RL locus represented by DefenseFinder as a four-profile model requiring Gao_RL__RL_A, Gao_RL__RL_B, Gao_RL__RL_C, and Gao_RL__RL_D.

A phage defense system in which an organism possesses a Gao_TerY locus represented by DefenseFinder as a three-profile model requiring Gao_TerY__TerYA, Gao_TerY__TerYB, and Gao_TerY__TerYC.

A phage defense system in which an organism possesses a Gao_Tmn locus represented by DefenseFinder as a single-profile model requiring Gao_Tmn__TmnA.

A phage defense system in which an organism possesses a Gao_Upx locus represented by DefenseFinder as a single-profile model requiring Gao_Upx__UpxA.

A phage defense system in which an organism possesses a Gamma-Mobile-Trio island-associated GAPS1 locus that can be triggered by a phage capsid protein to induce cell dormancy.

A phage defense system in which an organism possesses a GMT-encoded GAPS2 locus represented by DefenseFinder as a single-profile model, GAPS2__GAPS2, and experimentally linked to P1-vir and lambda-vir protection when expressed in E. coli.

A phage defense system in which an organism possesses a GMT-encoded GAPS4 locus represented by DefenseFinder as a two-profile model, GAPS4__GAPS4a and GAPS4__GAPS4b, and experimentally linked to T7, T4, P1-vir, and lambda-vir protection when expressed in E. coli.

A phage defense system in which an organism possesses a GMT-encoded GAPS6 locus represented by DefenseFinder as a two-profile model, GAPS6__GAPS6a and GAPS6__GAPS6b, and experimentally linked to T7, T4, P1-vir, and lambda-vir protection when expressed in E. coli.

An intracellular gas-filled proteinaceous inclusion that provides buoyancy, allowing planktonic bacteria and archaea to position themselves in the water column.

A phage defense system in which an organism possesses a bacterial gasdermin locus represented by the DefenseFinder GasderMIN__bGSDM profile, whose bGSDM effectors are associated with bacteriophage defense and can be proteolytically activated in characterized bGSDM-protease systems to assemble membrane pores, disrupt membrane integrity, and execute cell death.

A quality that is describing the percentage of guanine and cytosine nucleotides in genomic DNA, calculated as the ratio of GC base pairs to total base pairs.

A GC-content phenotype with genome-wide GC composition at or below approximately 42.65% (the METPO `GC_<=42.65` bin; note that the upstream label 'high' does not match this numeric threshold, but the synonym is preserved as the authoritative bin definition).

A GC-content phenotype with genome-wide GC composition between approximately 42.65% and 57.0% (the METPO `GC_42.65_57.0` bin; note that the upstream label 'low' does not match this mid-range numeric threshold, but the synonym is preserved as the authoritative bin definition).

A GC-content phenotype with genome-wide GC composition above approximately 66.3% (the METPO `GC_>66.3` bin; note that the upstream label 'mid1' does not match this high-end numeric threshold, but the synonym is preserved as the authoritative bin definition).

A GC-content phenotype with genome-wide GC composition between approximately 57.0% and 66.3% (the METPO `GC_57.0_66.3` bin).

A genome-sequence property describing strand asymmetry in guanine versus cytosine content between the leading and lagging replication strands, commonly used to locate the replication origin and terminus.

A phage defense system in which an organism possesses a Geb locus that can protect bacteria from bacteriophage infection.

A physiological enzyme-activity phenotype in which a cell produces active gelatinase protease.

A phenotype describing an organism with a broad ecological niche, capable of thriving across diverse environments or utilizing varied resources.

A quantitative genomics property describing the total length of an organism's genome (typically expressed in megabase pairs), which varies widely across prokaryotes and reflects lifestyle and evolutionary forces.

A genomics trait describing selective reduction of genome size and gene content in free-living microbes with very large effective population sizes, minimizing the cellular cost of replication and biosynthesis.

A genomics trait describing possession of a genomic island — a horizontally acquired chromosomal region (e.g. a pathogenicity, symbiosis, or metabolic island) that often retains mobility signatures such as flanking repeats and atypical nucleotide composition.

A motile in which an organism moves smoothly along solid surfaces without flagella or pili.

A physiological enzyme-activity phenotype in which a cell produces active glutamyl glutamic acid arylamidase enzymes that hydrolyze glutamyl-glutamic-acid arylamide substrates.

A physiological enzyme-activity phenotype in which a cell produces active glycine arylamidase enzymes that hydrolyze glycine arylamide substrates.

A type IV modification-dependent restriction system in which an organism possesses a GmrSD locus encoding either separate GmrS and GmrD proteins or a fused double-domain GmrSD-family protein, that targets glucosylated hydroxymethylcytosine-containing DNA.

A gram stain in which bacteria do not retain crystal violet dye and appear pink or red after staining, indicating a thin peptidoglycan layer and presence of an outer membrane.

A gram stain in which an organism retains crystal violet dye and appears purple under microscopy due to a thick peptidoglycan cell wall.

A phenotype where microorganisms are grouped based on their ability to retain crystal violet dye in the Gram staining procedure.

A gram stain in which bacteria from the same culture show both gram-positive and gram-negative staining characteristics, often due to age of culture or cell wall degradation.

A motile phenotype in which the speed of active propulsion is modulated according to orientation relative to gravity.

A motile phenotype in which the direction of active swimming is biased relative to gravity.

A phenotype in which growth is directionally oriented or reoriented in response to gravity.

A pigmentation phenotype in which microbial colonies or cultures appear green or blue-green due to pigments such as pyocyanin and pyoverdine.

A phenotype characterized by the span of values within which an organism can maintain growth.

A host association in which an organism is a persistent member of the gastrointestinal microbiota of an animal host, often contributing to host nutrition and physiology.

A motile phenotype in which the balance of gravitational and viscous torques biases an organism's swimming orientation.

An ecological classification of the primary environment or niche an organism inhabits (e.g. free-living vs host-associated; soil, rhizosphere, gut). Microbial taxa show biogeographic structure across such habitats.

A phage defense system in which an organism possesses a Hachiman antiphage locus encoding a HamA/HamB core.

A Hachiman system in which an organism possesses a HamA/HamB locus without a HamC component.

A Hachiman system in which an organism possesses a locus encoding HamA and HamB together with an additional HamC (DUF3223) component.

A phage defense system in which an organism possesses a Hailong locus encoding a HalB NTase DNA-signal enzyme and a HalA membrane effector complex that can be held inactive by HalB-derived oligodeoxyadenylate until viral DNA exonucleases release the primed HalA complex and induce protective host cell growth arrest.

A halophily preference in which an organism requires both high salt concentrations and alkaline pH for optimal growth.

A halophily preference in which an organism requires high concentrations of salt for growth and survival.

A phenotype that is relating to an organism's salt concentration requirements or tolerance for growth.

A halophily preference in which an organism can tolerate high salt concentrations but does not require them for growth.

Relates a microbe to a growth NaCl observation.

Relates a microbe to a growth oxygen observation.

Relates a microbe to a growth pH observation.

Relates a microbe to a growth temperature observation.

The maximum temperature (°C) associated with this observation.

The minimum temperature (°C) associated with this observation.

Relates a microbe to a NaCl tolerance breadth (delta) observation.

Relates a microbe to a NaCl observation.

A reported temperature value (°C) for this observation.

Relates a microbe to an optimum NaCl observation.

Relates a microbe to an optimum oxygen observation.

Relates a microbe to an optimum pH observation.

Relates a microbe to an optimum temperature observation.

Relates a microbe to a oxygen tolerance breadth (delta) observation.

Relates a microbe to an oxygen observation.

Relates a microbe to a pH tolerance breadth (delta) observation.

Relates a microbe to a pH observation.

Relates a microbe to a growth NaCl range observation.

Relates a microbe to a growth oxygen range observation.

Relates a microbe to a growth pH range observation.

Relates a microbe to a growth temperature range observation.

Relates a microbe to a temperature tolerance breadth (delta) observation.

Relates a microbe to a temperature observation.

Relates any instance to a numerical value

Free-text comments associated with this observation.

A stress response in which acute heat stress induces heat-shock proteins that refold or degrade denatured proteins to restore protein homeostasis.

A phage defense system in which an organism possesses the two-gene HEC-02 Hma-embedded candidate locus, encoding an ABC ATPase and an associated nuclease-related domain protein, that can reduce bacteriophage plaquing.

A phage defense system in which an organism possesses the two-gene HEC-03 Hma-embedded candidate locus, encoding an ABC ATPase and an associated PilT N-terminal domain protein, that can reduce bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene HEC-04 Hma-embedded candidate locus, encoding an ABC ATPase fused to a TOPRIM-family nuclease domain, that can reduce bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene HEC-05 Hma-embedded candidate locus, encoding a GmrSD-like protein closely matching BrxU, that can reduce bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene HEC-06 Hma-embedded candidate locus, encoding a GmrSD-like protein, that can reduce bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene HEC-07 Hma-embedded candidate locus, encoding a RelE domain-containing protein, that can reduce bacteriophage plaquing.

A phage defense system in which an organism possesses the single-gene HEC-08 Hma-embedded candidate locus, encoding a higher eukaryotes and prokaryotes nucleotide-binding domain-containing protein, that can reduce bacteriophage plaquing.

A cell shape in which an organism has a corkscrew-like helical cell body with curvature and twist along its long axis.

A phenotype describing the ability of an organism to lyse red blood cells.

A phenotype in which an organism is capable of lysing red blood cells.

A phage defense system in which an organism possesses a Hesat locus that can restrict bacteriophage infection.

A morphology trait in which a filamentous cyanobacterium differentiates specialized, thick-walled cells (heterocysts) that create a microoxic interior for oxygen-sensitive nitrogen fixation.

A fungal phenotype in which postfusion nonself recognition restricts the establishment or growth of viable vegetative heterokaryons.

A fungal phenotype characterized by the coexistence of genetically distinct nuclei within a shared cytoplasm.

A fungal phenotype in which sexual reproduction requires a separate, compatible mating partner.

A trophic type in which an organism obtains carbon from organic compounds rather than from carbon dioxide.

A physiological enzyme-activity phenotype in which a cell produces active histidine arylamidase enzymes that hydrolyze histidine arylamide substrates.

A phage defense system in which an organism possesses a genome-encoded Hma locus with predicted HmaA helicase, HmaB m5c methyltransferase, and HmaC ATPase components.

A phage defense system in which an organism possesses an Hna locus encoding a single SF2 helicase/nuclease effector that protects cells from bacteriophage infection by responding to phage single-stranded DNA-binding protein challenge, shifting toward dysregulated nuclease activation, and triggering abortive infection.

A morphology trait in which a bacterial cell produces a localized polar adhesive matrix called a holdfast that mediates permanent attachment to surfaces.

A stress response in which an organism remodels membrane lipid composition to maintain a functional membrane viscosity and fluidity when temperature changes perturb lipid packing.

A metabolism in which acetate is produced as the sole reduced end product from reduction of CO2 via the acetyl-CoA pathway.

A fungal phenotype enabling a culture founded from a single spore to reproduce sexually in isolation from a mating partner.

A morphological phenotype in which a filamentous cyanobacterium differentiates short, initially heterocyst-free filaments called hormogonia that are distinct from mature vegetative trichomes.

A habitat association in which an organism lives persistently on or in a plant or animal host (e.g. as a member of a host microbiome), spanning commensal, mutualistic, and pathogenic relationships.

A pathogen that infects organisms of the species Homo sapiens.

A metabolism in which an organism catabolizes a hydrocarbon, using it as a carbon and energy source.

A trophic type in which an organism uses molecular hydrogen as an electron donor for energy generation and carbon dioxide as the primary carbon source.

A methanogenesis in which carbon dioxide is reduced to methane using molecular hydrogen as the electron donor.

An OBJECT_PROPERTY relating an organism to a chemical substrate that the organism hydrolyses (cleaves by addition of water).

A temperature preference in which growth is favored at very high temperatures, typically ≥80 °C.

A phenotype in which vegetative fungal hyphae fuse to establish cytoplasmic continuity.

A phage defense system in which an organism possesses a Hypnos locus that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses a genome-encoded prokaryotic Schlafen nuclease fused to an immunoglobulin-like sensor domain that recognizes T5-like phage tail assembly chaperones and activates Schlafen tRNase defense.

An OBJECT_PROPERTY relating an organism to a chemical that the organism imports from the extracellular environment into the cytoplasm.

An assay that tests the ability of an organism to produce indole from tryptophan.

A phenotype in which an organism tests negative in the indole test, indicating it does not produce indole from tryptophan.

A phenotype in which an organism tests positive in the indole test, indicating it produces indole from tryptophan.

A genomic island trait in which an organism possesses an integrative and conjugative element, a self-transmissible mobile genetic element that integrates into host DNA, excises under induced expression, and encodes type IV secretion machinery for conjugative transfer to recipient cells.

A morphology trait describing a discrete intracellular body — a storage granule, gas-filled structure, or protein-bounded microcompartment/organelle — that compartmentalizes material or function within a prokaryotic cell.

An anaerobic respiration in which an organism uses iodate as the terminal electron acceptor for energy conservation.

An environmental tolerance in which an organism survives high doses of ionizing radiation (e.g. gamma rays), typically via efficient repair of DNA double-strand breaks and protection of the proteome from oxidative damage.

A metabolism in which an organism oxidizes ferrous iron (Fe2+) to ferric iron (Fe3+) to conserve energy, at acidic or circumneutral pH and under aerobic or anaerobic conditions.

A colony shape that has an irregular (non-round, non-rhizoid) outline.

A cell shape lacking a consistent geometric form across individual cells of a population.

True if this observation indicates no growth at the reported temperature (negative result).

An OBJECT_PROPERTY relating an organism to a chemical entity that is *not* required for that organism's growth (positive assertion of non-requirement). Functions as the negation companion of 'requires for growth'.

A sexual-reproduction phenotype in which the fusing gametes are similar in size.

A phage defense system in which an organism possesses a two-gene jukAB locus encoding a JukA sensor that binds a PhiKZ-like gp241 early phage protein at the EPI vesicle and directly recruits the pore-forming-toxin-like JukB effector to destabilize the vesicle, suppress early phage gene expression, and prevent phage DNA replication and nucleus assembly.

A phage defense system in which an organism possesses a Kamadhenu locus that can restrict bacteriophage infection.

A physiological phenotype in which a microbial organism selectively retains and uses nuclei acquired from prey.

A phage defense system in which an organism possesses a two-component Kiwa locus encoding the transmembrane sensor KwaA and DNA-binding effector KwaB that assemble into a membrane-associated supercomplex and coordinate phage-attachment sensing with inhibition of phage DNA replication and late transcription.

A physiological phenotype in which a microbial organism selectively retains plastids acquired from algal prey after discarding or digesting other prey components.

A phage defense system in which an organism possesses a Kongming locus that uses phage-triggered deoxyinosine triphosphate signaling to activate a KomBC effector complex and mediate NAD depletion-linked death of infected cells.

A fermentation in which sugars are converted mainly to lactate, with ATP generated by substrate-level phosphorylation. Homolactic fermentation yields ~2 lactate per glucose via glycolysis; heterolactic fermentation also yields ethanol/acetate and CO2. Characteristic of lactic acid bacteria (e.g. Lactobacillus, Lactococcus).

A Lamassu system in which an organism possesses a defense locus encoding a protease-domain LmuA effector together with a hydrolase-like protein, an SMC-like LmuB sensor, and LmuC.

A phage defense system in which an organism possesses a Lamassu locus built around a conserved SMC-like LmuB sensor paired with a modular LmuA effector and subfamily-specific partner architecture, enabling viral-DNA sensing and effector-mediated antiviral activity.

A Lamassu system in which an organism possesses a locus encoding the LmuA effector and SMC-like LmuB sensor but no LmuC component.

A Lamassu system in which an organism possesses a locus with an additional LmuC component alongside the LmuA effector module and SMC-like LmuB sensor.

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Amidase subtype locus represented by the Lamassu-Amidase rule row requiring the Lamassu-Fam__LmuA_effector_Amidase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Cap4_nuclease subtype locus represented by the Lamassu-Cap4_nuclease rule row requiring the Lamassu-Fam__LmuA_effector_Cap4_nuclease_II and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-FMO subtype locus represented by the Lamassu-FMO rule row requiring the Lamassu-Fam__LmuA_effector_FMO and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

A Lamassu system in which an organism possesses a locus encoding an HNH-domain LmuA effector, a short-form SMC-like LmuB sensor, and LmuC.

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Hydrolase subtype locus represented by the Lamassu-Hydrolase rule row requiring the Lamassu-Fam__LmuA_effector_Hydrolase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Lipase subtype locus represented by the Lamassu-Lipase rule row requiring the Lamassu-Fam__LmuA_effector_Lipase and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Mrr subtype locus represented by the Lamassu-Mrr rule row requiring the Lamassu-Fam__LmuA_effector_Mrr and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-PDDEXK subtype locus represented by the Lamassu-PDDEXK rule row requiring the Lamassu-Fam__LmuA_effector_PDDEXK and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Protease subtype locus represented by the Lamassu-Protease rule row requiring the Lamassu-Fam__LmuA_effector_Protease and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

A Lamassu system in which an organism possesses a genome-encoded DefenseFinder Lamassu-Sir2 subtype locus represented by the Lamassu-Sir2 rule row requiring the Lamassu-Fam__LmuA_effector_Sir2 and Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II profiles.

A Lamassu system in which an organism possesses a locus encoding an LmuA effector with a SMEK domain, an SMC-like LmuB sensor, and LmuC.

A phage defense system in which an organism possesses a lanthivirin lanthipeptide biosynthetic gene cluster that can confer anti-phage activity in a native Streptomyces context and after heterologous expression of complete lanthivirin systems.

A motility phenotype in which flagella emerge from the lateral side of the cell.

A physiological enzyme-activity phenotype in which a cell produces active lecithinases that hydrolyze lecithin or phosphatidylcholine.

A physiological enzyme-activity phenotype in which a cell produces active leucine arylamidase enzymes that hydrolyze leucine arylamide substrates.

A physiological enzyme-activity phenotype in which a cell produces active leucyl-glycine arylamidase enzymes that hydrolyze leucyl-glycine arylamide substrates.

A biopolymer-degradation metabolism in which an organism breaks down lignin, the recalcitrant aromatic heteropolymer of plant cell walls, using oxidative enzymes such as peroxidases and laccases.

A physiological enzyme-activity phenotype in which a cell produces active lipases that hydrolyze triglycerides at lipid-water interfaces.

A metabolism in which a microorganism hydrolyzes triacylglycerols into fatty acids and glycerol through lipase-catalyzed ester cleavage.

An autophagy phenotype in which a microbial cell degrades its lipid droplets by delivering them to lysosomal or vacuolar compartments.

A phage defense system in which an organism possesses a Lit locus represented by DefenseFinder as a single-profile model requiring Lit__Lit.

A trophic type in which an organism obtains energy from inorganic electron donors and carbon from carbon dioxide.

A trophic type in which an organism obtains energy from the oxidation of inorganic compounds while using organic compounds as the primary carbon source for biosynthesis.

A trophic type in which an organism uses inorganic compounds as electron donors for energy generation.

A Lamassu system in which an organism possesses a locus from the long-LmuB family, characterized by longer coiled-coil regions in its SMC-like LmuB sensor than in short Lamassu systems.

A flagellar arrangement with a tuft of multiple flagella at one pole of the cell.

A phage defense system in which an organism possesses a Lugos locus represented by a VCA0409 profile that can protect bacteria from bacteriophage infection.

A physiological enzyme-activity phenotype in which a cell produces active lysine decarboxylase enzymes that decarboxylate L-lysine to cadaverine and carbon dioxide.

A physiological phenotype in which a microbial organism internalizes bulk extracellular fluid by closing actin-driven plasma-membrane ruffles into large intracellular vesicles.

A phage defense system in which an organism possesses a methylation-associated defense system locus whose canonical architecture has mad1 through mad8 genes and whose methylation-coupled self/non-self discrimination can restrict bacteriophage infection.

A membrane-bounded intracellular organelle containing a magnetic iron-mineral crystal (magnetite or greigite); chains of magnetosomes allow magnetotactic bacteria to align with and navigate along geomagnetic field lines.

A behavioral physiology in which magnetosome-bearing motile cells align with geomagnetic field lines and navigate along that axis.

A metabolism in which microorganisms oxidize soluble Mn(II) to Mn(III) or Mn(IV) products through mechanisms including bacterial multicopper oxidases and fungal manganese peroxidases; many systems deposit insoluble manganese oxides.

An object or portion of a substance or mixture of substances that consists of matter

A fungal phenotype enabling conversion from one mating type to another, either reversibly or irreversibly.

A phage defense system in which an organism possesses a two-component MazEF toxin-antitoxin locus whose MazE antitoxin and MazF endoribonuclease can protect Escherichia coli against RNA phages and that DefenseFinder represents with mandatory MazEF__MazE and MazEF__MazF profiles.

A type IV modification-dependent restriction system in which an organism possesses an mcrBC locus encoding McrB DNA-binding and McrC cleavage-associated subunits that assemble into an McrBC restriction endonuclease complex targeting methylated cytosine-containing DNA.

A phage defense system in which an organism possesses a Menshen locus represented by NsnA, NsnB, and NsnC profile choices that can protect bacteria from bacteriophage infection.

A metal tolerance in which an organism grows in the presence of toxic inorganic or organic mercury compounds, typically via the mer operon, whose mercuric reductase (MerA) reduces reactive Hg(II) to volatile Hg(0).

A temperature preference in which growth is favored at intermediate temperatures, typically ~20–45 °C.

A biological process that maintains life in an organism.

An environmental tolerance in which an organism grows in the presence of elevated concentrations of toxic heavy-metal or metalloid ions, typically via efflux-based resistance determinants (RND-family CBA pumps, P-type ATPases, and cation diffusion facilitators).

A metabolism in which methane is produced as the primary end product through the reduction of carbon-containing compounds, formate, methanol, or acetate, exclusively performed by methanogenic archaea under strictly anaerobic conditions.

A metabolism in which an organism oxidizes methanol, typically to formaldehyde, as a carbon and energy source.

A trophic type in which an organism uses methane as the primary carbon and energy source through oxidation of methane to carbon dioxide.

An assay that tests the ability of an organism to produce and maintain stable acid end products from glucose fermentation.

A phenotype in which an organism tests negative in the methyl red test.

A phenotype in which an organism tests positive in the methyl red test, indicating mixed acid fermentation.

A methanogenesis in which methylated compounds donate methyl groups that are transferred to coenzyme M and reduced to methane.

A trophic type in which an organism obtains energy and carbon from reduced one-carbon compounds.

A phage defense system in which an organism possesses a Metis locus that senses phage-mediated host-genome degradation through N6-methyl-deoxyadenosine monophosphate and activates a type-specific toxic effector.

An oxygen preference that requires molecular oxygen (O₂) at concentrations lower than atmospheric.

An oxygen preference that tolerates low levels of molecular oxygen (O₂) without requiring it.

A material entity that is too small to be viewed by the unaided eye, typically requiring microscopy for observation. Used as the domain class for METPO organism-to-X object properties so that organism-level assertions can be expressed as `<microbe-instance> <METPO predicate> <object-class>`.

An autophagy phenotype in which a microbial cell selectively degrades its mitochondria by delivering them to lysosomal or vacuolar compartments.

A fermentation in which sugars are converted via the glycolytic pathway to a mixture of acids (lactic, acetic, formic, succinic) plus ethanol, CO2 and H2. Characteristic of enteric bacteria such as Escherichia coli.

A trophic type in which an organism can use both organic and inorganic carbon sources for growth.

A Wadjet system in which an organism possesses an MksBEFG derivative SMC locus encoding an MksBEF ATPase core and an MksG nuclease that degrades plasmid DNA.

A phage defense system in which an organism possesses an MMB gp29-gp30 locus that can protect bacteria from bacteriophage infection.

A genomics trait describing possession of DNA segments that can move within or between genomes and mediate horizontal gene transfer, including plasmids, prophages, transposable elements, and genomic islands.

A halophily preference where growth and proliferation requires high levels of sodium chloride, usually above or about 0.2 M.

A phage defense system in which an organism possesses a hok/sok toxin-antitoxin locus represented by DefenseFinder as the two-profile Mok_Hok_Sok model and experimentally linked to bacteriophage T4 exclusion by the plasmid R1 hok/sok locus.

A phage defense system in which an organism possesses a Mokosh locus represented by MkoA/MkoB type I or MkoC type II components that can protect bacteria from bacteriophage infection.

A flagellar arrangement with a single flagellum, typically located at one pole of the cell.

A motility in which an organism has the ability to move independently using metabolic energy.

A phenotype in which an organism has the capability to move independently through its environment, typically by means of flagella, pili, gliding mechanisms, or other locomotory structures.

A phage defense system in which an organism possesses a tripartite MqsRAC toxin-antitoxin-chaperone locus represented by DefenseFinder as a two-profile model requiring MqsRAC__mqsC and MqsRAC__mqsR.

A type IV modification-dependent restriction system in which an organism possesses an MspJI-family Mrr-like locus encoding a restriction endonuclease that recognizes methylcytosine- or hydroxymethylcytosine-modified DNA and cleaves both strands at a fixed distance from the modified cytosine.

A symbiosis in which both the microorganism and its host or partner benefit from the association, often through exchange of nutrients or services.

A morphology trait in which a bacterium grows as branching, filamentous hyphae that form a mycelium, often with subsequent differentiation into aerial hyphae and spores, as in Streptomyces.

A physiological phenotype in which a microbial organism feeds by aspirating prey cell contents through a localized feeding connection rather than engulfing the prey whole.

A salinity phenotype with numerical limits expressing the breadth (maximum minus minimum) of NaCl concentrations supporting growth of an organism.

A NaCl delta phenotype with a growth-supporting NaCl breadth above approximately 8% (w/v), characteristic of extreme-euryhaline organisms.

A NaCl delta phenotype with a narrow growth-supporting NaCl breadth of at most approximately 1% (w/v), characteristic of stenohaline organisms.

A NaCl delta phenotype with a growth-supporting NaCl breadth of approximately 1–3% (w/v), characteristic of organisms with modest salinity tolerance breadth.

A NaCl delta phenotype with a growth-supporting NaCl breadth of approximately 3–8% (w/v), characteristic of organisms with broad salinity tolerance.

A salinity phenotype with numerical limits that supports the most efficient growth and reproduction of an organism.

A NaCl optimum phenotype with the best-growth NaCl concentration above approximately 8% (w/v), corresponding to extreme-halophile physiology.

A NaCl optimum phenotype with the best-growth NaCl concentration at or below approximately 1% (w/v), corresponding to non-halophilic or halotolerant physiology.

A NaCl optimum phenotype with the best-growth NaCl concentration approximately between 1 and 3% (w/v), corresponding to slight-halophile or halotolerant physiology.

A NaCl optimum phenotype with the best-growth NaCl concentration approximately between 3 and 8% (w/v), corresponding to moderate-halophile or halotolerant physiology.

A salinity phenotype with numerical limits that bounds the minimum and maximum NaCl concentrations supporting growth of an organism.

A NaCl range phenotype in which the growth-supporting NaCl range extends above approximately 8% (w/v), characteristic of extreme-halophile organisms.

A NaCl range phenotype in which the upper bound of growth-supporting NaCl concentration is at or below approximately 1% (w/v), characteristic of non-halophilic or halotolerant organisms.

A NaCl range phenotype in which the growth-supporting NaCl range spans approximately 1–3% (w/v), characteristic of slight-halophilic or halotolerant organisms.

A NaCl range phenotype in which the growth-supporting NaCl range spans approximately 3–8% (w/v), characteristic of moderate-halophile organisms.

A physiological enzyme-activity phenotype in which a cell produces active NAD-dependent alcohol dehydrogenases that interconvert primary or secondary alcohols with aldehydes or ketones.

A phage defense system in which an organism possesses a Nantosuelta locus represented by a VCA0322 profile that can protect bacteria from bacteriophage infection.

A physiological enzyme-activity phenotype in which a cell produces active phosphohydrolases that hydrolyze naphthol-AS-BI-phosphate substrates.

A physiological state in which a cell takes up free extracellular DNA from the environment and integrates it into its genome (natural genetic transformation).

A phenotype in which germ-tube emergence or hyphal extension is directionally biased away from neighboring cells or hyphae of the same species.

A phage defense system in which an organism possesses a Nemetona locus represented by a VCA0441 profile that can protect bacteria from bacteriophage infection.

A pH growth preference characterized by optimal growth at near-neutral pH values, typically between pH 6.5 and 7.5.

A phage defense system in which an organism possesses an Nhi-family locus represented by the DefenseFinder Nhi__Nhi profile and exemplified by a single enzyme with nuclease and helicase activities that protects against diverse staphylococcal phages, prevents phage DNA accumulation, and is inferred to target and degrade phage-specific replication intermediates.

A metabolism in which an organism reduces nitrate, whether for energy conservation or for assimilation into biomass.

A nitrogen respiration in which nitrate is the terminal electron acceptor, reduced to nitrite or further reduced products.

A biological process in which ammonia is oxidized to nitrite (ammonia oxidation) and nitrite is oxidized to nitrate (nitrite oxidation), in two steps.

A nitrogen respiration in which nitrite is the terminal electron acceptor.

A metabolism in which an organism reduces atmospheric dinitrogen (N2) to ammonia using the nitrogenase enzyme complex, making fixed nitrogen biologically available (diazotrophy).

An anaerobic respiration in which an organism conserves energy by transferring electrons to an oxidized nitrogen compound as the terminal electron acceptor.

A mutualistic symbiosis in which a diazotrophic bacterium fixes atmospheric N2 for a host plant — classically rhizobia in legume root nodules — in exchange for photosynthate.

A phage defense system in which an organism possesses a NixI-family phage-satellite locus represented by the DefenseFinder NixI__NixI profile and exemplified by a PLE-encoded nicking endonuclease that cleaves ICP1 bacteriophage DNA, inhibits ICP1 genome replication, and reduces progeny production in Vibrio cholerae.

A phage defense system in which an organism possesses an NLR-related bacterial NACHT locus represented by DefenseFinder as an NLR_like_bNACHT01 or NLR_like_bNACHT09 single-profile model, encoding a NACHT-module STAND-family protein that can restrict bacteriophage production.

A halophily preference in which an organism does not require or prefer elevated salt concentrations for growth.

A motility in which an organism lacks the ability to move independently under its own power.

A phenotype in which an organism does not lyse red blood cells.

A sporulation in which an organism lacks the ability to produce endospores.

An autophagy phenotype in which a microbial cell degrades parts of its nucleus or an entire nucleus by delivering nuclear material to lysosomal or vacuolar compartments.

A trophic type that involves an organism's physiological and metabolic adaptations to specific nutrient availability.

A pH growth preference characterized by the requirement for acidic environments (pH below 5.5) for growth, with inability to grow at neutral or alkaline pH values.

An oxygen preference that requires molecular oxygen (O₂) for growth.

An alkaliphilic phenotype in which an organism requires alkaline conditions (typically pH above 8.5) for growth and cannot grow at neutral or acidic pH.

An oxygen preference in which molecular oxygen (O₂) inhibits or prevents growth.

A pressure growth preference in which an organism requires elevated hydrostatic pressure for growth and is unable to grow at atmospheric pressure (0.1 MPa).

A data-collection or measurement context in which trait-relevant qualities of organisms, samples, or conditions are recorded.

A phage defense system in which an organism possesses an Ogmios locus represented by a VCA0308 profile that can protect bacteria from bacteriophage infection.

A phage defense system in which an organism possesses an Old exonuclease locus represented by DefenseFinder as a single-profile model, Old_exonuclease__Old_exonuclease, and experimentally linked to interference with phage lambda by the bacteriophage P2 Old protein.

A nutrient adaptation characterized by the ability to thrive in environments with very low nutrient concentrations, typically possessing efficient nutrient uptake and utilization systems.

A phage defense system in which an organism possesses a two-component Olokun locus represented by OloA and OloB profiles that can protect bacteria from bacteriophage infection.

A sexual-reproduction phenotype in which large nonmotile female gametes fuse with smaller male gametes.

A phage defense system in which an organism possesses a three-gene Ophion locus encoding OpnA, OpnB, and OpnC components that can block jumbo-phage infection before phage-nucleus formation.

A host-association lifestyle in which a normally commensal or environmental microorganism causes disease only when host defenses are compromised or it reaches a normally sterile site.

A phenotype characterized by the value at which an organism exhibits maximum growth rate or activity.

An observation that identifies the temperature at which a microorganism exhibits maximum growth rate or metabolic activity.

A pigmentation phenotype in which microbial colonies or cells appear orange due to production and accumulation of orange pigments such as carotenoids.

The root OBJECT_PROPERTY for all organism-to-chemical interactions in the metabolism vocabulary; concrete uses (uses-as-X, ferments, produces, etc.) specialise this relation.

An anaerobic respiration in which an organism uses an organohalide as the terminal electron acceptor for energy conservation.

A trophic type characterized by the use of organic compounds as both electron donors and primary carbon sources for energy generation and biosynthesis.

A trophic type in which an organism obtains energy from the oxidation of organic compounds.

A physiological enzyme-activity phenotype in which a cell produces active ornithine decarboxylase enzymes that decarboxylate L-ornithine to putrescine and carbon dioxide.

A phage defense system in which an organism possesses an Oshun locus that can protect bacteria from bacteriophage infection.

A motile phenotype in which active locomotion produces net migration in response to a spatial gradient in external osmotic conditions.

A phenotype characterized by the ability to grow under high osmotic pressure (non-NaCl).

A cell shape characterized by an ellipsoidal morphology with rounded ends, resembling an elongated sphere.

A cell shape in which an organism has an oval morphology, rounded at both ends with one end often slightly broader than the other.

A physiological enzyme-activity phenotype in which a cell produces a terminal respiratory oxidase (notably cytochrome c oxidase); it is the basis of the diagnostic oxidase test.

Test-outcome phenotype where the oxidase test yields a negative result. The underlying enzyme-organism relation should additionally be asserted via <organism> METPO:2000303 'does not show activity of' GO:0004129 'cytochrome-c oxidase activity'.

A biochemical test that detects cytochrome c oxidase activity using a redox indicator. The test outcome (positive or negative) is captured by its child classes; this class itself does not assert oxidase activity.

A metabolism that generates ATP through the transfer of electrons from electron donors to electron acceptors via redox reactions, coupled to the pumping of protons across a membrane to create an electrochemical gradient.

A stress response that defends the cell against reactive oxygen species (e.g. superoxide and hydrogen peroxide) through detoxifying enzymes, regulators, and damage-repair systems.

An OBJECT_PROPERTY relating an organism to a chemical substrate that the organism oxidises (removes electrons or hydrogens from).

A phenotype that is relating to an organism's oxygen requirements or tolerance for growth.

A phototrophic metabolism that uses light energy to fix CO2, oxidizing water as the electron donor and releasing molecular oxygen. It uses two linked photosystems and chlorophyll, and is characteristic of cyanobacteria (and plant chloroplasts).

A sexual-reproduction phenotype in which two gametes produced by division within a single gametangium fuse with each other.

A physiological phenotype in which a microbial organism feeds by enveloping all or part of particulate food in an extruded membranous pallium, digesting it outside the main cell body, and taking up released nutrients.

A phage defense system in which an organism possesses a Panchino gp28 locus that can protect bacteria from bacteriophage infection.

A genomics trait describing the structure of a species' pangenome — the balance of core versus accessory genes and whether the pangenome is open (continually acquiring new genes across genomes) or closed.

A phage defense system in which an organism possesses a two-gene optSE locus encoding an OptS protein that constitutively produces cyclic dinucleotides and an OptE transmembrane effector that is released from cyclic-dinucleotide repression when phage Acb2-like proteins sequester those signals, leading to inner-membrane disruption.

A fungal phenotype enabling genetic reassortment through nuclear fusion followed by chromosome-loss-mediated ploidy reduction instead of conventional meiosis.

A symbiosis in which the microorganism benefits at the expense of its host's fitness, deriving resources from the host while causing it harm.

An abortive infection system in which an organism possesses a phage anti-restriction-induced system locus encoding an AriA ABC ATPase sensor and an AriB TOPRIM-family nuclease whose activation by phage anti-restriction or other foreign proteins releases AriB to inhibit translation through lysine tRNA cleavage and block bacteriophage propagation.

A phenotype where a microbe is a pathogen of some host organism.

A phage defense system in which an organism possesses a PD-Lambda-1 locus represented by DefenseFinder as a single-profile model, PD-Lambda-1__PD-Lambda-1, and experimentally linked to LambdaVir protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-Lambda-2 locus represented by DefenseFinder as a model with two mandatory profiles, PD-Lambda-2__PD-Lambda-2_A and PD-Lambda-2__PD-Lambda-2_B, plus the accessory PD-Lambda-2__PD-Lambda-2_C profile.

A phage defense system in which an organism possesses a PD-Lambda-3 locus represented by DefenseFinder as a two-profile model, PD-Lambda-3__PD-Lambda-3_A and PD-Lambda-3__PD-Lambda-3_B, and experimentally linked to LambdaVir protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-Lambda-4 locus represented by DefenseFinder as a two-profile model, PD-Lambda-4__PD-Lambda-4_A and PD-Lambda-4__PD-Lambda-4_B, and experimentally linked to T4, LambdaVir, SECphi27, and T7 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-Lambda-5 locus represented by DefenseFinder as a two-profile model, PD-Lambda-5__PD-Lambda-5_A and PD-Lambda-5__PD-Lambda-5_B, and experimentally linked to T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, and T7 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-Lambda-6 locus represented by DefenseFinder as a single-profile model, PD-Lambda-6__PD-Lambda-6, and experimentally linked to LambdaVir and T5 protection when expressed in E. coli.

A phage defense system in which an organism possesses a two-gene PD-T2-1 operon whose expression was experimentally linked to protection against T2, T6, Bas18, T4, and T5 phages.

A phage defense system in which an organism possesses a PD-T4-1 locus represented by DefenseFinder as a single-profile model, PD-T4-1__PD-T4-1, and experimentally linked to T2, T4, and T6 protection when expressed in E. coli.

An abortive infection system in which an organism possesses a PD-T4-10 locus represented by DefenseFinder as a two-profile model, PD-T4-10__PD-T4-10_A and PD-T4-10__PD-T4-10_B, and experimentally linked to T2, T4, T6, T5, and SECphi27 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T4-2 locus represented by DefenseFinder as a two-profile model requiring PD-T4-2__PD-T4-2_A and PD-T4-2__PD-T4-2_B, and experimentally linked to T2, T4, T6, T5, and SECphi27 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T4-3 locus represented by DefenseFinder as a single-profile model, PD-T4-3__PD-T4-3, and experimentally linked to T2, T4, and T6 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T4-4 locus represented by DefenseFinder as a two-profile model requiring PD-T4-4__PD-T4-4_A and PD-T4-4__PD-T4-4_B, and experimentally linked to T2, T4, T6, and SECphi17 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T4-5 locus represented by DefenseFinder as a single-profile model, PD-T4-5__PD-T4-5, and experimentally linked to T4, T6, LambdaVir, and T5 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T4-6 locus represented by DefenseFinder as a single-profile model, PD-T4-6__PD-T4-6, and experimentally linked to T2, T4, and T6 protection when expressed in E. coli.

An abortive infection system in which an organism possesses a PD-T4-7 locus represented by DefenseFinder as a single-profile model, PD-T4-7__PD-T4-7, and experimentally linked to T2, T4, and T6 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T4-8 locus represented by DefenseFinder as a single-profile model, PD-T4-8__PD-T4-8, and experimentally linked to T2, T4, T6, SECphi18, and SECphi27 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T7-1 locus represented by DefenseFinder as a single-profile model, PD-T7-1__PD-T7-1, and experimentally linked to T7 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T7-2 locus represented by DefenseFinder as a two-profile model, PD-T7-2__PD-T7-2_A and PD-T7-2__PD-T7-2_B, and experimentally linked to T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, and T7 protection when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T7-3 locus represented by DefenseFinder as a single-profile model, PD-T7-3__PD-T7-3, and experimentally linked to protection against T2, T4, T6, T5, SECphi17, T3, and T7 when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T7-4 locus represented by DefenseFinder as a single-profile model, PD-T7-4__PD-T7-4, and experimentally linked to protection against SECphi18, SECphi27, T3, and T7 when expressed in E. coli.

A phage defense system in which an organism possesses a PD-T7-5 locus represented by DefenseFinder as a single-profile model, PD-T7-5__PD-T7-5, and experimentally linked to SECphi17, T3, and T7 protection when expressed in E. coli.

A biopolymer-degradation metabolism in which an organism depolymerizes pectin into oligogalacturonides and catabolizes the released pectin breakdown products using pectinolytic enzymes.

An anaerobic respiration in which an organism uses perchlorate as the terminal electron acceptor and reduces it to chloride for energy conservation.

A flagellar arrangement with flagella distributed over the entire cell surface rather than localized to the poles.

Formation of dormant phenotypic variants (persister cells) that are transiently tolerant to antibiotics and other lethal stresses without carrying genetic resistance, arising stochastically in a population.

An autophagy phenotype in which a microbial cell selectively degrades its peroxisomes by delivering them to lysosomal or vacuolar compartments.

A phage defense system in which an organism possesses a Pf4 prophage-encoded PfiAT toxin-antitoxin locus represented by DefenseFinder as a two-profile model requiring PfiAT__PfiA and PfiAT__PfiT.

A pH phenotype with numerical limits expressing the breadth (maximum minus minimum) of external pH supporting growth of an organism.

A pH delta phenotype with a growth-supporting pH breadth of approximately 5–9 pH units, characteristic of euryphilic pH-tolerance physiology.

A pH delta phenotype with a growth-supporting pH breadth of approximately 1–2 pH units, characteristic of organisms with limited pH-tolerance breadth.

A pH delta phenotype with a growth-supporting pH breadth of approximately 2–3 pH units, characteristic of organisms with moderate pH-tolerance breadth.

A pH delta phenotype with a growth-supporting pH breadth of approximately 3–4 pH units, characteristic of organisms with broad pH-tolerance breadth.

A pH delta phenotype with a growth-supporting pH breadth of approximately 4–5 pH units, characteristic of organisms with wide pH-tolerance breadth.

A pH delta phenotype with a very narrow growth-supporting pH breadth of at most approximately 1 pH unit, characteristic of stenotopic pH-sensitive physiology.

A phenotype that describes how the rate and extent of population growth are affected by environmental pH.

A pH phenotype with numerical limits that represents the external pH conditions at which an organism exhibits the most efficient growth and reproduction.

A pH optimum phenotype with the best-growth external pH above approximately 8, corresponding to alkaliphilic or extreme-alkaliphilic physiology.

A pH optimum phenotype with the best-growth external pH at or below approximately 6, corresponding to acidophilic or extreme-acidophilic physiology.

A pH optimum phenotype with the best-growth external pH between approximately 6 and 7, corresponding to neutrophilic physiology.

A pH optimum phenotype with the best-growth external pH between approximately 7 and 8, corresponding to neutrophilic or moderately alkaliphilic physiology.

A phenotype characterized by specific pH values or ranges that define growth or activity limits.

A pH phenotype with numerical limits that bounds the minimum and maximum external pH supporting growth of an organism.

A pH range phenotype in which the growth-supporting external pH range spans approximately 10–14, characteristic of extreme-alkaliphile physiology.

A pH range phenotype in which the growth-supporting external pH range spans approximately 4–6, characteristic of acidophilic physiology.

A pH range phenotype in which the growth-supporting external pH range spans approximately 6–7, characteristic of neutrophilic physiology.

A pH range phenotype in which the growth-supporting external pH range spans approximately 7–8, characteristic of neutrophile or mild-alkaliphile physiology.

A pH range phenotype in which the growth-supporting external pH range spans approximately 8–10, characteristic of alkaliphile physiology.

A pH range phenotype in which growth extends to external pH at or below approximately 4, characteristic of extreme-acidophile physiology.

A motile phenotype in which active locomotion is directionally biased in response to an external pH gradient.

A phenotype in which polarized growth is directionally biased in response to a spatial gradient of external pH.

A genomics trait describing possession of one or more bacterial or archaeal immune systems that inhibit bacteriophage infection.

A physiological phenotype in which a microbial cell engulfs extracellular particles by enclosing them within its membrane and internalizes them into membrane-bound compartments.

A physiological phenotype in which a microbial organism ingests particulate food and assimilates nutrients derived from that food.

A quality that differentiates specific instances of a species from other instances of the same species.

A physiological enzyme-activity phenotype in which a cell produces active phenylalanine arylamidase enzymes that hydrolyze phenylalanine arylamide substrates.

A genomics trait describing possession of a DNA phosphorothioation-dependent antiviral locus in which host DNA phosphorothioate modification is paired with a Dnd-, Ssp-, or Pbe-family effector module to restrict invading viral DNA.

A trophic type characterized by the use of light as the energy source and carbon dioxide as the primary carbon source for biosynthesis.

A metabolism in which anoxygenic phototrophs use light energy to oxidize Fe(II) as an electron donor for carbon fixation and biomass formation.

A trophic type in which an organism uses light as the energy source and organic compounds as the primary carbon source for biosynthesis.

A motile phenotype in which the speed of active locomotion changes in response to illumination intensity, without requiring orientation toward or away from the light source.

A trophic type in which an organism obtains energy from light and carbon from carbon dioxide using inorganic electron donors.

A trophic type in which an organism uses light as the energy source and inorganic compounds as electron donors, typically with carbon dioxide as the primary carbon source.

A trophic type in which an organism obtains energy from light and carbon from organic compounds.

A phototrophic metabolism that uses light energy and chlorophyll- or bacteriochlorophyll-based photochemical reaction centers to drive electron flow, fixing CO2 and/or generating reducing power. Subdivided into oxygenic and anoxygenic photosynthesis.

A motile phenotype in which active locomotion is directionally biased toward or away from a light source in response to illumination.

A trophic type characterized by the use of light as the primary energy source for metabolic processes, regardless of carbon source.

A metabolism in which an organism captures light as its energy source. It encompasses chlorophyll-based photosynthesis (with photochemical reaction centers) and retinal-based (rhodopsin) light-driven ion pumping.

A phenotype in which growth is directionally oriented or reoriented toward or away from a light source in response to illumination.

A phage defense system in which an organism possesses a Phrann gp29-gp30 locus that can protect bacteria from bacteriophage infection.

An environmental growth preference in which an organism grows optimally at hydrostatic pressures substantially above atmospheric pressure (0.1 MPa), characteristic of deep-sea and deep-subsurface microorganisms.

A pressure growth preference in which an organism can grow under elevated hydrostatic pressure but grows at similar or faster rates at atmospheric pressure (0.1 MPa).

An abortive infection system in which an organism possesses an F-plasmid pif-family locus represented by the DefenseFinder Pif__PifA and Pif__PifC profiles and exemplified by the pif region that specifies abortive infection of T7 phage.

A phenotype characterized by the color of pigments produced by a microorganism.

A pigmentation phenotype in which microbial colonies or cells appear pink due to accumulation of pink or rose carotenoid pigments.

A physiological phenotype in which a microbial organism internalizes surrounding extracellular fluid and dissolved material into membrane-bound compartments formed from its plasma membrane.

A pathogen that infects organisms in the kingdom Viridiplantae.