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

Abstract

BackgroundA 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.ResultsWe isolated and sequenced eight mycobacteriophages using Mycobacterium smegmatis mc2155 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.ConclusionsWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-016-0734-3) contains supplementary material, which is available to authorized users.

Weirdo19ES is a novel singleton mycobacteriophage that selects for glycolipid deficient phage-resistant M. smegmatis mutants

“…Several mycobacteriophages were isolated and characterized by our group with the aim of exploring their diversity at a geographical location (South America) in which little work on that matter had been carried out [5][6][7]. Mycobacteriophages defining novel clusters and subclusters were detected by our group in spite of the reduced number of total isolates (less than 30) [8].…”

Mycobacteriophages as Potential Therapeutic Agents against Drug-Resistant Tuberculosis

“…Sequenced mycobacteriophages have been mostly isolated in M. smegmatis , although some of them are also reported to infect other mycobacterial species such as M. abscessus , M. aichiense , M. aurum , M. avium , M. phlei , and M. tuberculosis ; including 17 different strains among these species [ 72 ]. Phages are constantly assigned to these groups based on sequence similarity and clusters and sub-clusters created as new phage sequences are being discovered [ 91 , 92 , 93 ]. These mycobacteriophage clusters are based on sequence similarity, indicative of their mosaic architecture, which does not necessarily correlate with their biological and/or evolutionary significance.…”

Directed Evolution of a Mycobacteriophage

“…Currently, there are 10,454 phages described whose host belongs to Mycobacterium genus, of which 1751 are sequenced [13]. Most of these mycobacteriophages belong to the family Siphoviridae (with long, flexible, non-contractile tails) and, in a lower proportion, to the family Myoviridae (with contractile tails) [14]. Mycobacteriophages have provided a wealth of information on the diversity of phages that infect a common bacterial host.…”