A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

Genome Medicine

Volumn 9, Issue 1, 2017, Pages

  Hall, Andrew Brantley ^a,b   Yassour, Moran ^a,b   Sauk, Jenny ^b,h   Garner, Ashley ^a,b   Jiang, Xiaofang ^a,c   Arthur, Timothy ^a,b   Lagoudas, Georgia K ^a,c   Vatanen, Tommi ^a,b   Fornelos, Nadine ^a,b   Wilson, Robin ^b   Bertha, Madeline ^d   Cohen, Melissa ^b   Garber, John ^b   Khalili, Hamed ^b   Gevers, Dirk ^a,b,i   Ananthakrishnan, Ashwin N ^b   Kugathasan, Subra ^d   Lander, Eric S ^a,e,f   Blainey, Paul ^a,c   Vlamakis, Hera ^a,b   Xavier, Ramnik J ^a,b,c   Huttenhower, Curtis ^a,g   more..

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b MASSACHUSETTS GENERAL HOSPITAL   (United States)

^c Massachusetts Institute of Technology   (United States)

^d EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^f HARVARD MEDICAL SCHOOL   (United States)

^g HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^h UNIVERSITY OF CALIFORNIA   (United States)

ⁱ JANSSEN RESEARCH AND DEVELOPMENT   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ADHESION; ADULT; AGED; ARTICLE; BACTERIAL COLONIZATION; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM ISOLATE; CLADISTICS; CLINICAL ARTICLE; CLINICAL OUTCOME; COHORT ANALYSIS; CONTROLLED STUDY; DISEASE ACTIVITY; GENOMICS; GRAM NEGATIVE FACULTATIVELY ANAEROBIC RODS; HUMAN; INFLAMMATORY BOWEL DISEASE; INTESTINE FLORA; LONGITUDINAL STUDY; METAGENOMICS; MUCUS; NONHUMAN; OXIDATIVE STRESS; PRIORITY JOURNAL; RUMINOCOCCUS; RUMINOCOCCUS GNAVUS; TAXONOMIC RANK; WHOLE GENOME SEQUENCING; BACTERIAL GENOME; FECES; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MIDDLE AGED; PHYLOGENY; SPECIES DIFFERENCE; YOUNG ADULT;

ADULT; AGED; FECES; GASTROINTESTINAL MICROBIOME; GENOME, BACTERIAL; HUMANS; INFLAMMATORY BOWEL DISEASES; MIDDLE AGED; OXIDATIVE STRESS; PHYLOGENY; RUMINOCOCCUS; SPECIES SPECIFICITY; YOUNG ADULT;

EID: 85035359870     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-017-0490-5     Document Type: Article

References (33)

1. Khor B, Gardet A, Xavier RJ. Genetics and pathogenesis of inflammatory bowel disease. Nature. 2011;474:307-17.
2. Balmus IM, Ciobica A, Trifan A, Stanciu C. The implications of oxidative stress and antioxidant therapies in inflammatory bowel disease: clinical aspects and animal models. Saudi J Gastroenterol. 2016;22:3-17.
3. Poulsen NA, Andersen V, Møller JC, Møller HS, Jessen F, Purup S, et al. Comparative analysis of inflamed and non-inflamed colon biopsies reveals strong proteomic inflammation profile in patients with ulcerative colitis. BMC Gastroenterol. 2012;12:76.
4. Seril DN, Liao J, Yang G-Y, Yang CS. Oxidative stress and ulcerative colitis-associated carcinogenesis: studies in humans and animal models. Carcinogenesis. 2003;24:353-62.
5. Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 2012;13:R79.
6. Scholz M, Ward DV, Pasolli E, Tolio T, Zolfo M, Asnicar F, et al. Strain-level microbial epidemiology and population genomics from shotgun metagenomics. Nat Methods. 2016;13:435-8.
7. Truong DT, Tett A, Pasolli E, Huttenhower C, Segata N. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Res. 2017;27:626-38.
8. Geva-Zatorsky N, Sefik E, Kua L, Pasman L, Tan TG, Ortiz-Lopez A, et al. Mining the human gut microbiota for immunomodulatory organisms. Cell. 2017;168:928-43. e11.
9. Martinez-Medina M, Garcia-Gil LJ. Escherichia coli in chronic inflammatory bowel diseases: An update on adherent invasive Escherichia coli pathogenicity. World J Gastrointest Pathophysiol. 2014;5:213-27.
10. Yassour M, Vatanen T, Siljander H, Hämäläinen A-M, Härkönen T, Ryhänen SJ, et al. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci Transl Med. 2016;8:343ra81.
11. Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, et al. The long-term stability of the human gut microbiota. Science. 2013;341:1237439.
12. Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP, Bohannan BJM, et al. Identifying personal microbiomes using metagenomic codes. Proc Natl Acad Sci U S A. 2015;112:E2930-8.
13. Lewis JD, Chen EZ, Baldassano RN, Otley AR, Griffiths AM, Lee D, et al. Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohn's disease. Cell Host Microbe. 2015;18:489-500.
14. Shaw KA, Bertha M, Hofmekler T, Chopra P, Vatanen T, Srivatsa A, et al. Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease. Genome Med. 2016;8:75.
15. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207-14.
16. Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods. 2015;12:902-3.
17. Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol. 2012;8:e1002358.
18. Albenberg L, Esipova TV, Judge CP, Bittinger K, Chen J, Laughlin A, et al. Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Gastroenterology. 2014;147:1055-63. e8.
19. Kim S, De Jonghe J, Kulesa AB, Feldman D, Vatanen T, Bhattacharyya RP, et al. High-throughput automated microfluidic sample preparation for accurate microbial genomics. Nat Commun. 2017;8:13919.
20. Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe. 2014;15:382-92.
21. Moore WEC, Johnson JL, Holdeman LV. Emendation of Bacteroidaceae and Butyrivibrio and descriptions of Desulfomonas gen. nov. and ten new species in the genera Desulfomonas, Butyrivibrio, Eubacterium, Clostridium, and Ruminococcus. Int J Syst Evol Microbiol Microbiol Soc. 1976;26:238-52.
22. Nishiyama Y, Massey V, Takeda K, Kawasaki S, Sato J, Watanabe T, et al. Hydrogen peroxide-forming NADH oxidase belonging to the peroxiredoxin oxidoreductase family: existence and physiological role in bacteria. J Bacteriol. 2001;183:2431-8.
23. Masip L, Veeravalli K, Georgiou G. The many faces of glutathione in bacteria. Antioxid Redox Signal. 2006;8:753-62.
24. Kaitha S, Bashir M, Ali T. Iron deficiency anemia in inflammatory bowel disease. World J Gastrointest Pathophysiol. 2015;6:62-72.
25. Tailford LE, Owen CD, Walshaw J, Crost EH, Hardy-Goddard J, Le Gall G, et al. Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation. Nat Commun. 2015;6:7624.
26. Dabard J, Bridonneau C, Phillipe C, Anglade P, Molle D, Nardi M, et al. Ruminococcin A, a new lantibiotic produced by a Ruminococcus gnavus strain isolated from human feces. Appl Environ Microbiol. 2001;67:4111-8.
27. Rigottier-Gois L. Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis. ISME J. 2013;7:1256-61.
28. Hansen SGK, Skov MN, Justesen US. Two cases of Ruminococcus gnavus bacteremia associated with diverticulitis. J Clin Microbiol. 2013;51:1334-6.
29. Kim YJ, Kang HY, Han Y, Lee MS, Lee HJ. A bloodstream infection by Ruminococcus gnavus in a patient with a gall bladder perforation. Anaerobe. 2017;47:129-31.
30. Roux A-L, El Sayed F, Duffiet P, Bauer T, Heym B, Gaillard J-L, et al. Ruminococcus gnavus total hip arthroplasty infection in a 62-year-old man with ulcerative colitis. J Clin Microbiol. 2015;53:1428-30.
31. Fuentes S, Rossen NG, van der Spek MJ, Hartman JH, Huuskonen L, Korpela K, et al. Microbial shifts and signatures of long-term remission in ulcerative colitis after faecal microbiota transplantation. ISME J. 2017;11(8):1877-89.
32. Liu C, Finegold SM, Song Y, Lawson PA. Reclassification of Clostridium coccoides, Ruminococcus hansenii, Ruminococcus hydrogenotrophicus, Ruminococcus luti, Ruminococcus productus and Ruminococcus schinkii as Blautia coccoides gen. nov., comb. nov., Blautia hansenii comb. nov., Blautia hydrogenotrophica comb. nov., Blautia luti comb. nov., Blautia producta comb. nov., Blautia schinkii comb. nov. and description of Blautia wexlerae sp. nov., isolated from human faeces. Int J Syst Evol Microbiol. 2008;58:1896-902
33. Lawson PA, Finegold SM. Reclassification of Ruminococcus obeum as Blautia obeum comb. nov. Int J Syst Evol Microbiol. 2015;65:789-93.