Abstract
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.
Highlights
The “sterile urine” dogma based on traditional cultivation-dependent approaches of bacterial detection has been long questioned
We identified 1,729 core KEGG orthologs (KOs) and 316 modules in the genitourinary microbiota (Supplementary Tables 4, 5), and 97.05% cKOs and 96.24% modules of these were shared with the core functions of the gut representing 1,928 cKOs and 320 modules, respectively, demonstrating that the heterogeneous microbiome in these two body sites in asymptomatic individuals may have similar functions
To assess the impact of different types of possible contaminants while eliminating the effects of sequencing depth and sample size, we classified all samples into seven groups according to raw sequencing depth (G1-7: ≤20,000, 20,000–30,000, 30,000–40,000, 40,000–50,000, 50,000–60,000, 60,000–70,000, 70,000–80,000, ≥8,000), and extracted 110 samples from each group followed by the same contaminant identification operations
Summary
The “sterile urine” dogma based on traditional cultivation-dependent approaches of bacterial detection has been long questioned. Recent research has revealed that GM was dominated by genera like Lactobacillus, Streptococcus, Veillonella, Staphylococcus, and Neisseria (Aragon et al, 2018; Pohl et al, 2020). Jonquetella, Proteiniphilum, Saccharofermentans, and Parvimonas genera were only found in the urine of individuals older than 70 (Lewis et al, 2013); male samples tended to be enriched with Streptococcus, Veillonella, Staphylococcus, Gardnerella, Enterobacter sp., Neisseria, and Haemophilus, while female samples tended to be abundant of Lactobacillus and Prevotella (Pohl et al, 2020). GM research based on a larger samples size and targeted to certain subjects is needed
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