Comparative functional genomics of Lactobacillus spp. reveals possible mechanisms for specialization of vaginal lactobacilli to their environment - PubMed (original) (raw)

Comparative Study

. 2014 Apr;196(7):1458-70.

doi: 10.1128/JB.01439-13. Epub 2014 Jan 31.

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Comparative Study

Comparative functional genomics of Lactobacillus spp. reveals possible mechanisms for specialization of vaginal lactobacilli to their environment

Helena Mendes-Soares et al. J Bacteriol. 2014 Apr.

Abstract

Lactobacilli are found in a wide variety of habitats. Four species, Lactobacillus crispatus, L. gasseri, L. iners, and L. jensenii, are common and abundant in the human vagina and absent from other habitats. These may be adapted to the vagina and possess characteristics enabling them to thrive in that environment. Furthermore, stable codominance of multiple Lactobacillus species in a single community is infrequently observed. Thus, it is possible that individual vaginal Lactobacillus species possess unique characteristics that confer to them host-specific competitive advantages. We performed comparative functional genomic analyses of representatives of 25 species of Lactobacillus, searching for habitat-specific traits in the genomes of the vaginal lactobacilli. We found that the genomes of the vaginal species were significantly smaller and had significantly lower GC content than those of the nonvaginal species. No protein families were found to be specific to the vaginal species analyzed, but some were either over- or underrepresented relative to nonvaginal species. We also found that within the vaginal species, each genome coded for species-specific protein families. Our results suggest that even though the vaginal species show no general signatures of adaptation to the vaginal environment, each species has specific and perhaps unique ways of interacting with its environment, be it the host or other microbes in the community. These findings will serve as a foundation for further exploring the role of lactobacilli in the ecological dynamics of vaginal microbial communities and their ultimate impact on host health.

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Figures

FIG 1

FIG 1

Genome size and GC content of Lactobacillus species. Data represent average genome size and % GC content of the Lactobacillus species isolated from the vagina and from other habitats (gastrointestinal tract and food). Error bars denote standard deviations (SD). The Kruskal-Wallis rank sum test was done on vaginal versus nonvaginal Lactobacillus strains to compare the two groups, and significant differences (P < 0.05) are denoted with an asterisk (*).

FIG 2

FIG 2

Gene number in Lactobacillus species. Gene accumulation rarefaction curves across Lactobacillus strains were calculated based on the presence or absence of protein families using the “specaccum” function in the “vegan” package of R (

http://www.R-project.org/

) and were estimated by bootstrapping 100 permutations of randomized sample orders. The curves for all the genomes analyzed in this study (gray) and for the genomes of L. crispatus (pink), L. gasseri (yellow), L. jensenii (green), and L. iners (blue) are represented.

FIG 3

FIG 3

Hierarchical clustering of Lactobacillus strains based on dissimilarities in gene content. The dissimilarities were measured on binary data using Jaccard distance values, ranging from 0 to 1, to evaluate the presence or absence of each of the protein families. The bar on the left bottom of the figure represents a distance of 0.01. The different colors of the leaves represent the habitats from which the strains were isolated. Red represents strains isolated from food, green represents strains isolated from gastrointestinal tract, and blue represents strains isolated from the vagina.

FIG 4

FIG 4

Overrepresentation (green) and underrepresentation (red) of the Clusters of Orthologous Genes (COGs) in the genomes of the vaginal Lactobacillus species. The horizontal scale at the bottom represents the odds ratio calculated for each COG.

FIG 5

FIG 5

Cluster of Orthologous Genes (COGs) with over- and underrepresentation in vaginal Lactobacillus species. Data represent Clusters of Orthologous Genes (COGs) that were significantly overrepresented (odds ratio > 1) and underrepresented (odds ratio < 1) in the vaginal relative to nonvaginal Lactobacillus species. CoA, coenzyme A.

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