MOCHI: a comprehensive cross-platform tool for amplicon-based microbiota analysis

Moringa leaf meal exerts growth benefits in small ruminants through modulating the gastrointestinal microbiome

This study investigated the impact of feeding 17% moringa leaf meal (MLM) on the ruminal and fecal microbial composition and body weight gain (BWG) performance of lambs (Ovis aries) and kids (Capra hircus). A total of n = 28 lambs (n = 14, no-moringa, n = 14, 17% moringa) and 24 kids (n = 12, no-moringa, n = 12, 17% moringa) were involved in the experiment and body weight was recorded fortnightly. Metagenomic shotgun sequencing was performed on 28, 22, and 26 ruminal solid, liquid fraction, and fecal samples from lambs, and 23, 22, and 23 samples from kids. Moringa supplementation significantly increased BWG in lambs (21.09 ± 0.78 to 26.12 ± 0.81 kg) and kids (14.60 ± 1.29 to 18.28 ± 1.09 kg) (p-value ≤ 0.01). Microbiome analysis revealed an elevated Firmicutes:Bacteroidetes ratio in the moringa diet group. Moringa-fed animals exhibited increased microbial genera associated with volatile fatty acids (VFAs) production (Prevotella, Anaerovibrio, Lachnospiraceae, Butyrivibrio, Christensenella) and starch and fiber digesters (Proteobacteria, Ruminococcus). The increase in the bacterial genus Sharpea suggested possible methane reduction and decreased proportion of pathogens, Aliarcobacter_ID28198, Campylobacter_ID194 and Campylobacter_ID1660076 suggest health benefits. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated significant alterations in microbial gene pool and metabolic pathways related to carbohydrate, protein, lipid and energy metabolism, indicating potential improvements in animal health. Overall, moringa feeding showed higher energy recovery, improved growth, and potential benefits in methane reduction and reduced pathogenic bacteria.

The supplementation of Rothia as a potential preventive approach for bone loss in mice with ovariectomy-induced osteoporosis

There is an inseparable link between bone metabolism and gut microbiota, and the supplementation of probiotics exhibits a significant role in maintaining the homeostasis of gut microbiota and inhibiting bone loss. This study aims to explore the preventive and therapeutic potentials and the specific mechanisms of Rothia on osteoporosis. The mice models of osteoporosis induced by ovariectomy (OVX) were built, and the regular (once a day) and quantitative (200 μL/d) gavage of Rothia was performed for 8 weeks starting from 1 week after OVX. Microcomputed tomography was used to analyze the bone mass and bone microstructure of mice in each group after sacrifice. Histological staining and immunohistochemistry were then applied to identify the expression of pro-inflammatory cytokines, intestinal permeability, and osteogenic and osteoclastic activities of mice. The collected feces of mice in each group were used for 16S rRNA high-throughput sequencing to detect the alterations in composition, abundance, and diversity of gut microbiota. This study demonstrated that the gavage of Rothia alleviated bone loss in mice with OVX-induced osteoporosis, improved OVX-induced intestinal mucosal barrier injury, optimized intestinal permeability (zonula occludens protein 1 and occludin), reduced intestinal inflammation (tumor necrosis factor-α and interleukin-1β), and regulated imbalance of gut microbiota. Based on "gut-bone" axis, this study revealed that regular and quantitative gavage of Rothia can relieve bone loss in mice with OVX-induced osteoporosis by repairing the intestinal mucosal barrier injury, optimizing the intestinal permeability, inhibiting the release of pro-inflammatory cytokines, and improving the disorder of gut microbiota.

Translational informatics for human microbiota: data resources, models and applications

With the rapid development of human intestinal microbiology and diverse microbiome-related studies and investigations, a large amount of data have been generated and accumulated. Meanwhile, different computational and bioinformatics models have been developed for pattern recognition and knowledge discovery using these data. Given the heterogeneity of these resources and models, we aimed to provide a landscape of the data resources, a comparison of the computational models and a summary of the translational informatics applied to microbiota data. We first review the existing databases, knowledge bases, knowledge graphs and standardizations of microbiome data. Then, the high-throughput sequencing techniques for the microbiome and the informatics tools for their analyses are compared. Finally, translational informatics for the microbiome, including biomarker discovery, personalized treatment and smart healthcare for complex diseases, are discussed.