Ecological adaptation and succession of human fecal microbial communities in an automated in vitro fermentation system

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningfagfællebedømt

Longitudinal studies of gut microbiota following specific interventions are vital for understanding how they influence host health. However, robust longitudinal sampling of gut microbiota is a major challenge, which can be addressed using in vitro fermentors hosting complex microbial communities. Here, by employing 16S rRNA gene amplicon sequencing, we investigated the adaptation and succession of human fecal microbial communities in an automated multistage fermentor. We performed two independent experiments using different human donor fecal samples, one configured with two units of three colon compartments each studied for 22 days and another with one unit of two colon compartments studied for 31days. The fermentor maintained a trend of increasing microbial alpha diversity along colon compartments. Within each experiment, microbial compositions followed compartment-specific trajectories and reached independent stable configurations. While compositions were highly similar between replicate units, they were clearly separated between different experiments, showing that they maintained the individuality of fecal inoculum rather than converging on a fermentor-specific composition. While some fecal amplicon sequence variants (ASVs) were undetected in the fermentor, many ASVs undetected in the fecal samples flourished in vitro. These bloomer ASVs accounted for significant proportions of the population and included prominent healthassociated microbes such as Bacteroides fragilis and Akkermansia muciniphila. Turnover in community compositions is likely explained by feed composition and pH, suggesting that these communities can be easily modulated. Our results suggest that in vitro fermentors are promising tools to study complex microbial communities harboring important members of human gut microbiota.

OriginalsprogEngelsk
Artikelnummere00232-21
TidsskriftmSystems
Vol/bind6
Udgave nummer4
Antal sider18
ISSN2379-5077
DOI
StatusUdgivet - 2021

Bibliografisk note

Funding Information:
Novo Nordisk Foundation Center for Basic Metabolic Research is an independent research center, based at the University of Copenhagen, Denmark, and partially funded by an unconditional donation from the Novo Nordisk Foundation (www.cbmr.ku.dk) (grant number NNF18CC0034900). This work was supported by the Novo Nordisk Foundation grant NNF19OC0057169. C.A.-S. was supported by Novo Nordisk Foundation (grant number NNF16CC0020896). C.S. was supported by the Danish Council of Independent Research (grant number 6111-00471B). J.A.G. and O.H. were supported by Novo Nordisk Foundation Challenge program MicrobLiver (grant number NNF15OC0016692).

Publisher Copyright:
© 2021 Gnanasekaran et al.

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