A study published in Animal Microbiome demonstrates a novel role for host genetic variation in shaping lung microbiota composition. This may open new avenues for advancing lung microbiome research using animal models.
mice were mated within each cross at 10 weeks and included 11 pairs from each cross. Fmice were weaned at 3 weeks; males and females were housed in separate cages according to family, with mixed genotypes. Mice were maintained in individual ventilated cages , type II long in a specific pathogen-free facility with a 12-h light/dark cycle. Decalcified water and food were provided.
]. We chose the V1-V2 region of the 16S rRNA gene for multiple reasons. In particular, we made previous experience of this primer pair performing well in an earlier low biomass study of the same G], which also enables future cross-body site analyses. Three negative extraction controls from each extraction plate and one microbial community DNA standard were included. Host reads were removed from DNA extracts using “Kneaddata” , which removes host reads based on the provided reference database,.
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Effects of age, seasonality, and reproductive status on the gut microbiome of Southern White Rhinoceros (Ceratotherium simum simum) at the North Carolina zoo - Animal MicrobiomeBackground Managed southern white rhinoceros (Ceratotherium simum simum) serve as assurance populations for wild conspecifics threatened by poaching and other anthropocentric effects, though many managed populations experience subfertility and reproductive failure. Gut microbiome and host health are inextricably linked, and reproductive outcomes in managed southern white rhinoceros may be mediated in part by their diet and gut microbial diversity. Thus, understanding microbial dynamics within managed populations may help improve conservation efforts. We characterized the taxonomic composition of the gut microbiome in the managed population of female southern white rhinoceros (n = 8) at the North Carolina Zoo and investigated the effects of seasonality (summer vs. winter) and age classes (juveniles (n = 2; 0–2 years), subadults (n = 2; 3–7 years), and adults (n = 4; |7 years)) on microbial richness and community structure. Collection of a fecal sample was attempted for each individual once per month from July-September 2020 and January-March 2021 resulting in a total of 41 samples analyzed. Microbial DNA was extracted and sequenced using the V3-V4 region of the 16S rRNA bacterial gene. Total operational taxonomic units (OTUs), alpha diversity (species richness, Shannon diversity), and beta diversity (Bray-Curtis dissimilarity, linear discriminant analysis effect size) indices were examined, and differentially enriched taxa were identified. Results There were differences (p | 0.05) in alpha and beta diversity indices across individuals, age groups, and sampling months. Subadult females had higher levels of Shannon diversity (Wilcoxon, p | 0.05) compared to adult females and harbored a community cluster distinct from both juveniles and adults. Samples collected during winter months (January-March 2021) possessed higher species richness and statistically distinct communities compared to summer months (July-September 2020) (PERMANOVA, p | 0.05). Reproductively active (n
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Diets rich in fiber, plant protein, and unsaturated fat may beneficially modulate the gut microbiota involved in weight lossDiets rich in fiber, plant protein, and unsaturated fat may beneficially modulate the gut microbiota involved in weight loss Nutrients_MDPI CampusBioMedico fiber plantprotein diet plantbaseddiet mediterraneandiet weightloss gutmicrobiome
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ERStruct: a fast Python package for inferring the number of top principal components from whole genome sequencing data - BMC BioinformaticsBackground Large-scale multi-ethnic DNA sequencing data is increasingly available owing to decreasing cost of modern sequencing technologies. Inference of the population structure with such sequencing data is fundamentally important. However, the ultra-dimensionality and complicated linkage disequilibrium patterns across the whole genome make it challenging to infer population structure using traditional principal component analysis based methods and software. Results We present the ERStruct Python Package, which enables the inference of population structure using whole-genome sequencing data. By leveraging parallel computing and GPU acceleration, our package achieves significant improvements in the speed of matrix operations for large-scale data. Additionally, our package features adaptive data splitting capabilities to facilitate computation on GPUs with limited memory. Conclusion Our Python package ERStruct is an efficient and user-friendly tool for estimating the number of top informative principal components that capture population structure from whole genome sequencing data.
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Dublin: Man mistaken for animal and accidentally shotA man in his 40s has been taken to hospital after he was accidentally shot at a golf club near Dublin.
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Dublin: Man mistaken for animal and accidentally shotA man in his 40s has been taken to hospital after he was accidentally shot at a golf club near Dublin.
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Animal lovers in Preston invited to join RSPCA’s annual One Fun DayEntrance to the RSPCA in Preston Pic: Blog Preston RSPCA Preston and District Branch to host an event on Saturday June 17 Animal lovers are invited t
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