Comparative genome analyses of mycobacteria give better insights into their evolution.

Wei Yee Wee,Siew Woh Choo,Avirup Dutta,Seyed Ehtesham Hasnain

doi:10.1371/journal.pone.0172831

Wei Yee Wee, Siew Woh Choo + Show 2 more

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https://doi.org/10.1371/journal.pone.0172831

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Abstract

Mycobacteria a genus of Actinobacteria are widespread in nature ranging from soil-dwelling saprophytes to human and animal pathogens. The rate of growth has been a classifying factor for the Mycobacterium spp., dividing them into the rapid growers and the slow growers. Here we have performed a comparative genome study of mycobacterial species in order to get better understanding of their evolution, particularly to understand the distinction between the rapid and slow growers. Our study shows that the slow growers had generally gained and lost more genes compared to the rapid growers. The slow growers might haved eventually lost genes (LivFGMH operon, shaACDEFG genes and MspA porin) that could contribute to the slow growth rate of the slow growers. The genes gained and lost in mycobacteria had eventually helped these bacteria to adapt to different environments and have led to the evolution of the present day rapid and slow growers. Our results also show high number of Mycobacterium abscessus specific genes (811 genes) and some of them are associated with the known bacterial quorum sensing genes that might be important for Mycobacterium abscessus to adapt and survive in variety of unfavorable environments. Mycobacterium abscessus also does not contains genes involved in the bacterial defense system and together with the quorum sensing genes may have contributed to the high gene gain rate of Mycobacterium abscessus.

Highlights

Mycobacteria are a genus of Actinobacteria of the Mycobacteriacae family which are obligate aerobic, immobile, acid-fast Gram-positive bacteria with high G+C content, and are widespread in nature ranging from soil-dwelling saprophytes to pathogens of humans and animals [1,2]
28 different mycobacterial species comprising 16 rapid growing and 12 slow growing mycobacterial species were used in this study
The genome size of the 28 mycobacterial strains ranged from 4Mbp to 6Mbp except for Mycobacterium leprae TN which might due to genome degradation and Mycobacterium brisbanense UM_WWY which was the only mycobacterial genome having a genome size larger than 7Mbp

Summary

Introduction

Mycobacteria are a genus of Actinobacteria of the Mycobacteriacae family which are obligate aerobic, immobile, acid-fast Gram-positive bacteria with high G+C content, and are widespread in nature ranging from soil-dwelling saprophytes to pathogens of humans and animals [1,2]. Diseases in humans and animals, such as tuberculosis and leprosy respectively, are slow growers. Not all pathogenic NTMs are slow growers, such as M. abscessus a commonly isolated rapidly growing NTM is the third most common cause of lung disease [5]. Studies have shown that a distinction between the rapid and the slow growers is in the presence of ESX-5, which are exclusively present in the slow-growing mycobacteria [8]. We present a pan-genome analysis of 28 mycobacterial species (comprised of both rapid and slow growers). This study was performed with the objective to have a better understanding of the distinction between the rapid and the slow growers at the genomic level of the evolution of the mycobacterial genus

Materials and methods

Results and discussion

Conclusion