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Whole-Genome Sequencing and Comparative Analysis of Mycobacterium brisbanense Reveals a Possible Soil Origin and Capability in Fertiliser Synthesis.

Wee WY, Tan TK, Jakubovics NS, Choo SW - PLoS ONE (2016)

Bottom Line: It is likely that M. brisbanense UM_WWY is adapted to live in soil as its primary habitat since the genome contains many genes associated with nitrogen metabolism.These findings are consistent with the role of M. brisbanense as an opportunistic pathogen of humans.The whole-genome study of UM_WWY has provided the basis for future work of M. brisbanense.

View Article: PubMed Central - PubMed

Affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, Kuala Lumpur, 50603, Malaysia.

ABSTRACT
Mycobacterium brisbanense is a member of Mycobacterium fortuitum third biovariant complex, which includes rapidly growing Mycobacterium spp. that normally inhabit soil, dust and water, and can sometimes cause respiratory tract infections in humans. We present the first whole-genome analysis of M. brisbanense UM_WWY which was isolated from a 70-year-old Malaysian patient. Molecular phylogenetic analyses confirmed the identification of this strain as M. brisbanense and showed that it has an unusually large genome compared with related mycobacteria. The large genome size of M. brisbanense UM_WWY (~7.7Mbp) is consistent with further findings that this strain has a highly variable genome structure that contains many putative horizontally transferred genomic islands and prophage. Comparative analysis showed that M. brisbanense UM_WWY is the only Mycobacterium species that possesses a complete set of genes encoding enzymes involved in the urea cycle, suggesting that this soil bacterium is able to synthesize urea for use as plant fertilizers. It is likely that M. brisbanense UM_WWY is adapted to live in soil as its primary habitat since the genome contains many genes associated with nitrogen metabolism. Nevertheless, a large number of predicted virulence genes were identified in M. brisbanense UM_WWY that are mostly shared with well-studied mycobacterial pathogens such as Mycobacterium tuberculosis and Mycobacterium abscessus. These findings are consistent with the role of M. brisbanense as an opportunistic pathogen of humans. The whole-genome study of UM_WWY has provided the basis for future work of M. brisbanense.

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Related in: MedlinePlus

Schematic circular diagram of the UM_WWY genome.The following color bars represent: Dark red and light red are contigs, pink and orange represent forward and reverse CDS respectively, purple is tRNA, dark blue is genomic island, green is prophage, grey is virulence gene and the last track is the percentage of GC content.
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pone.0152682.g001: Schematic circular diagram of the UM_WWY genome.The following color bars represent: Dark red and light red are contigs, pink and orange represent forward and reverse CDS respectively, purple is tRNA, dark blue is genomic island, green is prophage, grey is virulence gene and the last track is the percentage of GC content.

Mentions: The genome of UM_WWY was shot-gun sequenced using the Illumina HiSeq2000 platform, generating 63,311,594 raw sequencing reads. These reads were pre-processed to remove adaptor sequences and trimmed at a Phred quality score of 20 using CLC Genomic Workbench version 5.1 (CLC bio, Denmark). The assembly of 53,995,482 pre-processed reads resulted in 130 contigs. The assembly has a genomic size of 7,690,050bp with a G+C content of 66.4%. The sequenced genome of UM_WWY has an N75 value of 74,225bp, N50 value of 112,506bp and N25 size of 198,038bp, indicating the high quality of this assembly. The UM_WWY genome was BLAST-searched against NCBI database of known plasmids and no plasmid sequences were detected in the genome. An overview of the UM_WWY genome is shown in Fig 1. Interestingly, a 980kbp intact prophage was predicted in the sequenced genome of UM_WWY by the PHAST software. This large intact prophage observed within contig suggest it was recently inserted, contains 98 putative protein-coding genes and most of them have unknown functions (S1 Fig). Further studies on the functions of these hypothetical proteins may give better insights into the functions or impact of this prophage on the traits of UM_WWY. There was evidence that this prophage is currently active as we observed the presence of reads aligned to a closed form of the origin of insertion (attP site), indicating that lytic phage were likely to have been present in the cultures (S2 Fig).


Whole-Genome Sequencing and Comparative Analysis of Mycobacterium brisbanense Reveals a Possible Soil Origin and Capability in Fertiliser Synthesis.

Wee WY, Tan TK, Jakubovics NS, Choo SW - PLoS ONE (2016)

Schematic circular diagram of the UM_WWY genome.The following color bars represent: Dark red and light red are contigs, pink and orange represent forward and reverse CDS respectively, purple is tRNA, dark blue is genomic island, green is prophage, grey is virulence gene and the last track is the percentage of GC content.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4816395&req=5

pone.0152682.g001: Schematic circular diagram of the UM_WWY genome.The following color bars represent: Dark red and light red are contigs, pink and orange represent forward and reverse CDS respectively, purple is tRNA, dark blue is genomic island, green is prophage, grey is virulence gene and the last track is the percentage of GC content.
Mentions: The genome of UM_WWY was shot-gun sequenced using the Illumina HiSeq2000 platform, generating 63,311,594 raw sequencing reads. These reads were pre-processed to remove adaptor sequences and trimmed at a Phred quality score of 20 using CLC Genomic Workbench version 5.1 (CLC bio, Denmark). The assembly of 53,995,482 pre-processed reads resulted in 130 contigs. The assembly has a genomic size of 7,690,050bp with a G+C content of 66.4%. The sequenced genome of UM_WWY has an N75 value of 74,225bp, N50 value of 112,506bp and N25 size of 198,038bp, indicating the high quality of this assembly. The UM_WWY genome was BLAST-searched against NCBI database of known plasmids and no plasmid sequences were detected in the genome. An overview of the UM_WWY genome is shown in Fig 1. Interestingly, a 980kbp intact prophage was predicted in the sequenced genome of UM_WWY by the PHAST software. This large intact prophage observed within contig suggest it was recently inserted, contains 98 putative protein-coding genes and most of them have unknown functions (S1 Fig). Further studies on the functions of these hypothetical proteins may give better insights into the functions or impact of this prophage on the traits of UM_WWY. There was evidence that this prophage is currently active as we observed the presence of reads aligned to a closed form of the origin of insertion (attP site), indicating that lytic phage were likely to have been present in the cultures (S2 Fig).

Bottom Line: It is likely that M. brisbanense UM_WWY is adapted to live in soil as its primary habitat since the genome contains many genes associated with nitrogen metabolism.These findings are consistent with the role of M. brisbanense as an opportunistic pathogen of humans.The whole-genome study of UM_WWY has provided the basis for future work of M. brisbanense.

View Article: PubMed Central - PubMed

Affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, Kuala Lumpur, 50603, Malaysia.

ABSTRACT
Mycobacterium brisbanense is a member of Mycobacterium fortuitum third biovariant complex, which includes rapidly growing Mycobacterium spp. that normally inhabit soil, dust and water, and can sometimes cause respiratory tract infections in humans. We present the first whole-genome analysis of M. brisbanense UM_WWY which was isolated from a 70-year-old Malaysian patient. Molecular phylogenetic analyses confirmed the identification of this strain as M. brisbanense and showed that it has an unusually large genome compared with related mycobacteria. The large genome size of M. brisbanense UM_WWY (~7.7Mbp) is consistent with further findings that this strain has a highly variable genome structure that contains many putative horizontally transferred genomic islands and prophage. Comparative analysis showed that M. brisbanense UM_WWY is the only Mycobacterium species that possesses a complete set of genes encoding enzymes involved in the urea cycle, suggesting that this soil bacterium is able to synthesize urea for use as plant fertilizers. It is likely that M. brisbanense UM_WWY is adapted to live in soil as its primary habitat since the genome contains many genes associated with nitrogen metabolism. Nevertheless, a large number of predicted virulence genes were identified in M. brisbanense UM_WWY that are mostly shared with well-studied mycobacterial pathogens such as Mycobacterium tuberculosis and Mycobacterium abscessus. These findings are consistent with the role of M. brisbanense as an opportunistic pathogen of humans. The whole-genome study of UM_WWY has provided the basis for future work of M. brisbanense.

Show MeSH
Related in: MedlinePlus