Biogeography & environmental conditions shape bacteriophage-bacteria networks across the human microbiome

Abstract

19Viruses and bacteria are critical components of the human microbiome and play important roles in health and 20 disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing 21 them to two separate communities. Such approaches are unable to capture how these microbial communities 22 interact, such as through processes that maintain community robustness or allow phage-host populations 23 to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network 24 diversity throughout the human body. We built these community networks using a machine learning algorithm 25 to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to 26 paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We 27 organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness 28 across the human body. We observed evidence that gut and skin network structures were person-specific 29 and not conserved among cohabitating family members. High-fat diets appeared to be associated with 30 less connected networks. Network structure differed between skin sites, with those exposed to the external Author Summary 37The human microbiome, the collection of microbial communities that colonize the human body, is a crucial 38 component to health and disease. Two major components to the human microbiome are the bacterial and 39 viral communities. These communities have primarily been studied separately using metrics of community 40 composition and diversity. These approaches have failed to capture the complex dynamics of interacting 41 bacteria and phage communities, which frequently share genetic information and work together to maintain 42 ecosystem homestatsis (e.g. kill-the-winner dynamics). Removal of bacteria or phage can disrupt or even 43 collapse those ecosystems. Relationship-based network approaches allow us to capture this interaction 44 information. Using this network-based approach with three independent human cohorts, we were able to 45 present an initial understanding of how phage-bacteria networks differ throughout the human body, so as to 46 provide a baseline for future studies of how and why microbiome networks differ in disease states.

The core seafloor microbiome in the Gulf of Mexico is remarkably consistent and shows evidence of recovery from disturbance caused by major oil spills

“…, it was recognized that a regression‐based model may effectively reconstruct the relative abundances of microbial groups across these regions. A machine learning method, random forest regression, was employed that has previously been successful in population distribution models (Cutler et al ., ; Oppel and Huettmann, ; Smith et al ., ; Wei et al ., ; Bradter et al ., ; Lima‐Mendez et al ., ; Hannigan et al ., ). As stated in the methods section, the model was constructed using the variables water depth, sediment depth, latitude and longitude as proxies for carbon input, redox state and geographic variations due to riverine inputs and differing geochronology across the GoM (Brooks et al ., ).…”

The Landscape of Genetic Content in the Gut and Oral Human Microbiome

“…The following references appear in the Supplemental Information: Andrei et al, 2019;Ayling et al, 2018;Bredon et al, 2018;Cabaná s et al, 2018;Carlos et al, 2018;Chen et al, 2018;Cheng, 2018;Delgado et al, 2019;Delsuc et al, 2018;Dong et al, 2017;Flota, n.d.;Georganas et al, 2018;Gerner et al, 2018;Graham et al, 2017;Graham et al, 2018;Han et al, 2018;Hannigan et al, 2018aHannigan et al, , 2018bHuang et al, 2018;Jackman et al, 2017;Kleiner et al, 2017;Kroeger et al, 2018;Kusy et al, 2018;Learman et al, 2019;Li et al, 2018;Martin et al, 2019;Maus et al, 2018;Mizzi et al, 2017;Nurk et al, 2017;O'Leary et al, 2016;P€ arn€ anen et al, 2016;Patin et al, 2018;Pedron et al, 2019;Rebollar et al, 2018;Rengasamy, 2018;Rengasamy et al, 2017;Roux et al, 2017;Royalty and Steen, 2018;Schulz et al, 2018;Shiller et al, 2017;Souvorov et al, 2018;…”

The Spatial Heterogeneity of the Gut Limits Predation and Fosters Coexistence of Bacteria and Bacteriophages

“…Using phage-bacterial model systems, dynamics of the coexistence of predators (or parasites) and preys (or hosts) have been the subject of theoretical and experimental studies, mostly performed in vitro and in silico (Betts et al 2014, Brockhurst et al 2006, Hannigan et al 2018a, Lenski and Levin 1985, Weitz et al 2013. In vivo, the interaction of phages and bacteria in the mammalian gut has been explored in mice and pigs (Galtier et al 2016, Galtier et al 2017, Looft et al 2014, Maura et al 2012a, Maura et al 2012b, Weiss et al 2009.…”