The commensal gut microbiota has been implicated as a determinant in several human diseases and conditions. There is mounting evidence that the gut microbiota of laboratory mice (Mus musculus) similarly modulates the phenotype of mouse models used to study human disease and development. While differing model phenotypes have been reported using mice purchased from different vendors, the composition and uniformity of the fecal microbiota in mice of various genetic backgrounds from different vendors is unclear. Using culture-independent methods and robust statistical analysis, we demonstrate significant differences in the richness and diversity of fecal microbial populations in mice purchased from two large commercial vendors. Moreover, the abundance of many operational taxonomic units, often identified to the species level, as well as several higher taxa, differed in vendor- and strain-dependent manners. Such differences were evident in the fecal microbiota of weanling mice and persisted throughout the study, to twenty-four weeks of age. These data provide the first in-depth analysis of the developmental trajectory of the fecal microbiota in mice from different vendors, and a starting point from which researchers may be able to refine animal models affected by differences in the gut microbiota and thus possibly reduce the number of animals required to perform studies with sufficient statistical power.

The gastrointestinal tract contains a vast community of microbes that to this day remain largely unculturable, making studies in this area challenging. With the newly affordable advanced sequencing technology, important breakthroughs in this exciting field are now possible. However, standardized methods of sample collection, handling, and DNA extraction have yet to be determined. To help address this, we investigated the use of 5 common DNA extraction methods on fecal samples from 5 different species. Our data show that the method of DNA extraction impacts DNA concentration and purity, successful NGS amplification, and influences microbial communities seen in NGS output dependent on the species of fecal sample and the DNA extraction method used. These data highlight the importance of careful consideration of DNA extraction method used when designing and interpreting data from cross species studies.

Tissue-resident macrophages (TRMs) are heterogeneous populations originating either from monocytes or embryonic progenitors, and distribute in lymphoid and non-lymphoid tissues. TRMs play diverse roles in many physiological processes, including metabolic function, clearance of cellular debris, and tissue remodeling and defense. Macrophages can be polarized to different functional phenotypes depending on their origin and tissue microenvironment. Specific macrophage subpopulations are associated with disease progression. In studies of fate-mapping and single-cell RNA sequencing methodologies, several critical molecules have been identified to induce the change of macrophage function. These molecules are potential markers for diagnosis and selective targets for novel macrophage-mediated treatment. In this review, we discuss some of the recent findings regarding less-known molecules and new functions of well-known molecules. Understanding the mechanisms of these molecules in macrophages has the potential to yield new macrophage-mediated treatments or diagnostic approaches to disease.

The influence of the microbiota on behavior and stress responses is poorly understood. Zebrafish larvae have unique characteristics that are advantageous for neuroimmune research, however, they are currently underutilized for such studies. Here, we used germ-free zebrafish to determine the effects of the microbiota on behavior and stress testing. The absence of a microbiota dramatically altered locomotor and anxiety-related behavior. Additionally, characteristic responses to an acute stressor were also obliterated in larvae lacking exposure to microbes. Lastly, treatment with the probiotic Lactobacillus plantarum was sufficient to attenuate anxiety-related behavior in conventionally-raised zebrafish larvae. These results underscore the importance of the microbiota in communicating to the CNS via the microbiome-gut-brain axis and set a foundation for using zebrafish larvae for neuroimmune research.

Horses are exquisitely sensitive to non-specific gastrointestinal disturbances as well as systemic and extraintestinal conditions related to gut health, yet minimal data are available regarding the composition of the microbiota present in the equine stomach, small intestine, and cecum and their relation to fecal microbiota. Moreover, there is minimal information regarding the concordance of the luminal and mucosal microbial communities throughout the equine gut. Illumina-based 16S rRNA gene amplicon sequencing of the luminal and mucosal microbiota present in seven regions of the gastrointestinal tract of nine healthy adult horses revealed a distinct compositional divide between the small and large intestines. This disparity in composition was more pronounced within the luminal contents, but was also detected within mucosal populations. Moreover, the uniformity of the gut microbiota was much higher in the cecum and colon relative to that in the stomach, jejunum and ileum, despite a significantly higher number of unique sequences detected in the colon. Collectively, the current data suggest that while colonic samples (a proxy for feces) may provide a reasonable profile of the luminal contents of the healthy equine large intestine, they are not informative with regard to the contents of the stomach or small intestine. In contrast to the distinct difference between the highly variable upper gastrointestinal tract microbiota and relatively uniform large bowel microbiota present within the lumen, these data also demonstrate a regional continuity present in mucosal microbial communities throughout the length of the equine gut.

The interplay between western diet and gut microbiota drives the development of non-alcoholic fatty liver disease and its progression to non-alcoholic steatohepatitis. However, the specific microbial and metabolic mediators contributing to non-alcoholic steatohepatitis remain to be identified. Here, a choline-low high-fat and high-sugar diet, representing a typical western diet, named CL-HFS, successfully induces male mouse non-alcoholic steatohepatitis with some features of the human disease, such as hepatic inflammation, steatosis, and fibrosis. Metataxonomic and metabolomic studies identify Blautia producta and 2-oleoylglycerol as clinically relevant bacterial and metabolic mediators contributing to CL-HFS-induced non-alcoholic steatohepatitis. In vivo studies validate that both Blautia producta and 2-oleoylglycerol promote liver inflammation and hepatic fibrosis in normal diet- or CL-HFS-fed mice. Cellular and molecular studies reveal that the GPR119/TAK1/NF-κB/TGF-β1 signaling pathway mediates 2-oleoylglycerol-induced macrophage priming and subsequent hepatic stellate cell activation. These findings advance our understanding of non-alcoholic steatohepatitis pathogenesis and provide targets for developing microbiome/metabolite-based therapeutic strategies against non-alcoholic steatohepatitis.