Microbiome and metabolome association network analysis identifies Clostridium_sensu_stricto_1 as a stronger keystone genus candidate than Bifidobacterium in the gut of common marmosets

• Published in: mSystems Vol. 10; no. 8; p. e0021425
• Main Authors: Hernandez, Jordan B., Hayer, Shivdeep S., Alvarez, Sophie, Fischer, Anne, Hassenstab, Haley R., Cooper, Katherine, Alsafwani, Zahraa W., Benson, Andrew K., Suhr Van Haute, Mallory J., Izard, Jacques, Song, Hyun-Seob, Clayton, Jonathan B.
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 07.07.2025
• Subjects: Animals; Bacteria; Bacteroidales; Bifidobacterium; Bile acids; bioinformatics; Captivity; Clostridium; Computational Biology; Diet; Disease; Feces; gut metabolome; gut microbiome; Gut microbiota; Intestinal microflora; marmoset; Metabolism; Metabolites; Metabolomics; Microbiomes; Microbiota; multi-omics; network analysis; Research Article; rRNA 16S; Social isolation; Taurine; Taxonomy; gut metabolome; gut microbiome; non-human primate; bioinformatics; multi-omics; amplicon sequencing; network analysis; marmoset; microbial ecology
• ISSN: 2379-5077; 2379-5077
• DOI: 10.1128/msystems.00214-25

Previous studies have identified significant individuality within the gut microbiome of common marmosets. The reasons for this inter-subject variability and how it relates to health in captivity are poorly understood, owing to a lack of knowledge regarding dynamic interactions between specific microbiota. To that end, this study characterized significant temporal associations between the gut microbiome and metabolome of healthy captive marmosets. Our findings suggest that certain microbial taxa exert a stronger influence within the gut than others. Specifically, Bifidobacterium was the most abundant genus and primary driving force behind subject-specific microbiome differences, while Clostridium_sensu_stricto_1 and bacteria from the order Bacteroidales were the main sources, respectively, for significant bacteria-metabolite and bacteria-bacteria associations. Together, this suggests that Bifidobacterium may compete with the other taxa for resources and a metabolic niche in the marmoset microbiome.