Author Correction: A catalog of the mouse gut metagenome (Nat. Biotechnol (2015), 33, 10, (1103-1108), 10.1038/nbt.3353);A catalog of the mouse gut metagenome

Nature Biotechnology

Volumn 33, Issue 10, 2015, Pages 1103-1108

  Xiao, Liang ^a   Feng, Qiang ^a,b   Liang, Suisha ^a   Sonne, Si Brask ^b   Xia, Zhongkui ^a   Qiu, Xinmin ^a   Li, Xiaoping ^a   Long, Hua ^c   Zhang, Jianfeng ^a   Zhang, Dongya ^a   Liu, Chuan ^a   Fang, Zhiwei ^a   Chou, Joyce ^c   Glanville, Jacob ^c   Hao, Qin ^b   Kotowska, Dorota ^b   Colding, Camilla ^b   Licht, Tine Rask ^d   Wu, Donghai ^e   Yu, Jun ^f   Sung, Joseph Jao Yiu ^f   Liang, Qiaoyi ^f   Li, Junhua ^a   Jia, Huijue ^a   Lan, Zhou ^a   Tremaroli, Valentina ^g   Dworzynski, Piotr ^d   Nielsen, H Bjørn ^d   Bäckhed, Fredrik ^g,h   Doré, Joël ^i,j   Le Chatelier, Emmanuelle ^j   Ehrlich, S Dusko ^j,k   Lin, John C ^c   Arumugam, Manimozhiyan ^a,h   Wang, Jun ^a,b,l,m   Madsen, Lise ^a,b,n   Kristiansen, Karsten ^a,b   more..

^a BGI SHENZHEN   (China)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c PFIZER INC   (United States)

^d TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^e GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH   (China)

^f and Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics   (Hong Kong)

^g UNIVERSITY OF GOTHENBURG   (Sweden)

^h Capital Region   (Denmark)

ⁱ CEMAGREF   (France)

^j University of Paris Saclay   (France)

^k GUY S HOSPITAL   (United Kingdom)

^l KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

^m MACAU UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Macao)

ⁿ INSTITUTE OF MARINE RESEARCH   (Norway)

more..

Author keywords

[No Author keywords available]

Indexed keywords

MAMMALS;

FECAL SAMPLES; GENETIC BACKGROUNDS; HIGH-FAT DIET; HUMAN GUTS; METAGENOMES; MICROBIOME; MOUSE STRAIN; NON-REDUNDANT;

GENE ENCODING;

ANIMAL TISSUE; ARTICLE; BACTERIAL STRAIN; DNA LIBRARY; DNA SEQUENCE; INTESTINE; METAGENOME; MICROBIOME; MOUSE; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS; ANIMAL; BACTERIAL GENOME; BACTERIUM; CHROMOSOME MAP; GENETIC DATABASE; GENETICS; HUMAN; METABOLISM; MICROBIOLOGY; MICROFLORA; PROCEDURES; PUBLICATION; SPECIES DIFFERENCE;

BACTERIAL PROTEIN;

ANIMALS; BACTERIA; BACTERIAL PROTEINS; CATALOGS AS TOPIC; CHROMOSOME MAPPING; DATABASES, GENETIC; GENOME, BACTERIAL; HUMANS; INTESTINES; MICROBIOTA; SPECIES SPECIFICITY;

EID: 84943607837     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt0119-102a     Document Type: Erratum

References (46)

1. Cho, I. and Blaser, M.J. The human microbiome: at the interface of health and disease. Nat. Rev. Genet. 13, 260-270 (2012).
2. Clemente, J.C., Ursell, L.K., Parfrey, L.W. and Knight, R. The impact of the gut microbiota on human health: an integrative view. Cell 148, 1258-1270 (2012).
3. Tremaroli, V. and Bäckhed, F. Functional interactions between the gut microbiota and host metabolism. Nature 489, 242-249 (2012).
4. Ridaura, V.K. et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341, 1241214 (2013).
5. Kamada, N., Seo, S.-U., Chen, G.Y. and Nuñez, G. Role of the gut microbiota in immunity and inflammatory disease. Nat. Rev. Immunol. 13, 321-335 (2013).
6. Cotillard, A. et al. ANR MicroObes consortium. Dietary intervention impact on gut microbial gene richness. Nature 500, 585-588 (2013).
7. Le Chatelier, E. et al. MetaHIT consortium. Richness of human gut microbiome correlates with metabolic markers. Nature 500, 541-546 (2013).
8. Ahern, P.P., Faith, J.J. and Gordon, J.I. Mining the human gut microbiota for effector strains that shape the immune system. Immunity 40, 815-823 (2014).
9. Huttenhower, C., Kostic, A.D. and Xavier, R.J. Inflammatory bowel disease as a model for translating the microbiome. Immunity 40, 843-854 (2014).
10. Faith, J.J., Ahern, P.P., Ridaura, V.K., Cheng, J. and Gordon, J.I. Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice. Sci. Transl. Med. 6, 220ra11 (2014).
11. Subramanian, S. et al. Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature 510, 417-421 (2014).
12. Thaiss, C.A. et al. Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis. Cell 159, 514-529 (2014).
13. Zhang, C. et al. Structural modulation of gut microbiota in life-long calorie-restricted mice. Nat. Commun. 4, 2163 (2013).
14. Qin, J. et al. MetaHIT Consortium. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65 (2010).
15. Li, J. et al. An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32, 834-841 (2014).
16. Gerlach, W. and Stoye, J. Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res. 39, e91 (2011).
17. Zhang, X. et al. Structural changes of gut microbiota during berberine-mediated prevention of obesity and insulin resistance in high-fat diet-fed rats. PLoS One 7, e42529 (2012).
18. Everard, A. et al. Microbiome of prebiotic-treated mice reveals novel targets involved in host response during obesity. ISME J. 8, 2116-2130 (2014).
19. Qin, J. et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490, 55-60 (2012).
20. Nielsen, H.B. et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat. Biotechnol. 32, 822-828 (2014).
21. Jensen, L.J. et al. eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res. 36, D250-D254 (2008).
22. Ogata, H. et al. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 27, 29-34 (1999).
23. Cantarel, B.L. et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37, D233-D238 (2009).
24. Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P.M. and Henrissat, B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42, D490-D495 (2014).
25. Anderson, M.J. A new method for non-parametric multivariate analysis of variance. Austral. Ecol. 26, 32-46 (2001).
26. McArdle, B.H. and Anderson, M.J. Fitting multivariate models to community data: A comment on distance-based redundancy analysis. Ecology 82, 290-297 (2001).
27. Zhao, L. The gut microbiota and obesity: from correlation to causality. Nat. Rev. Microbiol. 11, 639-647 (2013).
28. Zhang, C. et al. Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice. ISME J. 4, 232-241 (2010).
29. Zhang, C. et al. Structural resilience of the gut microbiota in adult mice under high-fat dietary perturbations. ISME J. 6, 1848-1857 (2012).
30. Suez, J. et al. Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature 514, 181-186 (2014).
31. Schwab, C. et al. Longitudinal study of murine microbiota activity and interactions with the host during acute inflammation and recovery. ISME J. 8, 1101-1114 (2014).
32. Lacombe, A. et al. Lowbush wild blueberries have the potential to modify gut microbiota and xenobiotic metabolism in the rat colon. PLoS One 8, e67497 (2013).
33. Friswell, M.K. et al. Site and strain-specific variation in gut microbiota profiles and metabolism in experimental mice. PLoS One 5, e8584 (2010).
34. Ley, R.E. et al. Obesity alters gut microbial ecology. Proc. Natl. Acad. Sci. USA 102, 11070-11075 (2005).
35. Turnbaugh, P.J. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027-1031 (2006).
36. Hildebrand, F. et al. Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice. Genome Biol. 14, R4 (2013).
37. Turnbaugh, P.J., Bäckhed, F., Fulton, L. and Gordon, J.I. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3, 213-223 (2008).
38. Turnbaugh, P.J. et al. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci. Transl. Med. 1, 6ra14 (2009).
39. Wu, G.D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105-108 (2011).
40. Patrone, V. et al. Short-term modifications in the distal gut microbiota of weaning mice induced by a high-fat diet. Microbiology 158, 983-992 (2012).
41. Parks, B.W. et al. Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice. Cell Metab. 17, 141-152 (2013).
42. David, L.A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559-563 (2014).
43. Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1, 18-23 (2012).
44. Kent, W.J. BLAT-the BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
45. Altschul, S.F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
46. Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A.C. and Kanehisa, M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182-W185 (2007).