Skip to main content
Close Search

Joy Scaria

Joy Scaria


Assistant Professor

Office Building

Animal Disease Research & Diagnostic Laboratory



Mailing Address

Animal Disease Research 114
Veterinary & Biomedical Sciences-Box 2175
University Station
Brookings, SD 57007


Ph.D - BITS, Pilani, India
Postdoc - Cornell University, New York

Academic Interests/Expertise

Bacterial genomics
Gut health
Food Safety

Creative Activities

1. Whole genome sequencing-based detection of antimicrobial resistance and virulence in non-typhoidal Salmonella enterica isolated from wildlife. Thomas M, Fenske GJ, Ghimire S, Antony L, Welsch R, Ramachandran A, Scaria J. Gut Pathogens 2017, 9:66 DOI 10.1186/s13099-017-0213-x

2. Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle. Thomas M, Webb M, Ghimire S, Blair A, Olson K, Fenske GJ, Fonder AT, Christopher-Hennings J, Brake D, Scaria J. Scientific Reports. 2017 Sep 25;7(1):12257. doi: 10.1038/s41598-017-12481-6.PMID: 28947833

3. Genome Sequences of Salmonella enterica subsp. enterica Serovar Lubbock Strains Isolated from Liver Abscesses of Feedlot Cattle. Amachawadi RG, Thomas M, Nagaraja TG, Scaria J.Genome Announc. 2016 May 5;4(3). pii: e00319-16. doi: 10.1128/genomeA.00319-16. PMID:27151794

4. Draft Genome Sequences of 37 Salmonella enterica Strains Isolated from Poultry Sources in Nigeria. Useh NM, Ngbede EO, Akange N, Thomas M, Foley A, Keena MC, Nelson E, Christopher-Hennings J, Tomita M, Suzuki H, Scaria J.Genome Announc. 2016 May 5;4(3). pii: e00315-16. doi: 10.1128/genomeA.00315-16.PMID:27151793

5. Draft Genome Sequences of Three Flavobacterium psychrophilum Strains Isolated from Coldwater Disease Outbreaks at Three Production Hatcheries. Neiger R, Thomas M, Das S, Barnes M, Fletcher B, Snekvik K, Thompson J, Scaria J.Genome Announc. 2016 Mar 10;4(2). pii: e00035-16. doi: 10.1128/genomeA.00035-16.PMID: 26966210

6. Distribution and factors associated with Salmonella enterica genotypes in a diverse population of humans and animals in Qatar using multi-locus sequence typing (MLST).Chang YC, Scaria J, Ibraham M, Doiphode S, Chang YF, Sultan A, Mohammed HO. J Infect Public Health. 2016 May-Jun;9(3):315-23. doi: 10.1016/j.jiph.2015.10.013.PMID:26631436

7. Complete Genome Sequence of a Highly Pathogenic Avian Influenza Virus (H5N2) Associated with an Outbreak in Commercial Chickens, Iowa, USA, 2015. Clement T, Kutish GF, Nezworski J, Scaria J, Nelson E, Christopher-Hennings J, Diel DG. Genome Announc. 2015 Jun 11;3(3). pii: e00613-15. doi: 10.1128/genomeA.00613-15.PMID: 26067961

8. High-Throughput Screening for Biomarker Discovery. Janvilisri T, Suzuki H, Scaria J, Chen JW, Charoensawan V. Dis Markers. 2015;2015:108064. doi: 10.1155/2015/108064. PMID: 26060333

9. Comparative genomic and phenomic analysis of Clostridium difficile and Clostridium sordellii, two related pathogens with differing host tissue preference.
Scaria J, Suzuki H, Ptak CP, Chen JW, Zhu Y, Guo XK, Chang YF. BMC Genomics. 2015 Jun 10;16:448. doi: 10.1186/s12864-015-1663-5.PMID:26059449

10. Comparative nutritional and chemical phenome of Clostridium difficile isolates determined using phenotype microarrays. Scaria J, Chen JW, Useh N, He H, McDonough SP, Mao C, Sobral B, Chang YF. Int J Infect Dis. 2014 Oct;27:20-5. doi: 10.1016/j.ijid.2014.06.018.PMID:25130165

11. Differential stress transcriptome landscape of historic and recently emerged hypervirulent strains of Clostridium difficile strains determined using RNA-seq. Scaria J, Mao C, Chen JW, McDonough SP, Sobral B, Chang YF. PLoS One. 2013 Nov 7;8(11):e78489. doi: 10.1371/journal.pone.0078489.PMID:24244315

12. Advances in molecular diagnostics. Janvilisri T, Bhunia AK, Scaria J.Biomed Res Int. 2013;2013:172521. doi: 10.1155/2013/172521. PMID:23781497

13. Proteomic comparison of historic and recently emerged hypervirulent Clostridium difficile strains. Chen JW, Scaria J, Mao C, Sobral B, Zhang S, Lawley T, Chang YF. J Proteome Res. 2013 Mar 1;12(3):1151-61. doi: 10.1021/pr3007528.PMID:23298230

14. Temporal differential proteomes of Clostridium difficile in the pig ileal-ligated loop model. Janvilisri T, Scaria J, Teng CH, McDonough SP, Gleed RD, Fubini SL, Zhang S, Akey B, Chang YF. PLoS One. 2012;7(9):e45608. doi: 10.1371/journal.pone.0045608.PMID:23029131

15. Phenotypic and transcriptomic response of auxotrophic Mycobacterium avium subsp. paratuberculosis leuD mutant under environmental stress.Chen JW, Scaria J, Chang YF. PLoS One. 2012;7(6):e37884. doi: 10.1371/journal.pone.0037884.PMID:22675497

16. Immunogenicity and protective efficacy of the Mycobacterium avium subsp. paratuberculosis attenuated mutants against challenge in a mouse model. Chen JW, Faisal SM, Chandra S, McDonough SP, Moreira MA, Scaria J, Chang CF, Bannantine JP, Akey B, Chang YF. Vaccine. 2012 Apr 19;30(19):3015-25. doi: 10.1016/j.vaccine.2011.11.029. PMID: 22107851

17. Identification of Escherichia coli genes associated with urinary tract infections.Mao BH, Chang YF, Scaria J, Chang CC, Chou LW, Tien N, Wu JJ, Tseng CC, Wang MC, Chang CC, Hsu YM, Teng CH.J Clin Microbiol. 2012 Feb;50(2):449-56. doi: 10.1128/JCM.00640-11.PMID:22075599

18. Clostridium difficile transcriptome analysis using pig ligated loop model reveals modulation of pathways not modulated in vitro.Scaria J, Janvilisri T, Fubini S, Gleed RD, McDonough SP, Chang YF.J Infect Dis. 2011 Jun 1;203(11):1613-20. doi: 10.1093/infdis/jir112.PMID:21592991

19. Analysis of Escherichia coli O157 clinical isolates by multilocus sequence typing.Rajkhowa S, Scaria J, Garcia DL, Musser KA, Akey BL, Chang YF.BMC Res Notes. 2010 Dec 21;3:343. doi: 10.1186/1756-0500-3-343.PMID:21176142

20. Analysis of ultra low genome conservation in Clostridium difficile.Scaria J, Ponnala L, Janvilisri T, Yan W, Mueller LA, Chang YF. PLoS One. 2010 Dec 8;5(12):e15147. doi: 10.1371/journal.pone.0015147.PMID: 21170335

21. Comparison of phenotypic and genotypic antimicrobial profiles in Escherichia coli and Salmonella enterica from the same dairy cattle farms.Scaria J, Warnick LD, Kaneene JB, May K, Teng CH, Chang YF. Mol Cell Probes. 2010 Dec;24(6):325-45. doi: 10.1016/j.mcp.2010.07.004.PMID:20688154

22. Transcriptional profiling of Clostridium difficile and Caco-2 cells during infection. Janvilisri T, Scaria J, Chang YF.J Infect Dis. 2010 Jul 15;202(2):282-90. doi: 10.1086/653484.PMID: 20521945

23. Development of a microarray for identification of pathogenic Clostridium spp.Janvilisri T, Scaria J, Gleed R, Fubini S, Bonkosky MM, Gröhn YT, Chang YF. Diagn Microbiol Infect Dis. 2010 Feb;66(2):140-7. doi: 10.1016/j.diagmicrobio.2009.09.014.PMID:19879710

24. Microarray identification of Clostridium difficile core components and divergent regions associated with host origin. Janvilisri T, Scaria J, Thompson AD, Nicholson A, Limbago BM, Arroyo LG, Songer JG, Gröhn YT, Chang YF. J Bacteriol. 2009 Jun;191(12):3881-91. doi: 10.1128/JB.00222-09.PMID:19376880

25. Microbial Diagnostic Array Workstation (MDAW): a web server for diagnostic array data storage, sharing and analysis.Scaria J, Sreedharan A, Chang YF.Source Code Biol Med. 2008 Sep 23;3:14. doi: 10.1186/1751-0473-3-14.PMID:18811969

26. Microarray for molecular typing of Salmonella enterica serovars.Scaria J, Palaniappan RU, Chiu D, Phan JA, Ponnala L, McDonough P, Grohn YT, Porwollik S, McClelland M, Chiou CS, Chu C, Chang YF.Mol Cell Probes. 2008 Aug;22(4):238-43. doi: 10.1016/j.mcp.2008.04.002.PMID:18554865

Area(s) of Research

Dr. Scaria conducts research in the areas of enteric diseases, role of prebiotics and probiotics in gut health, and the development of Next Generation sequencing (NGS) based diagnostic tools for pathogen detection. His primary research interest is to understand the mechanisms by which commensal gut bacteria provide colonization resistance against pathogens such as Clostridium difficile and Salmonella enterica. Current research efforts also includes transnational studies to control enteric infections using prebiotics and probiotics. A secondary focus of his research is the use of NGS for foodborne pathogen tracking and detection.