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Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium.
Flores, Vinicius S; Amgarten, Deyvid E; Iha, Bruno Koshin Vázquez; Ryon, Krista A; Danko, David; Tierney, Braden T; Mason, Christopher; da Silva, Aline Maria; Setubal, João Carlos.
Afiliação
  • Flores VS; Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil.
  • Amgarten DE; Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil.
  • Iha BKV; Hospital Israelita Albert Einstein, São Paulo, Brazil.
  • Ryon KA; Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil.
  • Danko D; Weill Cornell Medicine, New York, NY, USA.
  • Tierney BT; , Biotia, New York, NY, USA.
  • Mason C; Weill Cornell Medicine, New York, NY, USA.
  • da Silva AM; Harvard Medical School, Cambridge, MA, USA.
  • Setubal JC; Weill Cornell Medicine, New York, NY, USA.
Sci Rep ; 14(1): 7913, 2024 04 04.
Article em En | MEDLINE | ID: mdl-38575625
ABSTRACT
Bacteriophages are recognized as the most abundant members of microbiomes and have therefore a profound impact on microbial communities through the interactions with their bacterial hosts. The International Metagenomics and Metadesign of Subways and Urban Biomes Consortium (MetaSUB) has sampled mass-transit systems in 60 cities over 3 years using metagenomics, throwing light into these hitherto largely unexplored urban environments. MetaSUB focused primarily on the bacterial community. In this work, we explored MetaSUB metagenomic data in order to recover and analyze bacteriophage genomes. We recovered and analyzed 1714 phage genomes with size at least 40 kbp, from the class Caudoviricetes, the vast majority of which (80%) are novel. The recovered genomes were predicted to belong to temperate (69%) and lytic (31%) phages. Thirty-three of these genomes have more than 200 kbp, and one of them reaches 572 kbp, placing it among the largest phage genomes ever found. In general, the phages tended to be site-specific or nearly so, but 194 genomes could be identified in every city from which phage genomes were retrieved. We predicted hosts for 48% of the phages and observed general agreement between phage abundance and the respective bacterial host abundance, which include the most common nosocomial multidrug-resistant pathogens. A small fraction of the phage genomes are carriers of antibiotic resistance genes, and such genomes tended to be particularly abundant in the sites where they were found. We also detected CRISPR-Cas systems in five phage genomes. This study expands the previously reported MetaSUB results and is a contribution to the knowledge about phage diversity, global distribution, and phage genome content.
Assuntos

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Ferrovias / Bacteriófagos / Microbiota Idioma: En Revista: Sci Rep Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Brasil

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Ferrovias / Bacteriófagos / Microbiota Idioma: En Revista: Sci Rep Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Brasil