Unravelling the role of Bacteroides and Phocaeicola in the human gut: exploring evolutionary dynamics, mother-to-infant vertical transmission, and functional characteristics
The human gut microbiota is composed of trillions of microrganims and plays a major role in human health and disease by performing a series of physiological functions, such as protection against pathogens, energy production, maintenance of intestinal barrier integrity, and regulation of the immune system. Bacteroides is one of the major genera present in the human gut. Bacteroides colonise the gut soon after birth in vaginally born babies and its abundance increases after weaning. However, different studies have shown that Bacteroides are missing or present in lower relative abundance in infants born by caesarean section (CS). Lower Bacteroides relative abundance has been associated with higher risk of atopic sensitization, especially in children of Asian heritage. Bacteroides and Phocaeicola have been linked to both health and disease. In the gut, Bacteroides is often associated with health benefits, but it can become an opportunistic pathogen in other body sites. Herein, this thesis explored a number of research topics aimed at gaining a better understanding of the role of Bacteroides and Phocaeicola in the human gut, such as production of metabolites, genetic and evolutionary features, vertical transfer, persistence and relative abundance of Bacteroides and Phocaeicola in early life. Characterization of a new species of Bacteroides and a potential Phocaeicola probiotic strain were also carried out. In Chapter 1, the current knowledge about the association of Bacteroides and Phocaeicola with health and disease was explored. Metabolic conditions associated with altered levels of these species, as well as their role as opportunistic pathogens and the challenges associated with the use of Bacteroides and Phocaeicola as probiotic were investigated. Numerous pre-clinical studies showed the benefits of strains of Bacteroides and Phocaeicola in various conditions, however, more clinical research is needed to evaluate if these benefits extend to humans. Chapter 2 explores Bacteroides and Phocaeicola in early life. Metagenomic analysis was carried out to compare the relative abundance of these species in vaginally delivered (VD) and CS-born infants during the first year of life. The presence of vertically transferred strains and strains that were persistent across different time points were also evaluated. Whole genome sequence (WGS) was carried out and the average nucleotide identity (ANI) was used to determine whether different isolates were the same strain. A blast comparison of the whole genome was also carried out. Metabolomics analyses and γ-aminobutyric acid (GABA) production was carried out in a subset of the isolates. Metagenomic analysis showed that Bacteroides are absent in CS children who were not exposed to antibiotics before birth, but present in CS-born children whose mothers were exposed to antibiotics during pregnancy and VD infants. Five groups of isolates that were vertically transferred and/or persistent across different timepoints were identified. The metabolomics profile showed that Bacteroides and Phocaeicola strains were able to produce organic acids and indole. On Chapter 3 a comparative analysis of the genomes of P. dorei and P. vulgatus were performed. Nearly 4000 assemblies were used to build the pan-genome of these species and to evaluate functional differences, like Carbohydrate-Active enZymes (CAZyme) content, antimicrobial resistance profile and mobile genetic elements. Both species have an open pan-genome and a similar antimicrobial resistance profile, but different CAZyme content, indicating they might have evolved to occupy different niches. We also hypothesised that P. dorei evolved from a larger than average subclade of P. vulgatus. Chapter 4 describes a novel Bacteroides species, Bacteroides sp. nov. (strain MSB163), which was isolated from a healthy mother 4 weeks after giving birth. The WGS, metabolomic profile, respiratory quinones, polar lipids, growth conditions and fermentation of different carbohydrate sources were analysed. Apart from differences in the genome, the main differences between MSB163 and its closest relatives, B. cellulosilyticus and B. intestinalis are the presence of phosphatidylglycerol on its cell membrane and the ability to ferment melezitose and sorbitol. In chapter 5, we characterize strain MSB026 (P. dorei), a bacteriocin producer and potential probiotic candidate. MSB026 was isolated from a VD infant, not exposed to antibiotics. WGS, growth conditions, 2’FL utilization, and production of compounds of interest were analysed. The production of health beneficial compounds, like GABA and SCFAs, associated with the strain’s technological robustness make it a potential probiotic candidate. Bacteroides and Phoceicola play a major role in the prevention and onset of different health conditions. They are present in the gut from the first days of life, producing numerous metabolites and interacting with the host in differen ways. The results outlined in this thesis expand on the knowledge of two important commensal genera of the human gut that have an important role in host health.
Bacteroides, Phocaeicola, Probiotics, Mode of delivery, Early life, Gut microbiobe, Pan-genome, Metagenomics, Vertical transmission
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