Publications
2021
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
2020
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.
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. https://doi.org/10.1093/jas/skab054.156
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
https://kids.frontiersin.org/articles/10.3389/frym.2021.557762
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
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.
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
2019
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
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,
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,
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
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
2018
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.
2017
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.
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.
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
2016
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
2015
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
20 Janvilisri T, Bhunia AK, Scaria J.(2013) Advances in molecular diagnostics. Biomed Res Int.
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.
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