E.G. Zoetendal

High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota.

The human gastrointestinal (GI) tract microbiota plays a pivotal role in our health. For more than a decade a major input for describing the diversity of the GI tract microbiota has been derived from the application of small subunit ribosomal RNA (SSU rRNA)-based technologies. These not only provided a phylogenetic framework of the GI tract microbiota, the majority of which has not yet been cultured, but also advanced insights into the impact of host and environmental factors on the microbiota community structure and dynamics. In addition, it emerged that GI tract microbial communities are host and GI tract location-specific. This complicates establishing relevant links between the host’s health and the presence or abundance of specific microbial populations and argues for the implementation of novel high-throughput technologies in studying the diversity and functionality of the GI tract microbiota. Here, we focus on the recent developments and applications of phylogenetic microarrays based on SSU rRNA sequences and metagenomics approaches exploiting rapid sequencing technologies in unravelling the secrets of our GI tract microbiota.

Clinical trial: multispecies probiotic supplementation alleviates the symptoms of irritable bowel syndrome and stabilizes intestinal microbiota: CLINICAL TRIAL: PROBIOTICS IN IBS

Backgroundu2002 Irritable bowel syndrome is the most common diagnosis in gastroenterology. Trials suggest certain probiotics to be beneficial.

11 – Molecular Characterisation of Microbial Communities Based on 16S rRNA Sequence Diversity

The application of Temperature Gradient Gel Electrophoresis (TGGE), Denaturing Gradient Gel Electrophoresis (DGGE), and Single Strand Conformation Polymorphism (SSCP) to studies in microbial ecology is growing and the future perspectives are promising. The combination of reverse transcriptase-PCR, cloning, and fingerprinting of environmental samples may give an accurate description of a community. The power of these techniques is their reliability, speed, and ease of use. TGGE, DGGE, and SSCP are ideal for studying the temporal and spatial variation in microbial communities, both qualitatively and quantitatively. The only time-consuming aspect is the identification of specific amplicons in the profiles. The approach of combining 16S rDNA profiles and profiles of functional genes may enable the structure to be related to the function of an ecosystem. Another variant of this approach is the use of oligonucleotide microchips. The fingerprinting approach has already demonstrated that the dominant microbial community in adults is quite stable with time and differs for each individual. This approach can also be used to monitor the fate of certain bacteria, such as probiotic strains in the intestine. The impact of these strains on the microbial community in the gastrointestinal tract can be analyzed by quantifying similarities between the profiles or calculating microbial diversity and richness indices from profiles. Changes in band positions can be identified using cloning and sequencing analysis. The introduction of internal standards to the profiles may help the changes to be monitored quantitatively. These approaches will help in gaining an understanding of some aspects of the microbial community in the intestine.

Clinical trial: multispecies probiotic supplementation alleviates the symptoms of IBS and stabilises intestinal microbiota

Backgroundu2002 Irritable bowel syndrome is the most common diagnosis in gastroenterology. Trials suggest certain probiotics to be beneficial.

P672 Does the ileocecal valve functionally separate ileal and right-sided colon microbiota compositions?

there is current debate about a causal relation between retinoid treatment and inflammatory bowel disease (IBD). Patients have claimed that they developed acute intestinal inflammation during isotretinoin treatment or to develop inflammatory bowel disease (IBD) weeks or even years after cessation of the medication. We have previously shown that isotretinoin treatment has no adverse effects in two mouse models of inflammatory bowel disease [1]. Since the gut microbiota can metabolize retinoids, we investigated whether administration of retinoids might change the gut microbiota composition in a way that is favorable for the development of IBD. Methods: Balb/c mice were treated with isotretinoin (30mg/kg bodyweight) or vehicle orally for 2 weeks and kept for further 4 weeks to study potential direct and long-term effects. Fecal samples were collected before treatment, directly after the treatment period and four weeks later for analysis of gut microbiota composition by 16S rRNA gene sequencing on the GS-Flx 454 platform. Sequencing data were analyzed with the software QIIME to determine OTUs, calculate the relative abundance for each group and time point and to general principal coordinate analysis plots. Results: Principle coordinate analysis showed no formation of clusters neither depending on treatment nor on time point of investigation indicating no fundamental differences between the gut microbiota composition of isotretinoin or vehicle treated animals or between the different time points studied. Some differences with regard to alpha and beta diversity between the different treatment groups as well as between the different time points studied were observed and are currently under further investigation. Conclusions: Preliminary results with QIIME showed no substantial differences between isotretinoin and vehicle treated animals indicating that isotretinoin treatment had no fundamental effect on the composition of the murine gut microbiota. We are currently investigating the variations in alpha and beta diversity that were observed between groups exposed to isotretinoin and vehicle, as well as between the different time points.