The Putonti Lab studies bacteriophages in the environment.
Members of the Putonti Lab include computational scientists, molecular biologists and microbiologists: our research focus is bacterial viruses including questions of virus-host compatibility and the role of bacteriophages in regulating bacterial populations.
Viral genetic diversity. Bacteriophages (viruses that infect bacteria) are the most abundant and diverse members of most ecosystems on the planet. Phages are routinely discovered in every nook and cranny on Earth. When these new phage isolates are sequenced, we often find that their DNA sequences bear little or no resemblance to any sequences contained within current databases -- the diversity of phages on Earth is severely under sampled. It is therefore crucial to characterize these viruses and the critical roles that they have in directly impacting microbial communities. Our recent work has moved towards the development of a new network-based approach for classifying viruses found in different environments. Rather than just focus viral sequence analysis on what is know (what looks like something we've seen before), we are embracing the unknown. This work has the potential to open new avenues for exploring virus ecology and evolution from genomic data. This work was supported by NSF award #1661357.
Phages in the bladder. From our examination of bacteria isolated from the female urinary microbiota, we found something quite interesting: there are tons of phages! This included evidence of vertically and horizontally transmitted prophages, the latter characteristic of ongoing, pervasive phage infections of bladder bacteria. This led us to search for active phages in the bladder. We have characterized 7 novel phages isolated from UUI patients as well as several other phage species of the bladder microbiota (urobiome). Our preliminary surveys suggest that phages are abundant within the bladder microbiota and prompted our in-depth examination of the lysogenic phage species within bacteria isolated from the urobiome of 170 women.
Our Research in the Media: Our paper on the bacteriophages of the urinary microbiome has been featured in the press, including ASM and The Scientist.
Lake Michigan. Looking out from our beloved biology building at Lake Michigan, approximately 30 feet away, spurred us to expand our questions beyond model systems to that of the complex freshwater environment. So frequently we hear of Lake Michigan beaches closing due to elevated E. coli levels, but what role do bacteriophages play in the fluctuations of bacteria within near-shore waters? Our first challenge, however, was not molecular in nature, rather it was computational. Viruses have no universal markers like rRNA and, despite their omnipresence, only a few hundred bacteriophage species have been sequenced. Thus, we began development of new computational tools for the analysis of short sequencing reads from environmental viral species. Integrating these approaches with our previous knowledge of virus-host genome compatibility, we surveyed the phage diversity and density and its relationship with bacterial diversity and density in the Chicago are beach waters. This work was supported by NSF award #1149387.
Viral genetic diversity. Bacteriophages (viruses that infect bacteria) are the most abundant and diverse members of most ecosystems on the planet. Phages are routinely discovered in every nook and cranny on Earth. When these new phage isolates are sequenced, we often find that their DNA sequences bear little or no resemblance to any sequences contained within current databases -- the diversity of phages on Earth is severely under sampled. It is therefore crucial to characterize these viruses and the critical roles that they have in directly impacting microbial communities. Our recent work has moved towards the development of a new network-based approach for classifying viruses found in different environments. Rather than just focus viral sequence analysis on what is know (what looks like something we've seen before), we are embracing the unknown. This work has the potential to open new avenues for exploring virus ecology and evolution from genomic data. This work was supported by NSF award #1661357.
Phages in the bladder. From our examination of bacteria isolated from the female urinary microbiota, we found something quite interesting: there are tons of phages! This included evidence of vertically and horizontally transmitted prophages, the latter characteristic of ongoing, pervasive phage infections of bladder bacteria. This led us to search for active phages in the bladder. We have characterized 7 novel phages isolated from UUI patients as well as several other phage species of the bladder microbiota (urobiome). Our preliminary surveys suggest that phages are abundant within the bladder microbiota and prompted our in-depth examination of the lysogenic phage species within bacteria isolated from the urobiome of 170 women.
Our Research in the Media: Our paper on the bacteriophages of the urinary microbiome has been featured in the press, including ASM and The Scientist.
Lake Michigan. Looking out from our beloved biology building at Lake Michigan, approximately 30 feet away, spurred us to expand our questions beyond model systems to that of the complex freshwater environment. So frequently we hear of Lake Michigan beaches closing due to elevated E. coli levels, but what role do bacteriophages play in the fluctuations of bacteria within near-shore waters? Our first challenge, however, was not molecular in nature, rather it was computational. Viruses have no universal markers like rRNA and, despite their omnipresence, only a few hundred bacteriophage species have been sequenced. Thus, we began development of new computational tools for the analysis of short sequencing reads from environmental viral species. Integrating these approaches with our previous knowledge of virus-host genome compatibility, we surveyed the phage diversity and density and its relationship with bacterial diversity and density in the Chicago are beach waters. This work was supported by NSF award #1149387.