Exploring early-life microbiome transfer and therapeutic applications in bovines and humans

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Linehan, Kevin
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University College Cork
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The microbiome consists of intricate microbial communities, including bacteria, archaea, eukarya, viruses, bacteriophages, and their associated products. These dynamic entities establish symbiotic relationships with their bovine and human hosts, exerting direct or indirect influences on physiology throughout life, impacting both health and disease outcomes. The early-life microbiome exerts a profound impact on developmental trajectories and long-term health. The extent to which different maternal microbial sources and perinatal factors contribute and shape the initial colonisation, development, and functionality of the neonatal microbiome is a topic of ongoing research. Understanding these factors is crucial for comprehending the early establishment of the microbiome. Given the current antibiotic resistance crisis, there is significant importance in leveraging host-microbiome interactions to develop microbiome-based therapeutics. This thesis explores a number of research foci with a view to gain a better understanding of (1) the influence of different maternal microbial sources and perinatal factors on the initial establishment of the human infant gut microbiome, (2) harnessing the bioactive composition of bovine colostrum for bovine and human health applications, (3) characterising the virome of bovine colostrum and the influence of perinatal factors on its composition, and (4) the potential of microbiome-based therapeutics for disease treatment in bovines and humans. Chapter 1 discusses the impact of perinatal factors, including maternal nutrition, antibiotic use, gestational age, and mode of delivery, on the initial colonisation, development, and function of the human neonatal gut microbiome. The elucidation of the precise extent to which these factors influence gut microbiome establishment and identification of those with the most decisive effects on colonisation are essential for improving infant health. In Chapter 2, the diverse array of bioactive components in bovine colostrum suitable for the development of functional foods, nutraceuticals, and pharmaceuticals with veterinary and human health applications are discussed. The processing techniques used to produce high-value colostrum-based products, and recent studies utilizing bovine colostrum for veterinary and human health are also outlined. In Chapter 3, using a cohort of 18 healthy mother-infant dyads, the microbial composition of three potential maternal sources of microbial transmission (oral, vaginal and placental) to the microbiota of their new-born infant (oral and meconium microbiota) were characterised. This allowed investigation of the contribution of numerous transmission routes and the impact of various perinatal factors on the initial establishment of the infant gut and oral microbiome. The results of this study consolidate and corroborate recent findings surrounding the existence of a meconium microbiome and the absence of a placental microbiome. Furthermore, the study shows that significant vertical transfer, primarily from the maternal oral cavity to the infant oral cavity occurs in early life. In Chapter 4, a reproducible, low cost and high-throughput virome extraction method was developed for bovine colostrum. Shotgun sequencing and viral specific metagenomics bioinformatics were performed on samples from 72 dairy cows, given dry cow therapy (n=48) or naturally dried off (n=24). The impact of farm level variables (location and parity) were also assessed. Phages carrying multidrug resistance genes (smeS, lfrA, kdpE and baeS) were identified. Antibiotic treatments significantly impacted virome composition and the presence of resistance genes specific to the administered antibiotic. This study provides novel insights into disease development and transmission in animals and humans, and the contribution of viruses to the spread of global antimicrobial resistance. In Chapter 5, two novel Staphylococcus aureus bacteriophage species from the genus Phietavirus were isolated. Phages were lytic against several human and bovine mastitis causing strains of Staphylococcus aureus (including MRSA). Phages displayed excellent characteristics for in vivo experiments, with no resistance genes present, stability to variations in pH (4 to 9), temperature (up to 60 °C), chloroform resistant and capable of replicating in mastitic milk. Finally, in Chapter 6, a field trial was undertaken to investigate the efficacy of emulsion based postbiotic and live-biotherapeutic formulations of Lactococcus lactis DPC3147, producer of the bacteriocin lacticin 3147, as alternative therapeutics for bovine mastitis. Twenty eight cows with chronic mastitis were treated with emulsion-based formulations containing either viable L. lactis DPC3147 cells (n=15) or heat-killed L. lactis DPC3147 cells (n=13). The efficacies of the two formulations in stimulating a localised immune response (measuring interleukin-8 concentrations in milk) and cure rates (somatic cell counts reductions and pathogen absence) were evaluated. This study demonstrated that the presence of heat-inactivated bacteria (a postbiotic) was as effective as the live bio-therapeutic in eliciting a localised immune response in cows with chronic mastitis. The results outlined in this thesis provide valuable insights into the intricate dynamics of early-life microbiome transfer and outline novel microbiome-based therapeutics for applications in bovines and humans.
Microbiome , Virome , Live-biotherapeutics , Postbiotics , Bovine colostrum , Early-life microbiome transfer
Linehan, K. A. 2023. Exploring early-life microbiome transfer and therapeutic applications in bovines and humans. PhD Thesis, University College Cork.