For the second day of the IHMC congress at Hangzhou, morning presentations were related to data analysis and host-microbiome interactions.
Curtis Huttenhower, from Havard School of Public Health, discussed the fact that most studies focused on DNA, specifically bacterial DNA. However, transcript and proteins will turn to signaling molecules between cell type within microbial community and with host. He suggested to use MetaOmics analysis integrating metagenomics and metatranscriptomics. This method allows to connect ecology to pathway and their regulation.
Peer Bork, from EMBL, explained that metagenomic analysis now provides us with three levels of information : species abundance, genes abundance and nucleotide variation. Species abundance allows the description of enterotype community, defined as density ecological areas. Those enterotypes correlate with genes richness. Gene abundance permitted for instance to detect antibiotic resistance in a population. Nucleotide variations used as markers of strains over time permitted to describe the slow drift of donor strains to recipient strains in fecal transplantation. Those tools are included in the my.microbes project.
Junhua Li, from BGI, detailed how the gut microbiota gene catalog (used for many past and ongoing project) had been improved with an EMBL collaboration. Using 1267 sample, the catalog now reaches 10 millions genes with 57% complete genes. Low abundant species are now well covered, like Lactobacillus.
Joël Doré, from INRA, explained how metagenomics is not only about sequencing, but also screening. In fact, in his lab, different targets have been tested from carbohydrate metabolism to host inflammatory factors. Indeed, commensal bacteria and candidate food borne microbes (and not only pathogens) can establish crosstalk with human cells and tissues. Molecules of crosstalk could offer potential for new drug development.
Emilie B. Hollister, from Texas Children Hospital, presented her work on gut microbiome in childhood. The current hypothesis is that around 3 years of age the microbiota becomes as mature as that of adults. But her study shows that children can still be differentiated from adults, notably because Faecalibacterium and Bifidobacterium are often enriched in children. This is also true in terms of microbial functions, enriched in vitamin metabolism for instance.
Andrew Benson presented his study about associations between host loci (QTL) and microbial composition based on a mice model. His study shows 13 significant QTLs controlling the composition of microbiome based in classifier analysis. By adding a diet component, he was able to show that diet could modify allelic effect of microbiome modulating QTLs.