Comparative and functional genomics of pathogenic treponemes

Treponema pallidum subspecies pallidum is the causative agent of syphilis and is difficult to culture under in vitro conditions. This fact severely limits the use of standard genetic approaches to study this organism. Several genomic methods are being used in our lab to study this and related organisms.

1. Methods of functional genomics are used for identification of treponemal gene functions. These methods include heterologous expression in E. coli and other organisms.
2. Bacteria causing endemic treponematoses include Treponema pallidum subspecies pertenue (TPE) and endemicum (TEN) causing yaws and endemic syphilis (bejel), respectively. Genetic characterizations of these agents revealed a surprising genetic relatedness (over 99.7% at the whole genome level) to the causative agent of syphilis, Treponema pallidum subspecies pallidum (TPA). Moreover, the genetic analyses showed clustering of these agents congruent with clinical manifestations of these infections.
3. Closely related T. paraluisleporidarum is the etiologic agent of venereal spirochetosis of rabbits and hares and is not infectious to humans. Genomic comparisons of both treponemes can provide evidence of genetic diversity that can be related to the different pathogenicity of these closely related bacteria. About half of the free-living hares are infected by T. paraluisleporidarum.
4. A recent development of multilocus typing (MLST) scheme for TPA allowed a better direct diagnosis of syphilis cases and, in addition, the analysis of phylogenetic relationship of TPA in hundreds of human clinical TPA isolates. Until now, there are 796 fully typed human clinical TPA isolates in the public database for Treponema pallidum subsp. pallidum collecting results from the MLST typing. Since the MLST scheme reflects phylogenetic relatedness of TPA isolates and also reflects the whole genome diversity, the MLST is an important epidemiological tool that allows to map genetic diversity of syphilis strains and their geographical and temporal distribution.

Microbiome analyses and molecular genetics (bacteriocin research)

1. In the past decade, gut microbiota has been shown to be associated with a number of human diseases including metabolic syndrome, obesity-related diseases, inflammatory bowel disease, and colorectal cancer. To determine microbiome composition, 16S rRNA gene sequences from the gut microbiome and analysis of gut metagenome by whole-metagenome shotgun sequencing and subsequent analysis of gut metabolome are performed on samples previously taken from patients with various conditions.
2. Treatment of infectious diseases was revolutionized in the last century when antibiotics were introduced. However, an increasing emergence of antibiotic resistant bacteria more and more often prevents the effective use of these drugs and therefore there is an increasing clinical and scientific interest in alternative treatment regimens including the use of probiotics. Bacteriocins are exocellular bacterial protein toxins produced by some bacterial strains of the family Enterobacteriaceae. Their highly efficient ability to kill sensitive bacteria is facilitated by highly specific interactions between colicin molecule and the cell envelope proteins (and other components) of sensitive bacterium. We are studying probiotic potential of bacteriocin-producing E. coli strains. The main aim is a comprehensive characterization of genetic determinants and experimentally confirmed probiotic traits.