Human Placental Microbiome
This is a recent collaboration with the Department of Pediatrics and Human Development at MSU investigating role of placental microbiome in gestational diabetes.
Human Gut Microbiome
Intestinal microbial communities play an important role in hindering the growth of microbes that may compromise human health. The goal of this project is to examine differences in composition and abundance of these communities, in individuals with and without enteric infections. This work has been recently published and provides an insight to microbial features perturbed during acute infections.
Further, this project aims at understanding the functional characteristics of the community members based on whole genome shotgun sequencing, which is underway. Enhancing our understanding of intestinal community profiles and the factors that contribute to variation in these communities is useful for guiding future foodborne illness prevention strategies.
Cattle Gut Microbiome
Gut microbial communities are complex and diverse across animals and play an important role in their health by aiding in digestion and nutrient absorption; however, little is known about factors that influence variation. I am interested in determining factors that are responsible for intestinal community structure of these animals. I am currently analyzing gut communities from feed-lot and dairy farm animals that were collected in 2011-2012 from various farms in MI.
Association of foodborn pathogen specifically STEC and cattle Intestinal Microbiome is major focus of this project. Cattle is the main reservoir STEC along and the factors that influence this colonization are yet to be determined. I am interested in identifying microbial community factors driving this association
Venegas Vargas et al., Appl Environ Microbiol 2016
Deer Gut Microbiome
Deer is another ruminant that is found to be colonized by STEC. We have found evidence of transmission of STEC between deer and cattle sharing the same agroecosystem. Further, we are analyzing the intestinal community of white tailed deer to identify factors that aid in colonization of STEC.
Genetic characterization and ecology of STEC, a significant foodborne pathogen is very interesting. As a commensal E.coli resides in human intestines as beneficial community member, however acquisition of virulence factors such as bacteriophage encoded shiga-toxin, renders it pathogenic. My research involves performing comparative genomics to identify factors responsible for dynamic status of STEC and linking it to epidemiological data
Secondly, I also aim at performing genetic characterization of clinical STEC isolates specifically serotype O157, a leading serotype in clinical outbreaks and infections, based on Single Nucleotide Polymorphisms (SNP). The goal is to examine trends in clinical infections due to O157 over the years and identifying factors responsible for it.
Campylobacter, another important foodborn pathogen was recovered during our visits to MI farm. The aim of this project was to look antibiotic resistance and epidemiological factors linked to genetic characterization of Campylobacter. I performed WGS sequencing and comparative genomics study in this study to help answer some of these questions.
Cha et al., Front Microbiol 2016
S. agalacatiae or group B streptococcus (GBS) is a leading cause of neonatal infection and sepsis. I designed a high throughput SNP characterization method based on Illumina VeraCode technology for its genetic characterization.Additionally, I have also been involved in the projects assessing genetic makeup, pilli and capsular profile to invasive neonatal GBS in USA and Nigeria. Currently, I am performing comparative genomic studies on the hypervirulent strains to identify genetic factors responsible for their virulence.
Acknowledged in research article by Carl et.al., on Sepsis from the Gut [Clin Infect Dis. (2014) doi: 10.1093/cid/ciu084] for my technical expertise and bioinformatical help.