Investigating microbial co-occurrence patterns based on metagenomic compositional data

Bioinformatics

Volumn 31, Issue 20, 2015, Pages 3322-3329

  Ban, Yuguang ^a   An, Lingling ^b,c   Jiang, Hongmei ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

^b UNIVERSITY OF ARIZONA   (United States)

^c University of Arizona   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOLOGY; HIGH THROUGHPUT SEQUENCING; HUMAN; IMMUNIZATION; IMMUNOLOGY; METAGENOMICS; MICROBIOLOGY; PATHOPHYSIOLOGY; PROCEDURES; SKIN; SPECIES DIFFERENCE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; IMMUNIZATION; METAGENOMICS; SKIN; SPECIES SPECIFICITY;

EID: 84946878516     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv364     Document Type: Article

References (24)

1. Aitchison, J. (1981) A new approach to null correlations of proportions. J. Int. Assoc. Math. Geol., 13, 175-189.
2. Brook, I. et al. (1984) Synergistic effect of bacteroides, Clostridium, Fusobacterium, anaerobic cocci, and aerobic bacteria on mortality and induction of subcutaneous abscesses in mice. J. Infect. Dis., 149, 924-928.
3. Bryan, L.E. et al. (1979) Mechanism of aminoglycoside antibiotic resistance in anaerobic bacteria: Clostridium perfringens and Bacteroides fragilis. Antimicrob. Agents Chemother., 15, 7-13.
4. Chaffron, S. et al. (2010) A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res., 20, 947-959.
5. Chen, J., Li, H.Z. (2013) Variable selection for sparse Dirichlet-Multinomial regression with an application to microbiome data analysis. Ann Appl Stat., 7, 418-442.
6. Egozcue, J.J. et al. (2003) Isometric logratio transformations for compositional data analysis. Math Geol., 35, 279-300.
7. Faust, K. et al. (2012) Microbial co-occurrence relationships in the human microbiome. PLoS Comput. Biol., 8, e1002606.
8. Freilich, S. et al. (2010) The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucleic Acids Res., 38, 3857-3868.
9. Friedman, J., Alm, E.J. (2012) Inferring correlation networks from genomic survey data. PLoS Comput. Biol., 8, e1002687.
10. Hall-Stoodley, L. et al. (2004) Bacterial biofilms: from the natural environment to infectious diseases. Nat. Rev. Microbiol., 2, 95-108.
11. Hojo, K. et al. (2009) Bacterial interactions in dental biofilm development. J. Dent. Res., 88, 982-990.
12. Katsuyama, C. et al. (2009) Complementary cooperation between two syntrophic bacteria in pesticide degradation. J. Theor. Biol., 256, 644-654.
13. Kwaszewska, A.K. et al. (2006) Hydrophobicity and biofilm formation of lipophilic skin corynebacteria. Pol. J. Microbiol., 55, 189-193.
14. Kurtz, Z.D. et al. (2015) Sparse and compositionally robust inference of microbial ecological networks. PLoS Comput. Biol., 11, e1004226.
15. Leroy, S. et al. (2009) Genetic diversity and biofilm formation of Staphylococcus equorum isolated from naturally fermented sausages and their manufacturing environment. Int. J. Food Microbiol., 134, 46-51.
16. Lovell, D. et al. (2010) Caution! compositions! technical report and companion software (publicationtechnical). Technical Report EP10994, CSIRO.
17. Meinshausen, N., Bü hlmann, P. (2010) Stability selection. J. R. Stat. Soc. Ser. B Stat. Methodol., 72, 417-473.
18. Muscholl-Silberhorn, A. et al. (1997) Why does Staphylococcus aureus secrete an Enterococcus faecalis-specific pheromone. FEMS Microbiol. Lett., 157, 261-266.
19. Orphan, V.J. et al. (2001) Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science, 293, 484-487.
20. Otto, M. (2008) Staphylococcal biofilms. Curr. Topics Microbiol. Immunol., 322, 207-228.
21. Shah, R.D., Samworth, R.J. (2013) Variable selection with error control: another look at Stability Selection. J. R. Stat. Soc. Ser. B, 75, 55-80.
22. Srinivas, G. et al. (2013) Genome-wide mapping of gene-microbiota interactions in susceptibility to autoimmune skin blistering. Nat. Commun., 4, 2462.
23. Tibshirani, R. (1996) Regression shrinkage and selection via the Lasso. J. R. Stat. Soc. B Methodol., 58, 267-288.
24. Wexler, H.M. (2007) Bacteroides: the good, the bad, and the nitty-gritty. Clin. Microbiol. Rev., 20, 593-621.