Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries.

Background: Intra-continentally, vaginal microbiome signatures are reported to be significantly different between Black and Caucasian women, with women of African ancestry having the less well defined heterogenous bacterial community state type (CST) deficient of Lactobacillus species (CST IV). The objective of this study was to characterize the vaginal microbiomes across a more diverse intercontinental group of women (N = 151) of different ethnicities (African American, African Kenyan, Afro-Caribbean, Asian Indonesian and Caucasian German) using 16S rRNA gene sequence analysis to determine their structures and offer a comprehensive description of the non-Lactobacillus dominant CSTs and subtypes. Results: In this study, the bacterial composition of the vaginal microbiomes differed significantly among the ethnic groups. Lactobacillus spp. (L. crispatus and L. iners) dominated the vaginal microbiomes in African American women (91.8%) compared to European (German, 42.4%), Asian (Indonesian, 45.0%), African (Kenyan, 34.4%) and Afro-Caribbean (26.1%) women. Expanding on CST classification, three subtypes of CST IV (CST IV-A, IV-B and IV-C) (N = 56, 37.1%) and four additional CSTs were described: CST VI Gardnerella vaginalis-dominant (N = 6, 21.8%); CST VII (Prevotella-dominant, N = 1, 0.66%); CST VIII (N = 9, 5.96%), resembling aerobic vaginitis, was differentiated by a high proportion of taxa such as Enterococcus, Streptococcus and Staphylococcus (relative abundance [RA] > 50%) and CST IX (N = 7, 4.64%) dominated by genera other than Lactobacillus, Gardnerella or Prevotella (e.g., Bifidobacterium breve and Anaerococcus vaginalis). Within the vaginal microbiomes, 32 "taxa with high pathogenic potential" (THPP) were identified. Collectively, THPP (mean RA ~5.24%) negatively correlated (rs = -0.68, p < 2.2e-16) with Lactobacillus species but not significantly with Gardnerella/Prevotella spp. combined (r = -0.13, p = 0.1). However, at the individual level, Mycoplasma hominis exhibited moderate positive correlations with Gardnerella (r = 0.46, p = 2.6e-09) and Prevotella spp. (r = 0.47, p = 1.4e-09). Conclusions: These findings while supporting the idea that vaginal microbiomes vary with ethnicity, also suggest that CSTs are more wide-ranging and not exclusive to any particular ethnic group. This study offers additional insight into the structure of the vaginal microbiome and contributes to the description and subcategorization of non-Lactobacillus-dominated CSTs.

A novel approach for the identification and phylogenetic delineation of human Mycoplasma species and strains using genomic segment sequence analysis.

Human Mycoplasma are opportunistic, facultative pathogens that are site-specific in their colonization of mucosal surfaces. They are responsible for significant annual morbidity in humans by causing acute illnesses and chronic auto-inflammatory diseases via modulation of the host's immune system. Accurate and reliable identification of Mycoplasma species and their strains are thus of upmost importance. This study, analysed for the first time, the effectiveness of a short (50 kb) genome fragment (termed as R-segment), which includes the complete rRNA operon and the flanking region up to 50 kb, as a single phylogenetic marker for assessing the molecular taxonomy and determining the identity of human Mycoplasma species and their strains. The R-segments of human mycoplasmas were shown to have inherent genetic properties [average nucleotide identity (ANI), codon bias index (CBI), genome-to-genome distances (GGD) and % G + C] similar to their whole genome counterparts. Based on the results of our R segment analysis, a species of human Mycoplasma can simply be defined as a group of strains that share R-segments with ANIs ≥97%. Additionally, R-segments offered superiority to 16S rRNA gene sequences and multilocus sequences for the delineation of the human Mycoplasma species and their strains. The overall comparative genomic results suggest that R-segment analysis can be considered as a promising cost-effective tool for the epidemiological surveillance and differentiation of the closely related species and/or strains of human mycoplasmas.

Comparative genomics of four Mycoplasma species of the human urogenital tract: Analysis of their core genomes and virulence genes.

The variation in Mycoplasma lipoproteins attributed to genome rearrangements and genetic insertions leads to phenotypic plasticity that allows for the evasion of the host's defence system and pathogenesis. This paper compared for the first time the genomes of four human urogenital Mycoplasma species (M. penetrans HF-2, M. fermentans JER, M. genitalium G37 and M. hominis PG21) to categorise the metabolic functions of the core genes and to assess the effects of tandem repeats, phage-like genetic elements and prophages on the virulence genes. The results of this comparative in silico genomic analysis revealed that the genes constituting their core genomes can be separated into three distinct categories: nuclear metabolism, protein metabolism and energy generation each making up 52%, 31% and 23%, respectively. The genomes have repeat sequences ranging from 3.7% in M. hominis PG21 to 9.5% in M. fermentans JER. Tandem repeats (mostly minisatellites) and phage-like proteins (including DNA gyrases/topoisomerases) were randomly distributed in the Mycoplasma genomes. Here, we identified a coiled-coil structure containing protein in M. penetrans HF-2 which is significantly similar to the Mem protein of M. fermentans ɸMFV1. Therefore, a Mycoplasma prophage seems to be embedded within M. penetrans HF-2 unannotated genome. To the best of our knowledge, no Mycoplasma phages or prophages have been detected in M. penetrans. This study is important not only in understanding the complex genetic factors involved in phenotypic plasticity and virulence in the relatively understudied Mycoplasma species but also in elucidating the effective arrangement of their redundant minimal genomes.