top of page




71           Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate

               metabolism and mouth–gut axis. Prasoodanan P K V, Sharma AK, Mahajan S, Dhakan DB, Maji \

               A, Scaria J, Sharma VK. NPJ Biofilms Microbiomes. 2021 Oct 7;7(1):77. doi: 

               10.1038/s41522-021-00248-x. PMID: 34620880

70          Rice Bran and Quercetin Produce a Positive Synergistic Effect on Human Gut Microbiota,

              Elevate the Level of Propionate, and Reduce the Population of Enterobacteriaceae family when

              Determined using a Bioreactor Model. Ghimire, S; Wongkuna, S; Sankaranarayanan, R; Ryan, EP;

              Bhat, GJ;  and Scaria J*. Front Microbiol. 2021 Sep 30;12:751225. doi:

             10.3389/fmicb.2021.751225. eCollection 2021. PMID: 34659185

69           Analysis of 56,348 Genomes Identifies the Relationship between Antibiotic and Metal

               Resistance and the Spread of Multidrug-Resistant Non- Typhoidal Salmonella. Fenske GJ,

               Scaria J. Microorganisms. 2021 Jul 9;9(7):1468. doi: 10.3390/microorganisms9071468. PMID: 


68           Screening of Human Gut Bacterial Culture Collection Identifies Species That Biotransform

               Quercetin into Metabolites with Anticancer Properties. Sankaranarayanan R, Sekhon PK, Ambat

               A, Nelson J, Jose D, Bhat GJ, Scaria J. Int J Mol Sci. 2021 Jun 30;22(13):7045. doi:

              10.3390/ijms22137045 PMID: 34208885  

67           Description of Collinsella avium sp. nov., a new member of the Collinsella genus isolated from

               the ceacum of feral chicken. Wongkuna S, Ghimire S, Chankhamhaengdecha S, Janvilisri T,

               Scaria J. New Microbes New Infect. 2021 May 18;42:100902. doi: 10.1016/j.nmni.2021.100902.

               eCollection 2021 Jul. PMID: 34168883


65           Growth performance and gut health of Escherichia coli-challenged weaned pigs fed canola

               meal-containing diet. Hong J, Ariyibi S, Antony L, Scaria J, Dilberger-Lawson S, Francis D,

               Woyengo TA. J Anim Sci. 2021 Aug 1;99(8):skab196. doi: 10.1093/jas/skab196. PMID: 34159354

64            Mediterraneibacter catenae SW178 sp. nov., an intestinal bacterium of feral chicken.

                Wongkuna S, Ghimire S, Chankhamhaengdecha S, Janvilisri T, Scaria J. PeerJ. 2021 Apr

                27;9:e11050. doi: 10.7717/peerj.11050. eCollection 2021. PMID: 33986975


63            Genomics accurately predicts antimicrobial resistance in Staphylococcus pseudintermedius

                collected as part of Vet-LIRN resistance monitoring. Tyson GH, Ceric O, Guag J, Nemser S,

                Borenstein S, Slavic D, Lippert S, McDowell R, Krishnamurthy A, Korosec S, Friday C, Pople N,

                Saab ME, Fairbrother JH, Janelle I, McMillan D, Bommineni YR, Simon D, Mohan S, Sanchez S,

                Phillips A, Bartlett P, Naikare H, Watson C, Sahin O, Stinman C, Wang L, Maddox C, DeShambo

                V, Hendrix K, Lubelski D, Burklund A, Lubbers B, Reed D, Jenkins T, Erol E, Patel M, Locke S,

                Fortner J, Peak L, Balasuriya U, Mani R, Kettler N, Olsen K, Zhang S, Shen Z, Landinez MP,

                Thornton JK, Thachil A, Byrd M, Jacob M, Krogh D, Webb B, Schaan L, Patil A, Dasgupta S,

                Mann S, Goodman LB, Franklin-Guild RJ, Anderson RR, Mitchell PK, Cronk BD, Aprea M, Cui J,

                Jurkovic D, Prarat M, Zhang Y, Shiplett K, Campos DD, Rubio JVB, Ramanchandran A, Talent S,

                Tewari D, Thirumalapura N, Kelly D, Barnhart D, Hall L, Rankin S, Dietrich J, Cole S, Scaria J,

                Antony L, Lawhon SD, Wu J, McCoy C, Dietz K, Wolking R, Alexander T, Burbick C,

                Reimschuessel R. Vet Microbiol. 2021 Mar;254:109006.doi: 10.1016/j.vetmic.2021.109006. Epub

                2021 Feb 4. PMID: 33581494



62            Characterization of bovine ileal epithelial cell line for lectin binding, susceptibility to enteric

                pathogens, and TLR mediated immune responses. Katwal P, Uprety T, Okda F, Antony L,

                Thomas M, Chase C, Diel DG, Nelson E, Young A, Li F, Scaria J, Kaushik RS. Comp Immunol

                Microbiol Infect Dis. 2021 Feb;74:101581. doi: 10.1016/j.cimid.2020.101581. Epub 2020 Nov 17.

                PMID: 33260019


61            Growth Performance, Fecal Score, and Blood Immune Parameters of Nursery Pigs Challenged

                with Escherichia coli F18 Fed Canola Meal-based Diet. J Hong, S Ariyibi, J Scaria, S Dilberger-

                Lawson, D Francis, TA Woyengo. Journal of Animal Science, Volume 99, Issue Supplement_1,

                May 2021, Page 98.


60           Population structure of Salmonella enterica serotype Mbandaka reveals similar virulence

               potential irrespective of source and phylogenomic stratification. Antony L, Fenske G, Kaushik

               RS, Nagaraja TG, Thomas M, Scaria J. F1000Res. 2020 Sep 16;9:1142. doi:  

               10.12688/f1000research.25540.1. eCollection 2020. PMID: 33214877


59           How do we find the source of Foodborne superbug outbreaks?  Scaria J, Menon S, and Rovai M                Frontiers for Young Minds 2021. 9:557762



58            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 Nov 1;98(11):skaa338. doi: 10.1093/jas

                /skaa338. PMID: 33098648


57            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 

                PMID: 33083133


56           Population genomic analysis of Mycoplasma bovis isolates reveals transcontinental variations

               and potential virulence genes. Kumar, R; Register, K; Hennings, J; Moroni, P; Gioa, G; Garcia-

               Fernandez, N; Nelson, J; Jelinski, M; Lysnyansky, I; Bayles, D; and Scaria J*.  Microorganisms.

               2020 Oct 10;8(10):1561.PMID: 33050495



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; PMID: 32962221


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. . 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 



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. 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.

               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. 

               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.

               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. 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).

               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).  

             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. 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.  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 . 201 Jun 11;3(3).

            PMID: 26067961


22        Janvilisri T, Suzuki H, Scaria J, Chen JW, Charoensawan V.(2015) High-Throughput Screening  for

            Biomarker Discovery. Dis Markers. 2015:108064.   PMID: 26060333


Previous Publications


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. 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



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

bottom of page