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

virome. We can readily postulate that each bacterial species in the mammalian microbiome is infected or associated with multiple species of phage (Youle 2017). Given that there are thousands of bacterial species in the mammalian microbiome we could then postulate that there are tens of thousands of mammalian associated phage species and strains (Dutilh 2014; Kahrstrom 2013; Mirzaei 2017; Pride 2012). We would like to propose in this communication, for the first time, that phages play a role in maintaining the mammalian microbiome in several ways including protecting the microbiome genome, shielding the microbiome from the mammalian immune system, and protecting the mammalian host from pathogens and life- threatening virulence factors harbored in the microbiome itself. 1. Phages guard mammalian microbiome genomes, a recently derived concept consistent with biomatrix theory E.coli phages were the first phages studied, and hundreds of species have now been identified. Among the first phages discovered was the E.coli lambda phage discovered in 1950 by Esther Lederberg (Lederberg 1953). The lambda phage was discovered when bacteria growing as a lawn on a plate were lysed (viewed as a clear spot or plaque on the plate) when the bacterial plate culture was exposed to ultraviolet light. This is a fascinating temperate (lysogenic) phage system which involves insertion of the phage DNA into the mammalian E.coli DNA leaving the bacterial lifecycle largely undisturbed, but lyses bacteria when they are stressed by agents which in some cases can cause genetic alteration. Thus, lysogenic lambda phage can be viewed as acting like a guardian of the genome in some respects, helping to maintain the microbiome from collecting threatening mutations and genetic alteration similar in some ways to the endogenous protein guardians of the genome in eukaryotic cells. In addition, when a phage establishes lysogeny by integrating into the host genome, that bacterium becomes immune to lysis by identical and similar phages, helping to preserve the microbiome bacteria (Youle 2017). The lambda phage was not known in the 1950s for being involved with the microbiome. Since little was known about the microbiome as being a beneficial system, the focus on the lambda phage involved its temperate lifecycle and the genetic mechanisms at the molecular level. Indeed, it was a model system that helped start the field of molecular genetics leading to early discovery of gene expression mechanisms. In fact, to this day, it appears that lambda phage is known for its genetic mechanisms which help determine genetic function in other organisms rather than as a phage which may protect the microbiome (Gottesman, 2004). A search of databases like PubMed and others with the terms “lambda phage” and “microbiome” do not show any publications related to maintenance or protection of the mammalian microbiome. There is some indication however that phages may play a role in the microbiome as agents of bacterial innovation via gene transfer mechanisms (Kahrstrom 2013), but their role as protectors of the microbiome is not stressed. A recent text on phages suggests that phages may play a role in genome stability and change in the bacterium host, but does not refer to how this influences the microbiome at the ecological or organismal level (Youle 2017). 2. Mammalian associated phages possess mechanisms to shield bacteria from the immune system, phage cloaking theory It is well established that phages known to invade E.coli and other mammalian normal flora bacteria begin their infection process by binding to microbe associated molecular patterns (MAMPs) (Datta 1977; Simpson 2016). MAMPs are molecular patterns found in bacterial macromolecules, for example lipopolysacharride (LPS) or peptidoglycan (PG). MAMPS are located on all known bacteria (Owen et al. 2013). When released during cell death or present within dense concentrations of bacteria during infection, MAMPs are recognized by the pattern recognition receptors (PRRs) of the innate immune system (Owen et al. 2013). The innate immune system is now known to play a vital role in activating major pathways of the immune system (Owen et al. 2013). In some cases, instead of causing host protection, the immune response causes a life threatening reaction called sepsis. For example, gram-negative sepsis, a bacterial induced mechanism causes the death of hundreds of thousands of human patients each year, and is largely caused by pathogen released LPS and other MAMPs (Mossie 2013). One question raised by these facts is why the large numbers of normal flora bacteria, which all contain MAMPs, do not cause constant activation of the immune system and pose an ongoing threat of sepsis? We propose that phages possess mechanisms which allow them to coat bacteria and bind to cell free MAMPs thus shielding them from activating the mammalian immune system. A. Phage receptor binding proteins bind to MAMPs possibly hiding them from the mammalian immune system Phages bind to the MAMPs using receptors known as receptor binding proteins (RBPs) (Datta 1977; Rakhuba 2010; Simpson 2016). Fascinatingly, in databases of known RBPs, we have calculated that up to 90% of the documented RBPs bind known MAMPs (Silva 2015). Phages are known to quickly destroy their host bacterium, breaking open the cell (lysis) such that the cell becomes unrecognizable. However, we have found that many photographs of phage infection appear to show that phage bind to the surface of the bacterium in great abundance (Figure 1) (Caro 1966; Luria 1978). If the cell were rapidly and completely lysed, few of these photos could be obtained suggesting that phages can coat their bacterial hosts for a time before the lytic event occurs supporting the idea that phages are designed to continuously coat bacteria. In addition, there are primary and secondary binding sites for RBPs. The RBPs often bind in a reversible manner to the primary sites on the surface of the bacterium, allowing for movement of the phage on the bacterial surface and most likely promoting their tight packing on the surface (Youle 2017). On tailed phages the RBPs are often located on several phage tail fibers such that as one tail fiber becomes detached another can be attaching allowing for a “walking” type movement across the cell surface (Youle 2017). A secondary receptor can then be found and the phage binds irreversibly to this receptor. The secondary receptor serves as the site of infection whereby the phage can inject its DNA or RNA into the cell (Youle 2017). This can result in lysis or lysogeny. Curiously there are few secondary binding sites compared to the primary binding sites and they are often located at distinct sites on the cell surface (Youle 2017). We postulate that this design, which causes a time delay in lysis, is to promote coating of the bacteria prior to lysis, and to coat the MAMPs prior Francis et al. ◀ Bacteriophages as beneficial regulators ▶ 2018 ICC 153