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Nuts and dried fruit. © INRA, MAITRE Christophe

Microbiota: new insights on what happens to dietary fibre in the human gut

One of the major functions of our intestinal microbiota – which until recently was thought to reside only in the colon – is to break down dietary fibre (and namely complex polysaccharides). However, researchers from INRA working with CNRS1 used metagenomic screening to reveal fibrolytic potential in the ileum section of the small intestine. The results, published in Scientific Reports on 16 January 2017, shed new light on the function of fibre digestion and its impact on human health.

Updated on 01/31/2017
Published on 01/17/2017

Among dietary fibres, polysaccharides play an especially important role in our nutrition. These long chains of complex carbohydrates are found in such foods as fruit, vegetables and cereals and are digested in our intestine by the bacteria that make up our intestinal microbiota. These bacteria produce a wide range of enzymes to cut the fibres into smaller molecules, which are then used or transformed through microbial fermentation to generate the energy needed by the body’s cells. This collaboration between fibres, microbes and host helps us to stay in good health, and yet our knowledge of fibrolytic bacteria in the gut remains limited to bacteria found in the colon, located in the distal part of the intestine.

. © INRA
© INRA
A study led by INRA researchers working with the CNRS explored another intestinal site: the ileum, the terminal part of the small intestine located before the colon in the digestive tract. Although it is colonised by numerous bacteria, the ileum has rarely been studied due to difficult access. However, the researchers were able to analyse 20,000 metagenomic clones with large DNA fragment inserts from ileal mucosa-associated microbiota. Using functional metagenomic screening, the researchers identified 11 clones that were especially interesting. The clones carried genes involved in both the breakdown of complex polysaccharides that form the plant cell walls of our food and in the transport of sugars released by the bacteria. The researchers found 52 proteins involved in carbohydrate metabolism, half of which are enzymes known as CAZymes that break down various polysaccharides. Among these, 13 different families of glycoside hydrolases were found.

Homologs of the identified genes from ileal microbiota involved in carbohydrate metabolism were then searched in the MetaHit microbial gene catalogue built from fecal metagenomic samples (no catalogue exists for other intestinal sites). Their abundance was estimated in more than 1200 individuals. While some genes are shared between the colon and the ileum, others appear to be specific to the ileum. They most likely correspond to the bacterial genome of species established in the small intestine, or in very low abundance in the colon.

The functional and quantitative metagenomic screenings used in this study, in association with quantitative metagenomics, support the theory that fibrolytic bacteria occupy several ecological niches along the intestinal tract. Their role in the small intestine should be further studied, with a focus on the impact of carbohydrate metabolism on the particularly active dialogue occurring in this part of the intestine with the host’s cells (especially immune cells).

Functional metagenomic experiment: 212 plates such as this one containing 96 different metagenomic clones were screened for fibrolytic activity. The positive clones able to break down polysaccharides were identified through clear halos appearing around the bacterial colonies.. © INRA, Micalis, équipe FlnE
Functional metagenomic experiment: 212 plates such as this one containing 96 different metagenomic clones were screened for fibrolytic activity. The positive clones able to break down polysaccharides were identified through clear halos appearing around the bacterial colonies. © INRA, Micalis, équipe FlnE
                                                                       

Functional and quantitative metagenomics
This study used metagenomic approaches which have revolutionised our understanding of the intestinal microbiota in recent years. Metagenomics is a powerful approach used to analyse genomes and study the functions of nearly all microorganisms in an ecological niche, including those that cannot be cultivated and which often make up the majority of microorganisms. Quantitative metagenomics examines the genomes of species comprising this specific niche. Using this technique, scientists can analyse bacterial DNA diversity and establish the relative abundance of its components. Functional metagenomics is an approach that targets one or several microbial functions and provides access to completely unexplored biological resources. It allows scientists to study the mechanisms of interaction between microorganisms and food as well as the dialogue between bacteria and human cells. Functional screening (e.g., enzyme activity, immune modulation) of clone libraries with large metagenomic inserts helps researchers identify functional genes and complete metabolic pathways.

1 Architecture and function of biological macromolecules (AFMB, CNRS/Aix-Marseille University)

Contact(s)
Scientific contact(s):

  • Christel Béra-Maillet (33 (0)1 34 65 27 84) MICALIS - Joint Research Unit for Food and Gut Microbiology for Human Health
  • Hervé Blottière (33 (0)1 34 65 23 19) MICALIS - Joint Research Unit for Food and Gut Microbiology for Human Health
Press Relations:
INRA News Office (33 (0)1 42 75 91 86)
Associated Division(s):
Microbiology and the Food Chain
Associated Centre(s):
Jouy-en-Josas

Reference

Orlane Patrascu, Fabienne Béguet-Crespel, Ludovica Marinelli, Emmanuelle Le Chatelier, Anne-Laure Abraham, Marion Leclerc, Christophe Klopp, Nicolas Terrapon, Bernard Henrissat, Hervé M. Blottière, Joël Doré and Christel Béra-Maillet. A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic. Scientific Reports, 16 January 2017. DOI: 10.1038/srep40248