Abstract
The mammalian gut microbiome can potentially impact host health and disease state. It is known that the mouse-genome, eating-behavior, and exercise-status promotes higher taxonomic rank-level alterations (e.g. family to phyla-level) of the gut microbiota. Here, host genotype or activity status was investigated to determine if selection of individual bacterial species or strains could be discerned within the murine digestive system. For this study, the fecal bacterial community of adenylyl cyclase 5 knock-out (AC5KO, n = 7) mice or their wild-type (WT, n = 10) littermates under exercise or sedentary conditions were profiled by sequencing rRNA operons. AC5KO mice were chosen since this genotype displays enhanced longevity/exercise capacity and protects against cardiovascular/metabolic disease. Profiling of rRNA operons using the Oxford MinION yielded 65,706 2-D sequences (after size selection of 3.7–5.7 kb) which were screened against an NCBI 16S rRNA gene database. These sequences were binned into 1,566 different best BLAST hits (BBHs) and counted for each mouse sample. Non-metric multidimensional scaling (NMDS) of the gut microbial community demonstrated clustering by physical activity (p = 0.001) but not by host genotype. Additionally, sequence similarity and phylogenetic analysis demonstrated that different bacterial species (closely related to Muribaculum intestinale and Parasutterella excrementihominis) inhabit AC5KO or WT mice depending on activity status. Other bacterial species of the gut microbiota did not follow such patterning (e.g. Turicibacter sanguinis and Turicimonas muris). Our results support the need of improved taxonomic resolution for better characterization of bacterial communities to deepen our understanding of the role of the gut microbiome on host health.
Highlights
The mammalian gut microbiome can potentially impact host health and disease state
Two MinION sequencing libraries were created for rRNA operon amplicons from AC5KO and WT mice fecal samples and run for 18 or 22 h
To determine if the overall gut microbiome differed between the mouse genotypes or activity, a Bray-Curtis dissimilarity matrix was constructed using a fourth root transformation on the best BLAST hits (BBHs) sequences[34] and visualized via non-metric multidimensional scaling (NMDS; Fig. 1)
Summary
The mammalian gut microbiome can potentially impact host health and disease state. It is known that the mouse-genome, eating-behavior, and exercise-status promotes higher taxonomic ranklevel alterations (e.g. family to phyla-level) of the gut microbiota. Future studies will utilize newer Nanopore chemistries and base calling algorithms for rRNA operons profiling, the data analysis approach presented here is applicable for discerning cryptic variations within members of the bacterial communities that cannot be ascertained by screening short, variable regions against a 16S rRNA gene database This ability to discern species-level and strain-level differences between gut bacterial microbiota will greatly enhance our understanding of which microbes to target for further culturing/physiological studies; could lead to new clinical tools for optimizing the gut microbiome; and provides insight into how gut microbes and hosts interact to promote health
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