Global profiling of carbohydrate active enzymes in human gut microbiome

PLoS ONE

Volumn 10, Issue 11, 2015, Pages

  Bhattacharya, Tanudeep ^a   Ghosh, Tarini Shankar ^b   Mande, Sharmila S ^a  

^a Tain Square ^*

^b TATA CONSULTANCY SERVICES   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CARBOHYDRATE ACTIVE ENZYME; GH1 PROTEIN; GH3 PROTEIN; MICROBIAL ENZYME; UNCLASSIFIED DRUG; CARBOHYDRATE DIET; ESTERASE; GLYCOSIDASE; LYASE;

AGE; ARTICLE; BIFIDOBACTERIUM; BODY MASS; CARBOHYDRATE METABOLISM; COMPUTER MODEL; CORRELATIONAL STUDY; DIETARY INTAKE; ENZYME ANALYSIS; ETHNIC DIFFERENCE; FIRMICUTES; GEOGRAPHIC ORIGIN; HUMAN; INTESTINE FLORA; MICROBIAL COMMUNITY; NONHUMAN; OBESITY; PROTEIN FUNCTION; PROTEIN LOCALIZATION; TREND STUDY; ADULT; CARBOHYDRATE DIET; CHILD; GENETICS; METABOLISM; MICROFLORA;

ADULT; AGE FACTORS; CARBOHYDRATE METABOLISM; CHILD; DIETARY CARBOHYDRATES; ESTERASES; GASTROINTESTINAL MICROBIOME; GLYCOSIDE HYDROLASES; HUMANS; LYASES; MICROBIOTA;

EID: 84952650656     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0142038     Document Type: Article

References (30)

1. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010; 464(7285):59-65.
2. Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. Microbial degradation of complex carbohydrates in the gut. Gut Microbes. 2012; 3(4): 289-306.
3. Brandley BK, Schnaar RL. Cell-surface carbohydrates in cell recognition and response. J Leukoc Biol. 1986; 40(1): 97-111.
4. Hooper LV, Gordon JI. Glycans as legislators of host-microbial interactions: spanning the spectrum from symbiosis to pathogenicity. Glycobiology. 2001; 11(2): 1R-10R.
5. Hölemann A, Seeberger PH. Carbohydrate diversity: synthesis of glycoconjugates and complex carbohydrates. Current opinion in biotechnology. 2004; 15(6): 615-622.
6. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic acids research. 2009; 37. Suppl 1: D233-D238.
7. Lombard V, GolacondaRamulu H, Drula E, Coutinho PM, Henrissat B. The Carbohydrate-active enzymes database (CAZy) in 2013. Nucleic acids research. 2014; 42: D490-D495.
8. Xu J, Bjursell MK, Himrod J, Deng S, Carmichael LK, Chiang HC, et al. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science. 2003; 299(5615): 2074-6.
9. El Kaoutari A, Armougom F, Leroy Q, Vialettes B, Million M, Raoult D, et al. Development and Validation of a Microarray for the Investigation of the CAZymes Encoded by the Human Gut Microbiome. PLOS One. 2013; 8(12):e84033.
10. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006; 444(7122): 1027-131.
11. Turnbaugh PJ, Gordon JI. The core gut microbiome, energy balance and obesity. J. Physiol. 2009; 587 (17): 4153-4158.
12. Tsai F, Coyle WJ. The microbiome and obesity: is obesity linked to our gut flora? Current gastroenterology reports. 2009; 11(4): 307-313.
13. El Kaoutari A, Armougom F, Gordon JI, Raoult D, Henrissat B. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nature reviews Microbiology. 2013; 11(7): 497-504.
14. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. A core gut microbiome in obese and lean twins. Nature. 2009; 457(7228): 480-484.
15. Ghosh TS, Gupta SS, Bhattacharya T, Yadav D, Barik A, Chowdhury A, et al. Gut Microbiomes of Indian Children of Varying Nutritional Status. PLOS One. 2014; 9(4): e95547.
16. Gupta SS, Mohammed MH, Ghosh TS, Kanungo S, Nair GB, Mande SS. Metagenome of the gut of a malnourished child. Gut Pathog. 2011; 3:7.
17. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, et al. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci U S A. 2011; 108(1):4578-85.
18. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2014; 486(7402):222-7.
19. Ghosh TS, Gupta SS, Nair GB, Mande SS. In silico analysis of antibiotic resistance genes in the gut microflora of individuals from diverse geographies and age-groups. PLOS One. 2013; 8(12):e83823.
20. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A. 2010; 107(33):14691-6.
21. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, et al. Enterotypes of the human gut microbiome. Nature. 2011; 1473(7346):174-80 (2011).
22. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10.
23. Li W, Jaroszewski L, Godzik A. Clustering of highly homologous sequences to reduce the size of large protein database. Bioinformatics. 2001; 17:282-283.
24. Cantarel BL, Lombard V, Henrisaat B. Complex Carbohydrate Utilization by the Healthy Human Microbiome. PLOS One. 2012; 7(6):e28742.
25. Gini C. On the Measure of Concentration with Special Reference to Income and Statistics. Colorado College Publication. General Series. 1936. 208: 73-79.
26. Sharma AR. Using GINI Coefficients for analysing distribution of community forests in Nepal by development and ecological reasons. International Journal of Social Forestry (IJSF). 2010. 3(1):17-27.
27. Damgaard C, Weiner J. Describing inequality in plant size or fecundity. Ecology. 2000. 81(4): 1139-1142.
28. Baker M, Rayens W. Partial Least squares for discrimination. J. Chemometrics. 2003; 17:166-173.
29. Abdi H, Williams LJ. Principal Components Analysis.' Wiley Interdisciplinary reviews: Computational statistics (2010) 2.
30. Parks DH, Beiko RG. Identifying biologically relevant differences between metagenomic communities. Bioinformatics. 2010; 26(6):715-21.