Pallavi Singh

Assistant professor

My lab is focused on assessing ecology and dynamics of intestinal microbial communities of humans and animals. We investigate linkages between acute enteric infections utilizing cutting Next Generation molecular tools, epidemiological data and gut microbiome. These studies emphasize on commensal niche in host gut exhibiting beneficial interaction in the growth and development of the host.

Additionally, research is conducted to assess diversity and characterization of bacterial pathogens. This includes both genotypic (sequencing, Multilocus sequence typing) and phenotypic (biofilm) characterization. The pathogens we study are important due to food safety concerns and include Shiga-toxin producing E. coli, Salmonella and Campylobacter.

We also employ bioinformatical tools for analysis of large scale microbial community and genomics. The goals are to perform comparative genomics of bacterial pathogens based on whole genome sequencing, Singe nucleotide polymorphisms and functional annotation.

Representative Publications

Gendrin, J. Vornhagen, B. Armistead, P. Singh, C. Whidbey, S. Merillat, D. Knupp, R. Parker, LM. Rogers, P. Quach, L.M Iyer, L. Aravind, S.D. Manning, DM. Aronoff, L. Rajagopal. A non-hemolytic Group B Streptococcus strain exhibits hypervirulence. (J Infec. Dis. 2017 Mar.; 217(6):983-987).

Degado, P. Singh, KT. Scribner and SD. Manning. White-tailed deer’s fecal microbiota comparison between pathogenic Escherichia coli and Salmonella carriers and non-carriers. (Microb. Ecol. 2017: 1-11).

Medugu, KC. Iregbu, R. Parker, J.Plemmons, P. Singh, LI Audu, E. Efetie, HD. Davies and SD. Manning. Group B streptococcal colonization and transmission dynamics in pregnant women and their newborns in Nigeria: implications for prevention strategies (Clin Microbiol and Infec. 2017; 23(9): 673.e9-673.e16).

LA Boughner and P. Singh. Microbial Ecology: Where are we now? (Postdoc J. 2016 Nov; 4(11): 3–17.).

Singh and SD. Manning. Impact of age and gender on the composition and abundance of intestinal microbial communities in individuals with and without enteric infections. (Ann. Epidemiol. 2016;1-6).

Singh, D. Aronoff, H. Dele Davies and SD. Manning. Draft genome of an invasive Streptococcus agalactiae isolate lacking pigmentation. (Genome Announc. 2016, 4(1):e00015-16. doi:10.1128/genomeA.00015-16).

Cha, R. Mosci, SL. Wengert, P. Singh, DW. Newton, H. Salimnia, P. Lephart, W. Khalife, LS Mansfield, JT. Rudrick and SD. Manning. Antimicrobial susceptibility profiles of human Campylobacter jejuni isolates in Michigan and the association with phylogenetic lineage and disease severity. (Frontiers in Microbiol. 2016, 7:589. doi: 10.3389/fcimb.2016.00589).

Galli, V. Brusa, P. Singh, A. Cataldi, SD Manning and G. Leotta. High prevalence of Escherichia coli O157:H7 clade 8 isolated from retail meat and butcher shop environment. (Infect. Genet. Evol. 2016 doi:10.1016/j.meegid.2016.08.005).

Venegas-Vargas, S. Henderson, A. Khare, RE. Mosci, JD. Lehnert, P. Singh, L. Ouellette, B. Norby, JA. Funk, S. Rust, P. Bartlett, D. Grooms and SD. Manning. Factors associated with Shiga toxin producing Escherichia coli shedding in dairy and beef cattle. Appl. Environ. Microbiol. 2016, doi:10.1128/AEM.00829-16 AEM.00829-16).

Singh, T. Teal, T. Marsh, J. Tiedje, K.Jernigan, R. Mosci, A. Zell, D. Newton, H. Salimnia, P. Lephart, H. Salimnia, W. Khalife, D. Sundin, RA. Britton, JT. Rudrik, and SD. Manning. Intestinal microbial communities in patients with enteric infections and their family members. (Microbiome 2015, 3:45 doi:10.1186/s40168-015-0109-2).

Singh, R. Mosci, JT. Rudrik and SD. Manning. Draft genome sequence of a diarrheagenic Morganella morganii isolate (Genome Announc 2015, 3(5):e01165-15.).

Singh, Q. Sha, DW. Lacher, J. Del Valle, RE. Mosci, JA. Moore, KT. Scribner and SD. Manning. Characterization of enteropathogenic and Shiga toxin-producing Escherichia coli in cattle and deer in a shared agroecosystem. (Front Cell Infect Microbiol. 2015, 5:29.).

Amigo, E. Mercado, A. Bentancor, P. Singh, D. Vilte, E. Gerhardt, E. Zotta, C. Ibarra, SD. Manning, M. Larzabal and A.A Cataldi. Clade 8 and clade 6 strains of Escherichia coli O157:H7 from cattle in Argentina have hypervirulent-like phenotypes. (PLoS One. June1, 2015 DOI: 10.1371/journal.pone.0127710).

Singh and SD. Manning. Molecular Characterization of Shiga toxin producing Escherichia coli. In: DNA methods in Food Safety: Molecular Typing of Foodborne and Waterborne Bacterial Pathogens. (eds O. A. Oyarzabal and S. Kathariou), John Wiley & Sons, Ltd, Chichester, UK. 2014 doi: 10.1002/9781118278666.ch12

Springman, DW. Lacher, EA. Waymire, SL. Wengert, P. Singh, HD. Davies and SD. Manning. Pilus distribution among clonal lineages of group B Streptococcus: an evolutionary and clinical perspective. (BMC Microbiology.2014, 14:159 DOI: 10.1186/1471-2180-14-159).

Singh and YM. Kwon. Comparative analysis of Campylobacter populations within individual market age broilers using fla gene typing method. (Poult Sci. 2013 92:2135-2144; doi:10.3382/ps.2012-02615).

Singh, A. Karimi, K. Devendra, PW. Waldroup, KK. Cho, and YM. Kwon. Influence of penicillin on microbial diversity of the cecal microbiota in broiler chickens. (Poult Sci. 2013 Jan; 92(1):272-6. doi: 10.3382/ps.2012-02603).

Singh, SL. Foley, R. Nayak and YM. Kwon. Massively parallel sequencing of enriched target amplicons for high-resolution genotyping of Salmonella serovars. (Mol Cell Probes. 2013 Apr; 27(2):80-5. doi: 10.1016/j.mcp.2012.11.004. Epub 2012 Nov 29).

Singh, AC. Springman, HD. Davies and SD. Manning. Whole Genome Shotgun Sequencing of a colonizing ST17 Streptococcus agalactiae. (J Bacteriol. 2012 Nov; 194(21):6005. doi: 10.1128/JB.01378-12).

Singh, SL. Foley, R. Nayak and YM. Kwon. Multilocus sequence typing of Salmonella strains by high-throughput sequencing of selectively amplified target genes. (J Microbiol Methods. Jan 2012; 88 (1):127-33. Epub 2011 Nov 11).

P. Singh, R. Nayak and YM Kwon. Target-enrichment through amplification of hairpin-ligated universal targets for next-generation sequencing analysis. In: Methods in molecular biology. High-throughput next generation sequencing: Methods and applications. Edited by YM Kwon and Steven C. Ricke. (Clifton, N.J.). 2011;733: 267-78.



Curriculm Vitae


Ph.D., Cell and Molecular Biology University of Arkansas, Fayetteville, AR, 2010

M.Sc., Biotechnology, University of Madras, India, 2005

BSc., Biotechnology, Sardar Patel University, India, 2003

Fields of Interest

Human/animal microbiome, Bacterial pathogens, Comparative Genomics, One health, Food Safety.


Pallavi Singh 
Office: MO 359 (815) 753-7839
Lab:  MO 407
Dept. of Biological Sciences
Northern Illinois University
DeKalb, IL 60115

See also: