The International Human Microbiome Congress 2011 held in Vancouver this month could only have taken place in this era of next generation sequencing technologies. The microbiome, consisting of the microbial communities present at different body sites, is difficult to culture. Thus the ability to sequence directly either the genomes or the uniquely identifying 16S rDNA sequence of these colonies resulted in the interesting presentation of the ecological communities that exist within us both in health and disease.
With such large datasets, the need for standards in collecting and analyzing them was discussed in several talks. Owen White (University of Maryland) called for the ease of data sharing and analysis of these large metagenomic datasets, and Mani Arumugam (EMBL) discussed his approach for quantitative metagenomics allowing him to identify 3 different ‘phylotypes’ of bacteria in the human gut microbiome. Furthermore, Curtis Huttenhower (Harvard) showed that there is different information to be gained from analysing ‘who’ is there in a community (species analysis) vs how they’re living there (metabolic pathway analysis). However, returning to community-based analysis Andrew Fernandez (University of Western Ontario) discussed the limitations of current analysis techniques to define co-occurrence and co-exclusion in microbial communities.
Of the major biological themes at the meeting, the link between the gut microbiome, obesity and diet were much discussed. Liping Zhao (Shanghai Jiao Tong University) showed consistent effects of diet changes and lifespan upon the microbiome in mice. Claire Fraser-Liggett, (University of Maryland) on the other hand is studying humans using the unique conditions of a closed population as a background to analyze gut microbiomes and obesity. Alarmingly, Martin Blaser (NYU) presented work in mice linking antibiotic treatment to obesity and changes in gut microbiota. Several others presented talks on the use of probiotics and their ability to alter the composition of gut microbiota. However, Larry Forney’s (Univeristy of Idaho) talk on the vaginal microbiome showed a highly changing ecosystem, highlighting the challenges ahead if we are to manipulate these communities.
The need for more prospective studies with regard to changing microbiomes and disease was emphasised in a talk from Volker Mai (University of Florida) studying necrotising enterocolitis. This was echoed by Francisco Guarner (University Hospital Vall d’Hebron) at the end of his talk who asked whether the association of the bacterial species he found to be associated with ulcerative colitis are causal, a consequence or contributors. With the continued decreasing cost in sequencing, as emphasised by Rob Knight (University of Colorado) in his talk, it is likely that longitudinal studies are the next stage for the human microbiome. They will help us to decipher the microbiome as a cause or consequence of disease.
- Introducing the Genome Biology podcast – sequencing and disease mutations - 20th September 2011
- Help from a model organism in Genome Biology’s special issue on exome sequencing - 14th September 2011
- The International Human Microbiome Congress 2011 - 23rd March 2011