DNA-based studies have revealed the composition of the gut microbiota is changed in colorectal cancer (CRC) and implicated in its development and progression. However, these analyses are influenced by dead and dormant cell DNA, potentially leading to the overestimation of certain species contribution to the disease. Furthermore, gene expression is a regulated process and can be microbe-specific for the same stimuli which is overlooked by DNA-based analysis of functional potential. Therefore, to overcome these limitations, metatranscriptomes and 16S rDNA of faecal microbiota from CRC patients (n=10) and non-CRC volunteers (n=10) were subject to high throughput sequencing to characterise active microbial taxonomy and metabolic functions. These analyses revealed microbial abundance and activity are not always comparable. We describe sub-populations in both cohorts of ‘hyper-active’ (at least an order of magnitude higher levels of transcript relative to gene abundance) and dormant species, including CRC-associated
F. nucleatum and
B. fragilis, and probiotic genera
Lactobacillus and
Bifidobacterium respectively. This suggests that the CRC niche regulates species-specific changes in gene expression independently of genomic abundance. Surprisingly, the dominant and mostly conserved activity of the microbiome in both cohorts was metabolism of reactive oxygen species (ROS), a hallmark of inflammation, arguing the microbial population is responsible for maintaining physiological levels of ROS in the gut. Yet, the observed dysregulation of certain bacterial ROS scavenging pathways during CRC suggests a potentially transient mechanism for the gradual accumulation of genetic lesions that lead to disease development over time in an otherwise healthy individual. Taxonomic analysis also uncovered diminished activity of butyrate-producing bacteria and enhanced activity of clinically relevant ESKAPE, oral cavity and Enterobacteriaceae pathogens with no previous association to the malignancy. Functional analysis of expressed genomes uncovered a potential contribution of gut microbiota to known patient deficiencies for ferrous iron, carnitine, and folate, among others. This analysis also showed overexpression of multiple virulence factors, particularly genes related to host colonisation, biofilm formation, quorum sensing, genetic exchange, acid stress, and a highly expressed antibiotic (AB) resistome.
In vitro investigation of bacterial acid and AB resistance determinants (particularly of ESKAPE members) in response to CRC-specific environmental pressures exposed mechanisms of possible long-term transcriptional memory. Microbes which likely faced previous oxidative, osmotic and/or acid stresses within the CRC gut increased expression of these determinants upon repeat exposure to a significant degree in comparison to the same species isolated from healthy individuals. This pioneering work uncovered the CRC-specific changes to active population composition and metabolic pathway expression. Crucially, from this we propose the mechanisms by which the human gut microbiota may protect against or drive CRC and reveal that exposure of the microbiota to CRC-specific pressures may condition them to adapt more readily to future stresses.
Date of Award | Aug 2023 |
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Original language | English |
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Awarding Institution | |
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Sponsors | University Hospitals Coventry and Warwickshire NHS Trust |
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Supervisor | Igor Morozov (Supervisor), Steven Foster (Supervisor) & Ramesh Arasaradnam (Supervisor) |
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Taxonomic and Functional Signatures of the Active Human Gut Microbiota in Homeostasis and Colorectal Cancer
Lamaudiere, M. (Author). Aug 2023
Student thesis: Doctoral Thesis › Doctor of Philosophy