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.

James Daltro Lima-Junior,Michelle Cristiane Da Silva Rabello,Gabriel Esquitini Machado,Luciano Antonio Digiampietri,Sylvia Cardoso Leão,Daniel V Conde Oliveira,Cristina Viana-Niero,Daniel A Russell,Joaquim Martins-Junior,Graham F Hatfull,João Carlos Setubal,Aline Maria Da Silva,Deborah Jacobs-Sera,Layla Farage Martins,Welkin H Pope

doi:10.1186/s12866-016-0734-3

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.

Highlights

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 and extensive variation within those sharing evident nucleotide sequence similarity
We report the genome sequences of eight newly isolated phages providing insights into viral diversity and the first evidence for mycobacteriophage evolution within a geographically isolated niche
Isolation and identification of mycobacteria from composting material Several colonies of acid-fast bacteria were isolated from the São Paulo Zoo Park composting chambers 1, 2 and 3 at each time point, ranging from 2 to 20 per plate

Summary

Introduction

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. Results: We 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. Bacteriophages (phages) are the most abundant life forms on the planet, and can influence the entire bacterial ecosystem [1]. They are capable of delivering, through horizontal gene transfer, mechanisms of adaptation and resistance, toxins and photosynthesis genes to their hosts. More than 800 mycobacteriophage genomes have been sequenced (http://phagesdb.org) a collection that has grown rapidly due in part to the impact of integrated research-education programs [12, 13]

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