Gut Microbiota

A screen of more than 1,000 drugs shows that about a quarter of the non-antibiotic drugs inhibit the growth of at least one commensal bacterial strain in vitro.

Phospholipase Ds (PLDs) transform phosphatidylcholine to choline, which can then be converted to disease-associated trimethylamine. Here, PLDs are identified in gut bacteria that support growth of other bacteria and are potential therapeutic targets.

Infant nutrition and maternal weight gain during pregnancy impact early-life acquisition and function of the gut microbiome .

Comprehensive fecal metabolic profiling in 786 individuals from TwinsUK provides insights into the influence of host genetics and gut microbial composition on metabolites that may mediate microbiome-associated phenotypes.

Complex microbial communities shape the dynamics of various environments. In this Review, Knight and colleagues discuss the best practices for performing a microbiome study, including experimental design, choice of molecular analysis technology, methods for data analysis and the integration of multiple omics data sets.

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Metagenomic sequencing analysis of stool samples from 903 children as part of the TEDDY study shows that breastfeeding was the most important factor associated with microbiome structure, and the cessation of breast milk resulted in faster maturation of the gut microbiome.

An analysis of more than 10,000 metagenomes from the TEDDY study provides a detailed functional profile of the gut microbiome in relation to islet autoimmunity, and supports the protective effects of short-chain fatty acids in early-onset type 1 diabetes.

The authors compare human fecal viromes from three isolated villages of the Amazon rain forest with those from city dwellers. They report that the diversity of human viruses is not reduced in isolated villages, suggesting frequent viral introductions or increased susceptibility to enteric infections.

The effects of caesarean section delivery on mother-to-neonate transmission of microbiota are unclear. Here the authors show that caesarean section delivery can affect the transmission of specific microbial strains and the immunomodulatory potential of the microbiota.

Gut microbial dysbiosis in infancy is associated with childhood atopy and the development of asthma. Here, the authors show that gut microbiota perturbation is evident in the very earliest stages of postnatal life, continues throughout infancy, and can be partially rescued by Lactobacillus supplementation in high-risk for asthma infants.

The human gut microbiome has been associated with many health factors, but variability between studies limits exploration of these effects. Here, Jackson et al. analyse gut microbiota associations for 38 common diseases and 51 medications within >2700 members of the TwinsUK cohort.

Recent microbiome genome-wide association studies have identified numerous associations between human genetic variants and the gut microbiome. Here, the authors review how genetic variation in the host can alter the composition of the gut microbiome towards a disease state, with a focus on disorders of immunity and metabolism.

A new bioinformatic tool identifies a candidate source of bloodstream infection for better management and prevention of hospital-acquired infections.

Lipopeptides secreted by Bacillus bacteria block quorum sensing by Staphylococcus aureus and thereby inhibit the growth of this opportunistic pathogen in the gut, suggesting why people in rural Thailand who are colonized by Bacillus are not also colonized by S. aureus.

Genome-wide and metagenome-wide association study of 92 cardiovascular-diseases-related proteins identifies genetic and microbial factors that explain 76.6% of inter-individual variation, highlighting the role of gut microbiome in cardiovascular disease.

Current nutritional approaches to prevent and treat various diseases have limited effectiveness. Here, Zmora et al. review the major principles underlying effects of dietary constituents on the gut microbiota, resolving aspects of the diet–microbiota–host crosstalk, and present the promises and challenges of incorporating microbiome data into dietary planning.

Antimicrobial peptide resistance genes are found to be widespread in the gut microbiome but are exchanged at lower rates compared to antibiotic resistance genes, with functional compatibility between bacteria being important for gene exchange.

Klebsiella pneumoniae from the gut microbiota of patients with primary sclerosing cholangitis (PSC) can damage the intestinal epithelial barrier, resulting in bacterial translocation and T helper 17 cell responses in the liver, indicating a role in PSC pathogenesis.