Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria.

IF 13.8 1区 生物学 Q1 MICROBIOLOGY
Jiaying Zhu, Min-Zhi Jiang, Xue Chen, Min Li, Yu-Lin Wang, Chang Liu, Shuang-Jiang Liu, Wei-Hua Chen
{"title":"Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria.","authors":"Jiaying Zhu, Min-Zhi Jiang, Xue Chen, Min Li, Yu-Lin Wang, Chang Liu, Shuang-Jiang Liu, Wei-Hua Chen","doi":"10.1186/s40168-025-02156-0","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, there is a lack of large-scale experiments focusing on bacterial interactions within the human gut microbiome.</p><p><strong>Methods: </strong>We investigated the pairwise interactions of 113 bacterial strains isolated from healthy Chinese volunteers, selected for their high abundance and functional representation of the human gut microbiome. Using mGAM agar plates, a rich medium designed to maintain community structure, we established the \"PairInteraX\" dataset, which includes 3233 pair combinations of culturable human gut bacteria. This dataset was analyzed to identify interaction patterns and the key factors influencing these patterns.</p><p><strong>Results: </strong>Our analysis revealed that negative interactions were predominant among the bacteria in the PairInteraX dataset. When combined with in vivo gut metagenome datasets, we noted a diminishing mutualism and an increasing competition as microbial abundances increased; consequently, the maintenance of community diversity requires the participation of various types of interactions, especially the negative interactions. We also identified key factors influencing these interaction patterns including metabolic capacity and motility.</p><p><strong>Conclusions: </strong>This study provides a comprehensive overview of pairwise bacterial interactions within the human gut microbiome, revealing a dominance of negative interactions. Besides, metabolic capacity and motility were identified as the key factors to influence the pairwise interaction patterns. This large-scale dataset and analysis offer valuable insights for further research on microbial community dynamics and their implications for host health. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"161"},"PeriodicalIF":13.8000,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12235815/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Microbiome","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s40168-025-02156-0","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

Background: Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, there is a lack of large-scale experiments focusing on bacterial interactions within the human gut microbiome.

Methods: We investigated the pairwise interactions of 113 bacterial strains isolated from healthy Chinese volunteers, selected for their high abundance and functional representation of the human gut microbiome. Using mGAM agar plates, a rich medium designed to maintain community structure, we established the "PairInteraX" dataset, which includes 3233 pair combinations of culturable human gut bacteria. This dataset was analyzed to identify interaction patterns and the key factors influencing these patterns.

Results: Our analysis revealed that negative interactions were predominant among the bacteria in the PairInteraX dataset. When combined with in vivo gut metagenome datasets, we noted a diminishing mutualism and an increasing competition as microbial abundances increased; consequently, the maintenance of community diversity requires the participation of various types of interactions, especially the negative interactions. We also identified key factors influencing these interaction patterns including metabolic capacity and motility.

Conclusions: This study provides a comprehensive overview of pairwise bacterial interactions within the human gut microbiome, revealing a dominance of negative interactions. Besides, metabolic capacity and motility were identified as the key factors to influence the pairwise interaction patterns. This large-scale dataset and analysis offer valuable insights for further research on microbial community dynamics and their implications for host health. Video Abstract.

系统的成对共培养揭示了人类肠道细菌之间主要的负面相互作用。
背景:了解人类肠道中细菌的成对相互作用对于破译细菌相互作用的复杂网络及其对宿主健康的贡献至关重要。然而,缺乏针对人类肠道微生物群内细菌相互作用的大规模实验。方法:我们研究了从健康的中国志愿者中分离的113株细菌菌株的成对相互作用,选择这些菌株是因为它们的高丰度和人类肠道微生物组的功能代表。使用mGAM琼脂板(一种用于维持群落结构的富培养基),我们建立了“PairInteraX”数据集,其中包括3233对可培养的人类肠道细菌组合。对该数据集进行分析,以确定交互模式和影响这些模式的关键因素。结果:我们的分析显示,在PairInteraX数据集中,细菌之间的负相互作用占主导地位。当与体内肠道宏基因组数据集相结合时,我们注意到随着微生物丰度的增加,互惠互利的减少和竞争的增加;因此,维持社区多样性需要各种类型的互动,特别是消极互动的参与。我们还确定了影响这些相互作用模式的关键因素,包括代谢能力和运动性。结论:本研究提供了人类肠道微生物组内成对细菌相互作用的全面概述,揭示了负相互作用的优势。此外,代谢能力和运动能力被确定为影响两两相互作用模式的关键因素。这种大规模的数据集和分析为进一步研究微生物群落动态及其对宿主健康的影响提供了有价值的见解。视频摘要。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
Microbiome
Microbiome MICROBIOLOGY-
CiteScore
21.90
自引率
2.60%
发文量
198
审稿时长
4 weeks
期刊介绍: Microbiome is a journal that focuses on studies of microbiomes in humans, animals, plants, and the environment. It covers both natural and manipulated microbiomes, such as those in agriculture. The journal is interested in research that uses meta-omics approaches or novel bioinformatics tools and emphasizes the community/host interaction and structure-function relationship within the microbiome. Studies that go beyond descriptive omics surveys and include experimental or theoretical approaches will be considered for publication. The journal also encourages research that establishes cause and effect relationships and supports proposed microbiome functions. However, studies of individual microbial isolates/species without exploring their impact on the host or the complex microbiome structures and functions will not be considered for publication. Microbiome is indexed in BIOSIS, Current Contents, DOAJ, Embase, MEDLINE, PubMed, PubMed Central, and Science Citations Index Expanded.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信