Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents.

OBJECTIVE: Patients with renal failure suffer from symptoms caused by uraemic toxins, possibly of gut microbial origin, as deduced from studies in animals. The aim of the study is to characterise relationships between the intestinal microbiome composition, uraemic toxins and renal failure symptoms in human end-stage renal disease (ESRD). DESIGN: Characterisation of gut microbiome, serum and faecal metabolome and human phenotypes in a cohort of 223 patients with ESRD and 69 healthy controls. Multidimensional data integration to reveal links between these datasets and the use of chronic kidney disease (CKD) rodent models to test the effects of intestinal microbiome on toxin accumulation and disease severity. RESULTS: A group of microbial species enriched in ESRD correlates tightly to patient clinical variables and encode functions involved in toxin and secondary bile acids synthesis; the relative abundance of the microbial functions correlates with the serum or faecal concentrations of these metabolites. Microbiota from patients transplanted to renal injured germ-free mice or antibiotic-treated rats induce higher production of serum uraemic toxins and aggravated renal fibrosis and oxidative stress more than microbiota from controls. Two of the species, Eggerthella lenta and Fusobacterium nucleatum, increase uraemic toxins production and promote renal disease development in a CKD rat model. A probiotic Bifidobacterium animalis decreases abundance of these species, reduces levels of toxins and the severity of the disease in rats. CONCLUSION: Aberrant gut microbiota in patients with ESRD sculpts a detrimental metabolome aggravating clinical outcomes, suggesting that the gut microbiota will be a promising target for diminishing uraemic toxicity in those patients. TRIAL REGISTRATION NUMBER: This study was registered at ClinicalTrials.gov (NCT03010696).

Lactobacillus shenzhenensis sp. nov., isolated from a fermented dairy beverage.

Two Lactobacillus strains, designated LY-73(T) and LY-30B, were isolated from a dairy beverage, sold in Shenzhen market, China. The two isolates were Gram-positive, non-spore-forming, non-motile, facultatively anaerobic rods that were heterofermentative and did not exhibit catalase activity. Sequencing of the 16S rRNA, pheS and rpoA genes revealed that the two isolates shared 99.5, 99.8 and 99.9 % sequence similarity, which indicates that they belong to the same species. Phylogenetic analysis demonstrated clustering of the two isolates with the genus Lactobacillus. Strain LY-73(T) showed highest 16S rRNA gene sequence similarities with Lactobacillus harbinensis KACC 12409(T) (97.73%), Lactobacillus perolens DSM 12744(T) (96.96 %) and Lactobacillus selangorensis DSM 13344(T) (93.10 %). Comparative analyses of their rpoA and pheS gene sequences indicated that the novel strains were significantly different from other Lactobacillus species. Low DNA-DNA reassociation values (50.5 %) were obtained between strain LY-73(T) and its phylogenetically closest neighbours. The G+C contents of the DNA of the two novel isolates were 56.1 and 56.5 mol%. Straight-chain unsaturated fatty acids C18 : 1ω9c (78.85 and 74.29 %) were the dominant components, and the cell-wall peptidoglycan was of the l-Lys-d-Asp type. Based on phenotypic characteristics, and chemotaxonomic and genotypic data, the novel strains represent a novel species of the genus Lactobacillus, for which the name Lactobacillus shenzhenensis sp. nov. is proposed, with LY-73(T) ( = CCTCC M 2011481(T) = KACC 16878(T)) as the type strain.

Draft genome sequence of Escherichia coli LCT-EC106.

Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the intestine of warm-blooded organisms. Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans. Here, we present the complete genome sequence of Escherichia coli LCT-EC106, which was isolated from CGMCC 1.2385.

Characterization of the Genitourinary Microbiome of 1,165 Middle-Aged and Elderly Healthy Individuals.

Accumulated evidence shows that complex microbial communities resides in the healthy human urinary tract and can change in urological disorders. However, there lacks a comprehensive profiling of the genitourinary microbiota in healthy cohort. Here, we performed 16S rRNA gene sequencing of midstream urine specimens from 1,172 middle-aged and elderly healthy individuals. The core microbiota included 6 dominant genera (mean relative abundance >5%), including Prevotella, Streptococcus, Lactobacillus, Gardnerella, Escherichia-Shigella, and Veillonella, and 131 low-abundance genera (0.01-5%), displaying a distinct microbiome profiles to that of host-matched gut microbiota. The composition and diversity of genitourinary microbiome (GM) were distinct between genders and may fluctuate with ages. Several urotypes were identified by the stratification of microbiome profiles, which were mainly dominated by the six most predominant genera. The prevalence of urotypes was disparate between genders, and the male sample additionally harbored other urotypes dominated by Acinetobacter, Corynebacterium, Staphylococcus, or Sphingomonas. Peptoniphilus, Ezakiella, and Porphyromonas were co-occurred and co-abundant, and they may play crucial roles as keystone genera and be associated with increased microbial diversity. Our results delineated the microbial structure and diversity landscape of the GM in healthy middle-aged and elderly adults and provided insights into the influence of gender and age to it.

Systematic analysis of gut microbiota in pregnant women and its correlations with individual heterogeneity.

The woman's gut microbiota during pregnancy may support nutrient acquisition, is associated with diseases, and has been linked to infant health. However, there is limited information on gut microbial characteristics and dependence in pregnant women. In this study, we provide a comprehensive overview of the gut microbial characteristics of 1479 pregnant women using 16S rRNA gene sequencing of fecal samples. We identify a core microbiota of pregnant women, which displays a similar overall structure to that of age-matched nonpregnant women. Our data show that the gestational age-associated variation in the gut microbiota, from the ninth week of gestation to antepartum, is relatively limited. Building upon rich metadata, we reveal a set of exogenous and intrinsic host factors that are highly correlated with the variation in gut microbial community composition and function. These microbiota covariates are concentrated in basic host properties (e.g., age and residency status) and blood clinical parameters, suggesting that individual heterogeneity is the major force shaping the gut microbiome during pregnancy. Moreover, we identify microbial and functional markers that are associated with age, pre-pregnancy body mass index, residency status, and pre-pregnancy and gestational diseases. The gut microbiota during pregnancy is also different between women with high or low gestational weight gain. Our study demonstrates the structure, gestational age-associated variation, and associations with host factors of the gut microbiota during pregnancy and strengthens the understanding of microbe-host interactions. The results from this study offer new materials and prospects for gut microbiome research in clinical and diagnostic fields.

Genome Sequence of Enterobacter cancerogenus YZ1.

Enterobacter cancerogenus is usually known as an opportunistic human pathogen. Recently, it has attracted great attention for its capability to produce bioemulsifier, degrade xenobiotics, and resist alkalis and antibiotics. Here we report the complete genome of Enterobacter cancerogenus YZ1, isolated from a bran-feeding Coleoptera insect's frass.

Whole-Genome Sequencing of Lactobacillus shenzhenensis Strain LY-73T.

Lactobacillus shenzhenensis strain LY-73(T) is a novel species which was first isolated from fermented goods. Here, we report the draft genome sequence of Lactobacillus shenzhenensis LY-73(T).