Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community

Anna S. Weiss, Lisa S. Niedermeier, Alexandra von Strempel, Anna G. Burrichter, Diana Ring, Chen Meng, Karin Kleigrewe, Chiara Lincetto, Johannes Hübner and Bärbel Stecher ()
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Anna S. Weiss: Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich
Lisa S. Niedermeier: Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich
Alexandra von Strempel: Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich
Anna G. Burrichter: Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich
Diana Ring: Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich
Chen Meng: Technical University of Munich
Karin Kleigrewe: Technical University of Munich
Chiara Lincetto: Ludwig Maximilians University
Johannes Hübner: Ludwig Maximilians University
Bärbel Stecher: Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich

Nature Communications, 2023, vol. 14, issue 1, 1-16

Abstract: Abstract A challenging task to understand health and disease-related microbiome signatures is to move beyond descriptive community-level profiling towards disentangling microbial interaction networks. Using a synthetic gut bacterial community, we aimed to study the role of individual members in community assembly, identify putative keystone species and test their influence across different environments. Single-species dropout experiments reveal that bacterial strain relationships strongly vary not only in different regions of the murine gut, but also across several standard culture media. Mechanisms involved in environment-dependent keystone functions in vitro include exclusive access to polysaccharides as well as bacteriocin production. Further, Bacteroides caecimuris and Blautia coccoides are found to play keystone roles in gnotobiotic mice by impacting community composition, the metabolic landscape and inflammatory responses. In summary, the presented study highlights the strong interdependency between bacterial community ecology and the biotic and abiotic environment. These results question the concept of universally valid keystone species in the gastrointestinal ecosystem and underline the context-dependency of both, keystone functions and bacterial interaction networks.

Date: 2023
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DOI: 10.1038/s41467-023-40372-0

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