Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis

Abstract

BackgroundBacterial vaginosis (BV), the most common vaginal condition of reproductive-aged women, is associated with a highly diverse and heterogeneous microbiota. Here we present a proof-of-principle analysis to uncover the function of the microbiota using meta-RNA-seq to uncover genes and pathways that potentially differentiate healthy vaginal microbial communities from those in the dysbiotic state of bacterial vaginosis (BV).ResultsThe predominant organism, Lactobacillus iners, was present in both conditions and showed a differing expression profile in BV compared to healthy. Despite its minimal genome, L. iners differentially expressed over 10% of its gene complement. Notably, in a BV environment L. iners increased expression of a cholesterol-dependent cytolysin, and of mucin and glycerol transport and related metabolic enzymes. Genes belonging to a CRISPR system were greatly upregulated suggesting that bacteriophage influence the community. Reflective of L. iners, the bacterial community as a whole demonstrated a preference for glycogen and glycerol as carbon sources under BV conditions. The predicted end-products of metabolism under BV conditions include an abundance of succinate and other short-chain fatty-acids, while healthy conditions are predicted to largely contain lactic acid.ConclusionsOur study underscores the importance of understanding the functional activity of the bacterial community in addition to characterizing the population structure when investigating the human microbiome.

Lactobacillus-dominated cervicovaginal microbiota associated with reduced HIV/STI prevalence and genital HIV viral load in African women

“…Recent genomic and transcriptomic studies suggest that L. iners is highly adapted to the vaginal compartment (Macklaim et al, 2011). However, it differentially expresses over 10% of its genome in dysbiotic compared with healthy states, with increased expression of a cytolysin, mucin, glycerol transport and related metabolic enzymes (Macklaim et al, 2013). These changes likely result in the production of succinate and other short-chain fatty acids as the end product of metabolism as opposed to lactic acid, leading to an increased vaginal pH.…”

Comparison of Lactobacillus crispatus isolates from Lactobacillus-dominated vaginal microbiomes with isolates from microbiomes containing bacterial vaginosis-associated bacteria

“…Bacteriostatic and bactericidal activities are largely due to lactic acid, a product of lactate dehydrogenase enzymes, and to bacteriocins. Studies have shown that stability can be influenced by phage induction (Macklaim et al, 2013;Pavlova & Tao, 2000) but it may also be affected by things that confer resistance to harmful environmental stimuli, such as efflux pumps, or by factors that function in adaptation to changes in nutrient availability. We tested this by examining the whole genomes, the bactericidal activity (lactic acid production) and the stability (phage induction) of strains from women who were predominated by L. crispatus and did not have a history of BV, and comparing these parameters with strains from women with more diverse vaginal microbial profiles.…”

“…Excision can be spontaneous or induced by DNA-damaging agents that induce the global SOS stress response. One study indicates that CRISPR-related gene expression is elevated in L. iners during BV, suggesting that CRISPR activity may be a response to a phage-loaded environment (Macklaim et al, 2013). Cigarette smoking, which is associated with BV, may expose the vaginal lactobacilli to chemicals capable of inducing phage (Pavlova & Tao, 2000).…”

Normal flora and bacterial vaginosis in pregnancy: an overview

“…It is possible that each of the two forms of Gardnerella may be responsible for a different pathogenesis model (Swidsinski et al, 2010). However, as Hickey and Forney (2014) stressed, the correlation between G. vaginalis and BV does not necessarily indicate causation and hence responsibility of this bacterium for either of the two pathogenesis models (Macklaim et al, 2013). The intricate microbial structure of BV is said to result in increased cell lysis and subsequent carbohydrate availability.…”