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Joy Scaria

Scaria photo

Title

Associate Professor, Bacterial Genomics, Host-microbiome interactions

Office Building

Animal Disease Research & Diagnostic Laboratory

Office

117

Mailing Address

Animal Disease Research 117
Veterinary & Biomedical Sciences-Box 2175
University Station
Brookings, SD 57007

Education

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

Academic Interests/Expertise

Bacterial genomics
Gut health
Food Safety

Academic Responsibilities

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.

Creative Activities

PEER REVIEWED PUBLICATIONS
* indicates corresponding author
60 Canola meal in nursery pig diets: Growth performance and gut health. Hong J, Ndou SP, Adams S, Scaria J, Woyengo TA. J Anim Sci. 2020 Oct 24: doi: 10.1093/jas/skaa338. PMID: 33098648

59 Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces. Ghimire S, Wongkuna S, Scaria J*. PeerJ. 2020 Oct 5;8:e10071. doi: 10.7717/peerj.10071. PMID: 33083133

58 Population Genomic Analysis of Mycoplasma bovis Elucidates Geographical Variations and Genes associated with Host-Types. Kumar R, Register K, Christopher-Hennings J, Moroni P, Gioia G, Garcia-Fernandez N, Nelson J, Jelinski MD, Lysnyansky I, Bayles D, Alt D, Scaria J*. Microorganisms. 2020 Oct 10;8(10):E1561. doi: 10.3390/microorganisms8101561. PMID: 33050495

57 Taxono-genomics description of Olsenella lakotia SW165 T sp. nov., a new anaerobic bacterium isolated from cecum of feral chicken. Wongkuna S, Ghimire S, Janvilisri T, Doerner K, Chankhamhaengdecha S, Scaria J*. F1000Res. 2020 Sep 8;9:1103. doi: 10.12688/f1000research.25823.1. PMID: 33024551

56 Description of a new member of the family Erysipelotrichaceae: Clostridium fusiformis sp. nov., isolated from healthy human feces. Ghimire S, Wongkuna S, and Scaria J * PeerJ 8:e10071 https://peerj.com/articles/10071/

55 Antibiotic-Resistant Escherichia Coli and Sequence Type 131 in Fecal Colonization in Dogs in Taiwan. Chen, J; Huang, H; Chang, S; Scaria, J; Chiu, YL; Chen, CM; Ko, WC; Wang, JL;. Microorganisms. 2020, 8(9), 1439; https://doi.org/10.3390/microorganisms8091439 - 20 Sep 2020

54 Small Molecule Adjuvants Potentiate Colistin Activity and Attenuate Resistance Development in Escherichia coli by Affecting pmrAB System. Kathayat D, Antony L, Deblais L, Helmy YA, Scaria J, Rajashekara G. Infect Drug Resist. 2020 Jul 10;13:2205-2222. doi: 10.2147/IDR.S260766. eCollection 2020. PMID: 32764996

53 Identifying Clostridioides difficile-inhibiting gut commensals using culturomics, phenotyping, and combinatorial community assembly. Ghimire S, Roy C, Wongkuna S, Antony L, Fenske G, Maji A, Keena MC, Foley A, and Scaria J*. mSystems. 2020 Feb 4;5(1):e00620-19. doi: 10.1128/mSystems.00620-19. PMID: 32019832

52 The Gut Microbiota composition of Feral and Tamworth Pigs determined using High-Throughput Culturomics and Metagenomics Reveals Compositional Variations When Compared to the Commercial Breeds. Fenske G, Ghimire S, Antony L, Christopher-Hennings J, and Scaria J*. FEMS Microbiol Ecol. 2020 Mar 1;96(3):fiaa022. doi: 10.1093/femsec/fiaa022. PMID: 32031212

51 Genome sequence and description of Blautia brookingsii str SG772 nov., a new species of
anaerobic bacterium isolated from healthy human gut. Ghimire S, Kumar R, Nelson EA, Christopher-Hennings J, and Scaria J * New Microbes New Infect. 2020 Jan 7;34:100648. doi: 10.1016/j.nmni.2019.100648. eCollection 2020 Mar. PMID: 32055403

50 Sellimonas caecigallum sp. nov., description and genome sequence of a new member of the Sellimonas genus isolated from the cecum of feral chicken. Wongkuna S, Ghimire S, Antony L, Chankhamhaengdecha S, Janvilisri T, and Scaria J * New Microbes and New Infections 2019 PMID: 31993203

49 Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India. Gupta A, Dhakan DB, Maji A, Saxena R, Prasoodanan PK, Mahajan S, Pulikkan J, Kurian J, Gomez AM, Scaria J, Amato KR, Sharma AK, Sharma VK. mSystems. 2019 4:e00438-19. PMID: 31719139

48 Geography Shapes the Population Genomics of Salmonella enterica Dublin, Fenske G, Thachil A, McDonough P, Glaser, Scaria J *. Genome Biol Evol. 2019 Jul 22. pii: evz158. doi: 10.1093/gbe/evz158.PMID: 31329231

47 Amish (rural) versus non-Amish (urban) infant fecal microbiotas are highly diverse and their transplantation lead to differences in mucosal immune maturation in a humanized germfree piglet model. Dhakal, S; Gourapura RJ; Wang L; Antony L; Rank J; Bernardo P; Ghimire S; Bondra K; Siems C; Lakshmanappa YS; Sankar R, Hogshead B, Krakowka S, Kauffman M, Scaria J, LeJeune J, Zhongtang Y. Frontiers in Immunology, 10,1509,2019 PMID: 31379808

46 Gut Microbial Dynamics during Conventionalization of Germfree Chicken. "Thomas, M; Wongkuna, S; Ghimire S; Kumar R; Antony L; Doerner KC; Singery A; Nelson E; Woyengo T; Chankhamhaengdecha S, Janvilisri T, Scaria J*. mSphere, 2019 4,2,e00035-19, PMID: 30918057

45 Enhancing the one health initiative by using whole genome sequencing to monitor antimicrobial resistance of animal pathogens: Vet-LIRN collaborative project with veterinary diagnostic laboratories in United States and Canada, Ceric, O; Tyson GH; Goodman LB; Mitchell PK; Zhang Y; Prarat M; Cui J; Peak L; Scaria J; Antony L. et al ",BMC veterinary research,15,1,130, 2019, PMID: 31060608

44 Alternative Therapeutic Approaches For Multidrug Resistant Clostridium difficile. Janvilisri Tavan; Sorg J; Scaria J; Sadowsky MJ. Frontiers in Microbiology,10,,1216,2019, PMID: 31214150

43 Salmonella Typhimurium strain and tomato genotypes affect the persistence of Salmonella in tomato plants. Deblais L, Scaria J, Antony L, Vrisman C, Helmy Y, and Miller SA. PHYTOPATHOLOGY, Vol 109, P186, 2019

42 The Flavonoid Metabolite 2, 4, 6-Trihydroxybenzoic Acid Is a CDK Inhibitor and an Anti-Proliferative Agent: A Potential Role in Cancer Prevention", Sankaranarayanan R; Valiveti CK; Kumar DR; Kesharwani SS; Seefeldt T; Scaria J; Tummala H; Bhat GJ. Cancers,11,3,427, 2019, PMID: 30917530

41 Diagnostic tests, test performance, and considerations for interpretation. Christopher‐Hennings J; Erickson GA; Hesse RA; Nelson EA; Rossow S; Scaria J; Slavic D. Diseases of Swine. 75-97, 2019,"John Wiley & Sons

40 Salmonella Prevalence in Lymph Nodes of Sows and Market Hogs in the United States. Bessire BC; Thomas M; Gehring KB; Savell JW; Griffin DB; Taylor TM; Mikel WB; Campbell JA; Arnold AN; Scaria J. Meat and Muscle Biology, 2019 2,2,129-130

39 Effects of health-related claims on millennials’ willingness to pay for probiotics in the US: Implications for regulation. Kolady DE, Kattelmann K, Scaria J.
Journal of Functional Foods 60, 103434, 2019

38 Antimicrobial-Resistant Escherichia coli from Environmental Waters in Northern Colorado. Haberecht, Hannah B; Nealon, Nora Jean; Gilliland, Jake R; Holder, Amethyst V; Runyan, Connor; Oppel, Renee C; Ibrahim, Hend M; Mueller, Link; Schrupp, Forrest; Vilchez, Samuel; Antony L, Scaria J, Ryan EP. J Environ Public Health. 2019 Feb 18;2019:3862949 PMID : 30906330

37 The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches. Dhakan, DB; Maji, A; Sharma, AK; Saxena, R; Pulikkan, J; Grace, T; Gomez, A; Scaria, J; Amato, KR; Sharma, VK; Gigascience. 2019 Mar 1;8(3) 2019 PMID : 30698687

36 Genome divergence and increased virulence of outbreak associated Salmonella enterica subspecies enterica serovar Heidelberg. Antony L, Behr M, Sockett D, Miskimins D, Aulik N, Christopher-Hennings J, Nelson E, Allard MW, Scaria J*. Gut Pathog. 2018 Dec 24;10:53. doi: 10.1186/s13099-018-0279-0. eCollection 2018. PMID: 30603048

35 Draft Genome Sequences of Salmonella enterica subsp. enterica Serotype Heidelberg from Chicken and Turkey Farm Environments. Deblais L, Scaria J, Rajashekara G. Microbiol Resour Announc. 2018 Nov 21;7(20). pii: e01204-18. doi: 10.1128/MRA.01204-18. eCollection 2018 Nov. PMID: 30533829

34 Comparative Genomic Studies of Salmonella Heidelberg Isolated From Chicken- and Turkey-Associated Farm Environmental Samples. Deblais L, Lorentz B, Scaria J, Nagaraja KV, Nisar M, Lauer D, Voss S, Rajashekara G. Front Microbiol. 2018 Aug 10;9:1841. doi: 10.3389/fmicb.2018.01841. eCollection 2018. PMID: 30147682

33 Genotypic and Phenotypic Characterization of Salmonella Isolated from Fresh Ground Meats Obtained from Retail Grocery Stores in the Brookings, South Dakota, Area. Erickson AK, Murray DL, Ruesch LA, Thomas M, Lau Z, Scaria J. J Food Prot. 2018 Sep;81(9):1526-1534. doi: 10.4315/0362-028X.JFP-18-076. PMID: 30118346

32 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*. Sci Rep. 2017 Sep 25;7(1):12257. doi: 10.1038/s41598-017-12481-6. PMID: 28947833

31 Whole genome sequencing-based detection of antimicrobial resistance and virulence in non-typhoidal Salmonella enterica isolated from wildlife. Thomas M, Fenske GJ, Antony L, Ghimire S, Welsh R, Ramachandran A, Scaria J*. Gut Pathog. 2017 Nov 21;9:66. doi: 10.1186/s13099-017-0213-x. eCollection 2017.PMID: 29201148

30 Gudlavalleti, R. H., Bose, S. C., Verma, S. K., Khatri, P., Scaria, J., Dhewa, S., Chaubey, V. K.
A Novel Fluorometric Bio-Sensing-Based Arsenic Detection System for Groundwater. IEEE
SENSORS JOURNAL, (2017) (17), 5391-5398.

29 Palanisamy S, Chang YC, Scaria J, Penha RA, Peters KE, Mohammed HO. Genetic relatedness among STEC isolated along the animal food supply chain and in gastroenteritis cases in Qatar using multilocus sequence typing (MLST), Foodborne Pathogens and Disease. 2017 Jun;14(6):318-325. doi: 10.1089/fpd.2016.2209. PMID: 28358583

28 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 M, Nelson EA,
Christopher-Hennings J, Tomita M, Suzuki H and Scaria J*. GenomeA, 2016 May 5;4(3).
pii: e00315-16.PMID: 27151793

27 Genome Sequences of Salmonella enterica subsp. enterica Serovar Lubbock Isolated from
Liver Abscesses of Feedlot Cattle, Amachawadi RG, Thomas M, Nagaraja TG and Scaria J*.
GenomeA. 2016 May 5;4(3). pii: e00319-16 PMID: 27151794

26 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*. GenomeA. 2016 Mar 10;4(2).
pii: e00035-16 PMID: 26966210

25 Chang YC, Scaria J, Ibraham M, Doiphode S, Chang YF, Sultan A, Mohammed HO (2015)
Distribution and factors associated with Salmonella enterica genotypes in a diverse
population of humans and animals in Qatar using multi-locus sequence typing (MLST).J
Infect Public Health. 2015 Nov 26. pii: S1876-0341(15)00196-3. doi:
10.1016/j.jiph.2015.10.013 PMID: 26631436

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

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

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

21 Scaria J, Mao C, Chen JW, Sobral B, Chang YF. (2013) Differential Stress Transcriptome
Landscape of Historic and Recently Emerged Hypervirulent Strains of Clostridium difficile
Strains Determined Using RNA-seq. PLoS One. 2013 Nov 7;8(11):e78489. doi:
10.1371/journal.pone.0078489 PMID : 24244315.

20 Janvilisri T, Bhunia AK, Scaria J.(2013) Advances in molecular diagnostics. Biomed Res Int.
2013:172521. doi: 10.1155/2013/172521. Epub 2013 May 27 PMID: 23781497.

19 Chen JW, Scaria J, Mao C, Sobral B, Zhang S, Lawley TD, Chang YF. (2012) Proteomic
comparison of historic and recently emerged hypervirulent Clostridium difficile strains. J. of
Proteome Res. 2013 Mar 1;12(3):1151-61 PMID: 23298230

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

17 Chen JW, Scaria J, Chang YF. (2012) Transcriptomic and phenotypic response of
auxotrophic Mycobacterium avium subspecies paratuberculosis (MAP) leuD mutant under
environmental stresses. PLoS One. 2012;7(6):e37884. PMID:22675497

16 Chen JW, Faisal SM, Chandra S, McDonough SP, Moreira MA, Scaria J, Chang CF, Bannantine
JP, Akey B, Chang YF (2011) Immunogenicity and protective efficacy of the Mycobacterium
avium subsp. paratuberculosis attenuated mutants against challenge in a mouse model.
Vaccine. 2011 Nov 18. PMID: 22107851

15 Mao BH, Chang YF, Scaria J, Chang CC, Chou LW, Tien N, Wu JJ, Tseng CC, Wang MC, Chang
CC, Hsu YM, Teng CH (2011) Identification of Escherichia coli genes associated with urinary
tract infections. J Clin Microbiol. 2011 Nov 9. PMID:22075599

14 Scaria J, Janvilisri T, Fubini S, Gleed RD, McDonough SP, Chang YF (2010) Clostridium difficile
transcriptome analysis using pig ligated loop model reveals modulation of pathways not
modulated in vitro. J Infect Dis. 1;203(11):1613-20.PMID:21592991

13 Rajkhowa S, Scaria J, Garcia DL, Musser KA, Akey BL, Chang YF (2010) Analysis of Escherichia
coli O157 clinical isolates by multilocus sequence typing. BMC Res Notes.
21;3:343.PMID:21176142

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

11 Janvilisri T, Scaria J, Chang YF (2010) Transcriptional profiling of Clostridium difficile and
Caco-2 cells during infection. J Infect Dis. 202(2):282-90.PMID: 20521945

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

9 Janvilisri T, Scaria J, Chang YF (2010) Transcriptional profiling of Clostridium difficile and
Caco-2 cells during infection. J Infect Dis. 202(2):282-90.PMID: 20521945

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

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

6 Scaria J, Ramachandran S, Jain PK and Verma SK (2009) Construction and testing of EGFP
based bacterial biosensor for the detection of residual tetracycline in milk and water. R.
Journal of Microbiology, 4(3): 104-111.

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

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

3 Scaria J, Chandramouli U, Verma SK (2005) Antibiotic Resistance Genes Online (ARGO): a
Database on vancomycin and beta-lactam resistance genes. Bioinformation. 1(1):5-7.
PMID: 17597841

2 Raveender V, Scaria J and Verma SK (2004) Bioaccumulation and Biosorption of heavy metals
by Spirulina Platensis. International Journal of Biodeterioration and Biodegradation, 53(4):
229

1 Raveender V, Scaria J, Verma SK (2002) Application of mutant strains of Cyanobacteria for
Cd(2+) removal. Bull Environ Contam Toxicol. 69(5):632-7.PMID:12375109

Department(s)

Links

ResearchgateLoopLab webpage

Open Prairie

Open PRAIRIE - Public Research Access Institutional Repository and Information Exchange

Scaria lab webpage