title: Longitudinal Prediction of the Infant Gut Microbiome with Dynamic Bayesian Networks.
abstract: Sequencing of the 16S rRNA gene allows comprehensive assessment of bacterial community composition from human body sites. Previously published and publicly accessible data on 58 preterm infants in the Neonatal Intensive Care Unit who underwent frequent stool collection was used. We constructed Dynamic Bayesian Networks from the data and analyzed predictive performance and network characteristics. We constructed a DBN model of the infant gut microbial ecosystem, which explicitly captured specific relationships and general trends in the data: increasing amounts of Clostridia, residual amounts of Bacilli, and increasing amounts of Gammaproteobacteria that then give way to Clostridia. Prediction performance of DBNs with fewer edges were overall more accurate, although less so on harder-to-predict subjects (p = 0.045). DBNs provided quantitative likelihood estimates for rare abruptions events. Iterative prediction was less accurate (p < 0.001), but showed remarkable insensitivity to initial conditions and predicted convergence to a mix of Clostridia, Gammaproteobacteria, and Bacilli. DBNs were able to identify important relationships between microbiome taxa and predict future changes in microbiome composition from measured or synthetic initial conditions. DBNs also provided likelihood estimates for sudden, dramatic shifts in microbiome composition, which may be useful in guiding further analysis of those samples.
authors: Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA.
authors: Michael J
authors: MJ
authors: McGeachie
authors: Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA.
authors: Joanne E
authors: JE
authors: Sordillo
authors: Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA.
authors: Travis
authors: T
authors: Gibson
authors: The Jackson Laboratory for Genomic Medicine, Farmington, CT.
authors: George M
authors: GM
authors: Weinstock
authors: Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA.
authors: Yang-Yu
authors: YY
authors: Liu
authors: Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA.
authors: Diane R
authors: DR
authors: Gold
authors: Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA.
authors: Scott T
authors: ST
authors: Weiss
authors: Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA.
authors: Augusto
authors: A
authors: Litonjua
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D001499:Bayes Theorem; D000069196:Gastrointestinal Microbiome; D006801:Humans; D007231:Infant, Newborn; D016013:Likelihood Functions; D008137:Longitudinal Studies; D008962:Models, Theoretical; D012329:RNA, Bacterial / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S