HabitatMech

intestine environment

ENVO:2100002 ·resolve ·OTHER ·EXACT REVIEWED

An environmental system determined by an intestine. — ENVO

Source attestations

Each upstream vocabulary's own account of this habitat. Assertion counts are per-source units and are not comparable across sources — GOLD counts organisms, BacDive strains, PREGO taxa.

What each upstream vocabulary says about this habitat
SourceLabel / pathAssertionsUnit
ENVIRONMENTS_TABLE host_animal_endotherm_intestinal
Physicochemical parameter bands from kg-microbe's environment table.		 —
MADIN intestine environment 1963 TAXON
PREGO intestine environment 2406 TAXON

Broader habitats

Environmental parameters

Physicochemical parameters
ParameterValueSource
GRADIENTShighkg-microbe environments.csv (host_animal_endotherm_intestinal)
NUTRIENTShighkg-microbe environments.csv (host_animal_endotherm_intestinal)
ORGANIC_MATTERhighkg-microbe environments.csv (host_animal_endotherm_intestinal)
PRESSURElowkg-microbe environments.csv (host_animal_endotherm_intestinal)
SALINITYmediumkg-microbe environments.csv (host_animal_endotherm_intestinal)
SALINITY_VARIABILITYsmallkg-microbe environments.csv (host_animal_endotherm_intestinal)
STRUCTURAL_COMPLEXITYmediumkg-microbe environments.csv (host_animal_endotherm_intestinal)
TEMPERATUREmediumkg-microbe environments.csv (host_animal_endotherm_intestinal)
TEMPERATURE_VARIABILITYlowkg-microbe environments.csv (host_animal_endotherm_intestinal)
WATER_AVAILABILITYmediumkg-microbe environments.csv (host_animal_endotherm_intestinal)
WATER_VARIABILITYpermanently wetkg-microbe environments.csv (host_animal_endotherm_intestinal)

Causal graphs

Intestinal anaerobic glycan fermentation

Host epithelial oxygen consumption and intestinal glycan pools create anaerobic nutrient gradients that favor fermentative gut microbiota and short-chain fatty acid production.

Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.
Intestinal anaerobic glycan fermentation 8 nodes and 6 directed relationships. Labels and evidence are also available in the adjacent table. colonocyte beta-oxidation — reduces → low luminal oxygen; Evidence: PMID:28798125 reduces low luminal oxygen — selects for → obligate anaerobe dominance; Evidence: PMID:30498100 selects for intestine environment — provides → mucin O-glycans; Evidence: PMID:37442097 provides mucin O-glycans — fuels → microbial glycan fermentation; Evidence: PMID:37442097 fuels dietary fiber — fuels → microbial glycan fermentation; Evidence: PMID:29902436 fuels microbial glycan fermentation — produces → short-chain fatty acids; Evidence: PMID:29902436 produces intestine environment (HABITAT); intestine_environment; ENVO:2100002 HABITAT intestine environment colonocyte beta-oxidation (BIOLOGICAL_PROCESS); colonocyte_beta_oxidation BIOLOGICAL_PROCESS colonocyte beta-oxidation low luminal oxygen (ENVIRONMENTAL_PARAMETER); low_luminal_oxygen ENVIRONMENTAL_PARAMETER low luminal oxygen obligate anaerobe dominance (COMMUNITY_PROCESS); obligate_anaerobe_dominance COMMUNITY_PROCESS obligate anaerobe dominance dietary fiber (CHEMICAL); dietary_fiber CHEMICAL dietary fiber mucin O-glycans (CHEMICAL); mucin_o_glycans CHEMICAL mucin O-glycans microbial glycan fermentation (BIOLOGICAL_PROCESS); microbial_glycan_fermentation BIOLOGICAL_PROCESS microbial glycan fermentation short-chain fatty acids (CHEMICAL); short_chain_fatty_acids CHEMICAL short-chain fatty acids
intestinal_anaerobic_glycan_fermentation edges
EdgeSubjectPredicateObjectEvidence
beta_oxidation_limits_luminal_oxygen colonocyte beta-oxidation reduces
Colonic epithelial beta-oxidation limits oxygen availability in the intestinal lumen.		 low luminal oxygen PMID:28798125
Byndloss and colleagues describe microbiota-activated PPAR-gamma signaling as a driver of colonocyte beta-oxidation that restricts oxygen diffusing into the lumen.
low_oxygen_favors_obligate_anaerobes low luminal oxygen selects for
Low oxygen availability favors obligate anaerobic bacteria in the intestinal microbial community.		 obligate anaerobe dominance PMID:30498100
Litvak, Byndloss, and Baumler summarize the colonocyte oxygen sink as a host-controlled switch that shapes obligate versus facultative anaerobes in the colon.
intestinal_mucus_presents_o_glycans intestine environment provides
Intestinal mucus exposes O-glycans on MUC2 mucin to commensal gut microbes.		 mucin O-glycans PMID:37442097
Luis and Hansson describe O-glycosylated MUC2 as a major component of intestinal mucus.
mucin_glycans_feed_gut_microbes mucin O-glycans fuels
Gut microbiota use host mucin glycans as fermentable carbon sources.		 microbial glycan fermentation PMID:37442097
Luis and Hansson review commensal-microbiota interactions with host mucins and the proteins used to bind or cleave mucin glycans.
dietary_fiber_feeds_gut_microbes dietary fiber fuels
Dietary fibers directly supply gut microbes with fermentable carbohydrate substrates.		 microbial glycan fermentation PMID:29902436
Makki and colleagues review dietary fibers as food components that shape digestive-tract microbial communities.
glycan_fermentation_produces_scfas microbial glycan fermentation produces
Microbial fermentation of intestinal glycans produces short-chain fatty acids.		 short-chain fatty acids PMID:29902436
Makki and colleagues summarize short-chain fatty acids as major bacterial metabolites produced from dietary-fiber fermentation.

Associated taxa

Taxa reported from this habitat, which is weaker than being characteristic of it. rank is out of pool: a high rank in a pool of thousands of near-tied scores is a weak claim. Entries corroborated by a second, independent source are listed first.

Taxa reported from this habitat
TaxonSourceRankPoolCorroborated
Escherichia coli O157 NCBITaxon:1045010 PREGO 10 2406 MADIN
ruminococcus_flavefaciens NCBITaxon:1265 MADIN — 1963 PREGO
Staphylococcus aureus NCBITaxon:1280 MADIN — 1963 PREGO
Streptococcus salivarius NCBITaxon:1304 MADIN — 1963 PREGO
Streptococcus equinus NCBITaxon:1335 MADIN — 1963 PREGO
Enterococcus faecalis NCBITaxon:1351 MADIN — 1963 PREGO
Enterococcus faecium NCBITaxon:1352 MADIN — 1963 PREGO
Bacillus cereus NCBITaxon:1396 MADIN — 1963 PREGO
Bacillus pumilus NCBITaxon:1408 MADIN — 1963 PREGO
Methanothermobacter thermautotrophicus NCBITaxon:145262 MADIN — 1963 PREGO
clostridium_butyricum NCBITaxon:1492 MADIN — 1963 PREGO
Clostridium difficile NCBITaxon:1496 MADIN — 1963 PREGO
Clostridium perfringens NCBITaxon:1502 MADIN — 1963 PREGO
Anoxybacillus pushchinensis NCBITaxon:150248 MADIN — 1963 PREGO
clostridium_septicum NCBITaxon:1504 MADIN — 1963 PREGO
clostridium_aminophilum NCBITaxon:1526 MADIN — 1963 PREGO
clostridium_barati NCBITaxon:1561 MADIN — 1963 PREGO
Lactobacillus brevis NCBITaxon:1580 MADIN — 1963 PREGO
Lactobacillus helveticus NCBITaxon:1587 MADIN — 1963 PREGO
Lactobacillus plantarum NCBITaxon:1590 MADIN — 1963 PREGO
Lactobacillus gasseri NCBITaxon:1596 MADIN — 1963 PREGO
Lactobacillus reuteri NCBITaxon:1598 MADIN — 1963 PREGO
Lactobacillus fermentum NCBITaxon:1613 MADIN — 1963 PREGO
Lactobacillus salivarius NCBITaxon:1624 MADIN — 1963 PREGO
treponema_bryantii NCBITaxon:163 MADIN — 1963 PREGO

Showing 25 of 49 kept associations.

Also called

Curation

What a curator decided about this record, and why. A record built from several source concepts can carry one decision per concept.

  1. REVIEW 2026-08-15 · claude-opus-5

    Reviewed and endorsed the seeder's own resolution. Co-attestor review (#12): this source names the ontology CURIE itself, so its grounding is definitional rather than a lexical guess — the record IS the term the source pointed at. Recorded so the record it co-attests can reach REVIEWED, which needs every source concept decided. (source concept habitatmech:MADIN.38ed811a63)

  2. REVIEW 2026-08-15 · claude-opus-5

    Reviewed and endorsed the seeder's own resolution. Co-attestor review (#12): this source names the ontology CURIE itself, so its grounding is definitional rather than a lexical guess — the record IS the term the source pointed at. Recorded so the record it co-attests can reach REVIEWED, which needs every source concept decided. (source concept habitatmech:PREGO.5bfab021ea)

  3. ADD_CAUSAL_GRAPH 2026-09-04 · codex

    Added a mammalian intestinal anaerobic glycan-fermentation graph backed by PMID:28798125, PMID:30498100, PMID:37442097, and PMID:29902436.

Provenance

Generated by scripts/seed_from_sources.py from the committed inventories in data/raw/. View the record.