Colonization-Induced Host-Gut Microbial Metabolic Interaction

Claus, Sandrine P.; Ellero, Sandrine L.; Berger, Bernard; Krause, Lutz; Bruttin, Anne; Molina, Jérôme; Paris, Alain; Want, Elizabeth J.; Waziers, Isabelle de; Cloarec, Olivier; Richards, Selena E.; Wang, Yulan; Dumas, Marc; Ross, Alastair B.; Rezzi, Serge; Kochhar, Sunil; Bladeren, Peter van; Lindon, John C.; Holmes, Elaine; Nicholson, Jeremy K.

doi:10.1128/mbio.00271-10

Cited by 351 publications

(310 citation statements)

References 35 publications

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“…Tight associations have been shown between the abundance of Coriobacteriaceae and the hosts’ lipid metabolism. Coriobacteriaceae were positively associated with liver triglyceride levels and serum cholesterol levels and negatively associated with liver glucose and glycogen levels in laboratory rodents (Claus et al., 2011). Additionally, cholesterol excreted in bile had antibacterial effects on Coriobacteriaceae (Martínez et al., 2013).…”

Section: Discussionmentioning

confidence: 99%

Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux's sifakas (Propithecus verreauxi)

Springer

Fichtel

Al‐Ghalith

et al. 2017

Ecology and Evolution

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The intestinal microbiota plays a major role in host development, metabolism, and health. To date, few longitudinal studies have investigated the causes and consequences of microbiota variation in wildlife, although such studies provide a comparative context for interpreting the adaptive significance of findings from studies on humans or captive animals. Here, we investigate the impact of seasonality, diet, group membership, sex, age, and reproductive state on gut microbiota composition in a wild population of group‐living, frugi‐folivorous primates, Verreaux's sifakas (Propithecus verreauxi). We repeatedly sampled 32 individually recognizable animals from eight adjacent groups over the course of two different climatic seasons. We used high‐throughput sequencing of the 16S rRNA gene to determine the microbiota composition of 187 fecal samples. We demonstrate a clear pattern of seasonal variation in the intestinal microbiota, especially affecting the Firmicutes‐Bacteroidetes ratio, which may be driven by seasonal differences in diet. The relative abundances of certain polysaccharide‐fermenting taxa, for example, Lachnospiraceae, were correlated with fruit and fiber consumption. Additionally, group membership influenced microbiota composition independent of season, but further studies are needed to determine whether this pattern is driven by group divergences in diet, social contacts, or genetic factors. In accordance with findings in other wild mammals and primates with seasonally fluctuating food availability, we demonstrate seasonal variation in the microbiota of wild Verreaux's sifakas, which may be driven by food availability. This study adds to mounting evidence that variation in the intestinal microbiota may play an important role in the ability of primates to cope with seasonal variation in food availability.

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Section: Discussionmentioning

confidence: 99%

Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux's sifakas (Propithecus verreauxi)

Springer

Fichtel

Al‐Ghalith

et al. 2017

Ecology and Evolution

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“…Interestingly, not all important microbial functions were provided by dominant bacteria and Arumugam et al (2011) suggest that functional biomarkers are more robust than phylogenetic biomarkers for identifying enterotypes associated with host phenotype characteristics. The complementary metabolic pathways provided by the microbiome influence the phenotype of animals and humans and make them react differently to diet and drugs (Nicholson et al, 2005;Li et al, 2008;Claus et al, 2011).…”

Section: Linking Genomics and Metagenomics Data To Nutrition And Othementioning

confidence: 99%

Rumen microbial (meta)genomics and its application to ruminant production

Morgavi

Kelly

Janssen

et al. 2013

Animal

209

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Meat and milk produced by ruminants are important agricultural products and are major sources of protein for humans. Ruminant production is of considerable economic value and underpins food security in many regions of the world. However, the sector faces major challenges because of diminishing natural resources and ensuing increases in production costs, and also because of the increased awareness of the environmental impact of farming ruminants. The digestion of feed and the production of enteric methane are key functions that could be manipulated by having a thorough understanding of the rumen microbiome. Advances in DNA sequencing technologies and bioinformatics are transforming our understanding of complex microbial ecosystems, including the gastrointestinal tract of mammals. The application of these techniques to the rumen ecosystem has allowed the study of the microbial diversity under different dietary and production conditions. Furthermore, the sequencing of genomes from several cultured rumen bacterial and archaeal species is providing detailed information about their physiology. More recently, metagenomics, mainly aimed at understanding the enzymatic machinery involved in the degradation of plant structural polysaccharides, is starting to produce new insights by allowing access to the total community and sidestepping the limitations imposed by cultivation. These advances highlight the promise of these approaches for characterising the rumen microbial community structure and linking this with the functions of the rumen microbiota. Initial results using high-throughput culture-independent technologies have also shown that the rumen microbiome is far more complex and diverse than the human caecum. Therefore, cataloguing its genes will require a considerable sequencing and bioinformatic effort. Nevertheless, the construction of a rumen microbial gene catalogue through metagenomics and genomic sequencing of key populations is an attainable goal. A rumen microbial gene catalogue is necessary to understand the function of the microbiome and its interaction with the host animal and feeds, and it will provide a basis for integrative microbiome–host models and inform strategies promoting less-polluting, more robust and efficient ruminants.

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“…metagenomic (i.e., gut microbiota) effects and environmental factors. Indeed, both system-wide (i.e., whole organism) and organ-specific changes in biochemical processes have components driven by these factors (Martin et al 2009a, b;Nicholson et al 2005;Claus et al 2011;Mestdagh et al 2011;Merrifield et al 2011;Wikoff et al 2009).…”

Section: Electronic Supplementary Materialsmentioning

confidence: 99%

Current status on genome–metabolome-wide associations: an opportunity in nutrition research

et al. 2012

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Genome-wide association studies (GWASs) have become a very important tool to address the genetic origin of phenotypic variability, in particular associated with diseases. Nevertheless, these types of studies provide limited information about disease etiology and the molecular mechanisms involved. Recently, the incorporation of metabolomics into the analysis has offered novel opportunities for a better understanding of disease-related metabolic deregulation. The pattern emerging from this work is that gene-driven changes in metabolism are prevalent and that common genetic variations can have a profound impact on the homeostatic concentrations of specific metabolites. A particularly interesting aspect of this work takes into account interactions of environment and lifestyle with the genome and how this interaction translates into changes in the metabolome. For instance, the role of PY-ROXD2 in trimethylamine metabolism points to an interaction between host and microbiome genomes (host/ microbiota). Often, these findings reveal metabolic deregulations, which could eventually be tuned with a nutritional intervention. Here we review the development of gene-metabolism association studies from a single-gene/ single-metabolite to a genome-wide/metabolome-wide approach and highlight the conceptual changes associated with this ongoing transition. Moreover, we report some of our recent GWAS results on a cohort of 265 individuals from an ethnically diverse population that validate and refine previous findings on gene-urine metabolism interactions. Specifically, our results confirm the effect of PYROXD2 polymorphisms on trimethylamine metabolism and suggest that a previously reported association of N-acetylated compounds with the ALMS1/NAT8 locus is driven by SNPs in the ALMS1 gene.

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Colonization-Induced Host-Gut Microbial Metabolic Interaction

Cited by 351 publications

References 35 publications

Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux's sifakas (Propithecus verreauxi)

Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux's sifakas (Propithecus verreauxi)

Rumen microbial (meta)genomics and its application to ruminant production

Current status on genome–metabolome-wide associations: an opportunity in nutrition research

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