LABORATORY FOR MICROBIAL & ENVIRONMENTAL GENOMICS
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Research

VparaAt the Laboratory for Microbial and Environmental Genomics, we examine how microorganisms affect environmental health and human health. We are especially interested in how microbes evolve in response to ecosystem change. After all, the sum of the metabolic and evolutionary potential stored in the microbial community defines microorganisms as nature’s first responders.

Two primary areas of research are 1) assessing the intrinsic biodegradation of plastic debris in marine environments and 2) quantifying the prevalence of antibiotic resistance genes in urbanized estuaries. These two project are led by graduate students Lee Pinnell and James Tallman, respectively. Both students have received funding awards from Texas Sea Grant’s Grants-In-Aid of Research Program. Additionally, our plastic research is funded by Texas Research Development Fund and the Texas General Land Office Coastal Management Program. Although these projects are in the initiation stage, study sites have been selected and we will begin collecting data Spring 2016. Please check back in the near future to learn more about these exciting research projects.

More developed research projects include the analysis of multiple Vibrio genomes. The genus occurs naturally in marine environments and is frequently associated with disease in humans. However, these bacteria are not obligate parasites and pathogenicity is widely regarded as a consequence of genes that play a role in the marine environment but afford cross protection in a human host. More exploratory research projects include 1) the antimicrobial analysis of novel amino acid surfactants  (an interdisciplinary project coordinated with Dr. Feri Billiot and led by undergraduate student Devin Lovato) and 2) the evaluation of laser-induced plasma to sterilize food and medical tools (an interdisciplinary project coordinated with Dr. Magesh Thiyagarajan).

The abstracts below give a detailed description of current research. We will be showcasing these projects and more at the upcoming 2016 ASLO Ocean Sciences Meeting in New Orleans, LA.

Genomic Analysis of Attenuation in Pandemic Vibrio parahaemolyticus

Lee Pinnell1, James Tallman1, Rohinee Paranjpye2 and Jeffrey W. Turner1

1Texas A&M University at Corpus Christi, TX and 2NOAA’s Northwest Fisheries Science Center, Seattle, WA

A critical problem in the prevention and treatment of infectious disease is the ability to differentiate virulent from avirulent bacterial strains. The distinction is commonly based on the presence or absence of specific virulence-associated genes. Alternately, serotypic or phylogenetic typing can differentiate virulent from avirulent strains. When these approaches fail, more discriminatory analysis is needed. Pandemic Vibiro parahaemolyticus, distinguishable by genotyping (thermostable direct hemolysin or tdh), serotyping (O3:K6) and multilocus sequence typing (ST3), is regarded as a highly virulent clonal complex. We have previously shown, through population genetics and cytotoxicity testing, that some pandemic strains isolated from environmental sources are avirulent. To investigate the basis for attenuation, we sequenced the draft genomes of 10 pandemic V. parahaemolyticus isolates originating from environmental (N = 7) and clinical sources (N = 3). Genomic comparison of these 10 draft genomes, and the pandemic type strain (RIMD2210633), revealed a large core genome (5,158,719 bp) and a much smaller accessory genome (141,403 bp). The accessory genome was largely comprised of hypothetical proteins; however, several genes encoded phage-related proteins. Phylogenetic analysis, based on 2,902 single nucleotide polymorphisms in the core genome, did not reveal a discernable pattern. Current efforts are focused on the identification of insertions, deletions and point mutations that may alter protein expression or protein function. Preliminary results show the virulence-associated vacB gene (VP1890) is a pseudogene in attenuated strains. This gene encodes a 741 amino acid exoribonuclease homologous to exoribonucleases known to modulate virulence in Salmonella enterica and Helicobacter pylori. The correlation between attenuation and the absence of this gene, suggests that VP1890 plays an important role in human pathogenesis.

 

Genomic Analysis of Two Emergent Vibrio parahaemolyticus Ecotypes

Emille Moreno1, Marci Parks1, Lee Pinnell1, James Tallman1, Rohinee Paranjpye2 and Jeffrey W. Turner1

1Texas A&M University at Corpus Christi, TX and 2NOAA’s Northwest Fisheries Science Center, Seattle, WA

Vibrio parahaemolyticus [Vp] is a Gram-negative bacterium indigenous to marine coastal waters. Vp is also the causative agent of a mild to severe gastroenteritis associated with the consumption of raw or undercooked seafood. The majority of infections are caused by a genetically distinct ecotype commonly referred to as the pandemic clonal complex. However, localized outbreaks associated with non-pandemic ecotypes are frequently reported. In the East Pacific, two such ecotypes, identified as ST65 and ST417 by multilocus sequence typing, have been associated with outbreaks in Peru, Chile and the United States. In this study, we sequenced and assembled draft genomes from 4 clinical isolates (ST65: 3328, 3355; ST417: 3646, 3631) that were positive for both the thermostable direct hemolysin (tdh) and thermostable direct-related hemolysin (trh). When compared with the pandemic type strain (V. parahaemolyticus RIMD2210633), each of these isolates harbored more than 400 Kb of novel genetic material. Proteins encoded by this novel genetic material include CcdA-CcdB toxin-antitoxin systems, an efflux pump belonging to the multidrug and toxic efflux (MATE) family, and a repeats-in-toxin (RTX) gene cluster. These features share significant homology and synteny with virulence-associated features found in clinical V. vulnificus and Escherichia coli strains. We hypothesize that these features contribute to a pathogenic phenotype. The identification and characterization of multiple clinical ecotypes could improve efforts aimed at preventing V. parahaemolyticus infections. Further, a greater understanding of the species’ biogeography may lead to a more effective public health response.

 

Genome Sequencing and Analysis of a Highly Virulent Vibrio parahaemolyticus Strain Isolated from the Marine Environment

Marci Parks1, Emille Moreno1, Lee Pinnell1, James Tallman1,Rohinee Paranjpye2 and Jeffrey W. Turner1

1Texas A&M University at Corpus Christi, TX and 2NOAA’s Northwest Fisheries Science Center, Seattle, WA

Vibrio parahaemolyticus [Vp] is a Gram-negative bacterium and a natural inhabitant of coastal marine ecosystems worldwide. Vp is also a coincidental pathogen of humans. Virulent strains are commonly identified by the presence of the thermostable direct (tdh) or tdh-related (trh) hemolysin genes. However, virulence is multifaceted and many clinical Vp isolates do not carry tdh or trh. In this study, we sequenced and assembled the draft genome of a tdh and trh-negative environmental isolate (805) shown previously to be highly virulent in zebrafish. To investigate potential mechanisms of virulence, we compared 805 to the clinical V. parahaemolyticus type strain (RIMD2210633). Pairwise comparison revealed the presence of multiple genomic regions including an IncF conjugative pilus (1.3 Kb) and a colicin V plasmid (1.49 Kb). These features are homologous to genomic regions present in clinical V. vulnificus and V. cholerae strains. Genome comparison also revealed the presence of five toxin-antitoxin systems. Isolate 805 likely attained these new features through the lateral acquisition of mobile genomic material – a hypothesis supported by the aberrant GC content of these regions. Colicin V plasmids are a diverse group of IncF plasmids found in invasive bacterial strains. Similarly, an abundance of toxin-antitoxin systems have been linked to virulence in Gram-negative bacteria. Current efforts are focused on characterizing 142 coding features present in 805 but absent from the type strain.

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