6 WORLD GASTROENTEROLOGY NEWS JULY 2014 Editorial | Expert Point of View | WDHD News | WGO & WGOF News | WGO Global Guidelines | Calendar of Events Gut Microbes Virginia Robles-Alonso, MD Digestive System Research Unit University Hospital Vall d’Hebron, Ciberehd Barcelona, Spain Microbial communities: different approach, novel insights Until recent years, our knowledge on the human gut microbiota was largely limited to certain community members with potential pathogenicity by either translocation or production of toxins. Most of these potential pathogens were isolated in culture and recognized by traditional diagnostic techniques. However, culture-based techniques to identify bacteria have important limitations, and the large majority of bacteria in the human gut are considered ‘unculturable’ for the great difficulties for growing them in the laboratory. Their potential role in health or disease has been ignored. The notion of a host-microbe symbiotic relationship in the gut, in terms of proven benefits or mutual-ism among partners, is supported by studies carried out with animals born and bred under germ-free conditions1. Compared with colonized counter-parts, germ-free mammalians or birds exhibit major differences in body anatomy and physiology. These stud-ies clearly indicated that microbial communities colonizing the animal host have a strong influence on body growth and development, as well as on the induction and regulation of the immune system, thus contributing to maintenance of health during life. However, very little is known about nature and biological characteristics of the critical symbionts inducing beneficial effects on the animal host. The advent of high-throughput technologies has changed our perspec-tive dramatically. First, these tech-nologies are culture independent and, remarkably, they allow the character-ization of microbial communities as a whole, enabling a deeper and global view of all the community members and their relative abundance2. The novel approach for the analysis of microbial communities in environ-mental samples is called “metagenom-ics”, and is defined as the study of all the genetic material recovered directly from environmental samples bypass-ing the need to isolate and culture individual community members3. The metagenome is the collective genetic content of the combined genomes of the constituents of an ecological com-munity. The microbiome is defined as the collective genome of the microbial symbionts in a host animal4. The most common approach con-sists of the extraction of DNA from the biological sample, followed by the amplification and sequencing of 16S ribosomal RNA genes in the sample. The 16S rRNA gene is present in all bacteria and contains both conserved and variable regions. Thus, similari-ties and differences in the sequence of nucleotides of the 16S rRNA gene al-low taxonomic identification ranging from the domain and phylum level to the species level. Currently, around three million aligned and annotated 16S rRNA sequences are available in DNA databases (http://rdp.cme.msu. edu/). Taxonomic identification is based on comparison of 16S rRNA sequences in the sample with refer-ence sequences in the database. In this way, studies on the 16S rRNA gene provide information about microbial composition and diversity of species in a given sample. The most powerful molecular ap-proach is not limited to 16S rRNA sequencing but addresses all the genetic material in the sample. The decreasing cost and increasing speed of DNA sequencing, coupled with the advances in computational analyses of large datasets, have made it feasible to analyze complex mixtures of entire ge-nomes with reasonable coverage. The resulting information describes the collective genetic content of the com-munity from which functional and metabolic networks can be inferred. Thus, the full metagenomic approach has the advantage of not only provid-ing the phylogenetical characteriza-tion of the microbial community but Francisco Guarner, MD Digestive System Research Unit University Hospital Vall d’Hebron, Ciberehd Barcelona, Spain
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