MetaMIS: A metagenomic microbial interaction simulator based on microbial community profiles

BMC Bioinformatics

Volumn 17, Issue 1, 2016, Pages

  Shaw, Grace Tzun Wen ^a   Pao, Yueh Yang ^a   Wang, Daryi ^a  

^a BIODIVERSITY RESEARCH CENTER   (Taiwan)

Author keywords

Lotka Volterra; Metagenomics; Network dynamics

Indexed keywords

BACTERIA;

BRAY-CURTIS DISSIMILARITY; INTERACTION INFORMATION; LOTKA-VOLTERRA; METAGENOMICS; MICROBIAL INTERACTIONS; NETWORK DYNAMICS; OPERATIONAL TAXONOMIC UNITS; USER-FRIENDLY PLATFORMS;

PREDATOR PREY SYSTEMS;

ALGORITHM; BACTERIUM; BIOLOGY; CLASSIFICATION; ECOLOGY; FECES; FEMALE; GENETICS; HUMAN; MALE; METAGENOME; MICROBIOLOGY; MICROFLORA; ORGANISMAL INTERACTION; PROCEDURES; SOFTWARE;

ALGORITHMS; BACTERIA; COMPUTATIONAL BIOLOGY; ECOLOGY; FECES; FEMALE; HUMANS; MALE; METAGENOME; MICROBIAL INTERACTIONS; MICROBIOTA; SOFTWARE;

EID: 84997173322     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-016-1359-0     Document Type: Article

References (35)

1. Gilbert JA, Meyer F, Jansson J, Gordon J, Pace N, Tiedje J, Ley R, Fierer N, Field D, Kyrpides N, et al. The earth microbiome project: meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010. Stand Genomic Sci. 2010;3(3):249-53.
2. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature. 2007;449(7164):804-10.
3. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature. 2006;444(7122):1022-3.
4. Kamada N, Seo SU, Chen GY, Nunez G. Role of the gut microbiota in immunity and inflammatory disease. Nat Rev Immunol. 2013;13(5):321-35.
5. Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012;490(7418):55-60.
6. Danovaro R, Corinaldesi C, Dell'anno A, Fuhrman JA, Middelburg JJ, Noble RT, Suttle CA. Marine viruses and global climate change. FEMS Microbiol Rev. 2011;35(6):993-1034.
7. Faust K, Raes J. Microbial interactions: from networks to models. Nat Rev Microbiol. 2012;10(8):538-50.
8. Stolyar S, Van Dien S, Hillesland KL, Pinel N, Lie TJ, Leigh JA, Stahl DA. Metabolic modeling of a mutualistic microbial community. Mol Syst Biol. 2007;3:92.
9. Friedman J, Alm EJ. Inferring correlation networks from genomic survey data. PLoS Comput Biol. 2012;8(9):e1002687.
10. Fisher CK, Mehta P. Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression. PLoS One. 2014;9(7):e102451.
11. Berry D, Widder S. Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Front Microbiol. 2014;5:219.
12. Kurtz ZD, Muller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA. Sparse and compositionally robust inference of microbial ecological networks. PLoS Comput Biol. 2015;11(5):e1004226.
13. Tsai KN, Lin SH, Liu WC, Wang D. Inferring microbial interaction network from microbiome data using RMN algorithm. BMC Syst Biol. 2015;9:54.
14. Jansen W. A permanence theorem for replicator and Lotka-Volterra systems. J Math Biol. 1987;25(4):411-22.
15. Coyte KZ, Schluter J, Foster KR. The ecology of the microbiome: networks, competition, and stability. Science. 2015;350(6261):663-6.
16. Dam P, Fonseca LL, Konstantinidis KT, Voit EO. Dynamic models of the complex microbial metapopulation of lake mendota. NPJ Syst Biol Appl. 2016;2:16007.
17. Marino S, Baxter NT, Huffnagle GB, Petrosino JF, Schloss PD. Mathematical modeling of primary succession of murine intestinal microbiota. Proc Natl Acad Sci U S A. 2014;111(1):439-44.
18. Mounier J, Monnet C, Vallaeys T, Arditi R, Sarthou AS, Helias A, Irlinger F. Microbial interactions within a cheese microbial community. Appl Environ Microbiol. 2008;74(1):172-81.
19. Bastian M, Heymann S, Jacomy M. Gephi: an open source software for exploring and manipulating networks. ICWSM. 2009;8:361-2.
20. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498-504.
21. Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, Knights D, Gajer P, Ravel J, Fierer N, et al. Moving pictures of the human microbiome. Genome Biol. 2011;12(5):R50.
22. Levy R, Borenstein E. Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules. Proc Natl Acad Sci U S A. 2013;110(31):12804-9.
23. Edelstein-Keshet L. Mathematical models in biology, vol. 46: Siam; 1988.
24. Selwyn S, Marsh P, Sethna TN. In vitro and in vivo studies on antibiotics from skin micrococcaceae. Springer: Penicillins and Cephalosporins; 1976. p. 391-6.
25. Gonzalez B, Diez V. The effect of nitrite and starter culture on microbiological quality of "chorizo"-a Spanish dry cured sausage. Meat Sci. 2002;60(3):295-8.
26. Hill DA, Hoffmann C, Abt MC, Du Y, Kobuley D, Kirn TJ, Bushman FD, Artis D. Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis. Mucosal Immunol. 2010;3(2):148-58.
27. Ogle J, Finck A, Aho E. Production of Antimicrobial Substances by Nonpathogenic Neisseria Species. FASEB J. 2015;29(1 Supplement):575-7.
28. Nhamoyebonde S, Leslie A. Biological differences between the sexes and susceptibility to tuberculosis. J Infect Dis. 2014;209 suppl 3:S100-6.
29. Neyrolles O, Quintana-Murci L. Sexual inequality in tuberculosis. PLoS Med. 2009;6(12):e1000199.
30. Yurkovetskiy L, Burrows M, Khan AA, Graham L, Volchkov P, Becker L, Antonopoulos D, Umesaki Y, Chervonsky AV. Gender bias in autoimmunity is influenced by microbiota. Immunity. 2013;39(2):400-12.
31. Zhang H, Liao X, Sparks JB, Luo XM. Dynamics of gut microbiota in autoimmune lupus. Appl Environ Microbiol. 2014;80(24):7551-60.
32. Angly FE, Dennis PG, Skarshewski A, Vanwonterghem I, Hugenholtz P, Tyson GW. CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction. Microbiome. 2014;2:11.
33. Hofbauer J, Sigmund K. Evolutionary games and population dynamics. UK: Cambridge university press; 1998.
34. Wold H. Partial least squares, Encyclopedia of statistical sciences. 1985.
35. Lance G, Williams W. Computer programs for hierarchical polythetic classification ("similarity analyses"). Comput J. 1966;9(1):60-4.