Mechanistic insights into the cross-feeding of Ruminococcus gnavus and Ruminococcus bromii on host and dietary carbohydrates

Emmanuelle H. Crost, Gwenaelle Le Gall, Jenny A. Laverde-Gomez, Indrani Mukhopadhya, Harry J. Flint, Nathalie Juge*

*Corresponding author for this work

Research output: Contribution to journalArticle

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Abstract

Dietary and host glycans shape the composition of the human gut microbiota with keystone carbohydrate-degrading species playing a critical role in maintaining the structure and function of gut microbial communities. Here, we focused on two major human gut symbionts, the mucin-degrader Ruminococcus gnavus ATCC 29149, and R. bromii L2-63, a keystone species for the degradation of resistant starch (RS) in human colon. Using anaerobic individual and co-cultures of R. bromii and R. gnavus grown on mucin or starch as sole carbon source, we showed that starch degradation by R. bromii supported the growth of R. gnavus whereas R. bromii did not benefit from mucin degradation by R. gnavus. Further we analyzed the growth (quantitative PCR), metabolite production (1H NMR analysis), and bacterial transcriptional response (RNA-Seq) of R. bromii cultured with RS or soluble starch (SS) in the presence or absence of R. gnavus. In co-culture fermentations on starch, 1H NMR analysis showed that R. gnavus benefits from transient glucose and malto-oligosaccharides released by R. bromii upon starch degradation, producing acetate, formate, and lactate as main fermentation end-products. Differential expression analysis (DESeq 2) on starch (SS and RS) showed that the presence of R. bromii induced changes in R. gnavus transcriptional response of genes encoding several maltose transporters and enzymes involved in its metabolism such as maltose phosphorylase, in line with the ability of R. gnavus to utilize R. bromii starch degradation products. In the RS co-culture, R. bromii showed a significant increase in the induction of tryptophan (Trp) biosynthesis genes and a decrease of vitamin B12 (VitB12)-dependent methionine biosynthesis as compared to the monoculture, suggesting that Trp and VitB12 availability become limited in the presence of R. gnavus. Together this study showed a direct competition between R. bromii and R. gnavus on RS, suggesting that in vivo, the R. gnavus population inhabiting the mucus niche may be modulated by the supply of non-digestible carbohydrates reaching the colon such as RS.

Original languageEnglish
Article number2558
JournalFrontiers in Microbiology
Volume9
DOIs
Publication statusPublished - 5 Nov 2018

Fingerprint

Ruminococcus
Dietary Carbohydrates
Starch
Mucins
Coculture Techniques
formic acid
maltose phosphorylase
Vitamin B 12
Tryptophan
Fermentation
Colon
Carbohydrates
Maltose

Keywords

  • Cross-feeding
  • Gut bacteria
  • Mucin
  • Resistant starch
  • Ruminococcus

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

Cite this

Mechanistic insights into the cross-feeding of Ruminococcus gnavus and Ruminococcus bromii on host and dietary carbohydrates. / Crost, Emmanuelle H.; Le Gall, Gwenaelle; Laverde-Gomez, Jenny A.; Mukhopadhya, Indrani; Flint, Harry J.; Juge, Nathalie.

In: Frontiers in Microbiology, Vol. 9, 2558, 05.11.2018.

Research output: Contribution to journalArticle

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abstract = "Dietary and host glycans shape the composition of the human gut microbiota with keystone carbohydrate-degrading species playing a critical role in maintaining the structure and function of gut microbial communities. Here, we focused on two major human gut symbionts, the mucin-degrader Ruminococcus gnavus ATCC 29149, and R. bromii L2-63, a keystone species for the degradation of resistant starch (RS) in human colon. Using anaerobic individual and co-cultures of R. bromii and R. gnavus grown on mucin or starch as sole carbon source, we showed that starch degradation by R. bromii supported the growth of R. gnavus whereas R. bromii did not benefit from mucin degradation by R. gnavus. Further we analyzed the growth (quantitative PCR), metabolite production (1H NMR analysis), and bacterial transcriptional response (RNA-Seq) of R. bromii cultured with RS or soluble starch (SS) in the presence or absence of R. gnavus. In co-culture fermentations on starch, 1H NMR analysis showed that R. gnavus benefits from transient glucose and malto-oligosaccharides released by R. bromii upon starch degradation, producing acetate, formate, and lactate as main fermentation end-products. Differential expression analysis (DESeq 2) on starch (SS and RS) showed that the presence of R. bromii induced changes in R. gnavus transcriptional response of genes encoding several maltose transporters and enzymes involved in its metabolism such as maltose phosphorylase, in line with the ability of R. gnavus to utilize R. bromii starch degradation products. In the RS co-culture, R. bromii showed a significant increase in the induction of tryptophan (Trp) biosynthesis genes and a decrease of vitamin B12 (VitB12)-dependent methionine biosynthesis as compared to the monoculture, suggesting that Trp and VitB12 availability become limited in the presence of R. gnavus. Together this study showed a direct competition between R. bromii and R. gnavus on RS, suggesting that in vivo, the R. gnavus population inhabiting the mucus niche may be modulated by the supply of non-digestible carbohydrates reaching the colon such as RS.",
keywords = "Cross-feeding, Gut bacteria, Mucin, Resistant starch, Ruminococcus",
author = "Crost, {Emmanuelle H.} and {Le Gall}, Gwenaelle and Laverde-Gomez, {Jenny A.} and Indrani Mukhopadhya and Flint, {Harry J.} and Nathalie Juge",
note = "Funding: The authors gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC), this research was partly funded by the BBSRC Institute Strategic Programs for The Gut Health and Food Safety (BB/J004529/1), Gut Microbes and Health (BB/R012490/1) and Food Innovation and Health (BB/R012512/1) and by the BB/L008602/1 and BB/LL009951/1 BBSRC responsive mode grants. Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The reviewer GG and handling Editor declared their shared affiliation. Acknowledgments: Next-generation sequencing and library construction was delivered via the BBSRC National Capability in Genomics and Single Cell (BB/CCG1720/1) at the Earlham Institute by members of the Genomics Pipelines Group. We would like to thank Andrea Telatin from the Quadram Institute Bioscience for his help with the RNA-Seq data submission in ArrayExpress Data Availability Statement: The RNA-Seq data generated and analyzed for this study have been deposited in the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-7138.",
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AU - Crost, Emmanuelle H.

AU - Le Gall, Gwenaelle

AU - Laverde-Gomez, Jenny A.

AU - Mukhopadhya, Indrani

AU - Flint, Harry J.

AU - Juge, Nathalie

N1 - Funding: The authors gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC), this research was partly funded by the BBSRC Institute Strategic Programs for The Gut Health and Food Safety (BB/J004529/1), Gut Microbes and Health (BB/R012490/1) and Food Innovation and Health (BB/R012512/1) and by the BB/L008602/1 and BB/LL009951/1 BBSRC responsive mode grants. Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The reviewer GG and handling Editor declared their shared affiliation. Acknowledgments: Next-generation sequencing and library construction was delivered via the BBSRC National Capability in Genomics and Single Cell (BB/CCG1720/1) at the Earlham Institute by members of the Genomics Pipelines Group. We would like to thank Andrea Telatin from the Quadram Institute Bioscience for his help with the RNA-Seq data submission in ArrayExpress Data Availability Statement: The RNA-Seq data generated and analyzed for this study have been deposited in the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-7138.

PY - 2018/11/5

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N2 - Dietary and host glycans shape the composition of the human gut microbiota with keystone carbohydrate-degrading species playing a critical role in maintaining the structure and function of gut microbial communities. Here, we focused on two major human gut symbionts, the mucin-degrader Ruminococcus gnavus ATCC 29149, and R. bromii L2-63, a keystone species for the degradation of resistant starch (RS) in human colon. Using anaerobic individual and co-cultures of R. bromii and R. gnavus grown on mucin or starch as sole carbon source, we showed that starch degradation by R. bromii supported the growth of R. gnavus whereas R. bromii did not benefit from mucin degradation by R. gnavus. Further we analyzed the growth (quantitative PCR), metabolite production (1H NMR analysis), and bacterial transcriptional response (RNA-Seq) of R. bromii cultured with RS or soluble starch (SS) in the presence or absence of R. gnavus. In co-culture fermentations on starch, 1H NMR analysis showed that R. gnavus benefits from transient glucose and malto-oligosaccharides released by R. bromii upon starch degradation, producing acetate, formate, and lactate as main fermentation end-products. Differential expression analysis (DESeq 2) on starch (SS and RS) showed that the presence of R. bromii induced changes in R. gnavus transcriptional response of genes encoding several maltose transporters and enzymes involved in its metabolism such as maltose phosphorylase, in line with the ability of R. gnavus to utilize R. bromii starch degradation products. In the RS co-culture, R. bromii showed a significant increase in the induction of tryptophan (Trp) biosynthesis genes and a decrease of vitamin B12 (VitB12)-dependent methionine biosynthesis as compared to the monoculture, suggesting that Trp and VitB12 availability become limited in the presence of R. gnavus. Together this study showed a direct competition between R. bromii and R. gnavus on RS, suggesting that in vivo, the R. gnavus population inhabiting the mucus niche may be modulated by the supply of non-digestible carbohydrates reaching the colon such as RS.

AB - Dietary and host glycans shape the composition of the human gut microbiota with keystone carbohydrate-degrading species playing a critical role in maintaining the structure and function of gut microbial communities. Here, we focused on two major human gut symbionts, the mucin-degrader Ruminococcus gnavus ATCC 29149, and R. bromii L2-63, a keystone species for the degradation of resistant starch (RS) in human colon. Using anaerobic individual and co-cultures of R. bromii and R. gnavus grown on mucin or starch as sole carbon source, we showed that starch degradation by R. bromii supported the growth of R. gnavus whereas R. bromii did not benefit from mucin degradation by R. gnavus. Further we analyzed the growth (quantitative PCR), metabolite production (1H NMR analysis), and bacterial transcriptional response (RNA-Seq) of R. bromii cultured with RS or soluble starch (SS) in the presence or absence of R. gnavus. In co-culture fermentations on starch, 1H NMR analysis showed that R. gnavus benefits from transient glucose and malto-oligosaccharides released by R. bromii upon starch degradation, producing acetate, formate, and lactate as main fermentation end-products. Differential expression analysis (DESeq 2) on starch (SS and RS) showed that the presence of R. bromii induced changes in R. gnavus transcriptional response of genes encoding several maltose transporters and enzymes involved in its metabolism such as maltose phosphorylase, in line with the ability of R. gnavus to utilize R. bromii starch degradation products. In the RS co-culture, R. bromii showed a significant increase in the induction of tryptophan (Trp) biosynthesis genes and a decrease of vitamin B12 (VitB12)-dependent methionine biosynthesis as compared to the monoculture, suggesting that Trp and VitB12 availability become limited in the presence of R. gnavus. Together this study showed a direct competition between R. bromii and R. gnavus on RS, suggesting that in vivo, the R. gnavus population inhabiting the mucus niche may be modulated by the supply of non-digestible carbohydrates reaching the colon such as RS.

KW - Cross-feeding

KW - Gut bacteria

KW - Mucin

KW - Resistant starch

KW - Ruminococcus

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