What is CultureBotAI?

CultureBotAI is a research initiative at Lawrence Berkeley National Laboratory in Berkeley, California, that develops AI-driven tools and knowledge graphs for microbial cultivation and computational biology.

Who leads CultureBotAI?

CultureBotAI is led by Dr. Marcin P. Joachimiak, a scientist specializing in microbiology, knowledge graph development, and computational biology at Lawrence Berkeley National Laboratory.

Where is CultureBotAI based?

CultureBotAI is based at Lawrence Berkeley National Laboratory in Berkeley, California, within the Environmental Genomics and Systems Biology Division.

KG-Microbe is a comprehensive modular knowledge graph developed by Dr. Marcin P. Joachimiak that integrates diverse microbial data sources to enable AI-driven insights for growth prediction and culture optimization.

How can I access KG-Microbe?

KG-Microbe is available on GitHub at https://github.com/Knowledge-Graph-Hub/kg-microbe under the BSD-3-Clause license. The publication is available in GigaScience at https://doi.org/10.1093/gigascience/giag077

What does CultureBotAI work on?

CultureBotAI focuses on three main areas: (1) cultivation of isolated and novel organisms, (2) culture optimization through data-driven approaches, and (3) growth preference prediction using machine learning and AI methods.

Publications by Dr. Marcin P. Joachimiak — KG-Microbe and AI for Microbiology

Our research outputs led by Dr. Marcin P. Joachimiak span KG-Microbe knowledge graph development, AI applications in microbiology, and computational approaches to microbial cultivation.

Bibliography

Every publication, preprint, and software record from this work, with resolvable links. Individual pages link back to the entries relevant to them.

Journal Articles

Santangelo BE, Hegde H, Caufield JH, Reese J, Kliegr T, Hunter LE, Lozupone CA, Mungall CJ, Joachimiak MP. KG-Microbe — Building Modular and Scalable Knowledge Graphs for Microbiome and Microbial Sciences. GigaScience. 2026;giag077. doi:10.1093/gigascience/giag077
Máša P, Kliegr T, Joachimiak MP. Explainable rule-based prediction of cultivation media for microbes. Computational and Structural Biotechnology Journal. 2025;27:5194–5206. doi:10.1016/j.csbj.2025.10.014 · free full text

Preprints

Naseem S, Miller MA, Martinez-Gomez NC, Sun N, Joachimiak MP. MicroGrowAgents: An Agentic AI System for Microbial Cultivation Engineering. bioRxiv. 2026. doi:10.64898/2026.06.04.729985

Project page: MicroGrowAgents

Software and Data Records

Joachimiak MP. Knowledge Oriented Graph Unified Transformer (KOGUT) v0.1 [software]. DOE CODE; 2025. doi:10.11578/dc.20260210.3 · DOE CODE 175162

KOGUT is registered in DOE CODE and has no public source repository yet. See the tool entry for architecture and training details.
Joachimiak MP, Santangelo BE, Hegde H, Caufield JH, Reese J, Kliegr T, Hunter LE, Lozupone CA, Mungall CJ. kg-microbe: modular knowledge graph for microbiome and microbial sciences [software]. github.com/Knowledge-Graph-Hub/kg-microbe

License: BSD-3-Clause. See KG-Microbe.
CultureBotAI organization repositories — CultureMech, MediaIngredientMech, CommunityMech, TraitMech, and ProteinTraitsMech. github.com/CultureBotAI. Each repository carries its own citation and license; see Resources.
Joachimiak MP. KG-Microbe — Building Modular and Scalable Knowledge Graphs for Microbiome and Microbial Sciences [workflow]. WorkflowHub; v1. doi:10.48546/workflowhub.workflow.2044.1 · WorkflowHub 2044

The registered knowledge-graph construction workflow. License: BSD-3-Clause.

Talks and Presentations

Newest first. Titles are given as published by the hosting channel; ISCB truncates them with an ellipsis. Entries marked “poster and short talk” were presented as posters at ISMB, which also accepts a recorded short talk alongside the poster — that recording is what is linked.

Joachimiak MP. “RuleML/GOBLIN COST Action Lecture on Data Science: Teaching AI to Teach Humans About Microbiology.” RuleML / COST GOBLIN Action Seminar; 2026. Recording (published 5 August 2026)

Covers KG-Microbe and METPO, compares boosted trees, symbolic rule mining and relational graph deep learning for predicting taxa–growth-media pairings, and closes with MicroGrowAgents and KOGUT.
Joachimiak MP. “Knowledge-Graph-driven and LLM-enhanced Microbial…” BOKR COSI, ISMB/ECCB 2025. Recording (ISCB)
Santangelo BE. “Harmonizing human and microbial datasets to…” Bio-Ontologies COSI, ISMB 2024. Recording (ISCB)
Joachimiak MP. “Machine Learning to Uncover Microbial…” Function COSI poster and short talk, ISMB 2022. Recording (ISCB)
Joachimiak MP. PowerTalks Seminar Series. UAB Department of Biomedical Informatics and Data Science; 14 January 2022. Recording (UAB DBIDS)
Joachimiak MP. “KG-Microbe: a reference knowledge-graph and…” BOSC poster and short talk, ISMB/ECCB 2021. Recording (ISCB)

Methods and infrastructure this work builds on, co-authored by Dr. Joachimiak.

Caufield JH, Putman T, Schaper K, Unni DR, Hegde H, et al. (incl. Joachimiak MP). KG-Hub — building and exchanging biological knowledge graphs. Bioinformatics. 2023;39(7):btad418. doi:10.1093/bioinformatics/btad418 · free full text
Caufield JH, Hegde H, Emonet V, Harris NL, Joachimiak MP, et al. Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning. Bioinformatics. 2024;40(3):btae104. doi:10.1093/bioinformatics/btae104 · free full text
Joachimiak MP, Miller MA, Caufield JH, Ly R, Harris NL, et al. The Artificial Intelligence Ontology: LLM-Assisted Construction of AI Concept Hierarchies. Applied Ontology. 2024;19:408–418. doi:10.1177/15705838241304103
Clark T, Caufield H, Parker JA, Al Manir S, Amorim E, et al. (31 authors, incl. Joachimiak M). AI-readiness criteria for biomedical data. bioRxiv. 2026 (v6; first posted 2024). doi:10.1101/2024.10.23.619844

📬 Citation Information

Primary Citation for CultureBotAI Work

@article{santangelo2026kgmicrobe,
  title={KG-Microbe - Building Modular and Scalable Knowledge Graphs for Microbiome and Microbial Sciences},
  author={Santangelo, Brook E and Hegde, Harshad and Caufield, J Harry and Reese, Justin and Kliegr, Tomas and Hunter, Lawrence E and Lozupone, Catherine A and Mungall, Christopher J and Joachimiak, Marcin P},
  journal={GigaScience},
  year={2026},
  doi={10.1093/gigascience/giag077},
  url={https://doi.org/10.1093/gigascience/giag077}
}

Explainable Media Prediction

@article{masa2025explainable,
  title={Explainable rule-based prediction of cultivation media for microbes},
  author={M{\'a}{\v s}a, Petr and Kliegr, Tom{\'a}{\v s} and Joachimiak, Marcin P},
  journal={Computational and Structural Biotechnology Journal},
  volume={27},
  pages={5194--5206},
  year={2025},
  doi={10.1016/j.csbj.2025.10.014},
  url={https://doi.org/10.1016/j.csbj.2025.10.014}
}

Software Citation

Software citations will vary by specific GitHub repository within the CultureBotAI organization. Please refer to individual repository documentation for proper citation formats.

📧 Publication Updates

Stay updated on our latest publications:

Google Scholar: Dr. Joachimiak’s Profile
ORCID: 0000-0001-8175-045X

🤝 Collaboration & Co-authorship

We welcome collaboration opportunities and are open to:

Joint research projects combining AI and experimental microbiology
Data sharing initiatives for large-scale cultivation studies
Method development for computational microbiology tools
Review articles synthesizing advances in the field

Contact: MJoachimiak@lbl.gov for collaboration inquiries.

Frequently Asked Questions

How do I cite CultureBotAI’s work?

Cite the primary publication: Santangelo, B. E., et al. (2026). KG-Microbe - Building Modular and Scalable Knowledge Graphs for Microbiome and Microbial Sciences. GigaScience, giag077. https://doi.org/10.1093/gigascience/giag077

What is the DOI for the KG-Microbe publication?

The DOI is 10.1093/gigascience/giag077, available at https://doi.org/10.1093/gigascience/giag077

Where can I find Dr. Joachimiak’s publications?

Dr. Joachimiak’s publications are listed on Google Scholar at https://scholar.google.com/citations?user=zSlIlYQAAAAJ&hl=en and ORCID at https://orcid.org/0000-0001-8175-045X

What license is kg-microbe released under?

kg-microbe is released under the BSD-3-Clause License, allowing free use, modification, and distribution with proper attribution.

Can I use CultureBotAI’s software in my research?

Yes, kg-microbe and related tools are open-source and freely available for research use. Please cite the appropriate publications when using these resources.

Who are the co-authors on the KG-Microbe paper?

Co-authors include Brook E. Santangelo, Harshad Hegde, J. Harry Caufield, Justin Reese, Tomas Kliegr, Lawrence E. Hunter, Catherine A. Lozupone, Christopher J. Mungall, and Marcin P. Joachimiak.