Search Results (6)

Host genetics and environmental factors have been associated with effects on the mouse fecal microbiome; however, the commercial source of mice remains the dominant factor. Increasing evidence indicates that supplier-specific microbiomes confer differences in disease susceptibility in models of inflammatory conditions, as well as baseline behavior and body morphology. However, current knowledge regarding the compositional differences between suppliers is based on targeted-amplicon sequencing data, and functional differences between these communities remain poorly defined. We applied a multi-omic (metagenomic and metatranscriptomic) approach to biomolecules extracted from murine feces representative of two U.S. suppliers of research mice, which differ in composition, and influence baseline physiology and behavior as well as disease severity in models of intestinal disease. We reconstructed high-quality metagenome-assembled genomes, frequently containing genomic content unique to each supplier. Transcriptional activity and pathway analyses revealed key functional differences between the metagenomes associated with each supplier including carbohydrate, fatty acid, and sulfite metabolism. These data provide a detailed characterization of the baseline differences in the fecal metagenome of mice from two U.S. commercial suppliers, suggesting that these functional differences are influenced by differences in the initial inoculum of colony founders, as well as additional taxa gained during growth of the production colony. Full article

Obesity places a tremendous burden on individual health and the healthcare system. The gut microbiome (GM) influences host metabolism and behaviors affecting body weight (BW) such as feeding. The GM of mice varies between suppliers and significantly influences BW. We sought to determine whether GM-associated differences in BW are associated with differences in intake, fecal energy loss, or fetal growth. Pair-housed mice colonized with a low or high microbial richness GM were weighed, and the total and BW-adjusted intake were measured at weaning and adulthood. Pups were weighed at birth to determine the effects of the maternal microbiome on fetal growth. Fecal samples were collected to assess the fecal energy loss and to characterize differences in the microbiome. The results showed that supplier-origin microbiomes were associated with profound differences in fetal growth and excessive BW-adjusted differences in intake during adulthood, with no detected difference in fecal energy loss. Agreement between the features of the maternal microbiome associated with increased birth weight here and in recent human studies supports the value of this model to investigate the mechanisms by which the maternal microbiome regulates offspring growth and food intake. Full article

Research investigating the gut microbiome (GM) during a viral infection may necessitate inactivation of the fecal viral load. Here, we assess how common viral inactivation techniques affect 16S rRNA-based analysis of the gut microbiome. Five common viral inactivation methods were applied to cross-matched fecal samples from sixteen female CD-1 mice of the same GM background prior to fecal DNA extraction. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA. Treatment-dependent effects on DNA yield, genus-level taxonomic abundance, and alpha and beta diversity metrics were assessed. A sodium dodecyl sulfate (SDS)-based inactivation method and Holder pasteurization had no effect on measures of microbial richness, while two Buffer AVL-based inactivation methods resulted in a decrease in detected richness. SDS inactivation, Holder pasteurization, and the AVL-based inactivation methods had no effect on measures of alpha diversity within samples or beta diversity between samples. Fecal DNA extracted with TRIzol-treated samples failed to amplify and sequence, making it unsuitable for microbiome analysis. These results provide guidance in the 16S rRNA microbiome analysis of fecal samples requiring viral inactivation. Full article

Common hexaploid oat (Avena sativa L.) is an important global cereal crop. A Moroccan tetraploid sister species, A. magna Murphy et Terrel, was exclusively a wild species until recently. The goal of domestication was to exploit its superior groat-protein content and climatic tolerances. We set up replicated trials of 41 domesticated A. magna lines on eight Moroccan farms during the 2017–2018 and 2018–2019 growing seasons. Twenty traits were measured and analyses of variance detected significant differences among lines. The highest grain yield was at Berrechid in 2017–2018 (63.56 q/ha), with an average annual yield across sites of 43.50 q/ha, the site factor explaining 82% and the genotype-environment interaction explaining 15% of the variability. In the second year, El Kebab recorded the highest yield at 20.03 q/ha over the annual average of 14.78 q/ha. In this second year, the site factor was highly significant, explaining 42.25% of the variation, with the genotype-environment interaction explaining 26.61% of the variability. An additional main effect and multiplicative interaction analysis of the eight two-year trials identified several accessions with good yield stability. Twelve lines exhibited a ASVs ≤ 1.50, with five accessions (A34, A40, A23, A05, A04) exceeding the overall average yield of 29.53 and A34 having the greatest mean grain yield and stability. The versatility and stability of A. magna can provide a sustainable protein source and an economic resource for farmers seeking products that are resilient to climatic instability. Full article

Retinitis pigmentosa (RP) causes progressive photoreceptor loss resulting from mutations in over 80 genes. This study identified the genetic cause of RP in three members of a non-consanguineous pedigree. Detailed ophthalmic evaluation was performed in the three affected family members. Whole exome sequencing (WES) and whole genome sequencing (WGS) were performed in the three affected and the two unaffected family members and variants were filtered to detect rare, potentially deleterious variants segregating with disease. WES and WGS did not identify potentially pathogenic variants shared by all three affected members. However, WES identified a previously reported homozygous nonsense mutation in KIZ (c.226C>T, p.Arg76*) in two affected sisters, but not in their affected second cousin. WGS revealed a novel 1.135 kb homozygous deletion in a retina transcript of C21orf2 and a novel 30.651 kb heterozygous deletion in CACNA2D4 in the affected second cousin. The sisters with the KIZ mutation carried no copies of the C21orf2 or CACNA2D4 deletions, while the second cousin with the C21orf2 and CACNA2D4 deletions carried no copies of the KIZ mutation. This study identified two independent, homozygous mutations in genes previously reported in autosomal recessive RP in a non-consanguineous family, and demonstrated the value of WGS when WES fails to identify likely disease-causing mutations. Full article