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.
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.



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.



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.
Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.
James Daltro
JD
Lima-Junior
Departmento de Ciências Biológicas, Universidade Federal de São Paulo, campus Diadema, São Paulo, Brazil.
Cristina
C
Viana-Niero
Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.
Daniel V
DV
Conde Oliveira
Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.
Gabriel Esquitini
GE
Machado
Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil.
Michelle Cristiane da Silva
MC
Rabello
Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
Joaquim
J
Martins-Junior
Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
Layla Farage
LF
Martins
Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, Brazil.
Luciano Antonio
LA
Digiampietri
Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
Aline Maria
AM
da Silva
Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.|Virginia Bioinformatics Institute, Blacksburg, VA, 24060, USA.
João Carlos
JC
Setubal
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 1524, USA.
Daniel A
DA
Russell
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 1524, USA.
Deborah
D
Jacobs-Sera
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 1524, USA.
Welkin H
WH
Pope
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 1524, USA.
Graham F
GF
Hatfull
Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil. sylvia.leao@unifesp.br.
Sylvia Cardoso
SC
Leão
D001435:Bacteriophages / Q000235:genetics; D001483:Base Sequence; D001938:Brazil; D004269:DNA, Bacterial / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D014644:Genetic Variation; D016679:Genome, Viral; D005810:Multigene Family; D009160:Mycobacteriophages / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D009161:Mycobacterium / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000821:virology*; D020102:Mycobacterium smegmatis / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000821:virology; D010802:Phylogeny; D012987:Soil; D012988:Soil Microbiology
D004269:DNA, Bacterial; D004279:DNA, Viral; D012987:Soil
Composting; Mycobacteriophages; Mycobacterium smegmatis; Phage diversity; Whole genome sequencing