The gut microbiome is a complex ecosystem of bacteria, viruses, and fungi that strongly influences animal health. The bacterial component, for example, contributes orders of magnitude more gene products to host physiology than the host genome; thus, changes to the composition of these bacterial communities can have profound influences on the health of the animal. By infecting and lysing their hosts, viruses (particularly viruses infecting bacteria or phages) can affect critical functions in these environments, yet the consequences of these infections remain to be fully described. Most studies investigating gut viromes to date have focused on double-stranded DNA (dsDNA) phages and, consequently, little is known about the smaller single-stranded DNA (ssDNA) phages, which also inhabit gut environments. In this study, we investigated ssDNA phages of the Microviridae family within the gut of an invertebrate organism, Ciona robusta, used as a model system to better understand gut microbial interactions. As a filter feeder, Ciona concentrates dissolved organics and microbes as part of its diet, yet maintains a microbiome distinct from the surrounding water column. We identified 258 unique ssDNA phage genomes representing a diversity of Microviridae subgroups including novel members of the established Gokushovirinae subfamily and several proposed phylogenetic groups (Alpavirinae, Aravirinae, Group D, Parabacteroides prophages, and Pequeñovirus). Over 70% of the genomes belonged to the Gokushovirinae; however, 155 of these genomes did not group with previously described sequences. Our results highlight an unprecedented diversity of ssDNA phages from an animal gut. Furthermore, comparative analysis between samples collected from Ciona specimens with full and cleared guts as well as the surrounding water indicated that Ciona retains a unique and highly diverse community of ssDNA phages. The present study significantly expands the known diversity within the Microviridae family and suggests that Ciona is a promising system for studying the role of ssDNA phages within animal guts.

Humic substances, such as the closely related humic and fulvic acids are ubiquitous, naturally occurring organic macromolecules of complex but undefined structure. These compounds are known complexing agents due to their supramolecular like structures and are capable of binding a wide variety of compounds. Numerous studies have confirmed that humic and fulvic acids exhibit diverse medicinal and therapeutic properties. For this reason, alternative or “natural” medicinal preparations rich in these substances are being self-administered, often concomitantly with conventional drugs. The possibility exists that these humic substances, found in the alternative medicinal products, may result in drug-drug interactions and bind to simultaneously ingested drugs. Complex formation may affect absorption and alter overall bioavailability. Changes in these parameters may lead to reduced therapeutic effect or toxic side effects of prescribed drugs in patients. Similarly, these humic substances may bind to and alter the uptake of ingested nutrients, such as vitamins and minerals, obtained from food sources as well as dietary supplements. Changes in absorption may result in a loss of proper physiological functioning in the body or in unwanted effects of overdose. This study investigated the effect of fulvic and humic acids on the absorption of commonly administered classes of drugs, vitamins and minerals using the everted mouse gut model that was successfully used to assess the membrane transport of the test compounds. This model made use of everted segments of excised intestinal tissue placed in Krebs Ringer Buffer (pH7.4), where physiological functioning of the tissue is maintained for up to two hours after excision. The amount of test compound which crossed through the intestinal membrane without and in the presence of each humic substance was quantified using LC-MS/MS methods developed for each of the drugs and vitamins, and ICP-MS, in the case of the minerals. The amount of test compound absorbed alone was compared to the amount absorbed when in the presence of each humic substance. Changes in the uptake, for each test compound was noted, the extent of the absorption increase or decrease was compound specific. The changes in absorption observed could be attributed to changes in compound solubility and mechanism of transport across the intestinal membrane once in complex. Drugs and vitamins were seen to be more prone to decreases in absorption in the presence of the humic substances, whereas the majority of the minerals showed significantly increased absorption. Binding of the minerals to the humic substances through chelation, and not complex formation, could have a greater effect on compound solubility. Health care professionals, as well as individuals ingesting these and other substances concurrently, should be aware of the potential effects on absorption that may occur due to drug-drug interactions in order to avoid a loss of therapeutic/physiological activity or negative toxic symptoms. / Dissertation (MSc)--University of Pretoria, 2015. / tm2015 / Pharmacology / MSc / Unrestricted