Publications

1. Cuthbertson L, Löber U, Ish-Horowicz JS, McBrien CN, Churchward C, Parker JC, Olanipekun MT, Burke C, McGowan A, Davies GA, Lewis KE, Hopkin JM, Chung KF, O'Carroll O, Faul J, Creaser-Thomas J, Andrews M, Ghosal R, Piatek S, Willis-Owen SAG, Bartolomaeus TUP, Birkner T, Dwyer S, Kumar N, Turek EM, William Musk A, Hui J, Hunter M, James A, Dumas ME, Filippi S, Cox MJ, Lawley TD, Forslund SK, Moffatt MF, Cookson WOC.: Genomic attributes of airway commensal bacteria and mucosa. Commun Biol. 20242. Crobach MJT, Hornung BVH, Verduin C, Vos MC, Hopman J, Kumar N, Harmanus C, Sanders I, Terveer EM, Stares MD, Lawley TD, Kuijper EJ.: Screening for Clostridioides difficile colonization at admission to the hospital: a multi-centre study. Clin Microbiol Infect. 20233. Forster SC, Clare S, Beresford-Jones BS, Harcourt K, Notley G, Stares MD, Kumar N, Soderholm AT, Adoum A, Wong H, Morón B, Brandt C, Dougan G, Adams DJ, Maloy KJ, Pedicord VA, Lawley TD.: Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis. Nat Microbiol. 20224. Forster SC, Liu J, Kumar N, Gulliver EL, Gould JA, Escobar-Zepeda A, Mkandawire T, Pike LJ, Shao Y, Stares MD, Browne HP, Neville BA, Lawley TD.: Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome. Nat Commun. 20225. Beresford-Jones BS, Forster SC, Stares MD, Notley G, Viciani E, Browne HP, Boehmler DJ, Soderholm AT, Kumar N, Vervier K, Cross JR, Almeida A, Lawley TD, Pedicord VA.: The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping. Cell Host Microbe. 2022.6. Vervier K, Moss S, Kumar N, Adoum A, Barne M, Browne H, et al.: Two microbiota subtypes identified in irritable bowel syndrome with distinct responses to the low FODMAP diet. Gut. 2021.7. Browne HP, Almeida A, Kumar N, Vervier K, Adoum AT, Viciani E, Dawson NJR, Forster SC, Cormie C, Goulding D, Lawley TD.: Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle. Genome Biol. 2021.8. Strobbe F, Bénard MV, Rossen NG, de Vos WM, Kumar N, Lawley TD, Zoetendal EG, Hugenholtz F, Ponsioen CY.: A novel technique capable of taking 'protected' biopsies for reliable assessment of the distribution of microbiota along the colonic mucosa. J Microbiol Methods. 20219. Costa D, Lévesque S, Kumar N, Fresia P, Ferrés I, Lawley TD, Iraola G.: Pangenome analysis reveals genetic isolation in Campylobacter hyointestinalis subspecies adapted to different mammalian hosts. Sci Rep. 2021.10. Fitzpatrick Z, Frazer G, Ferro A, Clare S, Bouladoux N, Ferdinand J, Kumar N, Suchanek O, Tajsic T, Harcourt K, Scott K, Bashford-Rogers R, Helmy A, Reich DS, Belkaid Y, Lawley TD, McGavern DB, Clatworthy MR.: Gut-educated IgA plasma cells defend the meningeal venous sinuses. Nature. 2020.11. Shao Y, Forster SC, Tsaliki E, Vervier K, Strang A, Simpson N, Kumar N, Stares MD, Rodger A, Brocklehurst P, Field N, Lawley TD.: Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. Nature 201912. Kumar N*, Browne HP, Viciani E, Forster SC, Clare S, Harcourt K, Stares MD, Dougan G, Fairley DJ, Roberts P, Pirmohamed M, Clokie MRJ, Jensen MBF, Hargreaves KR, Ip M, Wieler LH, Seyboldt C, Norén T, Riley TV, Kuijper EJ, Wren BW, Lawley TD.: Adaptation of host transmission cycle during clostridium difficile speciation. Nature Genetics 2019 (*co-corresponding author).13. Forster SC*, Kumar N*, Anonye BO, Almeida A, Viciani E, Stares MD, Dunn M, Mkandawire TT, Zhu A, Shao Y, Pike LJ, Louie T, Browne HP, Mitchell AL, Neville BA, Finn RD, Lawley TD.: A human gut bacterial genome and culture collection for improved metagenomic analyses. Nature Biotechnology 2019. (*co-first author)14. Thomas-White K*, Forster SC*, Kumar N*, Van Kuiken M, Putonti C, Stares MD, Hilt EE, Price TK, Wolfe AJ, Lawley TD.: Culturing of female bladder bacteria reveals an interconnected urogenital microbiota. Nature Communications 2018. (*co-first author)15. Sharma C, Kumar R, Kumar N et al: Investigation of multiple resistance mechanisms in voriconazole resistant Aspergillus flavus clinical isolates from a chest hospital surveillance in Delhi, India. Antimicrob Agents Chemother 2018.16. Pike LJ, Viciani E, Kumar N: Genome watch: Microbial diversity knows no borders. Nat Rev Microbiol 2018.17. Fleurbaaij F, Henneman AA, Corver J, Knetsch CW, Smits WK, Nauta ST, Giera M, Dragan I, Kumar N, Lawley TD et al: Proteomic identification of Axc, a novel beta-lactamase with carbapenemase activity in a meropenem-resistant clinical isolate of Achromobacter xylosoxidans. Sci Rep 2018.18. Kumar N, Forster SC: Genome watch: Microbiota shuns the modern world. Nat Rev Microbiol 2017.19. Knetsch CW*, Kumar N* et al: Zoonotic transfer of Clostridium difficile harboring antimicrobial resistance between farm animals and humans. J Clin Microbiol 2017. (*co-first author)20. Iraola G, Forster SC, Kumar N et al: Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota. Nat Commun 2017.21. Howell KJ, Kraiczy J, Nayak KM, Gasparetto M, Ross A, Lee C, Mak TN, Koo BK, Kumar N, Lawley T et al: DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells from Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome. Gastroenterology 2017.22. Sharma C, Kumar N, Pandey R, Meis JF, Chowdhary A: Whole genome sequencing of emerging multidrug resistant Candida auris isolates in India demonstrates low genetic variation. New Microbes New Infect 2016.23. Kumar N, Miyajima F, He M et al: Genome-Based Infection Tracking Reveals Dynamics of Clostridium difficile Transmission and Disease Recurrence. Clin Infect Dis 2016.24. Fung TC, Bessman NJ, Hepworth MR, Kumar N et al: Lymphoid-Tissue-Resident Commensal Bacteria Promote Members of the IL-10 Cytokine Family to Establish Mutualism. Immunity 2016.25. Forster SC, Browne HP, Kumar N, Hunt M, Denise H, Mitchell A, Finn RD, Lawley TD: HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes. Nucleic Acids Res 2016.26. Browne HP, Forster SC, Anonye BO, Kumar N, Neville BA, Stares MD, Goulding D, Lawley TD: Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation. Nature 2016.27. Sharma C, Kumar N, Meis JF, Pandey R, Chowdhary A: Draft Genome Sequence of a Fluconazole-Resistant Candida auris Strain from a Candidemia Patient in India. Genome Announc 2015.28. Kumar N, Lad G, Giuntini E, Kaye ME, Udomwong P, Shamsani NJ, Young JP, Bailly X: Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum. Open Biol 2015.29. Bailly X, Giuntini E, Sexton MC, Lower RP, Harrison PW, Kumar N, Young JP: Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates. ISME J 2011.30. Bhardwaj A, Bhartiya D, Kumar N, Open Source Drug Discovery C, Scaria V: TBrowse: an integrative genomics map of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2009.