title: Personalized microbial network inference via co-regularized spectral clustering.
abstract: We use Human Microbiome Project (HMP) cohort (Peterson et al., 2009) to infer personalized oral microbial networks of healthy individuals. To determine clustering of individuals with similar microbial profiles, co-regularized spectral clustering algorithm is applied to the dataset. For each cluster we discovered, we compute co-occurrence relationships among the microbial species that determine microbial network per cluster of individuals. The results of our study suggest that there are several differences in microbial interactions on personalized network level in healthy oral samples acquired from various niches. Based on the results of co-regularized spectral clustering we discover two groups of individuals with different topology of their microbial interaction network. The results of microbial network inference suggest that niche-wise interactions are different in these two groups. Our study shows that healthy individuals have different microbial clusters according to their oral microbiota. Such personalized microbial networks open a better understanding of the microbial ecology of healthy oral cavities and new possibilities for future targeted medication. The scripts written in scientific Python and in Matlab, which were used for network visualization, are provided for download on the website http://learning-machines.com/.
authors.affiliation: Top Institute Food and Nutrition, Wageningen, The Netherlands; Research Group Microbiology and Systems Biology, TNO Earth, Environmental and Life Sciences, Zeist, The Netherlands; Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Amsterdam, The Netherlands. Electronic address: sultan.imangaliyev@tno.nl.
authors.forename: Sultan
authors.initials: S
authors.lastname: Imangaliyev
authors.affiliation: Top Institute Food and Nutrition, Wageningen, The Netherlands; Research Group Microbiology and Systems Biology, TNO Earth, Environmental and Life Sciences, Zeist, The Netherlands.
authors.forename: Bart
authors.initials: B
authors.lastname: Keijser
authors.affiliation: Top Institute Food and Nutrition, Wageningen, The Netherlands; Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, Amsterdam, The Netherlands.
authors.forename: Wim
authors.initials: W
authors.lastname: Crielaard
authors.affiliation: Top Institute Food and Nutrition, Wageningen, The Netherlands; Research Group Microbiology and Systems Biology, TNO Earth, Environmental and Life Sciences, Zeist, The Netherlands.
authors.forename: Evgeni
authors.initials: E
authors.lastname: Tsivtsivadze
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D059013:Microbial Consortia; D064307:Microbiota / Q000235:genetics*
keywords: Metagenomics; Oral health; Personalized network; Spectral clustering