The proportions of bacterial genera in urine and swab specimens are similar.

<p>The y-axis shows percentage classified sequence reads corresponding to each genera, bars corresponding to urine and swab are in gray and black, respectively. Error bars indicate one unit of standard error. The 15 most abundant genera, corresponding to 89.48% and 83.52% of classifiable sequences from STI positive and negative specimens, respectively, are shown. (A). STI (positive test for <i>C. trachomatis</i>, <i>N. gonorrhoeae</i>, and or <i>T. vaginalis</i>) positive group (n = 10), (B) STI negative group (n = 22).</p

Bacterial lineages suspected to be zoonotic pathogens and the host species and rodent community in which they were detected.

<p>Bacterial lineages suspected to be zoonotic pathogens and the host species and rodent community in which they were detected.</p

Bacterial prevalence in G<i>erbillus andersoni</i> (green), <i>G. pyramidum</i> (purple), and <i>G. gerbillus</i> (red) as a function of host species richness.

<p>Lineages found in at least two host individuals are shown in the main figures, and unique lineages are included in the right-hand inserts. Numbers in the right-hand inserts indicate the total number of unique lineages observed for each host species.</p

Relationships between bacterial lineage diversity (means ± SE of Fisher alpha) and rodent species richness.

<p>Relationships are quantified at different scales and for different organization levels. A- in individual hosts, B- at the plot scale in a population of hosts, C- at the plot scale in a community of hosts, D- at the regional scale in a population of hosts, E- at the regional scale in a community of hosts. The relationships between bacterial diversity and host diversity in individual hosts and host populations are illustrated separately for each host species (G<i>erbillus andersoni</i> is indicated in green, <i>G. pyramidum</i> in purple and <i>G. gerbillus</i> in red).</p

Results summary for ranked bacterial lineage occupancy analyses for the three rodent communities.

<p>Results summary for ranked bacterial lineage occupancy analyses for the three rodent communities.</p

Statistical results testing the effects of host species, host diversity and their interaction on diversity measures of bacterial communities of individual rodents, rodent populations, and rodent communities.

<p>Statistical results testing the effects of host species, host diversity and their interaction on diversity measures of bacterial communities of individual rodents, rodent populations, and rodent communities.</p

DataSheet_1_Association of Chlamydia trachomatis burden with the vaginal microbiota, bacterial vaginosis, and metronidazole treatment.docx

Bacterial vaginosis (BV), a dysbiosis of the vaginal microbiota, is a common coinfection with Chlamydia trachomatis (Ct), and BV-associated bacteria (BVAB) and their products have been implicated in aiding Ct evade natural immunity. Here, we determined if a non-optimal vaginal microbiota was associated with a higher genital Ct burden and if metronidazole, a standard treatment for BV, would reduce Ct burden or aid in natural clearance of Ct infection. Cervicovaginal samples were collected from women at enrollment and, if testing positive for Ct infection, at a follow-up visit approximately one week later. Cervical Ct burden was assessed by inclusion forming units (IFU) and Ct genome copy number (GCN), and 16S rRNA gene sequencing was used to determine the composition of the vaginal microbiota. We observed a six-log spectrum of IFU and an eight-log spectrum of GCN in our study participants at their enrollment visit, but BV, as indicated by Amsel’s criteria, Nugent scoring, or VALENCIA community state typing, did not predict infectious and total Ct burden, although IFU : GCN increased with Amsel and Nugent scores and in BV-like community state types. Ct burden was, however, associated with the abundance of bacterial species in the vaginal microbiota, negatively with Lactobacillus crispatus and positively with Prevotella bivia. Women diagnosed with BV were treated with metronidazole, and Ct burden was significantly reduced in those who resolved BV with treatment. A subset of women naturally cleared Ct infection in the interim, typified by low Ct burden at enrollment and resolution of BV. Abundance of many BVAB decreased, and Lactobacillus increased, in response to metronidazole treatment, but no changes in abundances of specific vaginal bacteria were unique to women who spontaneously cleared Ct infection.</p

Similarity of CS and urine taxa

<p>. A-C) Weighted Unifrac comparison of the microbiotas in select groups of specimens (Sanger data-set). A) All CS (red) and all urine (blue) specimens. B) Circumcised (red) and uncircumcised (blue) CS specimens. C) Circumcised (red) and uncircumcised (blue) urine specimens.</p

Temporal stability of CS and urine taxa

<p>. Lin’s concordance correlation coefficients (Y-axis) were calculated to assess agreement of abundance of taxa, (X-axis), in sequential (A) CS, or (B) urine specimens from the same participants (three intervals: months 0–1, 1–2, 2–3), the red trend line indicates mean of the three intervals. Bars indicate 95% confidence intervals.</p

The microbiota of the CS is more stable than that of urine.

<p>Sørenson’s similarity indices calculated between pairwise specimens within each participant’s (month = 0, 1, 2, 3) CS and urine samples, separately. A linear mixed-effects model was used to test if the index differed between CS and urine samples, taking into account multiple specimens from the same participants (clustered data). Participants are indicated at left, Sørenson similarity values are on the Y-axis, and blue dots indicate unique specimens.</p