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Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.
Bickhart, Derek M; Watson, Mick; Koren, Sergey; Panke-Buisse, Kevin; Cersosimo, Laura M; Press, Maximilian O; Van Tassell, Curtis P; Van Kessel, Jo Ann S; Haley, Bradd J; Kim, Seon Woo; Heiner, Cheryl; Suen, Garret; Bakshy, Kiranmayee; Liachko, Ivan; Sullivan, Shawn T; Myer, Phillip R; Ghurye, Jay; Pop, Mihai; Weimer, Paul J; Phillippy, Adam M; Smith, Timothy P L.
Afiliación
  • Bickhart DM; Cell Wall Biology and Utilization Laboratory, Dairy Forage Research Center, USDA, Madison, WI, 53706, USA.
  • Watson M; Division of Genetics and Genomics, The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK.
  • Koren S; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
  • Panke-Buisse K; Cell Wall Biology and Utilization Laboratory, Dairy Forage Research Center, USDA, Madison, WI, 53706, USA.
  • Cersosimo LM; Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA.
  • Press MO; Phase Genomics Inc, Seattle, WA, 98109, USA.
  • Van Tassell CP; Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
  • Van Kessel JAS; Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
  • Haley BJ; Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
  • Kim SW; Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
  • Heiner C; Pacific Biosciences, Menlo Park, CA, USA.
  • Suen G; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
  • Bakshy K; Cell Wall Biology and Utilization Laboratory, Dairy Forage Research Center, USDA, Madison, WI, 53706, USA.
  • Liachko I; Phase Genomics Inc, Seattle, WA, 98109, USA.
  • Sullivan ST; Phase Genomics Inc, Seattle, WA, 98109, USA.
  • Myer PR; Department of Animal Science, University of Tennessee, Knoxville, TN, 37996, USA.
  • Ghurye J; Department of Computer Science, University of Maryland, College Park, MD, 20742, USA.
  • Pop M; Department of Computer Science, University of Maryland, College Park, MD, 20742, USA.
  • Weimer PJ; Cell Wall Biology and Utilization Laboratory, Dairy Forage Research Center, USDA, Madison, WI, 53706, USA.
  • Phillippy AM; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
  • Smith TPL; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
Genome Biol ; 20(1): 153, 2019 08 02.
Article en En | MEDLINE | ID: mdl-31375138
We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Virus / Farmacorresistencia Microbiana / Análisis de Secuencia de ADN / Metagenómica / Microbiota Límite: Animals Idioma: En Revista: Genome Biol Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Virus / Farmacorresistencia Microbiana / Análisis de Secuencia de ADN / Metagenómica / Microbiota Límite: Animals Idioma: En Revista: Genome Biol Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido