Isolation and characterisation of Faecalibacterium prausnitzii in New Zealand calves : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Microbiology at Massey University, Manawatū, New Zealand
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2022
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Massey University
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Abstract
Faecalibacterium is an oxygen-sensitive bacterium found in the intestines of many animals and is of considerable interest due to the benefits it contributes to gastrointestinal tract (GIT) health and homeostasis. Faecalibacterium produces the short-chain fatty acid, butyrate, which is an important energy source for gut epithelial cells and acts as an anti-inflammatory agent in the GIT. In New Zealand, artificially reared calves that are raised in the absence of their dams are highly susceptible to gastrointestinal diseases which can result in morbidity and mortality. Understanding the roles of beneficial GIT microorganisms, and how these may enhance GIT health in calves, is highly desirable to improve calf health, growth and development. This project aimed to isolate and characterise Faecalibacterium strains from whole milk-fed New Zealand calves. Cultivation trials from calf faecal samples were conducted on Faecalibacterium enriching agar media in Petri plates or roll tubes and more than 300 colonies were screened to identify Faecalibacterium. A polymerase chain reaction (PCR) screen selective for Faecalibacterium was developed using a combination of universal and Faecalibacterium-specific 16S rRNA gene primers, and only one isolate was identified as Faecalibacterium via 16S rRNA gene sequencing. However, other closely related members of the Ruminococcaceae have also been isolated: two Fournierella massiliensis isolates and one member of Gemmiger. Genome sequencing and analyses showed that in both the Faecalibacterium and Gemmiger isolates, genes in the pathway from pyruvate to butyrate were present, consistent with their ability to produce butyrate. The Fournierella isolates were not observed to produce butyrate, and instead, ethanol was a major fermentation end-product. The genome of the Faecalibacterium isolate had an average nucleotide identity (ANI) of 96.05% compared to that of the human-derived F. prausnitzii strain A2-165, and an ANI of 85.01% compared to the F. prausnitzii type strain 27768T, suggesting genomic differences between calf and human-derived isolates. This study will provide a better understanding of microbial diversity and function within New Zealand calves, and the bacteria isolated in this study may serve as beneficial microbes to help reduce scours or other gastrointestinal diseases.
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Figures 1-1, 1-2 and 3-16 are re-used with permission.