![]() ![]() At the same time, however, studies using embryo transplantation, litter cross-fostering and other variation in mouse rearing and housing have shown that experimental manipulations, environmental and stochastic factors (for example, founder effects) can exert dominating contributions in microbiota taxonomic composition ( Friswell et al., 2010). ![]() ![]() Strong evidence exists that the global host genotype influences specific microbiota composition (beta diversity) ( Benson et al., 2010 Kovacs et al., 2011), and mutations and inactivation of specific genes have been associated with discrete community changes, in some cases linked to metabolic diseases (for example, obesity, diabetes and metabolic syndrome) (reviewed in Spor et al. Such studies have used both conventionally reared and germ-free animals inoculated selectively with different bacterial isolates or natural microbiota samples. Significant advances in understanding the individual roles of host and environmental factors on the composition of vertebrate gut microbiota have resulted from studies on genetically inbred mouse lines (reviewed in Spor et al. Such complex interactions between deterministic (genetic and developmental), environmental and stochastic factors in the assembly and dynamics of vertebrate gut microbiota are being studied intensely, from fundamental ecological perspectives to its impact on host health and disease ( Dethlefsen et al., 2006 Ley et al., 2006 Dethlefsen et al., 2007 Palmer et al., 2007 Ley et al., 2008a Turnbaugh et al., 2009 Reid et al., 2011 Spor et al., 2011). Distinct community structure and composition characterizes different vertebrate and invertebrate species in their natural environments, global microbiota and interspecies relatedness, reflecting host phylogeny and incorporating elements of developmental and nutritional specialization ( Ley et al., 2008a, 2008b Ochman et al., 2010 Yidirim et al., 2010). Even for more complex animal gut microbial communities, acquired and maintained dynamically after hatching or birth, there are likely host-microbe specificity determinants, as revealed by natural colonization and experimental microbiota transplantation across host species ( Rawls et al., 2004 Rawls et al., 2006 Palmer et al., 2007 Morowitz et al., 2011). In some cases, extensive genetic coevolution between the animal host and microbes has resulted in obligate, highly specific, nutritional symbioses involving one or a few vertically transmitted microbial species, such as the endosymbionts of some hydrothermal vent invertebrates and those of plant sap-feeding insects ( Moran, 2007 Dubilier et al., 2008). Specific microbial eco-physiological traits have led to a wide range of associations between metazoan taxa and members of the bacterial and archaeal domains. Throughout their evolutionary history, animals have been in continuous, direct contact with the microbial diversity that thrives in all environments on earth. This study provides a baseline analysis of intestinal bacterial communities in the eight CC progenitor strains and will be linked to integrated host genotype, phenotype and microbiota research on the resulting CC panel. Cohabitation of different strains of mice revealed an interaction of host genetic and environmental factors in shaping gut bacterial consortia, in which bacterial communities became more similar but retained strain specificity. We identified bacterial phylotypes that appear to be discriminative and strain-specific to each mouse line used. Cohabitation and litter had a reduced, although detectable effect, and the microbiota response to these factors varied by strain. Significant correlations were found between the mouse strains and their gut microbiota, reflected by distinct bacterial communities. Diversity of gut microbiota was characterized by complementing phylogenetic and distance-based, sequence-clustering approaches. Eight of these strains are the foundation of the Collaborative Cross (CC), a panel of mice derived from a genetically diverse set of inbred founder strains, designed specifically for complex trait analysis. We employed barcoded pyrosequencing of V1-2 and V4 regions of bacterial small subunit ribosomal RNA genes to characterize the effects of host genetics and environment on cecum assemblages in 10 genetically distinct, inbred mouse strains. A synergy of host genetic and environmental factors shape these communities and account for their variability, but their individual contributions and the selective pressures involved are still not well understood. The mammalian gut harbors complex and variable microbial communities, across both host phylogenetic space and conspecific individuals. ![]()
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