Chicken Gut Microbiome
The aim of this project was to look at the effect of Penicillin on the intestinal community of chickens, as at sub-therapeutic levels, antibiotics may be used as growth promoters that may inturn lead to antibiotic resistance spreading from farm to fork . The ability to process cecal samples from chickens and understand their gut community based on 16S rRNA gene sequencing, a conserved gene across microbial community members, while being able to distinguish hundreds of bacterial species was very exciting.
This helped me get an insight at the role of gut microbial community plays in the growth and development of its host. We were also able to understand that diet of these birds was instrumental in defining their core microbiome which in turn affected their health. This work was recognized and awarded for excellence in research for the talk I gave at the annual meeting of the Poultry Science association held in Denver, CO, in 2010
Singh et.al., Poultry Science 2013
Campylobacter is an important foodborne pathogen for which poultry animals are an important reservoir. Characterization of this bug in individual market age broilers based on short variable region of the flaA gene provided with an insight to genetic diversity and effect of host-microbial interaction on the ecology of Campylobacter. This work was presented at the Arkansas Association for Food Protection and was placed second in poster awards
Singh and Kwon, Poultry Science 2013
Salmonella is another important pathogen that is responsible for causing outbreaks and havoc. I developed a novel genetic characterization technique MLST-seq with higher resolution as compared to the gold standards; MLST (Multilocus Sequence Typing) and PFGE (Pulse Field Gel Electrophoresis). This method was based on 21 target genes that were selectively amplified simultaneously based on target enrichment techniques that I developed taking advantage of the NextGen Sequencing. The two target enrichment strategies were: 1) Hairpin Selector based ligation and 2) Hairpin-primed Multiplex amplification. With Salmonella as a model organism for each technique, target genes amplified were characterized using MLST-seq, can be applied to other bacterial pathogens.
Tuberculosis is one of the leading bacterial infections responsible for almost 3 million deaths per year. According to CDC, about a third of the world’s population is infected with Mycobacterium tuberculosis (Mtb) and 5 to 10% of the infected population will develop disease during their life time. The incidence of Tuberculosis is rising significantly in many parts of the world, especially in Asia and Africa. Owing to the resurgence of the multi drug resistant (MDR) strains, there is today a greater need than ever to identify antigens of Mtb that can serve as immunodiagnostic agents and/or vaccine candidates. Tuberculosis is completely curable with the antituberculosis drugs, if detected at the right stage. Large number of protein antigens in addition to carbohydrate and glycolipid components are being tested for immunodiagnosis, however, the desired sensitivity and specificity is difficult due to the cross reactivity of proteins from Mtb H37Rv (a laboratory strain) and with other environmental non-pathogenic or saprophytic mycobacterium species. Purified antigens and the use of monoclonal antibodies have helped with cross reactivity of crude extracts. In this project, I searched for novel Mtb antigens from clinical isolates, which were prevalent (40%) in patients from Chengalpet in South India and may therefore have higher virulence. These clinical isolates harbored single copy of IS6110, a transposon found by RFLP studies. The antigenic profiles were compared with standard laboratory strain H37Rv. Strains were characterized for differential expression of new and potent antigens due to insertion of the transposon.