As part of the Repositive team, I have recently attended the Microbiome forum in Amsterdam, that brought together academic, clinical and industrial researchers as well as business developers.
In her previous post, Charlotte has already explained why studying microbiome is becoming more and more popular. Based on the scientific program of the forum and recent publications^1, one can see that there are more and more areas where microbiota is found to play a crucial role.
My personal favourite
was the keynote lecture by Elena Verdu from the Division of Gastroenterology, McMaster University, Canada, about the role of intestinal microbiota in gluten metabolism and its implications for celiac disease.
Celiac disease is a common autoimmune condition occurring in genetically susceptible persons (but the presence of susceptibility genes is not sufficient to induce autoimmunity). It appears to be triggered by peptides - partially degraded fragments of gluten, which itself is a mix of proteins. Clinical studies have demonstrated alterations in the microbiota of celiac patients compared with healthy controls. It has been hypothesised that microbial factors modulate celiac risk in people with genetic predisposition. In Verdu's group, they studied gluten metabolism by opportunistic pathogens and commensal bacteria isolated from duodenum of people with and without celiac disease. Certain bacterial species metabolised gluten to immunogenic peptides (i.e. they could cause immune response in gluten sensitive organisms), whereas other species metabolised them further leading to non-immunogenic peptide products.
The works of Verdu's group demonstrate how exactly different small intestinal bacteria metabolise gluten and how the resulting peptides increase or reduce gluten immunogenicity.
There were many other interesting examples of how microbiota is involved in different aspects of human life. For example, vaginal microbiota - maternal host interactions are important in pregnancy ^2; microbiota clearly plays a role IBD and its extra-intestinal manifestations^3; cutaneous microbiome is involved in inflammatory skin diseases ^5 and so on.
In some cases, analysing tissue microbiota (e.g. blood) allows to see correlations with different diseases and can be used in diagnostics for early detection. To learn more, please check the works of Benjamin Lelouvier from Vaiomer.
It occurred to me that people do not yet combine (or do it very seldom) sequencing data of bacteria (16S rRNA sequencing) with sequencing hosts, i.e. human genomic data that we at Repositive are most interested in. This happens mainly because of the higher costs of the latter and (!) the absence of clarity on which questions to ask? Since this is a new paradigm, no clear pathways exist yet, but we come across more and more scientists who would like to have the combination of human and bacterial genomic data. We are looking forward to the developments in this field and hope to add more data to our Microbiome data collection.
==To access the Microbiome collection, please visit== https://discover.repositive.io/collections
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P.S. And this is how some of our 'bugs' look like!
Low-temperature electron micrograph of a cluster of E. coli bacteria, magnified 10,000 times. Each individual bacterium is oblong shaped. By Photo by Eric Erbe, digital colorisation by Christopher Pooley, both of USDA, ARS, EMU. Public domain, via Wikimedia Commons
^2: http://stm.sciencemag.org/content/8/350/350ra102 Kindinger LM et al. Relationship between vaginal microbial dysbiosis, inflammation, and pregnancy outcomes in cervical cerclage Science Translational Medicine 2016; Vol. 8, Issue 350, pp. 350ra102
^3: http://www.gastrojournal.org/article/S0016-5085(16)34696-0/fulltext Eppinga H, et al. Gut Microbiota Developments With Emphasis on Inflammatory Bowel Disease: Report From the Gut Microbiota for Health World Summit 2016
^4: https://link.springer.com/article/10.1007%2Fs11926-013-0407-2 Eppinga H, et al. The Microbiome and Psoriatic Arthritis Current Rheumatology Reports 2014, 16:407
^5: http://bit.ly/2qgln6n Rodrigues Hoffmann A The cutaneous ecosystem: the roles of the skin microbiome in health and its association with inflammatory skin conditions in humans and animals Vet Dermatol 2017, 28: 60–e15.