Integrated multi-omics study of the human gut microbiome in four families with multiple cases of type 1 diabetes

Gut microbial communities display inter-individual variation and current research focuses on studying the gastrointestinal microbiome at both compositional and functional levels. Type 1 diabetes mellitus (T1DM) is a disease conditioned by an interplay of both genetics and environment. Links between gut microbiota and T1DM are still uncertain.

A recent study, led by Dr. Paul Wilmes from the Luxembourg Centre for Systems Biomedicine at the University of Luxembourg (Luxembourg), adds new insights about the human microbiome in type 1 diabetes mellitus (T1DM) from an integrated multi-omics analysis.

The researchers studied a cohort of 20 individuals from four families of at least two generations presenting at least two cases of T1DM. For studying the gastrointestinal microbiome at both structural and functional levels, metagenomic, metratranscriptomic and metaproteomic data were considered.

Analysis of both intra- and inter-individual data showed that human family membership has a pronounced effect on both the structural and functional composition of the gastrointestinal microbiome. Specifically, intra-individual variability was greater at the metatranscriptome and metaproteome levels, which emphasizes that the stability of the gut microbiota within the same individual is reflected at the functional level whereas consistent compositional changes were not found across families.

Regarding T1DM, differences in the levels of certain human pancreatic enzymes in the stool were found and they correlated with thiamine synthesis and glycolysis genes involved in metabolism. These results may indicate that different microbial populations can contribute to functional differences between samples, therefore justifying the use of integrated multi-omics analyses for establishing host-microbe phenotypic associations in the context of human disease research.

On the whole, multi-omic characteristics of the gut microbiome in individuals with T1DM compared to healthy relatives show a greater influence of microbes rather than genetics (family-dependent effects) of T1DM. This study identifies the expression of T1DM-associated microbial functions to distinct taxa, which demonstrates the need for integrated omics analyses (metagenomics, metatranscriptomics and metaproteomics) for depicting a clearer picture of host-microbe interactions.




Heintz-Buschart A, May P, Laczny CC, et al. Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes. Nat Microbiol. 2016; 2:16180. doi: 10.1038/nmicrobiol.2016.180.

Paul Enck
Paul Enck
Prof. Dr. Paul Enck, Director of Research, Dept. of Psychosomatic Medicine and Psychotherapy, University Hospital Tübingen, Germany. His main interests are gut functions in health and disease, including functional and inflammatory bowel disorders, the role of the gut microbiota, regulation of eating and food intake and its disorders, of nausea, vomiting and motion sickness, and the psychophysiology and neurobiology of the placebo response, with specific emphasis on age and gender contributions. He has published more than 170 original data paper in scientific, peer-reviewed journals, and more than 250 book chapters and review articles. He is board member/treasurer of the European Society of Neurogastroenterology and Motility and of the German Society of Neurogastroenterology and Motility, and has served as reviewer for many international journals and grant agencies.