Table 1.
Characteristics of 73 “Ca. M. girerdii” positive vaginal samples.
Table 2.
Associations of vaginal carriage of bacterial taxa with common vaginal infections.
Figure 1.
Detection of “Ca. Mycoplasma girerdii” in mid-vaginal samples.
Panel (A) shows relative abundance of major taxonomic groups in “Ca. M. girerdii” positive samples (1% 16S rRNA threshold): “Ca. M. girerdii” is colored red (A). Light colored bars represent other taxa. Dark blue circles represent samples positive for T. vaginalis by qRT-PCR, light gray circles represent negative samples. Panels (B–E) show fluorescence in situ hybridization detection of bacteria in mid-vaginal samples from two participants with clinically diagnosed trichomoniasis (subject 1, panels B, C and D; subject 2, panel E) by confocal laser scanning microscopy. Most bacteria were detected with fluorescein-labeled broad-range bacteria probe Eub338 (turquoise). “Ca. M. girerdii” was also stained with a Cy5-labeled probe targeting 16S rDNA (red). Nuclei were labeled with 4′6′-diamidine-2-phenylindole, dehydrochloride (DAPI, blue). Negative control with reverse complementary probe of Eub338 did not hybridize to any bacteria (data not shown). Scale bar = 10 µm.
Figure 2.
Cluster analysis of mid-vaginal samples positive for “Ca. M. girerdii”.
Relative abundance of microbial taxa in mid-vaginal bacterial communities of “Ca. M. girerdii” positive women is shown. The dendrogram was generated using Ward’s method with Manhattan distance. This analysis includes only mid-vaginal samples that exhibited at least 0.1% “Ca. M. girerdii” by 16S rDNA profiling. Clinical diagnosis is indicated in the first bar, and presence of T. vaginalis by RT-PCR is indicated in the second bar (orange designates a negative result and pink designates a positive result). The three samples dominated by L. crispatus and the three samples with the highest prevalence of L. iners were negative for T. vaginalis.
Table 3.
“Ca. M. girerdii” is associated with African American race and elevated vaginal pH.
Figure 3.
Representation of “Ca. M. girerdii” genomes.
A circular representation of the “Ca. M. girerdii” reference genome (strain VCU_M1) assembled from metagenomic sequences from a mid-vaginal sample. Position 1 is set to the start of the dnaA gene. Outermost circles (1–3) show the alignment (97% or greater identity) of contigs of three different strains from metagenomic assemblies from mid-vaginal samples containing high proportions of “Ca. M. girerdii”. Circle 4 (red) represents the reference strain (VCU_M1). Circles 5 (dark red) and 6 (blue) represent the predicted coding sequences in the forward and reverse orientations respectively. Circle 7 (black) shows the GC content, and circle 8 shows GC skew (pink (-), green (+)).
Figure 4.
Phylogenetic tree of 16SrRNA shows uncultured “Ca. M. girerdii” clusters most closely with other uncultivated organisms in the Pneumoniae Group.
The maximum likelihood tree was inferred by RAxML 7.2.7 using the gamma-distributed heterogeneity rate categories with 1,000 bootstraps. The 16S rRNA gene alignments were manually inspected. The Hominis Group is shaded in blue, the Pneumoniae Group in green, the Hemoplasma Group in gray and the Spiroplasma Group in purple. The 16S rRNA sequence of “Ca. M. girerdii” VCU_M1, “Ca. M. girerdii” VCU_PA1, “Ca. M. girerdii” VCU JB1 and “Ca. M. girerdii” VCU_G1 were identical. “Ca. M. girerdii” groups most closely with “Mnola”, which shows 100% identity in 16S rRNA sequence, uncultivated organisms from the oral sample of a low birth weight infant (HG764209, HG764210, and HG764212) and uncultivated species from rumen and termite gut in the Pneumoniae Group. A partial 16S rRNA sequence from the vaginal sample of a woman who delivered full term (JX871253) also exhibits 99% identity with “Ca. M. girerdii”, but was not included in the analysis due to its length.
Figure 5.
Phylogenetic Tree based on inferred amino acid sequences confirms placement of “Ca. M. girerdii” in the Pneumoniae group.
“Ca. M. girerdii” is located within the Pneumoniae group, denoted in green, in a subclade along with the Ureaplasma species, M. iowae and M. penetrans. The tree was inferred using amino acid sequences of 57 orthologs (Tables S4, S5, and S6). Numbers at nodes correspond to the support values from 1,000 bootstrap replicates.
Figure 6.
Unique strategies of “Ca. M. girerdii”.
Putative transporters, enzymes involved in carbohydrate metabolism and virulence factors are represented in red for “Ca. M. girerdii”. Comparisons with other genital mycoplasmas are indicated with color-coded boxes: M. genitalium (MG, blue) U. parvum (UP, green) and M. hominis (MH, purple). Arrows indicate direction of transport. Light gray arrows represent metabolic strategies unique to other genital mycoplasma. Metabolic reconstruction was performed using ASGARD and careful inspection of manual annotations.
Figure 7.
Expanded “Ca. M. girerdii” BspA-like protein family.
The diverse family of 26 BspA-like protein family members from the “Ca. M. girerdii” strain VCU_M1 is depicted in panel (A). Predicted transmembrane domains and TpLRR domains are represented. An alignment of TpLRR domains from Tannerella forsythia BspA (AAC82625.1, bases 382–1347), “Ca. M. girerdii” strain VCU_M1 MGM1_3780 (bases 449–782) and T.vaginalis BspA-like TVAG_495790 (XP_001327783.1, bases 112–1077) is shown in panel (B).