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

Research output: Contribution to journalJournal articlepeer-review

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Ecological adaptation and succession of human fecal microbial communities in an automated in vitro fermentation system. / Gnanasekaran, Thiyagarajan; Geraldo, Juliana Assis; Ahrenkiel, David Wilczek; Alvarez-Silva, Camila; Saenz, Carmen; Khan, Adnan; Hanteer, Obaida; Gunalan, Vithiagaran; Trost, Kajetan; Moritz, Thomas; Arumugam, Manimozhiyan.

In: mSystems, Vol. 6, No. 4, e00232-21, 2021.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Gnanasekaran, T, Geraldo, JA, Ahrenkiel, DW, Alvarez-Silva, C, Saenz, C, Khan, A, Hanteer, O, Gunalan, V, Trost, K, Moritz, T & Arumugam, M 2021, 'Ecological adaptation and succession of human fecal microbial communities in an automated in vitro fermentation system', mSystems, vol. 6, no. 4, e00232-21. https://doi.org/10.1128/mSystems.00232-21

APA

Gnanasekaran, T., Geraldo, J. A., Ahrenkiel, D. W., Alvarez-Silva, C., Saenz, C., Khan, A., Hanteer, O., Gunalan, V., Trost, K., Moritz, T., & Arumugam, M. (2021). Ecological adaptation and succession of human fecal microbial communities in an automated in vitro fermentation system. mSystems, 6(4), [e00232-21]. https://doi.org/10.1128/mSystems.00232-21

Vancouver

Gnanasekaran T, Geraldo JA, Ahrenkiel DW, Alvarez-Silva C, Saenz C, Khan A et al. Ecological adaptation and succession of human fecal microbial communities in an automated in vitro fermentation system. mSystems. 2021;6(4). e00232-21. https://doi.org/10.1128/mSystems.00232-21

Author

Gnanasekaran, Thiyagarajan ; Geraldo, Juliana Assis ; Ahrenkiel, David Wilczek ; Alvarez-Silva, Camila ; Saenz, Carmen ; Khan, Adnan ; Hanteer, Obaida ; Gunalan, Vithiagaran ; Trost, Kajetan ; Moritz, Thomas ; Arumugam, Manimozhiyan. / Ecological adaptation and succession of human fecal microbial communities in an automated in vitro fermentation system. In: mSystems. 2021 ; Vol. 6, No. 4.

Bibtex

@article{b622ca9788de4c6ca1b7a2da371175b0,
title = "Ecological adaptation and succession of human fecal microbial communities in an automated in vitro fermentation system",
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. ",
keywords = "Fecal microbiota, In vitro fermentor",
author = "Thiyagarajan Gnanasekaran and Geraldo, {Juliana Assis} and Ahrenkiel, {David Wilczek} and Camila Alvarez-Silva and Carmen Saenz and Adnan Khan and Obaida Hanteer and Vithiagaran Gunalan and Kajetan Trost and Thomas Moritz and Manimozhiyan Arumugam",
note = "Publisher Copyright: {\textcopyright} 2021 Gnanasekaran et al.",
year = "2021",
doi = "10.1128/mSystems.00232-21",
language = "English",
volume = "6",
journal = "mSystems",
issn = "2379-5077",
publisher = "American Society for Microbiology",
number = "4",

}

RIS

TY - JOUR

T1 - Ecological adaptation and succession of human fecal microbial communities in an automated in vitro fermentation system

AU - Gnanasekaran, Thiyagarajan

AU - Geraldo, Juliana Assis

AU - Ahrenkiel, David Wilczek

AU - Alvarez-Silva, Camila

AU - Saenz, Carmen

AU - Khan, Adnan

AU - Hanteer, Obaida

AU - Gunalan, Vithiagaran

AU - Trost, Kajetan

AU - Moritz, Thomas

AU - Arumugam, Manimozhiyan

N1 - Publisher Copyright: © 2021 Gnanasekaran et al.

PY - 2021

Y1 - 2021

N2 - 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.

AB - 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.

KW - Fecal microbiota

KW - In vitro fermentor

U2 - 10.1128/mSystems.00232-21

DO - 10.1128/mSystems.00232-21

M3 - Journal article

C2 - 34313459

AN - SCOPUS:85112249487

VL - 6

JO - mSystems

JF - mSystems

SN - 2379-5077

IS - 4

M1 - e00232-21

ER -

ID: 283752991