The human intestinal microbiota is known to play an important role in human health and disease, and with the advent of novel molecular techniques, disease-specific variations in its composition have been found. However, analysis of the intestinal microbiota has not yet been applicable in large-scale clinical research or routine diagnostics because of the complex and expensive nature of the techniques needed. Here, we describe a new PCR-based profiling technique for high-throughput analysis of the human intestinal microbiota, which we have termed IS-pro. This technique combines bacterial species differentiation by the length of the 16S-23S rDNA interspace region with instant taxonomic classification by phylum-specific fluorescent labeling of PCR primers. We validated IS-pro in silico, in vitro, and in vivo, on human colonic biopsies and feces, and introduced a standardized protocol for data analysis. IS-pro is easy to implement in general clinical microbiological laboratories with access to capillary gel electrophoresis, and the high-throughput nature of the test makes analysis of large numbers of samples feasible. This combination renders IS-pro ideally suited for use in clinical research and routine diagnostics.

Intestinal microbial community structure is driven by host genetics in addition to environmental factors such as diet. In comparison with environmental influences, the effect of host genetics on intestinal microbiota, and how host-driven differences alter host metabolism is unclear. Additionally, the interaction between host genetics and diet, and the impact on the intestinal microbiome and possible down-stream effect on host metabolism is not fully understood, but represents another aspects of inter-individual variation in disease risk. The objectives of this study were to investigate how diet and genetic background shape microbial communities, and how these diet- and genetic-driven microbial differences relate to cardiometabolic phenotypes. To determine these effects, we used the 8 progenitor strains of the collaborative cross/diversity outbred mapping panels (C57BL/6J, A/J, NOD/ShiLtJ, NZO/HILtJ, WSB/EiJ, CAST/EiJ, PWK/PhJ, and 129S1/SvImJ). 16s rRNA profiling of enteric microbial communities in addition to the assessment of phenotypes central to cardiometabolic health was conducted under baseline nutritional conditions and in response to diets varying in atherogenic nutrient (fat, cholesterol, cholic acid) composition. These studies revealed strain-driven differences in enteric microbial communities which were retained with dietary intervention. Diet–strain interactions were seen for a core group of cardiometabolic-related microbial taxa. In conclusion, these studies highlight diet and genetically regulated cardiometabolic-related microbial taxa. Furthermore, we demonstrate the progenitor model is useful for nutrigenomic-based studies and screens seeking to investigate the interaction between genetic background and the phenotypic and microbial response to diet.Electronic supplementary materialThe online version of this article (doi:10.1007/s00335-014-9540-0) contains supplementary material, which is available to authorized users.

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This study aimed to understand how diet and genetics influence the intestinal microbiome and cardiometabolic risk factors. To achieve this aim, inbred mouse strains varying in metabolic disease susceptibility were selected as follows: C57Bl/6J, A/J, 129S1/SvlmJ, NOD/LtJ, NZO/HilLtJ, CAST/EiJ, PWK/PhJ, WSB/EiJ. All strains were randomized to receive either an atherogenic high fat cholic acid diet or control diet for 16 weeks. Before and after this diet period, the intestinal microbiome community was assessed by 16s rRNA gene sequencing, and plasma trimethylamine‐N‐oxide (TMAO), lipids, glucose and insulin concentrations were measured. Aortic lesions were measured at the study close. Principal Coordinates Analysis highlighted by‐strain separation in microbial diversity at baseline. Between‐diet separation in community diversity was also observed. Interestingly, a strain X diet interaction was evident, with certain strains exhibiting greater separation between the atherogenic and control diets. Several differentially abundant taxa were consistently related to the cardiometabolic parameters. In conclusion, this study has identified diet and genetic‐regulated taxa related to metabolic risk factors. Future work will focus on directly investigating these taxa in order to understand mechanism of effect, and to develop targeted microbiome‐focused treatments for metabolic disease.