Gut microbial interactions based on network construction and bacterial pairwise cultivation  

作　　者：Min-Zhi Jiang Chang Liu Chang Xu He Jiang Yulin Wang Shuang-Jiang Liu 

机构地区：[1]State Key Laboratory of Microbial Technology,Shandong University,Qingdao 266000,China [2]State Key Laboratory of Microbial Resources,and Environmental Microbiology Research Center(EMRC),Institute of Microbiology,Chinese Academy of Sciences,Beijing 100101,China [3]University of Chinese Academy of Sciences,Beijing 100049,China

出　　处：《Science China(Life Sciences)》2024年第8期1751-1762,共12页中国科学（生命科学英文版）

基　　金：supported by the National Key Research and Development Program of China(2021YFA0717002);Taishan Young Scholars(tsqn202306029).

摘　　要：Association networks are widely applied for the prediction of bacterial interactions in studies of human gut microbiomes.However,the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated bacteria.In this study,we addressed this challenge by integrating in vitro time series network(TSN)associations and cocultivation of TSN taxon pairs.Fecal samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 days.Enriched cells were harvested for DNA extraction and metagenomic sequencing.A total of 198 metagenome-assembled genomes(MAGs)were recovered.Temporal dynamics of bacteria growing on the YCFA agar were used to infer microbial association networks.To experimentally validate the interactions of taxon pairs in networks,we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank,respectively,for pairwise co-cultures.The co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism(51.67%),followed by commensalism(21.67%),amensalism(18.33%),competition(5%)and exploitation(3.33%).Genome-centric analysis further revealed that the commensal gut bacteria(helpers and beneficiaries)might interact with each other via the exchanges of amino acids with high biosynthetic costs,short-chain fatty acids,and/or vitamins.We also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7%of these strains was significantly promoted.This approach provides new insights into the gut microbiome complexity and microbial interactions in association networks.Our work highlights that the positive relationships in gut microbial communities tend to be overestimated,and that amino acids,short-chain fatty acids,and vitamins are contributed to the positive relationships.

关 键 词：human gut microbiome gut microbial pairwise interaction CO-CULTURE association network microbial community 

分 类 号：R37[医药卫生—病原生物学]