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ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Infectious Bacterial Diseases Research » Research » Publications at this Location » Publication #372366
Research Project: Characterization of Antigens, Virulence Markers, and Host Immunity in the Pathogenesis of Johne’s Disease

Location: Infectious Bacterial Diseases Research

Title: Genetic diversity among Mycobacterium avium subspecies revealed by analysis of complete genome sequences

Author
item Bannantine, John
item CONDE, CYRIL - Universite De Tours
item Bayles, Darrell
item BRANGER, MAXINE - Universite De Tours
item BIET, FRANCK - Universite De Tours

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/29/2020
Publication Date: 8/7/2020
Citation: Bannantine, J.P., Conde, C., Bayles, D.O., Branger, M., Biet, F. 2020. Genetic diversity among Mycobacterium avium subspecies revealed by analysis of complete genome sequences. Frontiers in Microbiology. 11. https://doi.org/10.3389/fmicb.2020.01701.
DOI: https://doi.org/10.3389/fmicb.2020.01701

Interpretive Summary: This study takes a comprehensive look at the genome structure of Mycobacterium avium subspecies paratuberculosis (MAP) and other M. avium subspecies bacteria. By focusing our analysis only on complete genome sequences, we were able to define what makes MAP MAP (this is known as the core genome of MAP). The primary finding from this study was the remarkable stability of the MAP genome, yet the dynamic changing of the other M. avium subspecies bacteria. Other findings suggest unique phylogenetic relationships between these strains. Overall, this work is of interest to researchers in the field, animal health specialists and genome scientists.

Technical Abstract: At the time this study was designed, there were 29 complete genome sequences available for the diverse Mycobacterium avium complex (MAC), which comprises four subspecies. Members of the MAC contain both human and veterinary pathogens. Twenty-eight of these genomes have been reannotated as RefSeq genomes, facilitating direct comparisons. These genomes represent strains from around the world. The Mycobacterium avium subspecies paratuberculosis (Map) genome size was remarkably consistent despite being distributed across five continents, averaging 4.8 Mb with a variance of only 29,657 bps among the 13 strains. When considering the larger genome size and variance among Mycobacterium avium subspecies avium (Maa) and Mycobacterium avium subspecies hominissuis (Mah) strains (), this may suggest a general lack of horizontal gene transfer within the Map subspecies. The most evolutionally distinct Map strain was an ovine strain, designated Telford, which had >1,000 SNPs compared to the bovine K-10 reference strain. Furthermore, an additional 15 Mycobacterium avium genome sequences not belonging to the subspecies paratuberculosis were compared to Map genomes to reveal single nucleotide variants. These analyses demonstrated the conserved nature of Map versus the mosaic nature of non-Map M. avium strains. Finally, core and pan genomes were developed for Map and Mah. These data were also used to determine the genetic diversity and most unique features of this sample of complete genomes. The core genome of Map was revealed and provides a framework for genome diversity in the MAC.