The Proceedings of the Eighth International Conference on Creationism (2018)

Francis, J.W., M. Ingle, and T.C. Wood. 2018. Bacteriophages as beneficial regulators of the mammalian microbiome. In Proceedings of the Eighth International Conference on Creationism , ed. J.H. Whitmore, pp. 152–157. Pittsburgh, Pennsylvania: Creation Science Fellowship. BACTERIOPHAGES AS BENEFICIAL REGULATORS OF THE MAMMALIAN MICROBIOME Joseph W. Francis , The Master’s University, 21726 Placerita Canyon Rd, Santa Clarita, CA 91321, jfrancis@masters.edu Matthew Ingle , The Master’s University, 27126 Placerita Canyon Rd, Santa Clarita, CA 91321, mingle@masters.edu Todd Charles Wood , Core Academy of Science P.O. Box 1076 Dayton, TN 3732, tcw@coresci.org ABSTRACT Much of the research on viruses has concentrated on their disease causing ability. The creation model biomatrix theory predicts that viruses play a beneficial role in cells and organisms. In this report we present a new theory which proposes that mammalian phages (bacteriophages), the most abundant organism associated with mammals, guard and regulate growth of the mammalian microbiome. We base this theory on nearly a century of published evidence that demonstrates that phage can insert into the bacterial genome and cover the surface of bacteria. We propose that this “cloaking” of the bacterial cell surface is an elegant mechanism whereby the normal flora bacteria are protected from immune detection and pathogenic bacteria can be directly lysed by the same phage. Additionally, both phage genome integration and cloaking can be used to prevent normal flora bacteria from conversion to a pathogenic state. Further support for the phage cloaking aspect of our theory has been demonstrated in recent studies which show that phage proteins bind specifically to microbial-associated molecular patterns (MAMPs), which are known to be the major ligands that activate the mammalian immune system. Although these phenomena have been documented separately over decades, we postulate for the first time that these functions work together to promote the integrity of the mammalian microbiome. KEY WORDS virus, bacteriophage, virome, microbiome, biomatrix, bacteriome, phage Copyright 2018 Creation Science Fellowship, Inc., Pittsburgh, Pennsylvania, USA www.creationicc.org 152 INTRODUCTION Creationists have noted that the exquisite design in structural composition, life-cycle and genetic control within viruses suggests that they were created as part of God’s original good creation (Bergman 1999, 2002; Davidheiser 1965; Coppedge 2011; Doyle 2008; Francis 2003, 2008; Greunke 2004; Kim 2006, 2007, 2008; Liu and Soper 2009; Liu 2007, 2015; Larson 2000; Wood 2003; Peet 2006; Sarfati 2008). Relatedly the biomatrix theory is a creation theory postulating that the microbes (including viruses) that exist on earth perform beneficial activities consistent with their good creation, with most bacteria involved in life sustaining biogeochemical cycles (Francis 2003). Instances of beneficial viral activity however are more difficult to document. Although viruses display design features at the molecular-genetic level, they are often viewed as parasitic (Lucas and Wood 2006) and there is a lack of in-depth analysis and theory building in the creationist literature regarding viral function within the biomatrix. A fruitful approach to determining viral function within the biomatrix may be to assess animal associated viruses because animals possess some of the most densely populated biomatrix communities. Furthermore, the biblical creation model suggests that community is an important part of the living world, and assessing viral functionwithin the larger community ofmulticellular organisms may aid in determining the “good” function of viruses (Francis 2009). In this report we analyze the role of bacteriophages associated with mammalian commensual bacteria (the microbiome). PHAGES AND THE BIOMATRIX Biomatrix theory predicts that all prokaryote and eukaryote cells possess multiple viral symbionts or parasites. One major function of phages in the biomatrix appears to be the control of bacterial populations (Francis 2003, Gruenke 2004). Two examples of population control by phages in the marine biomatrix are instructive and may help to formulate hypotheses about the role of phages in the mammalian microbiome. In one example, a vibriophage is known to decrease the population of Vibrio cholerae bacteria in the ocean, the causative agent of cholera. Cholera is often associated with weather patterns that produce monsoon rains, which are postulated to lower the vibriophage populations and correspondingly increase Vibrio cholerae populations (Francis 2013; Faruque 2005). Secondly, cyanophages can influence the population of cyanobacteria which are one of the most populous carbon fixers on earth (Shestakov and Karbysheva 2015). Given that phages control populations of the free living microbiome we predict that mammalian associated phages may play a similar role in the mammalian microbiome. PHAGES AND THE MAMMALIAN MICROBIOME The human bacteriome is composed of at least 50 trillion cells (current theory predicts that there are about one bacterium associated with each human body cell) and each bacterial cell may be associated with at up to 10 viral partners (Dewart 2016; Virgin 2014). Thus we predict that there may be greater than 500 trillion viruses on the adult human body. Phages are the most abundant virus associated with mammals and yet they are largely ignored as members of the mammalian