MetaModules identifies key functional subnetworks in microbiome-related disease

Bioinformatics

Volumn 32, Issue 11, 2016, Pages 1678-1685

  May, Ali ^a,b,c   Brandt, Bernd W ^b   El Kebir, Mohammed ^a,d,e   Klau, Gunnar W ^a,c,e   Zaura, Egija ^b   Crielaard, Wim ^b   Heringa, Jaap ^a,c   Abeln, Sanne ^a,c  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

^b UNIVERSITY OF AMSTERDAM   (Netherlands)

^c AMSTERDAM INSTITUTE FOR MOLECULES   (Netherlands)

^d Brown Univerity   (United States)

^e CWI   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; DENTAL CARIES; HUMAN; MICROFLORA;

ALGORITHMS; DENTAL CARIES; HUMANS; MICROBIOTA;

EID: 84973369805     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv526     Document Type: Article

References (50)

1. Abubucker, S. et al. (2012) Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput. Biol., 8, e1002358.
2. Ajdic, D. et al. (2002) Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen. Proc. Natl. Acad. Sci. USA, 99, 14434-14439.
3. Beisser, D. et al. (2010) BioNet: an R-Package for the functional analysis of biological networks. Bioinformatics, 26, 1129-1130.
4. Belda-Ferre, P. et al. (2012) The oral metagenome in health and disease. ISME J., 6, 46-56.
5. Bradshaw, D. J. et al. (1989) Effects of carbohydrate pulses and pH on population shifts within oral microbial communities in vitro. J. Dent. Res., 68, 1298-1302.
6. Burne, R. A. et al. (2012) Progress dissecting the oral microbiome in caries and health. Adv. Dent. Res., 24, 77-80.
7. Caspi, R. et al. (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res., 42, D459-D471.
8. Chan, P. P. and Lowe, T. M. (2009) GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res., 37, D93-D97.
9. Chang, M. C. et al. (2013) Butyrate induces reactive oxygen species production and affects cell cycle progression in human gingival fibroblasts. J. Periodont. Res., 48, 66-73.
10. Dejong, M. H. and Vanderhoeven, J. S. (1987) The growth of oral bacteria on saliva. J. Dent. Res., 66, 498-505.
11. Dinkla, K. et al. (2014) eXamine: exploring annotated modules in networks. BMC Bioinformatics, 15, 201.
12. Dittrich, M. T. et al. (2008) Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics, 24, I223-I231.
13. Edgar, R. C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
14. Franzosa, E. A. et al. (2014) Relating the metatranscriptome and metagenome of the human gut. Proc. Natl. Acad. Sci. USA, 111, E2329-E2338.
15. Harper, D. S. and Loesche, W. J. (1984) Growth and acid tolerance of human dental plaque bacteria. Arch. Oral. Biol., 29, 843-848.
16. Huson, D. H. et al. (2007) MEGAN analysis of metagenomic data. Genome Res, 17, 377-386.
17. Huttenhower, C. et al. (2012) Structure, function and diversity of the healthy human microbiome. Nature, 486, 207-214.
18. Ideker, T. et al. (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 18, S233-S240.
19. Jorth, P. et al. (2014) Metatranscriptomics of the human oral microbiome during health and disease. mBio, 5, e01012-e01014.
20. Kanehisa, M. and Goto, S. (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res., 28, 27-30.
21. Kiliç, A. O. et al. (2004) Involvement of Streptococcus gordonii beta-glucoside metabolism systems in adhesion, biofilm formation, and in vivo gene expression. J. Bacteriol., 186, 4246-4253.
22. Koopman, J. E. et al. (2015) Stability and resilience of oral microcosms toward acidification and Candida outgrowth by arginine supplementation. Microb. Ecol., 69, 422-433.
23. Kopylova, E. et al. (2012) SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics, 28, 3211-3217.
24. Langendijk, P. S. et al. (1999) Sulfate-reducing bacteria in periodontal pockets and in healthy oral sites. J. Clin. Periodontol., 26, 596-599.
25. Langendijk, P. S. et al. (2000) Sulfate-reducing bacteria in association with human periodontitis. J. Clin. Periodontol., 27, 943-950.
26. Leimena, M. M. et al. (2013) A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets. BMC Genomics, 14.
27. Levine, M. (1985) The role for butyrate and propionate in mediating Hela-cells growth-inhibition by human dental plaque fluid from adult periodontal-disease. Arch. Oral. Biol., 30, 155-159.
28. Ling, L. L. et al. (2015) A new antibiotic kills pathogens without detectable resistance. Nature, 517, 455-459.
29. Liu, B. and Pop, M. (2011) MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasets. BMC Proc., 5, S9.
30. Love, M. I. et al. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15, 550.
31. Luo, C. et al. (2013) A user's guide to quantitative and comparative analysis of metagenomic datasets. Meth. Enzymol., 531, 525-547.
32. Man, S. M. et al. (2011) The role of bacteria and pattern-recognition receptors in Crohn's disease. Nat. Rev. Gastro. Hepat., 8, 152-168.
33. Marchetti, A. et al. (2012) Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability. Proc. Natl. Acad. Sci. USA, 109, E317-E325.
34. Mitra, K. et al. (2013) Integrative approaches for finding modular structure in biological networks. Nat. Rev. Genet., 14, 719-732.
35. Morgan, X. C. et al. (2012) Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol., 13, R79.
36. Oliveira, A. P. et al. (2008) Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks. BMC Syst. Biol., 2, 17.
37. Patil, K. R. and Nielsen, J. (2005) Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc. Natl. Acad. USA, 102, 2685-2689.
38. Peterson, S. N. et al. (2014) Functional expression of dental plaque microbiota. Front. Cell. Infect. Microbiol., 4, 108.
39. Pihlstrom, B. L. et al. (2005) Periodontal diseases. Lancet, 366, 1809-1820.
40. Pounds, S. and Morris, S. W. (2003) Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values. Bioinformatics, 19, 1236-1242.
41. Qin, J. et al. (2012) A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature, 490, 55-60.
42. Quast, C. et al. (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res., 41, D590-D596.
43. Rath, C. M. and Dorrestein, P. C. (2012) The bacterial chemical repertoire mediates metabolic exchange within gut microbiomes. Curr. Opin. Microbiol., 15, 147-154.
44. Robinson, M. D. et al. (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139-140.
45. Selwitz, R. H. et al. (2007) Dental caries. Lancet, 369, 51-59.
46. Shannon, P. et al. (2003) Cytoscape: a software environment for integratedmodels of biomolecular interaction networks. Genome Res., 13, 2498-2504.
47. Singer, R. E. and Buckner, B. A. (1981) Butyrate and propionate-important components of toxic dental plaque extracts. Infect. Immunol., 32, 458-463.
48. Subramanian, A. et al. (2005) Gene set enrichment analysis: a knowledgebased approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. USA, 102, 15545-15550.
49. Turnbaugh, P. J. et al. (2009) A core gut microbiome in obese and lean twins. Nature, 457, 480-484.
50. Wang, Z. et al. (2011) Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature, 472, 57-63.