Tipping elements in the human intestinal ecosystem

Nature Communications

Volumn 5, Issue , 2014, Pages

  Lahti, Leo ^a,b   Salojärvi, Jarkko ^a   Salonen, Anne ^c   Scheffer, Marten ^b   De Vos, Willem M ^a,b,c  

^a UNIVERSITY OF HELSINKI   (Finland)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c UNIVERSITY OF HELSINKI   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

HOST FACTOR;

ABUNDANCE; AGING; BACTERIUM; MICROBIAL COMMUNITY; PHYLOGENETICS;

ADULT; AGED; ARTICLE; BACTEROIDES FRAGILIS; BODY MASS; CLOSTRIDIUM DIFFICILE; CONTROLLED STUDY; CROSS HYBRIDIZATION; DNA EXTRACTION; ECOSYSTEM HEALTH; FAECALIBACTERIUM PRAUSNITZII; FECES MICROFLORA; FEMALE; FOLLOW UP; GEOGRAPHIC DISTRIBUTION; HUMAN; INFECTION RISK; INTESTINE FLORA; LACTOBACILLUS PLANTARUM; MAJOR CLINICAL STUDY; MALE; METHANOBREVIBACTER; METHANOGENIC ARCHAEON; NONHUMAN; PHYLOGENY; PREVOTELLA MELANINOGENICA; PREVOTELLA ORALIS; BACTERIUM; BIODIVERSITY; CLASSIFICATION; COHORT ANALYSIS; ECOSYSTEM; GENETICS; GROWTH, DEVELOPMENT AND AGING; INTESTINE; ISOLATION AND PURIFICATION; MICROBIOLOGY; MICROFLORA; MIDDLE AGED;

ADULT; BACTERIA; BIODIVERSITY; COHORT STUDIES; ECOSYSTEM; FEMALE; HUMANS; INTESTINES; MALE; MICROBIOTA; MIDDLE AGED; PHYLOGENY;

EID: 84904014790     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms5344     Document Type: Article

References (45)

1. Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65 (2010).
2. Zoetendal, E. G., Rajilić-Stojanović, M. & de Vos, W. M. High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 57, 1605-1615 (2008).
3. de Vos, W. M. & de Vos, E. A. J. Role of the intestinal microbiome in health and disease: from correlation to causation. Nutr. Rev. 70, S45-S56 (2012).
4. Cho, I. & Blaser, M. J. The human microbiome: at the interface of health and disease. Nat. Rev. Genet. 13, 260-270 (2012).
5. Costello, E. K., Stagaman, K., Dethlefsen, L., Bohannan, B. J. M. & Relman, D. A. The application of ecological theory toward an understanding of the human microbiome. Science 336, 1255-1262 (2012).
6. The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214 (2012).
7. Jeffery, I. B., Claesson, M. J., O'Toole, P. W. & Shanahan, F. Categorization of the gut microbiota: enterotypes or gradients? Nat. Rev. Microbiol. 10, 591-592 (2012).
8. Scheffer, M. Critical Transitions in Nature and Society (Princeton Univ. Press, 2009).
9. Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174-180 (2011).
10. Koren, O. et al. A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput. Biol. 9, e1006863 (2013).
11. Lenton, T. M. et al. Tipping elements in the earth's climate system. Proc. Natl Acad. Sci. USA 105, 1786-1793 (2008). (Pubitemid 351439417)
12. Rajilić-Stojanović, M. et al. Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ. Microbiol. 11, 1736-1751 (2009).
13. Hirota, M., Holmgren, M., van Nes, E. H. & Scheffer, M. Global resilience of tropical forest and savanna to critical transitions. Science 334, 232-235 (2011).
14. Livina, V. N., Kwasniok, F. & Lenton, T. M. Potential Analysis reveals changing number of climate states during the last 60 kyr. Clim. Past 6, 77-82 (2010).
15. Tibshirani, R. & Walter, G. Cluster validation by prediction strength. J. Comput. Graph. Stat. 14, 511-528 (2005). (Pubitemid 41442147)
16. Lappi, J. et al. Intake of whole-grain and fiber-rich rye bread versus refined wheat bread does not differentiate intestinal microbiota composition in Finnish adults with metabolic syndrome. J. Nutr. 143, 648-655 (2013).
17. Salonen, A. et al. Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men. ISME J. doi:10.1038/ismej.2014.63 (2014).
18. David, L. A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 23, 559-563 (2014).
19. Martínez, I. et al. Gut microbiome composition is linked to whole grain-induced immunological improvements. ISME J. 7, 269-280 (2013).
20. Kato, H. et al. Colonisation and transmission of Clostridium difficile in healthy individuals examined by PCR ribotyping and pulsed-field gel electrophoresis. J. Med. Microbiol. 50, 720-727 (2001). (Pubitemid 32664902)
21. van Nood, E. et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N. Engl. J. Med. 368, 407-415 (2013).
22. Gough, E., Shaikh, H. & Manges, A. R. Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection. Clin. Infect. Dis. 53, 994-1002 (2011).
23. Scheffer, M. et al. Early-warning signals for critical transitions. Nature 461, 53-59 (2009).
24. Dridi, B., Henry, M., El Khéchine, A., Raoult, D. & Drancourt, M. High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS One 4, e7063 (2009).
25. Salonen, A. et al. Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J. Microbiol. Methods 81, 127-134 (2010).
26. Faust, K. et al. Microbial co-occurrence relationships in the human microbiome. PLoS Comput. Biol. 8, e1006606 (2012).
27. Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222-227 (2012).
28. Lozupone, C. & Knight, R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71, 8228-8235 (2005). (Pubitemid 41803949)
29. Chatelier, E. L. et al. Richness of human gut microbiome correlates with metabolic markers. Nature 500, 541-546 (2013).
30. Scheffer, M., Carpenter, S., Foley, J. A., Folke, C. & Walker, B. Catastrophic shifts in ecosystems. Nature 413, 591-596 (2001). (Pubitemid 32964052)
31. Lan, Y., Kriete, A. & Rosen, G. L. Selecting age-related functional characteristics in the human gut microbiome. Microbiome 1, 2 (2013).
32. Biagi, E. et al. Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians. PLoS ONE 5, e10667 (2010).
33. Rueffler, C., Van Dooren, T. J. M., Leimar, O. & Abrams, P. A. Disruptive selection and then what? Trends Ecol. Evol. 21, 238-245 (2006). (Pubitemid 43669032)
34. Faust, K. & Raes, J. Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10, 538-550 (2012).
35. Claesson, M. J. et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 488, 178-184 (2012).
36. Holmes, I., Harris, K. & Quince, C. Dirichlet multinomial mixtures: generative models for microbial metagenomics. PLoS ONE 7, e30126 (2012).
37. Lemon, K. P., Armitage, G. C., Relman, D. A. & Fischbach, M. A. Microbiota-targeted therapies: an ecological perspective. Sci. Transl. Med. 4, 137rv5 (2012).
38. Kuczynski, J. et al. Experimental and analytical tools for studying the human microbiome. Nat. Rev. Genet. 13, 47-58 (2011).
39. Claesson, M. J. et al. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS ONE 4, e6669 (2009).
40. Lahti, L., Torrente, A., Elo, L. L., Brazma, A. & Rung, J. A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases. Nucleic Acids Res. 41, e110 (2013).
41. Lahti, L., Elo, L. L., Aittokallio, T. & Kaski, S. Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays. IEEE/ACM Trans. Comput. Biol. Bioinform. 8, 217-225 (2011).
42. Scott, D. W. Multivariate Density Estimation: Theory, Practice, and Visualization (John Wiley & Sons, 1992).
43. Gower, J. C. Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53, 325-328 (1966).
44. Chen, J. et al. Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics 28, 2106-2113 (2012).
45. Dewulf, E. M. et al. Insight into the prebiotic concept: lessons from an exploratory, double blind intervention study with inulin-type fructans in obese women. Gut 62, 1112-1121 (2013).