Lima-Junior JD et al. (2016), Characterization of mycobacteria and mycobacter...

ECB-ART-44763

BMC Microbiol 2016 Jun 17;161:111. doi: 10.1186/s12866-016-0734-3.

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Characterization of mycobacteria and mycobacteriophages isolated from compost at the São Paulo Zoo Park Foundation in Brazil and creation of the new mycobacteriophage Cluster U.

Lima-Junior JD , Viana-Niero C , Conde Oliveira DV , Machado GE , Rabello MC , Martins-Junior J , Martins LF , Digiampietri LA , da Silva AM , Setubal JC , Russell DA , Jacobs-Sera D , Pope WH , Hatfull GF , Leão SC .

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BACKGROUND: A large collection of sequenced mycobacteriophages capable of infecting a single host strain of Mycobacterium smegmatis shows considerable genomic diversity with dozens of distinctive types (clusters) and extensive variation within those sharing evident nucleotide sequence similarity. Here we profiled the mycobacterial components of a large composting system at the São Paulo zoo. RESULTS: We isolated and sequenced eight mycobacteriophages using Mycobacterium smegmatis mc(2)155 as a host. None of these eight phages infected any of mycobacterial strains isolated from the same materials. The phage isolates span considerable genomic diversity, including two phages (Barriga, Nhonho) related to Subcluster A1 phages, two Cluster B phages (Pops, Subcluster B1; Godines, Subcluster B2), three Subcluster F1 phages (Florinda, Girafales, and Quico), and Madruga, a relative of phage Patience with which it constitutes the new Cluster U. Interestingly, the two Subcluster A1 phages and the three Subcluster F1 phages have genomic relationships indicating relatively recent evolution within a geographically isolated niche in the composting system. CONCLUSIONS: We predict that composting systems such as those used to obtain these mycobacteriophages will be a rich source for the isolation of additional phages that will expand our view of bacteriophage diversity and evolution.

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Genes referenced: LOC115918857 LOC115925287 LOC115925415 span

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	Fig. 1. PRA-hsp65 patterns of isolates recovered from composting materials. BstE II and Hae III restriction patterns of the 441 bp amplicon of the hsp65 gene are shown in the upper and lower figure, respectively. The figure was produced from different gels with the BioNumerics program v. 7.5 (Applied Maths, Sint-Martens-Latem, Belgium). M: 50 kb ladder (Invitrogen, USA). 1: M. peregrinum type 3; 2: M. fortuitum type 2; 3: M. fortuitum type 1; 4: M. septicum type 1; 5: M. peregrinum type 1; 6: M. terrae type 1; 7: M. insubricum type 1; 8: M. kumamotonense type 1
	Fig. 2. Genome comparisons of Subcluster A1 phages Barriga and Nhonho. Each genome map is shown with the coordinates in kbp flanked by genes represented as boxes positioned above (transcribed rightwards) or below (transcribed leftwards); the phams to which each gene belongs are indicated above or below genes (and colored accordingly) with the number of pham members in parentheses. Pairwise nucleotide sequence similarity between genomes is shown as spectrum-colored shading between the genomes as determined with BLASTN; greatest similarity is shown in purple and weakest similarity (above a threshold level of 10−4) shown in red. Barriga and Nhonho have similar gene contents and genome architectures but with a notable insertion/deletion between the recB and immunity repressor genes. The nucleotide similarity between the two phages is quite high in the capsid genes in the left arm, disappears almost entirely downstream of the major capsid protein, and reemerges in the minor tail proteins
	Fig. 3. Gene content-based network relationships among Subcluster A mycobacteriophages. Splitstree [59] was used to present the relationships between Cluster A mycobacteriophages, using the Phamerator database ‘Actinobacteriophage_554’, filtering for taxa within Cluster A. Colored circles indicate the different subclusters, and the phages isolated from the Sao Paulo zoo are boxed
	Fig. 4. Genome comparisons of Cluster B phages Numberten, Pops, Godines and Ares. Phages Numberten and Pops are highly similar in both nucleotide sequence and gene content across entire genome spans, as are Godines and Ares; see Fig. 2 for figure annotation details. All four Cluster B phages have similar gene contents and genome architectures, with insertion/deletions reflected in interruptions in the purple shaded regions between genome pairs
	Fig. 5. Genome comparisons of Cluster F mycobacteriophages Florinda, Girafales, Quico, Danaerys, and Boomer. Florinda has close similarity with Danaerys capsid and packaging genes near the left end; Girafales and Quico have greatest similarity in this region to Boomer. All three newly sequenced phages have a region containing 12 genes in common adjacent to the integrase that are either not present or rare in other Cluster F phages
	Fig. 6. Gene content-based network relationships among Subcluster F1 mycobacteriophages. Splitstree [59] was used to present the relationships between Subcluster F1 phages, using the Phamerator database ‘Actinobacteriophage_554’, filtering for taxa within Subcluster F1. Phages isolated from the Sao Paulo zoo are highlighted in yellow
	Fig. 7. Genome comparisons of Cluster U phages Madruga and Patience. Phages Madruga and Patience share extensive nucleotide sequence similarity with three notable insertion/deletions, and constitute the new Cluster U; see Fig. 2 for figure annotation details

References [+] :

Ackermann, Bacteriophage observations and evolution. 2003, Pubmed