Difference between revisions of "Linking variations in gene composition of the microbiome to health conditions"

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(New page: {{Projectproposal |Contact person=Douwe Molenaar |Contact person2=Remco Kort |Master areas=Systems Biology, Bioinformatics |Fulfilled=No }} This internship concerns the identification of b...)
 
 
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|Contact person=Douwe Molenaar
 
|Contact person2=Remco Kort
 
|Contact person2=Remco Kort
|Master areas=Systems Biology, Bioinformatics
 
 
|Fulfilled=No
 
|Fulfilled=No
 
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This internship concerns the identification of bacterial genetic factors by a comparative genome analysis of 28 sequenced genomes and 12 reference genomes of ''Lactobacilus crispatus'', the most predominant bacterium in the human vagina.  
 
This internship concerns the identification of bacterial genetic factors by a comparative genome analysis of 28 sequenced genomes and 12 reference genomes of ''Lactobacilus crispatus'', the most predominant bacterium in the human vagina.  
 
This study is a collaboration between the VU Amsterdam and TNO Microbiology and Systems Biology, Zeist. Bacterial Vaginosis (BV) is an aberrant state of the vagina characterized by a reduced fraction of of lactobacilli, an increased pH and a more diverse vaginal microbiota, including  ''Gardnerella vaginalis'', and species of the genera ''Peptostreptococcus'' and ''Mobiluncus'', as well as anaerobic Gram-negative rod-shaped species such as ''Prevotella'' and ''Bacteroides''. BV is associated with increased risk for pre-term birth and acquirement of sexually transmitted diseases. A healthy vagina is dominated by one ''Lactobacillus'' species, mostly ''L. crispatus'', or ''L. gasseri'', ''L. jensenii'', and ''L. iners''. For this study we determined the full genome sequence of ''L. crispatus'' species (28) isolated from equal numbers of BV and non-BV subjects. The aim of this project is to identify, by pan-genome analysis, genetic factors in ''L. crispatus'' that are responsible for the loss of the ability of this organism to dominate the vaginal microbiota. This study will contribute to a better understanding of the aberrant microbiome of BV as well as of the ecology of complex bacterial communities in general.
 
This study is a collaboration between the VU Amsterdam and TNO Microbiology and Systems Biology, Zeist. Bacterial Vaginosis (BV) is an aberrant state of the vagina characterized by a reduced fraction of of lactobacilli, an increased pH and a more diverse vaginal microbiota, including  ''Gardnerella vaginalis'', and species of the genera ''Peptostreptococcus'' and ''Mobiluncus'', as well as anaerobic Gram-negative rod-shaped species such as ''Prevotella'' and ''Bacteroides''. BV is associated with increased risk for pre-term birth and acquirement of sexually transmitted diseases. A healthy vagina is dominated by one ''Lactobacillus'' species, mostly ''L. crispatus'', or ''L. gasseri'', ''L. jensenii'', and ''L. iners''. For this study we determined the full genome sequence of ''L. crispatus'' species (28) isolated from equal numbers of BV and non-BV subjects. The aim of this project is to identify, by pan-genome analysis, genetic factors in ''L. crispatus'' that are responsible for the loss of the ability of this organism to dominate the vaginal microbiota. This study will contribute to a better understanding of the aberrant microbiome of BV as well as of the ecology of complex bacterial communities in general.

Latest revision as of 10:05, 24 August 2016


About Linking variations in gene composition of the microbiome to health conditions


Description

|free text=}} This internship concerns the identification of bacterial genetic factors by a comparative genome analysis of 28 sequenced genomes and 12 reference genomes of Lactobacilus crispatus, the most predominant bacterium in the human vagina. This study is a collaboration between the VU Amsterdam and TNO Microbiology and Systems Biology, Zeist. Bacterial Vaginosis (BV) is an aberrant state of the vagina characterized by a reduced fraction of of lactobacilli, an increased pH and a more diverse vaginal microbiota, including Gardnerella vaginalis, and species of the genera Peptostreptococcus and Mobiluncus, as well as anaerobic Gram-negative rod-shaped species such as Prevotella and Bacteroides. BV is associated with increased risk for pre-term birth and acquirement of sexually transmitted diseases. A healthy vagina is dominated by one Lactobacillus species, mostly L. crispatus, or L. gasseri, L. jensenii, and L. iners. For this study we determined the full genome sequence of L. crispatus species (28) isolated from equal numbers of BV and non-BV subjects. The aim of this project is to identify, by pan-genome analysis, genetic factors in L. crispatus that are responsible for the loss of the ability of this organism to dominate the vaginal microbiota. This study will contribute to a better understanding of the aberrant microbiome of BV as well as of the ecology of complex bacterial communities in general.

Skills

  • Working in a linux environment
  • Sequence analysis
  • Statistical analysis