Influence of the host diet on the structure & function of the mammalian gut microbiome.
Brian Muegge, Washington University School of Medicine
Not part of the sequencing centre, they do their own sequencing. Small lab.
Working on the Human Microbiome. Microbiome: totality of microes, their genetic elements, and environmental interactions in a defined environment. Metagenomics is the genomic analysis of a population of microorganism.
Gut is divided into different segments, and the microbial communities vary across the length. Stomach is different than small intestine, which is again different from large intestine. In this case, Stool bacteria is studied as a proxy for the large gut.
Past work: researcher went to zoos and started looking at mammalian stool, looking at 16S rRNA. Strong clustering by diet type, just looking at species of the gut.
started by looking at 39 mammalian fecal samples from previous study. Range of 3 diet classes, both free living and zoos.
also used 18 humans who are practising long-term caloric restriction with optimal nutrition. They were selected because they keep great records of what they eat, not because of the caloric restrictions.
Method: Single fecal sample from each individual. DNA isolation, then sequencing on 454 FLX. Two kinds of seq: V2 directed 16S rRNA sequencing and shotgun gene sequencing and functional annotation. Used blasts against Kegg to figure out what the genes are doing.
What they found:
- community phylogeny structure predicts functional profile.
- Host diet is associated with different bacterial metabolic patterns (eg amino acids)
- Human dietary intake correlates with microbiota structure.
Discuss new type of analyses: procrustes analysis. [I’ve never heard of it before. seems to involve transforming data until you find a good fit, rotating through various axes to generate the best overlay to find the best clustering… Hope I got that right.]
Example of analysis shown for omnivore, herbivore, carnivore. Clustering is apparent by diet type. Fit is much better than expected than chance. Omnivores sometimes cluster with herbivores, sometimes on their own. Occasionally with carnivore.
Similar results obtained for several different classes of enzymes.
What is the biology separating the different groups? Used E.C. annotations, looking for things that separate groups. Amino acid metabolism enzymes not found in carnivores, but (12/20) enriched in herbivores. Amino acid degredation found in carnivores (9/20) found in carnivores, but only 3/20 in herbivores. [Nice map shown, indicating which enzymes are found in herbivores and which are in carnivores.]
Herbivores are making amino acids, carnivores are breaking them down.
On to humans. Regression was core of analysis. If you know how much protein they consume, you can explain about 30% of the variation. 36% can be explained by OTU.
- Adaptations by gut microbiome to host diet is reproducible across diverse mammalian hosts.
- Phylogenetic data can be used to predict functional provile
- E.C. level metabolic reconstrcution reveals reaction pathway differences.
- And the human stuff written above. Diet reflects variation in human gut microbiome.