LMdist: Local Manifold distance accurately measures beta diversity in ecological gradients.

Motivation: Differentiating ecosystems poses a complex, high-dimensional problem constrained by capturing relevant variation across species profiles. Researchers use pairwise distances and subsequent dimensionality reduction to highlight variation in a few dimensions. Despite popularity in analysis of ecological data, these low-dimensional visualizations can contain geometric abnormalities such as "arch" and "horseshoe" effects, potentially obscuring the impact of environmental gradients.

Industrialized human gut microbiota increases CD8+ T cells and mucus thickness in humanized mouse gut.

Immigration to a highly industrialized nation has been associated with metabolic disease and simultaneous shifts in microbiota composition, but the underlying mechanisms are challenging to test in human studies. Here, we conducted a pilot study to assess the differential effects of human gut microbiota collected from the United States (US) and rural Thailand on the murine gut mucosa and immune system. Colonization of germ-free mice with microbiota from US individuals resulted in an increased accumulation of innate-like CD8 T cells in the small intestine lamina propria and intra-epithelial compartments when compared to colonization with microbiota from Thai individuals.

A Guide to Dietary Pattern-Microbiome Data Integration.

The human gut microbiome is linked to metabolic and cardiovascular disease risk. Dietary modulation of the human gut microbiome offers an attractive pathway to manipulate the microbiome to prevent microbiome-related disease. However, this promise has not been realized.

Saliva Testing Is Accurate for Early-Stage and Presymptomatic COVID-19.

Although nasopharyngeal samples have been considered the gold standard for COVID-19 testing, variability in viral load across different anatomical sites could cause nasopharyngeal samples to be less sensitive than saliva or nasal samples in certain cases. Self-collected samples have logistical advantages over nasopharyngeal samples, making them amenable to population-scale screening. To evaluate sampling alternatives for population screening, we collected nasopharyngeal, saliva, and nasal samples from two cohorts with varied levels and types of symptoms.

Calprotectin (S100A8/A9) Is an Innate Immune Effector in Experimental Periodontitis.

Upregulated in inflammation, calprotectin (complexed S100A8 and S100A9; S100A8/A9) functions as an innate immune effector molecule, promoting inflammation, and also as an antimicrobial protein. We hypothesized that antimicrobial S100A8/A9 would mitigate change to the local microbial community and promote resistance to experimental periodontitis . To test this hypothesis, S100A9 and wild-type (WT; S100A9) C57BL/6 mice were compared using a model of ligature-induced periodontitis.

Alteration of the Gut Microbiome in Normal and Overweight School Children from Selangor with Fermented Milk Administration.

Childhood obesity is a serious public health problem worldwide. Perturbations in the gut microbiota composition have been associated with the development of obesity in both children and adults. Probiotics, on the other hand, are proven to restore the composition of the gut microbiome which helps reduce the development of obesity.

Bacterial community structure and function distinguish gut sites in captive red-shanked doucs (Pygathrix nemaeus).

The mammalian order primates contains wide species diversity. Members of the subfamily Colobinae are unique amongst extant primates in that their gastrointestinal systems more closely resemble those of ruminants than other members of the primate order. In the growing literature surrounding nonhuman primate microbiomes, analysis of microbial communities has been limited to the hindgut, since few studies have captured data on other gut sites, including the foregut of colobine primates.