title: Investigating a holobiont: Microbiota perturbations and transkingdom networks.
abstract: The scientific community has recently come to appreciate that, rather than existing as independent organisms, multicellular hosts and their microbiota comprise a complex evolving superorganism or metaorganism, termed a holobiont. This point of view leads to a re-evaluation of our understanding of different physiological processes and diseases. In this paper we focus on experimental and computational approaches which, when combined in one study, allowed us to dissect mechanisms (traditionally named host-microbiota interactions) regulating holobiont physiology. Specifically, we discuss several approaches for microbiota perturbation, such as use of antibiotics and germ-free animals, including advantages and potential caveats of their usage. We briefly review computational approaches to characterize the microbiota and, more importantly, methods to infer specific components of microbiota (such as microbes or their genes) affecting host functions. One such approach called transkingdom network analysis has been recently developed and applied in our study. (1) Finally, we also discuss common methods used to validate the computational predictions of host-microbiota interactions using in vitro and in vivo experimental systems.
authors.affiliation: a College of Veterinary Medicine, Oregon State University , Corvallis , OR , USA.
authors.forename: Renee
authors.initials: R
authors.lastname: Greer
authors.affiliation: b College of Pharmacy, Oregon State University , Corvallis , OR , USA.
authors.forename: Xiaoxi
authors.initials: X
authors.lastname: Dong
authors.affiliation: b College of Pharmacy, Oregon State University , Corvallis , OR , USA.
authors.forename: Andrey
authors.initials: A
authors.lastname: Morgun
authors.affiliation: b College of Pharmacy, Oregon State University , Corvallis , OR , USA.
authors.forename: Natalia
authors.initials: N
authors.lastname: Shulzhenko
mesh_terms: D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001419:Bacteria / Q000187:drug effects* / Q000235:genetics / Q000378:metabolism; D001424:Bacterial Infections / Q000382:microbiology*; D019295:Computational Biology; D054884:Host-Pathogen Interactions / Q000187:drug effects*; D006801:Humans; D064307:Microbiota / Q000187:drug effects*
chemical_list: D000900:Anti-Bacterial Agents
keywords: antibiotics; bipartite betweenness centrality; germfree mice; holobiont; metagenomics; microbiome; microbiota; systems biology; transkingdom networks