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Items: 50

1.

Recent Advancements in the Development of Modern Probiotics for Restoring Human Gut Microbiome Dysbiosis.

Kumar R, Sood U, Gupta V, Singh M, Scaria J, Lal R.

Indian J Microbiol. 2020 Mar;60(1):12-25. doi: 10.1007/s12088-019-00808-y. Epub 2019 May 25. Review.

PMID:
32089570
2.

Synthesis and applications of various bimetallic nanomaterials in water and wastewater treatment.

Scaria J, Nidheesh PV, Kumar MS.

J Environ Manage. 2020 Apr 1;259:110011. doi: 10.1016/j.jenvman.2019.110011. Epub 2020 Jan 10. Review.

PMID:
32072958
3.

Genome sequence and description of Blautia brookingsii SG772 sp. nov., a novel bacterial species isolated from human faeces.

Ghimire S, Wongkuna S, Kumar R, Nelson E, Christopher-Hennings J, Scaria J.

New Microbes New Infect. 2020 Jan 7;34:100648. doi: 10.1016/j.nmni.2019.100648. eCollection 2020 Mar.

4.

Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome.

Fenske GJ, Ghimire S, Antony L, Christopher-Hennings J, Scaria J.

FEMS Microbiol Ecol. 2020 Feb 7. pii: fiaa022. doi: 10.1093/femsec/fiaa022. [Epub ahead of print]

PMID:
32031212
5.

Identification of Clostridioides difficile-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly.

Ghimire S, Roy C, Wongkuna S, Antony L, Maji A, Keena MC, Foley A, Scaria J.

mSystems. 2020 Feb 4;5(1). pii: e00620-19. doi: 10.1128/mSystems.00620-19.

6.

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, Scaria J.

New Microbes New Infect. 2019 Nov 29;33:100626. doi: 10.1016/j.nmni.2019.100626. eCollection 2020 Jan.

7.

Defining the Environmental Adaptations of Genus Devosia: Insights into its Expansive Short Peptide Transport System and Positively Selected Genes.

Talwar C, Nagar S, Kumar R, Scaria J, Lal R, Negi RK.

Sci Rep. 2020 Jan 24;10(1):1151. doi: 10.1038/s41598-020-58163-8.

8.

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, P K VP, Mahajan S, Pulikkan J, Kurian J, Gomez AM, Scaria J, Amato KR, Sharma AK, Sharma VK.

mSystems. 2019 Nov 12;4(6). pii: e00438-19. doi: 10.1128/mSystems.00438-19.

9.

Amish (Rural) vs. 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, Wang L, Antony L, Rank J, Bernardo P, Ghimire S, Bondra K, Siems C, Lakshmanappa YS, Renu S, Hogshead B, Krakowka S, Kauffman M, Scaria J, LeJeune JT, Yu Z, Renukaradhya GJ.

Front Immunol. 2019 Jul 16;10:1509. doi: 10.3389/fimmu.2019.01509. eCollection 2019.

10.

Geography Shapes the Population Genomics of Salmonella enterica Dublin.

Fenske GJ, Thachil A, McDonough PL, Glaser A, Scaria J.

Genome Biol Evol. 2019 Aug 1;11(8):2220-2231. doi: 10.1093/gbe/evz158.

11.

Editorial: Alternative Therapeutic Approaches For Multidrug Resistant Clostridium difficile.

Janvilisri T, Sorg JA, Scaria J, Sadowsky MJ.

Front Microbiol. 2019 May 31;10:1216. doi: 10.3389/fmicb.2019.01216. eCollection 2019. No abstract available.

12.

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, Thomas M, Nemser SM, Anderson R, Thachil AJ, Franklin-Guild RJ, Slavic D, Bommineni YR, Mohan S, Sanchez S, Wilkes R, Sahin O, Hendrix GK, Lubbers B, Reed D, Jenkins T, Roy A, Paulsen D, Mani R, Olsen K, Pace L, Pulido M, Jacob M, Webb BT, Dasgupta S, Patil A, Ramachandran A, Tewari D, Thirumalapura N, Kelly DJ, Rankin SC, Lawhon SD, Wu J, Burbick CR, Reimschuessel R.

BMC Vet Res. 2019 May 6;15(1):130. doi: 10.1186/s12917-019-1864-2.

13.

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 Mar 27;4(2). pii: e00035-19. doi: 10.1128/mSphere.00035-19.

14.

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, Van Slambrouck S, Kesharwani SS, Seefeldt T, Scaria J, Tummala H, Bhat GJ.

Cancers (Basel). 2019 Mar 26;11(3). pii: E427. doi: 10.3390/cancers11030427.

15.

Antimicrobial-Resistant Escherichia coli from Environmental Waters in Northern Colorado.

Haberecht HB, Nealon NJ, Gilliland JR, Holder AV, Runyan C, Oppel RC, Ibrahim HM, Mueller L, Schrupp F, Vilchez S, Antony L, Scaria J, Ryan EP.

J Environ Public Health. 2019 Feb 18;2019:3862949. doi: 10.1155/2019/3862949. eCollection 2019.

16.

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). pii: giz004. doi: 10.1093/gigascience/giz004.

17.

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.

18.

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.

19.

Improved production of cellulase by Trichoderma reesei (MTCC 164) from coconut mesocarp-based lignocellulosic wastes under response surface-optimized condition.

Dey P, Singh J, Scaria J, Anand AP.

3 Biotech. 2018 Sep;8(9):402. doi: 10.1007/s13205-018-1421-x. Epub 2018 Sep 8.

20.

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.

21.

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
22.

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.

23.

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.

24.

Genetic Relatedness Among Shiga Toxin-Producing Escherichia coli Isolated Along the Animal Food Supply Chain and in Gastroenteritis Cases in Qatar Using Multilocus Sequence Typing.

Palanisamy S, Chang Y, Scaria J, Penha Filho RAC, Peters KE, Doiphode SH, Sultan A, Mohammed HO.

Foodborne Pathog Dis. 2017 Jun;14(6):318-325. doi: 10.1089/fpd.2016.2209. Epub 2017 Mar 30.

PMID:
28358583
25.

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.

26.

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.

27.

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.

28.

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. Epub 2015 Nov 27.

29.

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.

30.

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. Epub 2015 Apr 28. No abstract available.

31.

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.

32.

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. Epub 2014 Aug 12.

33.

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. eCollection 2013.

34.

Advances in molecular diagnostics.

Janvilisri T, Bhunia AK, Scaria J.

Biomed Res Int. 2013;2013:172521. doi: 10.1155/2013/172521. Epub 2013 May 27. No abstract available.

35.

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. Epub 2013 Jan 25.

PMID:
23298230
36.

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. Epub 2012 Sep 18.

37.

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. Epub 2012 Jun 4.

38.

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. Epub 2011 Nov 19.

PMID:
22107851
39.

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. Epub 2011 Nov 9.

40.

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.

41.

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.

42.

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.

43.

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. Epub 2010 Aug 3.

44.

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.

45.

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. Epub 2009 Oct 30.

46.

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. Epub 2009 Apr 17.

47.

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.

48.

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. Epub 2008 May 1.

49.
50.

Application of mutant strains of cyanobacteria for Cd(2+) removal.

Raveender V, Scaria J, Verma SK.

Bull Environ Contam Toxicol. 2002 Nov;69(5):632-7. No abstract available.

PMID:
12375109

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