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

Thiyagarajan Gnanasekaran, Juliana Assis Geraldo, David Wilczek Ahrenkiel, Camila Alvarez-Silva, Carmen Saenz, Adnan Khan, Obaida Hanteer, Vithiagaran Gunalan, Kajetan Trost, Thomas Moritz, Manimozhiyan Arumugam*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

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.

Original languageEnglish
Article numbere00232-21
JournalmSystems
Volume6
Issue number4
Number of pages18
ISSN2379-5077
DOIs
Publication statusPublished - 2021

Bibliographical note

Publisher Copyright:
© 2021 Gnanasekaran et al.

Keywords

  • Fecal microbiota
  • In vitro fermentor

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