More than 9,000,000 unique genes in human gut bacterial community: Estimating gene numbers inside a human body

PLoS ONE

Volumn 4, Issue 6, 2009, Pages

  Yang, Xing ^a,b   Xie, Lu ^a   Li, Yixue ^a,c,d   Wei, Chaochun ^a,c  

^a SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

^b TONGJI UNIVERSITY   (China)

^c SHANGHAI JIAO TONG UNIVERSITY   (China)

^d Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTEROIDES; CLOSTRIDIUM; CONTROLLED STUDY; ESCHERICHIA COLI; GENE NUMBER; GENOME ANALYSIS; INTESTINE FLORA; METAGENOMICS; MICROBIAL COMMUNITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE CONSTRUCTION METHOD; RNA SEQUENCE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; DNA SEQUENCE; GENETICS; HUMAN; INTESTINE; MICROBIOLOGY; SEQUENCE ALIGNMENT; THEORETICAL MODEL;

BACTERIA (MICROORGANISMS);

COMPUTATIONAL BIOLOGY; GENES, BACTERIAL; GENOME, BACTERIAL; HUMANS; INTESTINES; MODELS, GENETIC; MODELS, THEORETICAL; RNA, RIBOSOMAL, 16S; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 67650685282     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0006074     Document Type: Article

References (24)

1. Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, et al. (2000) Gene index analysis of the human genome estimates approximately 120,000 genes. Nat Genet 25: 239-240.
2. Fields C, Adams MD, White O, Venter JC (1994) How many genes in the human genome? Nat Genet 7: 345-346.
3. Das M, Burge CB, Park E, Colinas J, Pelletier J (2001) Assessment of the total number of human transcription units. Genomics 77: 71-78.
4. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
5. Wei C, Brent MR (2006) Using ESTs to Improve the Accuracy of de novo Gene Prediction. BMC Bioinformatics 7: 327.
6. Wei C, Lamesch P, Arumugam M, Rosenberg J, Hu P, et al. (2005) Closing in on the C. elegans ORFeome by Cloning TWINSCAN predictions. Genome Res 15: 577-582.
7. Lederberg J (2000) Infectious history. Science 288: 287-293.
8. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, et al. (2007) The human microbiome project. Nature 449: 804-810.
9. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, et al. (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031.
10. Backhed F, Ding H, Wang T, Hooper LV, Koh GY, et al. (2004) The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A 101: 15718-15723.
11. Backhed F, Manchester JK, Semenkovich CF, Gordon JI (2007) Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci U S A 104: 979-984.
12. Cani PD, Amar J, Iglesias MA, Poggi M, Knauf C, et al. (2007) Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 56: 1761-1772.
13. Holmes E, Loo RL, Stamler J, Bictash M, Yap IK, et al. (2008) Human metabolic phenotype diversity and its association with diet and blood pressure. Nature 453: 396-400.
14. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, et al. (2009) A core gut microbiome in obese and lean twins. Nature 457: 480-484.
15. Zhu J, Zhang B, Schadt EE (2008) A systems biology approach to drug discovery. Adv Genet 60: 603-635.
16. Chen Y, Zhu J, Lum PY, Yang X, Pinto S, et al. (2008) Variations in DNA elucidate molecular networks that cause disease. Nature 452: 429-435.
17. Backhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI (2005) Host-bacterial mutualism in the human intestine. Science 307: 1915-1920.
18. Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R (2005) The microbial pan-genome. Curr Opin Genet Dev 15: 589-594.
19. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009) GenBank. Nucleic Acids Res 37: D26-31.
20. Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, et al. (2007) The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 35: D169-172.
21. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-145.
22. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2005) At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71: 7724-7736.
23. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, et al. (2005) Diversity of the human intestinal microbial flora. Science 308: 1635-1638.
24. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, et al. (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A 102: 13950-13955.