Evidence map›Paper›PMID 42534443›Full record

ArticleiMeta2026

Beyond omics: From descriptive profiling to causal and scalable design of fermentation microbiomes.

Dongze Niu, Huili Pang, Xuekai Wang, Liang Song, Jing Zhang, Ansah Terry, Junfeng Li, Jingwen Cao, Qinhua Liu, Dayong Han and 13 more

Abstract readLetter
PubMed Full text at PMC Publisher
In one paragraph

Article in iMeta, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

23 authors.

Dongze NiuNational-Local Joint Engineering Research Center of Biomass Refining and High-Quality Utilization, Institute of Urban and Rural Mining Changzhou University Changzhou China.ORCID https://orcid.org/0000-0001-6554-885X
Huili PangState Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agriculture and Biomanufacturing Zhengzhou University Zhengzhou China.
Xuekai WangCollege of Grassland Science and Technology China Agricultural University Beijing China.
Liang SongInstitute of Microbiology Chinese Academy of Sciences Beijing China.
Jing ZhangCollege of Food Science & Engineering Nanjing University of Finance and Economics Nanjing China.
Ansah TerryFaculty of Agriculture, Food and Consumer Sciences University for Development Studies Tamale Ghana.
Junfeng LiCollege of Agro-Grassland Science Nanjing Agricultural University Nanjing China.
Jingwen CaoSchool of Agriculture and Biology Shanghai Jiao Tong University Shanghai China.
Qinhua LiuFaculty of Animal Science and Technology Yunnan Agricultural University Kunming China.
Dayong HanInstitute of Microbiology Chinese Academy of Sciences Beijing China.
Jidong WangState Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agriculture and Biomanufacturing Zhengzhou University Zhengzhou China.
Jong Geun KimInstitute of Green Bio Science & Technology Seoul National University Pyeongchang Korea.
Kazuo AtakuDepartment of Dairy Science Rakuno Gakuen University Hokkaido Japan.
Smerjai BureenokFaculty of Agricultural Innovation and Technology Rajamangala University of Technology Isan Nakhon Ratchasima Thailand.
Zhongfang TanState Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agriculture and Biomanufacturing Zhengzhou University Zhengzhou China.
Fengyan BaiCollege of Food Science & Engineering Nanjing University of Finance and Economics Nanjing China.
Tao ShaoCollege of Agro-Grassland Science Nanjing Agricultural University Nanjing China.
Taoli HuheNational-Local Joint Engineering Research Center of Biomass Refining and High-Quality Utilization, Institute of Urban and Rural Mining Changzhou University Changzhou China.
Lifeng WangCollege of Food Science & Engineering Nanjing University of Finance and Economics Nanjing China.
Peijie HanInstitute of Microbiology Chinese Academy of Sciences Beijing China.
Chuncheng XuCollege of Engineering China Agricultural University Beijing China.
Fuyu YangCollege of Grassland Science and Technology China Agricultural University Beijing China.
Yimin CaiState Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agriculture and Biomanufacturing Zhengzhou University Zhengzhou China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

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.

Identifiers

PMID42534443
PMCPMC13420143

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.