Systems approaches to computational modeling of the oral microbiome

Abstract

Current microbiome research has generated tremendous amounts of data providing snapshots of molecular activity in a variety of organisms, environments, and cell types. However, turning this knowledge into whole system level of understanding on pathways and processes has proven to be a challenging task. In this review we highlight the applicability of bioinformatics and visualization techniques to large collections of data in order to better understand the information that contains related diet—oral microbiome—host mucosal transcriptome interactions. In particular, we focus on systems biology of Porphyromonas gingivalis in the context of high throughput computational methods tightly integrated with translational systems medicine. Those approaches have applications for both basic research, where we can direct specific laboratory experiments in model organisms and cell cultures, and human disease, where we can validate new mechanisms and biomarkers for prevention and treatment of chronic disorders.

The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health

“…This view takes into account that system components (modules, layers) cannot be considered from isolated perspectives[127]. In this regard, Meta-OMIC modeling and network-view approaches are just beginning to emerge to characterize oral microbiome dynamics and predict health and disease states [64, 126, 128]. However, there is a clear necessity for more applications of such models into risk assessment in the early oral cavity.…”

Recent Advances in Studies of Polymicrobial Interactions in Oral Biofilms

“…Computational analysis promises to add meaning to big data sets by combining metagenomic, transcriptomic, proteomic, and metabolomic studies, and building pathways to investigate global processes within whole communities [80,104]. At the same time, it is important not to forget the power of small, simple in vitro model systems that can illustrate the mechanisms of individual inter-species interactions that are relevant in vivo with elegance and class.…”

Oral Biosciences: The annual review 2014

“…Proteomics studies have proven very insightful in the revelation of biological events that are relevant to multispecies bacterial interactions [142]. Systems approaches, which have been successful in modeling and simulating gut microbiome-host intestinal transcriptome interactions, are gaining momentum in their application to the further understanding of oral microbiome interactions [143]. Moreover, an understanding of the complex interactions between the diverse oral microbial community and the host, as well as of the potential mechanism(s) whereby the oral microbiome impact a disease, is starting to emerge.…”