Khera, Tanya (2012) The diversity and distribution of Mycobacterium species in varying ecological and climatic environments. PhD thesis, University of Warwick.

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Abstract

The species within the genus Mycobacterium are commonly detected in a variety of environments including soil, water and dust. Many species within the group are capable of causing opportunistic diseases and are hypothesised to be responsible for the reduction in BCG efficacy in tropical countries. Consequently it is important to understand the diversity and biogeography of mycobacteria in the environment. Soil and water samples were collected from a total of 42 residential sites in 9 different climatic regions. To determine community composition, community DNA was extracted and amplicon pyrosequencing was employed to target the 16S rRNA gene of the Mycobacterium genus and slow-growing mycobacteria. Quantitative PCR was employed to quantify the total abundance of Mycobacterium species and specifically members of the M. tuberculosis complex. The study revealed a greater diversity of both fast-growing and slow-growing mycobacteria than previously reported. Prevalent species in soil were closely related to the fast growers M. neglectum, M. moriokaense and the slow growers M. malmoense and M. colombiense, in contrast to water had a high abundance of sequences related to the fast growers M. aurum sp. ATCC 23070, M. neoaurum and the slow-growers M. gordonae and M. colombiense. The abundance of the Mycobacterium genus ranged from 3.35 x 101 to 8.01 x108 gene copies per gram/ml. M. bovis was detected in six environmental samples using qPCR. Biogeographical analysis demonstrated the importance of elevation and temperature for the community composition of mycobacteria in soil. A nonlinear relationship was observed between elevation and the outcome variables Mycobacterium species richness, diversity and abundance with a peak midelevation. In contrast latitude was the primary factor to explain the composition and diversity of mycobacteria in water samples. To our knowledge this is the first time that the diversity and abundance of mycobacteria has been elucidated on a large geographical scale using pyrosequencing and multivariate analyses. Results indicate ample opportunity for human exposure to mycobacteria with potentially pathogenic species in soil and water substrates. These results have implications for the risk of infection and similar biogeographical surveys on a worldwide scale may provide improved correlations with BCG vaccine efficacy.

Item Type:	Thesis or Dissertation (PhD)
Subjects:	Q Science > QR Microbiology
Library of Congress Subject Headings (LCSH):	Mycobacteria -- Ecology
Date:	September 2012
Institution:	University of Warwick
Theses Department:	School of Life Sciences
Thesis Type:	PhD
Publication Status:	Unpublished
Supervisor(s)/Advisor:	Wellington, E. M. H. (Elizabeth M. H.), 1954- ; Courtenay, Orin
Extent:	xvii, 254 leaves : illustrations, charts, maps
Language:	eng
URI:	http://wrap.warwick.ac.uk/id/eprint/51639

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