Longitudinal Prediction of the Infant Gut Microbiome with Dynamic Bayesian Networks

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Mcgeachie, Michael J ^a   Sordillo, Joanne E ^a   Gibson, Travis ^a   Weinstock, George M ^b   Liu, Yang Yu ^a   Gold, Diane R ^a   Weiss, Scott T ^a   Litonjua, Augusto ^a  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

^b JACKSON LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RNA 16S;

BACTERIUM; BAYES THEOREM; CLASSIFICATION; GENETICS; HUMAN; INTESTINE FLORA; ISOLATION AND PURIFICATION; LONGITUDINAL STUDY; NEWBORN; SEQUENCE ANALYSIS; STATISTICAL MODEL; THEORETICAL MODEL;

BACTERIA; BAYES THEOREM; GASTROINTESTINAL MICROBIOME; HUMANS; INFANT, NEWBORN; LIKELIHOOD FUNCTIONS; LONGITUDINAL STUDIES; MODELS, THEORETICAL; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, RNA;

EID: 84957566691     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep20359     Document Type: Article

References (35)

1. Ley, R. E. et al. Evolution of mammals and their gut microbes. Science 320, 1647-1651 (2008).
2. Muegge, B. D. et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332, 970-974 (2011).
3. LeBlanc, J. G. et al. Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Curr. Opin. Biotechnol. 24, 160-168 (2013).
4. Carmody, R. N., Turnbaugh, P. J. Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics. J. Clin. Invest. 124, 4173-4181 (2014).
5. Bengmark, S. Gut microbiota, immune development and function. Pharmacol. Res. 69, 87-113 (2013).
6. Weng, M., Walker, W. A. The role of gut microbiota in programming the immune phenotype. J. Dev. Orig Health. Dis. 4, 203-214 (2013).
7. West, C. E. et al. The gut microbiota and inflammatory noncommunicable diseases: associations and potentials for gut microbiota therapies. J. Allergy Clin. Immunol. 135, 3-13, quiz 14 (2015).
8. Wopereis, H., Oozeer, R., Knipping, K., Belzer, C., Knol, J. The first thousand days-intestinal microbiology of early life: establishing a symbiosis. Pediatr. Allergy Immunol. 25, 428-438 (2014).
9. Adlerberth, I. Factors influencing the establishment of the intestinal microbiota in infancy. Nestle Nutr. Workshop Ser. Pediatr. Program. 62, 13-29; discussion 29-33 (2008).
10. Adlerberth, I., Wold, A. E. Establishment of the gut microbiota in Western infants. Acta Paediatr. 98, 229-238 (2009).
11. Ardissone, A. N. et al. Meconium microbiome analysis identifies bacteria correlated with premature birth. PLoS One 9, e90784 (2014).
12. Wassenaar, T. M., Panigrahi, P. Is a foetus developing in a sterile environment? Lett. Appl. Microbiol. 59, 572-579 (2014).
13. La Rosa, P. S. et al. Patterned progression of bacterial populations in the premature infant gut. Proc. Natl. Acad. Sci. USA. 111, 12522-12527 (2014).
14. Faust, K., Raes, J. Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10, 538-550 (2012).
15. Ljung, L. System identification: theory for the user (1999).
16. Fisher, C. K., Mehta, P. Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression. PLoS One 9, e102451 (2014).
17. Stein, R. R. et al. Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLoS Comput. Biol. 9, e1003388 (2013).
18. Marino, S., Baxter, N. T., Huffnagle, G. B., Petrosino, J. F., Schloss, P. D. Mathematical modeling of primary succession of murine intestinal microbiota. Proc. Natl. Acad. Sci. USA. 111, 439-444 (2014).
19. Bucci, V., Bradde, S., Biroli, G., Xavier, J. B. Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota. PLoS Comput. Biol. 8, e1002497 (2012).
20. Åström, K. J., Eykhoff, P. System identification-a survey. Automatica 7, 123-162 (1971).
21. Gerber, G. K., Onderdonk, A. B., Bry, L. Inferring dynamic signatures of microbes in complex host ecosystems. PLoS Comput. Biol. 8, e1002624 (2012).
22. Larjo, A., Shmulevich, I., Lahdesmaki, H. Structure learning for Bayesian networks as models of biological networks. Methods Mol. Biol. 939, 35-45 (2013).
23. Milns, I., Beale, C. M., Smith, V. A. Revealing ecological networks using Bayesian network inference algorithms. Ecology 91, 1892-1899 (2010).
24. van Gerven, M. A., Taal, B. G., Lucas, P. J. Dynamic Bayesian networks as prognostic models for clinical patient management. J. Biomed. Inform. 41, 515-529 (2008).
25. Zhu, J. et al. Characterizing dynamic changes in the human blood transcriptional network. PLoS Comput. Biol. 6, e1000671 (2010).
26. Pe'er, D., Regev, A., Elidan, G., Friedman, N. Inferring subnetworks from perturbed expression profiles. Bioinformatics 17 Suppl 1, S215-24 (2001).
27. McGeachie, M. J. CGBayesNets: Conditional Guassian Bayesian Networks package. (Accessed June 14, 2014, at www.cgbayesnets. com) (2013).
28. McGeachie, M. J., Chang, H. H., Weiss, S. T. CGBayesNets: conditional Gaussian Bayesian network learning and inference with mixed discrete and continuous data. PLoS Comput. Biol. 10, e1003676 (2014).
29. Kass, R. E., Raftery, A. E. Bayes Factors. Journal of the American Statistical Association 90, 773-795 (1995).
30. Dogra, S. et al. Dynamics of infant gut microbiota are influenced by delivery mode and gestational duration and are associated with subsequent adiposity. MBio 6, 10.1128/mBio.02419-14 (2015).
31. Koenig, J. E. et al. Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl. Acad. Sci. USA. 108 Suppl 1, 4578-4585 (2011).
32. Sharon, I. et al. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res. 23, 111-120 (2013).
33. Trosvik, P., Stenseth, N. C., Rudi, K. Convergent temporal dynamics of the human infant gut microbiota. ISME J. 4, 151-158 (2010).
34. Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174-180 (2011).
35. Dethlefsen, L., et al. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6, 2383-2400 (2008).