Beyond omics: From descriptive profiling to causal and scalable design of fermentation microbiomes
Fermentation microbiomes play essential roles in food production, feed preservation, waste valorization, and diverse sustainable industrial processes. Although multi-omics and systems biology have substantially advanced our understanding of their assembly, interactions, and functional dynamics, industrial translation remains constrained by fragmented datasets, limited causal validation, and transport constraints during scale-up. Large language models act as upper-level knowledge and workflow orchestrators, accelerating data integration, hybrid AI-mechanistic modeling, hypothesis generation, and perturbation-guided learning. Collectively, these advances enable fermentation microbiome research to move beyond descriptive omics toward mechanism-guided synthetic microbial community design, causal validation, and scalable biomanufacturing.
Authors
- Dongze Niu (ORCID: https://orcid.org/0000-0001-6554-885X)
- S. Bureenok (ORCID: https://orcid.org/0000-0002-6756-4981)
- Taoli Huhe
- Chuncheng Xu (ORCID: https://orcid.org/0000-0003-0219-3304)
- Junfeng Li (ORCID: https://orcid.org/0000-0001-6739-7805)
- Xuekai Wang (ORCID: https://orcid.org/0000-0002-8072-0467)
- Huili Pang (ORCID: https://orcid.org/0000-0002-6846-7518)
- Jingwen Cao
- Qinhua Liu (ORCID: https://orcid.org/0000-0002-3218-046X)
- Jing Zhang (ORCID: https://orcid.org/0000-0002-6566-6693)
- Jidong Wang (ORCID: https://orcid.org/0000-0002-7127-2244)
- Zhongfang Tan
- Fuyu Yang
- Yimin Cai
- Peijie Han
- Fengyan Bai
- Kazuo Ataku
- Lifeng Wang
- Ansah Terry
- Liang Song
- Jong Geun Kim
- Dayong Han
- Tao Shao
Institutions
- Nanjing Agricultural University (CN)
- Rajamangala University of Technology Isan (TH)
- Nanjing University of Finance and Economics (CN)
- Guizhou University (CN)
- Shanghai Jiao Tong University (CN)
- Yunnan Agricultural University (CN)
- Chinese Academy of Sciences (CN)
- Zhengzhou University (CN)
- Korea Environmental Industry and Technology Institute (KR)
- Guiyang University (CN)
- Institute of Microbiology (CN)
- Changzhou University (CN)
- China Agricultural University (CN)
- Rakuno Gakuen University (JP)
- University for Development Studies (GH)
Publication Details
- Journal
- iMeta
- Published
- 2026-07-30
- DOI
- https://doi.org/10.1002/imt2.70161
- Primary Topic
- Microbial Metabolic Engineering and Bioproduction
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Natural Science Foundation of China
- Tianjin Municipal Science and Technology Bureau