1
|
Bearhart JM, Bethke JL, Christian CS, Cour FN, Creasey KR, Crowe EJ, Dahl JG, Hanson LA, Jaecks AL, Lamantia VA, Madison M, Roskowiak AL, Scheberl JD, VanEperen BM, Wurst ME, Klyczek KK. Complete genome sequence of Microbacterium paraoxydans phage Damascus. Microbiol Resour Announc 2024:e0128723. [PMID: 38624212 DOI: 10.1128/mra.01287-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/17/2024] [Indexed: 04/17/2024] Open
Abstract
Phage Damascus was isolated from soil in northwestern Wisconsin using Microbacterium paraoxydans as the host. The Damascus genome is 56,477 bp with 3' single-stranded overhangs and 56.5% G+C content. Damascus was assigned to cluster EL and shares 42.6%-91.7% gene content with the three other phages in this cluster.
Collapse
Affiliation(s)
- Julisa M Bearhart
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Jenna L Bethke
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Cassie S Christian
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Faith N Cour
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Karleigh R Creasey
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Emily J Crowe
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Julia G Dahl
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Lindsey A Hanson
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Abby L Jaecks
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Vincent A Lamantia
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Mercedes Madison
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Autumn L Roskowiak
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Justin D Scheberl
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Bekkah M VanEperen
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Morgan E Wurst
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| | - Karen K Klyczek
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, USA
| |
Collapse
|
2
|
Baumgartner BM, Bono KA, McIntosh DR, Vu AM, Adams CF, Benik BC, Chavez J, Gresky SJ, Sotelo A, Ray JI, Peister A, Kimberley KW, McKenna CC, Theoret JR, Yoon EJ, Windsor EJ. Genome sequences of actinobacteriophages JorRay, Blocker23, Nibbles, and OlgasClover. Microbiol Resour Announc 2024; 13:e0125623. [PMID: 38445868 PMCID: PMC11008117 DOI: 10.1128/mra.01256-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
JorRay, Blocker23, Nibbles, and OlgasClover are actinobacteriophages belonging to clusters G1, B2, CT, and DJ, respectively. JorRay and Blocker23 were identified in host bacterium Mycobacterium smegmatis mc2155. Nibbles and OlgasClover were identified in host bacterium Gordonia rubripertincta NRRL B-16540.
Collapse
Affiliation(s)
| | - Kayla A. Bono
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Dawn R. McIntosh
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Anna M. Vu
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Chanel F. Adams
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Brooklyn C. Benik
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Jessica Chavez
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Samantha J. Gresky
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Andres Sotelo
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Jordan I. Ray
- Department of Biology, Morehouse College, Atlanta, Georgia, USA
| | | | - Kendra W. Kimberley
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Chelsey C. McKenna
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - James R. Theoret
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Earl J. Yoon
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| | - Erin J. Windsor
- Department of Biological Sciences, College of Southern Nevada, Las Vegas, Nevada, USA
| |
Collapse
|
3
|
Tatum B, Murray P, Bicknell C, Webb SA, Kanak A. Genome sequence and annotation of Arthrobacter globiformis phage Ruchi (AS1) isolated from soil in Lumpkin County, Georgia. Microbiol Resour Announc 2024; 13:e0122423. [PMID: 38466103 PMCID: PMC11008183 DOI: 10.1128/mra.01224-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 02/28/2024] [Indexed: 03/12/2024] Open
Abstract
Ruchi, a temperate, AS1 subcluster bacteriophage isolated in Lumpkin County, Georgia using host Arthrobacter globiformis, possesses a genome of 38,571 bp and 67.7% GC. Annotation of this virus revealed 64 predicted reading frames, no predicted tRNA genes, and a close evolutionary relationship to AS1 phage Basilisk.
Collapse
Affiliation(s)
- Brooke Tatum
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Payton Murray
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Claire Bicknell
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Shane A. Webb
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Alison Kanak
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| |
Collapse
|
4
|
Barnes O, Workman CJ, Patterson NC, Oesch R, Johnson KL, Goncz K, Sharbrough J, DeVeaux LC. Desert diversity: genome sequence of Gordonia rubripertincta cluster DJ phage Mossy and cluster DV phage Erutan. Microbiol Resour Announc 2024; 13:e0124523. [PMID: 38470028 PMCID: PMC11008172 DOI: 10.1128/mra.01245-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Lytic bacteriophages Mossy and Erutan were directly isolated from desert soil on Gordonia rubripertincta and characterized by their morphologies and genomes. Mossy, part of the DJ cluster of Actinobacteriophage, has a genome of 61,183 bp. The genome of Erutan, part of the DV cluster, is 66,957 bp.
Collapse
Affiliation(s)
- October Barnes
- Department Biology, New Mexico Institute of Mining and Technology, Socorro, New Mexico, USA
| | - Christopher J. Workman
- Department Biology, New Mexico Institute of Mining and Technology, Socorro, New Mexico, USA
| | - Noah C. Patterson
- Department Biology, New Mexico Institute of Mining and Technology, Socorro, New Mexico, USA
| | - Riley Oesch
- Department Biology, New Mexico Institute of Mining and Technology, Socorro, New Mexico, USA
| | - Katie L. Johnson
- Department Biology, New Mexico Institute of Mining and Technology, Socorro, New Mexico, USA
| | - Kaarin Goncz
- Department Biology, New Mexico Institute of Mining and Technology, Socorro, New Mexico, USA
| | - Joel Sharbrough
- Department Biology, New Mexico Institute of Mining and Technology, Socorro, New Mexico, USA
| | - Linda C. DeVeaux
- Department Biology, New Mexico Institute of Mining and Technology, Socorro, New Mexico, USA
| |
Collapse
|
5
|
Kumar SV, Schaffer N, Bharmal Z, Mood Q, Erill I, Caruso SM. Complete genome and characteristics of cluster BC bacteriophage SoJo, isolated using Streptomyces mirabilis NRRL B-2400 in Columbia, MD. Microbiol Resour Announc 2024; 13:e0006824. [PMID: 38394246 PMCID: PMC11008112 DOI: 10.1128/mra.00068-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Here, we present bacteriophage SoJo, a siphovirus infecting Streptomyces mirabilis, with a circularly permuted genome of 39 kbp and GC content of 71.5%. Its genome length and content are similar to that of other phages in the Actinobacteriophage Database BC cluster. SoJo was isolated from soil in Columbia, MD, USA.
Collapse
Affiliation(s)
- Soven Verma Kumar
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Nicholas Schaffer
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Zainab Bharmal
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Quinn Mood
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | | | - Ivan Erill
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
- Departament d’Enginyeria de la Informació i de les Comunicacions, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Steven M. Caruso
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| |
Collapse
|
6
|
Bailey DS, Dotson DR, Berkes C, Agbede O, Augustin M, Blackman-Murray I, Chambers T, Felber N, Fleming D, Frazier L, Gray N, Harrison A, Hernandez G, Iwuchukwu N, Iwuji C, Jackson T, Jefferson A, Jordan D, Jordan M, Nicolas B, Person M, Richardson G, Roman A, Stevens C, Suggs M, Thompson N, Timmons-Smith S, Wilfong S, Wilson-Wheatley M. Complete genome sequence of Mycobacterium smegmatis phage Rummer, a subcluster A3 actinophage. Microbiol Resour Announc 2024; 13:e0126823. [PMID: 38466105 PMCID: PMC11008113 DOI: 10.1128/mra.01268-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
Bacteriophage Rummer is a siphovirus morphology actinophage isolated from Mycobacterium smegmatis. Rummer has a 50,908 base pair genome encoding 89 predicted protein-coding genes and three tRNAs. Based on gene content similarity to sequenced actinobacteriophages, Rummer is assigned to phage subcluster A3.
Collapse
Affiliation(s)
- Dondra S. Bailey
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Dominique R. Dotson
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Charlotte Berkes
- Department of Biology, Merrimack College, North Andover, Massachusetts, USA
| | - Oluwanifemi Agbede
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Marcelaine Augustin
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | | | - Talaeya Chambers
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Nicolas Felber
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Dy'Mon Fleming
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Loretta Frazier
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Natalie Gray
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Ayanna Harrison
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Genesis Hernandez
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Nina Iwuchukwu
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Chika Iwuji
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Taysha Jackson
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Angelic Jefferson
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Daya Jordan
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Miracle Jordan
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Brian Nicolas
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Monae Person
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Ga'Nayah Richardson
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Ashley Roman
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Christian Stevens
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - My'Sean Suggs
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Nahshon Thompson
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Summer Timmons-Smith
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | - Shiaishea Wilfong
- Department of Natural Sciences, Coppin State University, Baltimore, Maryland, USA
| | | |
Collapse
|
7
|
Adams RM, Britton HA, Bruce ED, De La Paz Y, Kratz EN, Pfeifer EJ, Priddy DE, Schotter BI, Stuffle WA, Wagner J, Weiss MR, Watt DK, Connerly PL, Rueschhoff EE. Genome sequence of Soos: a siphovirus of the CP cluster infecting Gordonia rubripertincta . Microbiol Resour Announc 2024; 13:e0120423. [PMID: 38526095 PMCID: PMC11008160 DOI: 10.1128/mra.01204-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/03/2024] [Indexed: 03/26/2024] Open
Abstract
Novel actinobacteriophage Soos was isolated and purified from Southern Indiana soil using host Gordonia rubripertincta NRRL B-16540. Sequencing revealed a 57,509 bp circularly permuted genome encoding 87 predicted protein-coding genes. Soos is only the third phage in cluster CP, along with phages Clawz and Sting.
Collapse
Affiliation(s)
- Reese M. Adams
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Holly A. Britton
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Emily D. Bruce
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Yucita De La Paz
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Emily N. Kratz
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Emma J. Pfeifer
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Daisy E. Priddy
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Brooklyn I. Schotter
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Wyatt A. Stuffle
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Jordyn Wagner
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Meredith R. Weiss
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Danielle K. Watt
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | - Pamela L. Connerly
- School of Natural Sciences, Indiana University Southeast, New Albany, Indiana, USA
| | | |
Collapse
|
8
|
Easterwood JC, Katsanos JM, Lloyd J. The genomic characterization of three Microbacterium foliorum-specific bacteriophages, "Nucci," "MCubed," and "QMacho". Microbiol Resour Announc 2024:e0020324. [PMID: 38597796 DOI: 10.1128/mra.00203-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024] Open
Abstract
Nucci, MCubed, and QMacho are microbacteriophages that were isolated from soil samples in Charlotte, NC. They were classified into EA10, EA2, and EB clusters, respectively. Nucci and MCubed each had 63 predicted genes, while QMacho had 73 predicted genes.
Collapse
Affiliation(s)
| | | | - Jenna Lloyd
- Department of Biology, Queens University of Charlotte, Charlotte, North Carolina, USA
| |
Collapse
|
9
|
Chuhran L, Whitlow C, Teems C, Kanak A, Webb SA. Genome sequence and annotation of Arthrobacter globiformis phage Vulpecula (AS1) isolated from soil in Dahlonega, Georgia. Microbiol Resour Announc 2024; 13:e0009024. [PMID: 38385671 DOI: 10.1128/mra.00090-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024] Open
Abstract
Vulpecula, a temperate bacteriophage collected from soil in Dahlonega, Georgia using host Arthrobacter globiformis, is an AS1 subcluster virus of 37,766 bp (67.7% GC). Genome annotation suggests 64 open reading frames, no predicted tRNA genes, and ~98% sequence similarity to AS1 phages Ruchi (from GA) and Jamun (New Hampshire).
Collapse
Affiliation(s)
- Lily Chuhran
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Chase Whitlow
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Carson Teems
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Alison Kanak
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Shane A Webb
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| |
Collapse
|
10
|
Diggins AE, Gubitose MG, Hinrichsen EG, Jones PT, Kearns BS, Lord CE, Parsons MT, Pitt RA, Woods IA, Zarakotas TR, Wilkes BM. Genome sequence of Arthrobacter globiformis phage MaGuCo. Microbiol Resour Announc 2024; 13:e0117923. [PMID: 38376341 DOI: 10.1128/mra.01179-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
MaGuCo is a temperate phage isolated from soil collected in Alton, NH, USA, using Arthrobacter globiformis. Its genome is 43,924 base pairs long and contains 63 protein-encoding genes, 44 of which were assigned putative functions. MaCuGo is assigned to cluster AZ2 based on gene content similarity to actinobacteriophages.
Collapse
Affiliation(s)
- Amanda E Diggins
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Mary G Gubitose
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Elijah G Hinrichsen
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Patrick T Jones
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Brian S Kearns
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Caitlynn E Lord
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Mary T Parsons
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Rachel A Pitt
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Isabella A Woods
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Teagan R Zarakotas
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| | - Beth M Wilkes
- Department of Natural Sciences, NHTI - Concord's Community College, Concord, New Hampshire, USA
| |
Collapse
|
11
|
Migueletti MR, García Rey J, Micheloni J, Lomanto C, Martelli E, Sánchez G, Colombo JM, Vallecillo LM, Lamagni F, Giusti T, Acosta F, Villagrán F, Gvozdenovich M, Pricco Frakich A, Pianesi T, Tulin G, Mascali FC, Petitti TD, Torres Manno MA, Fusari CM, Buttigliero L, Giordana MF, Gramajo H, Diacovich L, Espariz M, Mussi MA. Complete genome sequence of the Microbacterium foliorum bacteriophage Garey24. Microbiol Resour Announc 2024; 13:e0121523. [PMID: 38315107 DOI: 10.1128/mra.01215-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
In this work, we report the discovery and characterization of Garey24, a bacteriophage that forms medium-size plaques with halo rings isolated from a soil sample in Funes, Argentina. Its 41,522 bp circularly permuted genome contains 63 putative protein-coding genes. Based on gene content similarity, Garey24 was assigned to subcluster EA1.
Collapse
Affiliation(s)
- Matías R Migueletti
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Julieta García Rey
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Josefina Micheloni
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Camila Lomanto
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Elisa Martelli
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Gastón Sánchez
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Julián M Colombo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Luciano M Vallecillo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Francisco Lamagni
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Tomás Giusti
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Fabrina Acosta
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Franco Villagrán
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Martín Gvozdenovich
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Abril Pricco Frakich
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Tulio Pianesi
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Gonzalo Tulin
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Florencia C Mascali
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Tomás D Petitti
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Mariano A Torres Manno
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Corina M Fusari
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | | | | | - Hugo Gramajo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Lautaro Diacovich
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Martín Espariz
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - María Alejandra Mussi
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| |
Collapse
|
12
|
Oliveros AM, McDougall SA, Snyder MA, Snowden SK, Richard JD, Rao CM, Ponce M, Pitonza CJ, Ozcelik M, Mannina SS, Magna JR, Lopez AS, Gustafson LC, Glackin BK, Dolge AE, DeLancy ND, Davis ABC, Davis TP, Blagodar M, Natale SN, Dennis MK, Godin EA. Genome sequence of bacteriophage Djungelskog isolated from an Arthrobacter globiformis culture. Microbiol Resour Announc 2024; 13:e0129423. [PMID: 38376224 DOI: 10.1128/mra.01294-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
Actinobacteriophage Djungelskog was isolated from a sample of degraded organic material in Poughkeepsie, NY, using Arthrobacter globiformis B-2979. Its genome is 54,512 bp and encodes 86 putative protein-coding genes. Djungelskog has a siphovirus morphology and is assigned to cluster AW based on gene content similarity to actinobacteriophages.
Collapse
Affiliation(s)
| | | | - Miles A Snyder
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Sara K Snowden
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Joseph D Richard
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | | | - Marybeth Ponce
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | | | - Mira Ozcelik
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Sofia S Mannina
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Juliana R Magna
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Andrew S Lopez
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | | | - Brynn K Glackin
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Abigail E Dolge
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Nate D DeLancy
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Andrew B C Davis
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Thomas P Davis
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Max Blagodar
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Sydney N Natale
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | - Megan K Dennis
- Department of Biology, Marist College, Poughkeepsie, New York, USA
| | | |
Collapse
|
13
|
Ngove Z, Matthews R, Goedken J, Huntington S, Kirkle L, Coleman ST. Complete genome sequences of bacteriophages Guetzie and SirVictor, isolated from Microbacterium foliorum. Microbiol Resour Announc 2024; 13:e0107423. [PMID: 38294214 DOI: 10.1128/mra.01074-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/21/2024] [Indexed: 02/01/2024] Open
Abstract
Cluster EA4 Guetzie and SirVictor are lytic siphoviral bacteriophages that were isolated from soil in Waverly, Iowa, using Microbacterium foliorum NRRL B-24224 as the host. The Guetzie and SirVictor genomes are both 39,758 bp each, and both contain 58 predicted protein-coding genes with one tRNA gene each.
Collapse
Affiliation(s)
- Zefanias Ngove
- Biology Department, Wartburg College, Waverly, Iowa, USA
| | | | - Jack Goedken
- Biology Department, Wartburg College, Waverly, Iowa, USA
| | | | - Lauren Kirkle
- Biology Department, Wartburg College, Waverly, Iowa, USA
| | - Sean T Coleman
- Biology Department, Wartburg College, Waverly, Iowa, USA
| |
Collapse
|
14
|
Rossier O, Labarre C, Lopes A, Auberdiac M, Tambosco K, Delaruelle D, Abes H, Arteni AA, Ouldali M, Pieri L, Afgoun R, Anacleto L, Beaure N, Beghdad M, Bellom N, Ben Hamou-Kuijpers E, Boukamel A, Carron J, Carta V, Castelneau L, Chadaillac Z, Chaouat E, Desmat S, Favel K, Gabillot E, Gargar M, Gautheret M, Gilles E, Lager C, Le Deit A, Le vay Y, Lemercier L, Litvinov A, Moussi S, Prevot M, Rehala M, Rodrigues C, Sambe R, Srimoorthy A, Tillay TM, Verhoeven C, Vittaz P, Wu J, Regeard C. Genome sequence of PSonyx, a singleton bacteriophage infecting Corynebacterium glutamicum. Microbiol Resour Announc 2024; 13:e0115523. [PMID: 38236045 PMCID: PMC10868258 DOI: 10.1128/mra.01155-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024] Open
Abstract
PSonyx is a newly isolated phage that infects Corynebacterium glutamicum. This siphovirus was isolated from a French pond in the south of Paris by students from Paris-Saclay University. Its 80,277-bp singleton genome carries 136 protein-coding genes and 5 tRNAs.
Collapse
Affiliation(s)
- Ombeline Rossier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Cécile Labarre
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Anne Lopes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Monique Auberdiac
- Faculté des Sciences d’Orsay, Université Paris-Saclay, Orsay, France
| | - Kevin Tambosco
- Faculté des Sciences d’Orsay, Université Paris-Saclay, Orsay, France
| | - Daniel Delaruelle
- Faculté des Sciences d’Orsay, Université Paris-Saclay, Orsay, France
| | - Hakima Abes
- Faculté des Sciences d’Orsay, Université Paris-Saclay, Orsay, France
| | - Ana A. Arteni
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Malika Ouldali
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Laura Pieri
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Ryan Afgoun
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Leonor Anacleto
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Nathan Beaure
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Meyssa Beghdad
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Nolwenn Bellom
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | | | - Aïda Boukamel
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - James Carron
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Vincent Carta
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Lauriane Castelneau
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Zoe Chadaillac
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Elsa Chaouat
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Soline Desmat
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Keylian Favel
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Eva Gabillot
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Melissa Gargar
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Madeleine Gautheret
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Esther Gilles
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Claire Lager
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Amandine Le Deit
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Yoann Le vay
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Laure Lemercier
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | | | - Samir Moussi
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Marion Prevot
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Marion Rehala
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Chloë Rodrigues
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Ramatoulaye Sambe
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Ashvini Srimoorthy
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | | | - Cerise Verhoeven
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Pauline Vittaz
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Jacqueline Wu
- Ecole Universitaire de Premier Cycle, Université Paris-Saclay, Orsay, France
| | - Christophe Regeard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| |
Collapse
|
15
|
Prout AE, Swerdlow SJ. Genome sequences of Microbacterium foliorum phages, BabyYoda and Lynlen. Microbiol Resour Announc 2024; 13:e0100623. [PMID: 38132671 PMCID: PMC10871031 DOI: 10.1128/mra.01006-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
BabyYoda and Lynlen are two cluster EB phages that were discovered at Thiel College using Microbacterium foliorum NRRL B-24224. Both BabyYoda and Lynlen are predicted to be lytic, with siphovirus morphologies, with genome sizes of 41,557 and 41,448 base pairs, respectively.
Collapse
Affiliation(s)
- Ashley E. Prout
- Biology Department, Thiel College, Greenville, Pennsylvania, USA
| | - Sarah J. Swerdlow
- Department of Natural Sciences-Biological Sciences, University of Pittsburgh-Greensburg, Greensburg, Pennsylvania, USA
| |
Collapse
|
16
|
Makhoul JC, Valentine M, Campbell C, McLaughlin EG, Vereline FH, Collins JM, Crandall SIG, Rabideau EL, Tender WJ, Fairweather SL, Miller CJ, Mcleish KQY, Izquierdo JD, Gallagher LN, Tyrrell LP, Gleichsner AM. Genome sequence of Microbacterium foliorum phage CandC. Microbiol Resour Announc 2024; 13:e0111723. [PMID: 38231186 PMCID: PMC10868228 DOI: 10.1128/mra.01117-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/15/2023] [Indexed: 01/18/2024] Open
Abstract
We report the discovery and genome sequence of CandC, a lytic bacteriophage with siphovirus morphology. CandC was isolated from a soil sample from Plattsburgh, NY, USA (Fall 2021). It has a genome size of 62,344 bp with 106 predicted protein-encoding genes, 30 of which are assigned putative functions.
Collapse
Affiliation(s)
- Joëlle C. Makhoul
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Megan Valentine
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Caila Campbell
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Emma G. McLaughlin
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Frank H. Vereline
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Jenna M. Collins
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Sophia I. G. Crandall
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Emma L. Rabideau
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Wesley J. Tender
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Shaniah L. Fairweather
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Carson J. Miller
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Kori Q. Y. Mcleish
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Justin D. Izquierdo
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Leah N. Gallagher
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Luke P. Tyrrell
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| | - Alyssa M. Gleichsner
- Department of Biological Sciences, State University of New York, College at Plattsburgh, Plattsburgh, New York, USA
| |
Collapse
|
17
|
Andro MN, Cansler AJJ, Conley OS, Cruz NO, Dionne JA, Edwards JI, Furtuna D, Green CJ, Huber M, Hudson GJ, Humphries IR, Karazin AA, Mombille PI, Pell MM, Shickle G, Shipp ZJ, Timmons CA, Trembush JI, Turnmire CD, Yemofio NY, Burleson MD, Gainey MD. From Cullowhee Creek to Conley: genome sequence and annotation of a cluster DJ Gordonia phage. Microbiol Resour Announc 2024; 13:e0117623. [PMID: 38133170 PMCID: PMC10868162 DOI: 10.1128/mra.01176-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
We report the discovery of Gordonia phage Conley, a siphovirus isolated from Cullowhee Creek in the Fall of 2022. The 60,078bp genome contains 90 predicted protein-coding genes all transcribed in the same direction and has been assigned to genetic cluster DJ based on gene content similarity.
Collapse
Affiliation(s)
- Mindy N. Andro
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - AJ J. Cansler
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Olivia S. Conley
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Naidelyn O. Cruz
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Joshua A. Dionne
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Jordan I. Edwards
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Daniel Furtuna
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Carlee J. Green
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Miriam Huber
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Gunnar J. Hudson
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Isabella R. Humphries
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Amanda A. Karazin
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Patrizia I. Mombille
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Montana M. Pell
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Gabriela Shickle
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Zahria J. Shipp
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Chloe A. Timmons
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Jasmine I. Trembush
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Cameron D. Turnmire
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Naa Yemoley Yemofio
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Mathew D. Burleson
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Maria D. Gainey
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| |
Collapse
|
18
|
Alexander WK, Allen RR, Anderson JD, Brumfield AN, Cook TM, Dana GM, Ethridge GJ, Gailey EC, Netzley RA, Nguyen JV, Souza PJ, Yoder BM, Wallen JR, Gainey MD, Bates TC, Wisner EM. From compost to culver: genome sequence and annotation of a cluster CQ1 Gordonia phage. Microbiol Resour Announc 2024; 13:e0106623. [PMID: 38132830 PMCID: PMC10868165 DOI: 10.1128/mra.01066-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
Phage Culver, with a siphovirus morphology, was isolated using Gordonia terrae CAG3. Culver is assigned to phage cluster CQ1 based on gene content similarity to actinobacteriophages. Notably, Culver is predicted to encode eight tRNAs, lysin A by two adjacent genes, and, unlike other CQ1 phages, two putative integrase genes.
Collapse
Affiliation(s)
- William K. Alexander
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Rianna R. Allen
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Jaden D. Anderson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Amber N. Brumfield
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Tiffany M. Cook
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Giana M. Dana
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Gregory J. Ethridge
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Emily C. Gailey
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Rebekah A. Netzley
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Joshua V. Nguyen
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Phillip J. Souza
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Briggs M. Yoder
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Jamie R. Wallen
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Maria D. Gainey
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina, USA
| | - Tonya C. Bates
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Ellen M. Wisner
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| |
Collapse
|
19
|
Radersma MD, Lathrop G, Moleakunnel KC, Harlow LA, Baker AE, Chen AJ, Churu JG, Dole CA, Doorn SL, Hill EM, Howland A, Janvier A, Kramer CM, Minasian MJ, Nieze JR, Perezrios IK, Ramsey FJ, Seinen KL, Swierenga SK, Veenstra MM, Weaver GE, White AC, Yoon E, Wertz JT, DeJong RJ. Complete genome sequences of nine Rhodococcus equi phages. Microbiol Resour Announc 2024; 13:e0108823. [PMID: 38179906 PMCID: PMC10868187 DOI: 10.1128/mra.01088-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024] Open
Abstract
We report genomes of nine phages isolated from Actinobacteria Rhodococcus equi NRRL B-16538. Six of these phages belong to actinobacteriophage cluster CR, which otherwise contains Gordonia phages; two form the CF cluster; and one is a singleton. Genome lengths are 62,017-80,980 bp with 63.9%-67.3% GC content.
Collapse
Affiliation(s)
- Myles D. Radersma
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Gabrielle Lathrop
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | | | - Luke A. Harlow
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Aerin E. Baker
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Alison J. Chen
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Jason G. Churu
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Carly A. Dole
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Sophia L. Doorn
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Ethan M. Hill
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Anna Howland
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Amanda Janvier
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Catie M. Kramer
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Matt J. Minasian
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Jocelyn R. Nieze
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | | | - Fiona J. Ramsey
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Katie L. Seinen
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | | | | | - Grace E. Weaver
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | | | - Esther Yoon
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - John T. Wertz
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Randall J. DeJong
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| |
Collapse
|
20
|
Cao Yao JC, Garcia Cehic D, Quer J, Méndez JN, Gorrín AD, Hevia LG, Fernández MTT. Complete Genome Sequences of Four Mycobacteriophages Involved in Directed Evolution against Undisputed Mycobacterium abscessus Clinical Strains. Microorganisms 2024; 12:374. [PMID: 38399778 PMCID: PMC10893344 DOI: 10.3390/microorganisms12020374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Phage therapy is still in its infancy, but it is increasingly promising as a future alternative for treating antibiotic-resistant bacteria. To investigate the effect of phages on Mycobacterium abscessus complex (MABC), we isolated 113 environmental phages, grown them to high titres, and assayed them on MABC clinical strains through the spot test. Of all the phages, only 16 showed killing activity. Their activity was so temperate to MABC that they could not generate any plaque-forming units (PFUs). The Appelmans method of directed evolution was carried out to evolve these 16 phages into more lytic ones. After only 11 of 30 rounds of evolution, every single clinical strain in our collection, including those that were unsusceptible up to this point, could be lysed by at least one phage. The evolved phages were able to form PFUs on the clinical strains tested. Still, they are temperate at best and require further training. The genomes of one random parental phage and three random evolved phages from Round 13 were sequenced, revealing a diversity of clusters and genes of a variety of evolutionary origins, mostly of unknown function. These complete annotated genomes will be key for future molecular characterisations.
Collapse
Affiliation(s)
- Juan Carlos Cao Yao
- Department of Molecular Biology and Biomedicine, University of Cantabria, 39011 Santander, Spain (A.D.G.); (L.G.H.)
| | - Damir Garcia Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Hospital Universitari Vall d’Hebron, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (D.G.C.); (J.Q.)
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Hospital Universitari Vall d’Hebron, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (D.G.C.); (J.Q.)
- CIBER de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Jesús Navas Méndez
- Department of Molecular Biology and Biomedicine, University of Cantabria, 39011 Santander, Spain (A.D.G.); (L.G.H.)
- Instituto de Investigación Valdecilla (IDIVAL), 39011 Santander, Spain
| | - Alexis Dorta Gorrín
- Department of Molecular Biology and Biomedicine, University of Cantabria, 39011 Santander, Spain (A.D.G.); (L.G.H.)
- Instituto de Investigación Valdecilla (IDIVAL), 39011 Santander, Spain
| | - Lorena García Hevia
- Department of Molecular Biology and Biomedicine, University of Cantabria, 39011 Santander, Spain (A.D.G.); (L.G.H.)
- Instituto de Investigación Valdecilla (IDIVAL), 39011 Santander, Spain
| | - María Teresa Tórtola Fernández
- Mycobacteria Unit, Clinical Laboratories, Microbiology Service, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| |
Collapse
|
21
|
Gong C, Chakraborty D, Koudelka GB. A prophage encoded ribosomal RNA methyltransferase regulates the virulence of Shiga-toxin-producing Escherichia coli (STEC). Nucleic Acids Res 2024; 52:856-871. [PMID: 38084890 PMCID: PMC10810198 DOI: 10.1093/nar/gkad1150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 01/26/2024] Open
Abstract
Shiga toxin (Stx) released by Shiga toxin producing Escherichia coli (STEC) causes life-threatening illness. Its production and release require induction of Stx-encoding prophage resident within the STEC genome. We identified two different STEC strains, PA2 and PA8, bearing Stx-encoding prophage whose sequences primarily differ by the position of an IS629 insertion element, yet differ in their abilities to kill eukaryotic cells and whose prophages differ in their spontaneous induction frequencies. The IS629 element in ϕPA2, disrupts an ORF predicted to encode a DNA adenine methyltransferase, whereas in ϕPA8, this element lies in an intergenic region. Introducing a plasmid expressing the methyltransferase gene product into ϕPA2 bearing-strains increases both the prophage spontaneous induction frequency and virulence to those exhibited by ϕPA8 bearing-strains. However, a plasmid bearing mutations predicted to disrupt the putative active site of the methyltransferase does not complement either of these defects. When complexed with a second protein, the methyltransferase holoenzyme preferentially uses 16S rRNA as a substrate. The second subunit is responsible for directing the preferential methylation of rRNA. Together these findings reveal a previously unrecognized role for rRNA methylation in regulating induction of Stx-encoding prophage.
Collapse
Affiliation(s)
- Chen Gong
- Department of Biological Sciences University at Buffalo, Buffalo, NY 14260, USA
| | | | - Gerald B Koudelka
- Department of Biological Sciences University at Buffalo, Buffalo, NY 14260, USA
| |
Collapse
|
22
|
Stamm J, Merkle JA, Abernathy A, Ackerman E, Brown J, Harris A, Hoffman K, Hoskins A, Jahn A, Jones N, Kitch A, Mathavan N, Rose N, Taylor J. Complete genome sequences of Streptomyces griseus phages Spelly and Phredrick. Microbiol Resour Announc 2024; 13:e0104923. [PMID: 38112473 PMCID: PMC10793280 DOI: 10.1128/mra.01049-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 11/29/2023] [Indexed: 12/21/2023] Open
Abstract
We present the complete genome sequences of two viruses with siphovirus morphology, isolated from soils collected in Southwestern Indiana using the host Streptomyces griseus. Spelly is a BE2 cluster phage with a 131,347-bp genome. Phredrick is a BK1 cluster phage with a 128,873-bp genome.
Collapse
Affiliation(s)
- Joyce Stamm
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Julie A. Merkle
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Ava Abernathy
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Elizabeth Ackerman
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - John Brown
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Abbey Harris
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Kayli Hoffman
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Ashleigh Hoskins
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Abbie Jahn
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Nathan Jones
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Ashley Kitch
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Nandini Mathavan
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Nat Rose
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | - Joey Taylor
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| |
Collapse
|
23
|
Anders KR, Abeyta A, Andrade CC, Bonilla CY, Braley AB, Bratt AG, Duncan KA, Hayes SG, Robinson CJ, Smith-Flores H, Ettinger ASH, Ettinger WF, Fay MM, Haydock J, McKenzie SK, Garlena RA, Russell DA, Poxleitner MK. Genome sequences of 31 mycobacteriophages isolated on Mycobacterium smegmatis mc 2155 at room temperature. Microbiol Resour Announc 2024; 13:e0108623. [PMID: 38099681 DOI: 10.1128/mra.01086-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 11/29/2023] [Indexed: 01/18/2024] Open
Abstract
We report the genome sequences of 31 mycobacteriophages isolated on Mycobacterium smegmatis mc2155 at room temperature. The genomes add to the diversity of Clusters A, B, C, G, and K. Collectively, the genomes include 70 novel protein-coding genes that have no close relatives among the actinobacteriophages.
Collapse
Affiliation(s)
- Kirk R Anders
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Antonio Abeyta
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Christy C Andrade
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Carla Y Bonilla
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Amanda B Braley
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Alexandra G Bratt
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Kaya A Duncan
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Stephen G Hayes
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Ciara J Robinson
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | | | | | | | - Marta M Fay
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Joseph Haydock
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Sean K McKenzie
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh , Pittsburgh, Pennsylvania, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh , Pittsburgh, Pennsylvania, USA
| | | |
Collapse
|
24
|
Baliraine FW, Mathews KE, Livingston EG, Martinez CA, Donnelly OL, Pledger TM, Feroz T, Harbison ZJ, Schlimme SG, Andrade C, Salazar KN, Berryhill EC, DeLosSantos MM, Foree HL, Gicheru W, Jett AM, Mendez SN, Odebiyi TM, Pitman JI, Tan MJ, McLoud JD, Baliraine FN. Complete genome sequences and characteristics of mycobacteriophages Diminimus, Dulcita, Glaske16, and Koreni. Microbiol Resour Announc 2024; 13:e0101023. [PMID: 38063427 DOI: 10.1128/mra.01010-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 11/10/2023] [Indexed: 01/18/2024] Open
Abstract
Complete genome sequences of four novel mycobacteriophages, Diminimus, Dulcita, Glaske16, and Koreni, isolated from soil are presented. All these bacteriophages belong to subcluster M1, except Koreni that belongs to subcluster A4. Moreover, all have siphovirus morphologies, with genome sizes ranging from 51,055 to 81,156 bp.
Collapse
Affiliation(s)
- Faith W Baliraine
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Kaitlyn E Mathews
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Emma G Livingston
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Clarissa A Martinez
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Olivia L Donnelly
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Taryn M Pledger
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Tadeen Feroz
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Zoe J Harbison
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Sarah G Schlimme
- Department of Electrical, Computer, and Biomedical Engineering, LeTourneau University , Longview, Texas, USA
| | - Camila Andrade
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Keren N Salazar
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Elise C Berryhill
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | | | - Hannah L Foree
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Wanjiru Gicheru
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Adrienne M Jett
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Sofia N Mendez
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Toluwalope M Odebiyi
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Jacob I Pitman
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Michael J Tan
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | - Josh D McLoud
- Department of Biology and Kinesiology, LeTourneau University , Longview, Texas, USA
| | | |
Collapse
|
25
|
Dojs M, Fleischacker C, Ackerman S, Boyle B, Feiring S, Fleischacker T, Frank J, Jackson S, Schaefbauer A, Vigness C, Webb R. Genome sequences of bacteriophage Shambre1 and Renna12, isolated from Arthrobacter globiformis. Microbiol Resour Announc 2024; 13:e0085823. [PMID: 38088575 DOI: 10.1128/mra.00858-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/18/2023] [Indexed: 01/18/2024] Open
Abstract
Bacteriophages Shambre1 and Renna12 were isolated from soil in Bismarck, ND, using Arthrobacter globiformis. Genomic characterization and analyses allowed Renna12 to be assigned to phage cluster AS3, while Shambre1, which is not closely related to any phage, is a singleton.
Collapse
Affiliation(s)
- Madeline Dojs
- Department of Biology, University of Mary , Bismarck, North Dakota, USA
| | | | - Skylar Ackerman
- Department of Biology, University of Mary , Bismarck, North Dakota, USA
| | - Blaise Boyle
- Department of Biology, University of Mary , Bismarck, North Dakota, USA
| | - Shambre Feiring
- Department of Biology, University of Mary , Bismarck, North Dakota, USA
| | | | - Jaycee Frank
- Department of Biology, University of Mary , Bismarck, North Dakota, USA
| | - Sarah Jackson
- Department of Biology, University of Mary , Bismarck, North Dakota, USA
| | | | - Corinna Vigness
- Department of Biology, University of Mary , Bismarck, North Dakota, USA
| | - Rylie Webb
- Department of Biology, University of Mary , Bismarck, North Dakota, USA
| |
Collapse
|
26
|
Cousins SR, Dufour GR, Law K, Nichols RM, Sladek BJ, Aniapam CR, Tarbox BP, Savage EF. Genome sequence of the lytic bacteriophage Alucard, a cluster EE actinophage. Microbiol Resour Announc 2024; 13:e0101723. [PMID: 38051077 DOI: 10.1128/mra.01017-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/08/2023] [Indexed: 12/07/2023] Open
Abstract
Bacteriophage Alucard is a lytic phage isolated from the soil collected in southern Maine on Microbacterium foliorum NRRL B-24224. Alucard has siphovirus morphology with a 17,363-bp genome encoding 25 putative genes. Based on gene content similarity to actinobacteriophages, Alucard is assigned to cluster EE.
Collapse
Affiliation(s)
- Samuel R Cousins
- Biology, Southern Maine Community College , South Portland, Maine, USA
| | - Gemma R Dufour
- Biology, Southern Maine Community College , South Portland, Maine, USA
| | - Kendra Law
- Biology, Southern Maine Community College , South Portland, Maine, USA
| | - Robert M Nichols
- Biology, Southern Maine Community College , South Portland, Maine, USA
| | - Bradi J Sladek
- Biology, Southern Maine Community College , South Portland, Maine, USA
| | | | - Brian P Tarbox
- Biology, Southern Maine Community College , South Portland, Maine, USA
| | - Emily F Savage
- Biology, Southern Maine Community College , South Portland, Maine, USA
| |
Collapse
|
27
|
Bazinet N, Biro E, Geydoshek A, Hodgkin G, Jestel E, Klute E, MacDonald C, Russano M, Thatcher J, Neely MN, Molloy S. Characterization of the genomes of cluster CT Gordonia terrae phages, Horseradish and Yummy. Microbiol Resour Announc 2023; 12:e0074723. [PMID: 37982651 PMCID: PMC10720472 DOI: 10.1128/mra.00747-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/16/2023] [Indexed: 11/21/2023] Open
Abstract
The genomes of lytic, cluster CT Gordonia terrae phages, Horseradish and Yummy, are 45,764 and 45,878 bp in length, respectively, and each encodes 71 protein-coding genes. The genomes are identical in sequence with the exception of a 38-bp insertion/deletion in the minor tail protein, gp26.
Collapse
Affiliation(s)
- Nicole Bazinet
- The Honors College, University of Maine, Orono, Maine, USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Esther Biro
- The Honors College, University of Maine, Orono, Maine, USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Ashley Geydoshek
- The Honors College, University of Maine, Orono, Maine, USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Grace Hodgkin
- The Honors College, University of Maine, Orono, Maine, USA
- School of Biology and Ecology, University of Maine, Orono, Maine, USA
| | - Eric Jestel
- The Honors College, University of Maine, Orono, Maine, USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Emily Klute
- The Honors College, University of Maine, Orono, Maine, USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Clare MacDonald
- The Honors College, University of Maine, Orono, Maine, USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Marcus Russano
- The Honors College, University of Maine, Orono, Maine, USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Jayson Thatcher
- The Honors College, University of Maine, Orono, Maine, USA
- School of Biology and Ecology, University of Maine, Orono, Maine, USA
| | - Melody N. Neely
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Sally Molloy
- The Honors College, University of Maine, Orono, Maine, USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| |
Collapse
|
28
|
Guerrero JA, Maldonado N, Mbajiofor EO, Ramirez L, Valencia MJ, Healy CD, Garza AA, Mizell SA, Jackson BN, Vargas Ayala M. Characterization and genome sequence of Microbacterium foliorum phage Morrigan, of cluster EA6 with siphovirus morphology. Microbiol Resour Announc 2023; 12:e0071923. [PMID: 37975671 PMCID: PMC10720499 DOI: 10.1128/mra.00719-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/12/2023] [Indexed: 11/19/2023] Open
Abstract
Bacteriophage Morrigan, which was isolated from soil using Microbacterium foliorum NRRL B-24224, is lytic with siphovirus morphology. Morrigan's 40,509-bp genome has a GC content of 62.8% and 66 putative protein-coding genes, of which 31 could be assigned putative functions. Based on gene content similarity to actinobacteriophages, Morrigan is assigned to subcluster EA6.
Collapse
Affiliation(s)
- Jennifer A. Guerrero
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Nery Maldonado
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Emmanuella O. Mbajiofor
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Lisette Ramirez
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Mary Jo Valencia
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Creehan D. Healy
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Alejandro A. Garza
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Samantha A. Mizell
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Brianna N. Jackson
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Mayra Vargas Ayala
- Department of Integrative Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| |
Collapse
|
29
|
Markov SA, Olusoga KO, Oni PO, Henderson GA. Genome sequence of Microbacterium foliorum bacteriophage DumpQuist isolated from soil in Clarksville, Tennessee. Microbiol Resour Announc 2023; 12:e0092323. [PMID: 37991355 PMCID: PMC10720438 DOI: 10.1128/mra.00923-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 10/19/2023] [Indexed: 11/23/2023] Open
Abstract
Bacteriophage DumpQuist was isolated from soil collected in Clarksville, TN, using the bacterium Microbacterium foliorum. Electron microscopy revealed that DumpQuist has a podovirus morphology. DumpQuist has a 53,924-bp genome that contains 54 predicted protein-coding genes and is most similar to phages in actinobacteriophage cluster EK1.
Collapse
Affiliation(s)
- Sergei A. Markov
- Biology Department, Austin Peay State University, Clarksville, Tennessee, USA
| | - Kehinde O. Olusoga
- Biology Department, Austin Peay State University, Clarksville, Tennessee, USA
| | - Patience O. Oni
- Biology Department, Austin Peay State University, Clarksville, Tennessee, USA
| | - Grace A. Henderson
- Biology Department, Austin Peay State University, Clarksville, Tennessee, USA
| |
Collapse
|
30
|
McLean N, Jackson T, Govardhan Y, Dharanendiran A, Bost C, Brown F, Cowen B, Deselem J, Parkhurst N, Stewart J, Leonard J, Collins DP. Genome sequences of cluster GA phages Phonegingi and Dropshot. Microbiol Resour Announc 2023; 12:e0091823. [PMID: 38014965 PMCID: PMC10720569 DOI: 10.1128/mra.00918-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 10/25/2023] [Indexed: 11/29/2023] Open
Abstract
Bacteriophages Phonegingi and Dropshot were isolated from soil in North Carolina using the host Microbacterium foliorum. Both phages have siphovirus morphologies. Based on gene content similarity to one another and to other actinobacteriophages, both phages are assigned to phage cluster GA.
Collapse
Affiliation(s)
- Natalie McLean
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Tabitha Jackson
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Yajat Govardhan
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Aditi Dharanendiran
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Caden Bost
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Frederick Brown
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Benjamin Cowen
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Jenna Deselem
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Nico Parkhurst
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Jacob Stewart
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - Justin Leonard
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| | - D. Parks Collins
- Department of Natural Sciences, Mitchell Community College, Statesville, North Carolina, USA
| |
Collapse
|
31
|
Wood PR, Sullivan EA, Mathison RT, Hepworth SM, Graves RS, Danklefsen B, Almahie O, Serna C, Hunt DJ, Brewster R, Bartholomew S, Shurley JF, Grinath AS, Thomas MA. Isolation and genome sequence annotation of SallyK, a newly discovered cluster EG bacteriophage infecting Microbacterium. Microbiol Resour Announc 2023; 12:e0094323. [PMID: 37991360 PMCID: PMC10720488 DOI: 10.1128/mra.00943-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 10/15/2023] [Indexed: 11/23/2023] Open
Abstract
Discovered from soil in a flower planter in Pocatello, Idaho and using Microbacterium foliorum, SallyK is a lytic bacteriophage with a siphovirus morphology. It has a 62,883 bp-long genome with 103 putative genes. Based on gene content similarity to actinobacteriophages, SallyK is assigned to cluster EG.
Collapse
Affiliation(s)
- Paige R. Wood
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Emily A. Sullivan
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Rylee T. Mathison
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Sariah M. Hepworth
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - R. Scott Graves
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Breanna Danklefsen
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Omer Almahie
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Carlos Serna
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Dylan J. Hunt
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Reganne Brewster
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Skylar Bartholomew
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Jack F. Shurley
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Anna S. Grinath
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Michael A. Thomas
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| |
Collapse
|
32
|
Loney RE, Delesalle VA, Chaudry BE, Czerpak M, Guffey AA, Goubet-McCall L, McCarty M, Strine MS, Tanke NT, Vill AC, Krukonis GP. A Novel Subcluster of Closely Related Bacillus Phages with Distinct Tail Fiber/Lysin Gene Combinations. Viruses 2023; 15:2267. [PMID: 38005943 PMCID: PMC10674732 DOI: 10.3390/v15112267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Bacteriophages (phages) are the most numerous entities on Earth, but we have only scratched the surface of describing phage diversity. We isolated seven Bacillus subtilis phages from desert soil in the southwest United States and then sequenced and characterized their genomes. Comparative analyses revealed high nucleotide and amino acid similarity between these seven phages, which constitute a novel subcluster. Interestingly, the tail fiber and lysin genes of these phages seem to come from different origins and carry out slightly different functions. These genes were likely acquired by this subcluster of phages via horizontal gene transfer. In conjunction with host range assays, our data suggest that these phages are adapting to hosts with different cell walls.
Collapse
Affiliation(s)
- Rachel E. Loney
- University Program in Genetics and Genomics, School of Medicine, Duke University, Durham, NC 27708, USA
| | - Véronique A. Delesalle
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA; (M.C.); (M.M.)
| | | | - Megan Czerpak
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA; (M.C.); (M.M.)
| | - Alexandra A. Guffey
- Janssen Scientific Affairs, LLC. 200 Tournament Dr., Horsham, PA 19044, USA;
| | - Leo Goubet-McCall
- Department of Biology, The Pennsylvania State University, 201 Huck Life Sciences Building, University Park, PA 16802, USA;
| | - Michael McCarty
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA; (M.C.); (M.M.)
| | - Madison S. Strine
- Department of Immunobiology, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA;
| | - Natalie T. Tanke
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Albert C. Vill
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA;
| | - Greg P. Krukonis
- Department of Biology, Angelo State University, Cavness Science Building 101, ASU Station #10890, San Angelo, TX 76909, USA;
| |
Collapse
|
33
|
Nesbit AE, Kanak AE. Genomic sequence identification of Arthrobacter phage Ascela. Microbiol Resour Announc 2023; 12:e0077623. [PMID: 37905911 PMCID: PMC10652938 DOI: 10.1128/mra.00776-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023] Open
Abstract
Arthrobacter phage Ascela was isolated in North Georgia. Its genome is 44,192 bp with 71 open reading frames and a GC content of 67.4%. It shares 99.29% nucleotide identity with Arthrobacter phage Iter. Actinobacteriophages that share over 50% nucleotide identity are sorted into clusters, with Ascela in cluster AZ and subcluster AZ1.
Collapse
Affiliation(s)
- Audrey E. Nesbit
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| | - Alison E. Kanak
- Department of Biology, University of North Georgia, Dahlonega, Georgia, USA
| |
Collapse
|
34
|
Cleary KE, Pelagalli C, Cassford M, Berry N, Aguas E, Kim B, deCarvalho T, Jacobs-Sera D, Caruso SM, Cornely K. Genome sequence of Streptomyces BM cluster phage Frankenweenie. Microbiol Resour Announc 2023; 12:e0059223. [PMID: 37830805 PMCID: PMC10652959 DOI: 10.1128/mra.00592-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/09/2023] [Indexed: 10/14/2023] Open
Abstract
Frankenweenie is a newly isolated bacteriophage that infects Streptomyces scabiei RL-34. Frankenweenie was discovered in Gaithersburg, MD, and has 366 genes comprising a 200,048-bp genome. Frankenweenie is grouped in cluster BM and is predicted to possess a unique tailspike protein that potentially widens its host range.
Collapse
Affiliation(s)
- Katherine E. Cleary
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Charles Pelagalli
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Marly Cassford
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Nathan Berry
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Elizabeth Aguas
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Brandon Kim
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Tagide deCarvalho
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Steven M. Caruso
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Kathleen Cornely
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| |
Collapse
|
35
|
Almahie O, Danklefsen B, Graves RS, Hepworth SM, Mathison RT, Sullivan EA, Wood PR, Bartholomew S, Brewster R, Hunt DJ, Serna C, Shurley JF, Grinath AS, Thomas MA. Isolation and genome sequence annotation of KillerTomato, a newly discovered cluster EE bacteriophage infecting Microbacterium. Microbiol Resour Announc 2023; 12:e0085223. [PMID: 37877714 PMCID: PMC10652884 DOI: 10.1128/mra.00852-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 09/27/2023] [Indexed: 10/26/2023] Open
Abstract
Discovered in Pocatello, Idaho, soil near a tomato garden, siphovirus KillerTomato infects Microbacterium foliorum NRRL B-24224. KillerTomato is a lytic cluster EE phage with a 17,442-bp genome and 68.6% GC content. Of 25 genes, 20 were assigned putative functions, including a putative tail assembly chaperone protein with a programmed frameshift and an endolysin.
Collapse
Affiliation(s)
- Omer Almahie
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Breanna Danklefsen
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - R. Scott Graves
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Sariah M. Hepworth
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Rylee T. Mathison
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Emily A. Sullivan
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Paige R. Wood
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Skylar Bartholomew
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Reganne Brewster
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Dylan J. Hunt
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Carlos Serna
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Jack F. Shurley
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Anna S. Grinath
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Michael A. Thomas
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| |
Collapse
|
36
|
Sasaoka A, Arellano O, Hatch XR, Garcia Costas AM. Genome sequence of bacteriophage Aoka, a cluster FO phage isolated using Arthrobacter globiformis. Microbiol Resour Announc 2023; 12:e0045423. [PMID: 37737618 PMCID: PMC10586098 DOI: 10.1128/mra.00454-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/03/2023] [Indexed: 09/23/2023] Open
Abstract
We report the discovery and genome sequence of bacteriophage Aoka, an actinobacteriophage isolated from a soil sample in Pueblo, Colorado using Arthrobacter globiformis, B2880-SEA. Its genome length is 36,744 base pairs with 54 protein-coding genes. Based on gene content similarity to other actinobacteriophages, Aoka is assigned to cluster FO.
Collapse
Affiliation(s)
- Aidan Sasaoka
- Department of Biology, Colorado State University-Pueblo, Pueblo, Colorado, USA
| | - Olivia Arellano
- Department of Biology, Colorado State University-Pueblo, Pueblo, Colorado, USA
| | - Xavier R. Hatch
- Department of Biology, Colorado State University-Pueblo, Pueblo, Colorado, USA
| | | |
Collapse
|
37
|
Niblock DJ, Winkler AR, Curtin CE, Kokinda JF, Danker WA, Llorente Fernandez I, Smith AR, Ali A, Cruz GG, Givvines LC, Lee-Soety JY. Isolating and characterizing cluster AB Mycobacteriophage NoShow, which encodes lysis proteins shared with cluster H2 phages. Microbiol Resour Announc 2023; 12:e0064923. [PMID: 37747255 PMCID: PMC10586156 DOI: 10.1128/mra.00649-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 08/09/2023] [Indexed: 09/26/2023] Open
Abstract
We present here Mycobacteriophage NoShow, isolated from a soil sample collected on the Maguire Campus of Saint Joseph's University in Merion Station, Pennsylvania. Even though NoShow's 52,825 bp genome is most similar to phages in cluster AB, its lysA and lysB genes are most similar to phages in cluster H2.
Collapse
Affiliation(s)
- Danielle J. Niblock
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | - Anne R. Winkler
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | - Caroline E. Curtin
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | - Jacqui F. Kokinda
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | - Walter A. Danker
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | | | - Ava R. Smith
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | - Asad Ali
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | - Gabrielle G. Cruz
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | - Leya C. Givvines
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | - Julia Y. Lee-Soety
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| |
Collapse
|
38
|
LaBianca K, Butura J, McKnight A, Pan K, Whelan S, Punska E, Pause R, Igbinosa B, Ribbe A, Chien P, Russell D, Garlena R, Hatfull G, Jacobs-Sera D, Rocheleau J. Complete genome sequence of phi29-like Microbacterium foliorum podovirus phage PineapplePizza. Microbiol Resour Announc 2023; 12:e0047823. [PMID: 37671874 PMCID: PMC10586137 DOI: 10.1128/mra.00478-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/16/2023] [Indexed: 09/07/2023] Open
Abstract
Bacteriophage PineapplePizza is a podovirus infecting Microbacterium foliorum NRRL B-24224. The genome is 16,662 bp long and contains 23 predicted protein-coding genes. Interestingly, PineapplePizza shows amino acid similarities to well-studied Bacillus subtilis phage phi29.
Collapse
Affiliation(s)
- Kylie LaBianca
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Jessica Butura
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Arden McKnight
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Karin Pan
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Sean Whelan
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Elizabeth Punska
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Robert Pause
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Bright Igbinosa
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Alexander Ribbe
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts, USA
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Daniel Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rebecca Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Graham Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jessica Rocheleau
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| |
Collapse
|
39
|
Meng B, Bleau A, Bombaywala RR, DeGraw AS, Deol MS, Dollard KE, Gentile N, Jebaraj J, Kayayan GN, Miranda BC, Momoh AE, Morales E, Nunes AC, Oropallo AM, Otterstedt SC, Pridell AT, Roberts JI, Ruiz GA, Sangasani D, Smith RD, Tarar M, Singh V, Jayachandran P. Complete genome sequences of G ordonia rubripertincta phages OtterstedtS21 and Patos. Microbiol Resour Announc 2023; 12:e0071823. [PMID: 37772859 PMCID: PMC10586170 DOI: 10.1128/mra.00718-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 08/24/2023] [Indexed: 09/30/2023] Open
Abstract
We report the genomes of two viruses with siphovirus morphology, OtterstedtS21 and Patos, from Albany, New York, using Gordonia rubripertincta. The genomes of OtterstedtS21 and Patos are ~68 kbp long with 58% GC content. Both phages group with cluster DV based on gene content similarity to phages in the Actinobacteriophage database.
Collapse
Affiliation(s)
- Bowen Meng
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Alexander Bleau
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Riddhi R. Bombaywala
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Audrey S. DeGraw
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Manjot S. Deol
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Kendall E. Dollard
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Nicolas Gentile
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Julianna Jebaraj
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Gregory N. Kayayan
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Briana C. Miranda
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Ayobamidele E. Momoh
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Elias Morales
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Amalia C. Nunes
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Antonia M. Oropallo
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Sophia C. Otterstedt
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Anna T. Pridell
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Jenna I. Roberts
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Gabriel A. Ruiz
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Dhatri Sangasani
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Renee D. Smith
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Mahad Tarar
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Vir Singh
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Pradeepa Jayachandran
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| |
Collapse
|
40
|
Fakhri AM, Warner MH, DeGiorgis JA, Cornely K. Mycobacteriophage Rita: a cluster F1 phage discovered in North Easton, Massachusetts. Microbiol Resour Announc 2023; 12:e0051023. [PMID: 37638726 PMCID: PMC10508093 DOI: 10.1128/mra.00510-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/30/2023] [Indexed: 08/29/2023] Open
Abstract
Mycobacteriophage Rita infects Mycobacterium smegmatis mc2155 and was isolated from a soil sample collected in North Easton, Massachusetts. Assigned to cluster F1 based on sequence similarity to other phages in the same cluster, Rita has a 58,771 bp genome and encodes 104 genes. Rita is 98% similar to phage Bipolar.
Collapse
Affiliation(s)
- Anna M. Fakhri
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| | - Marcie H. Warner
- Department of Natural Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joseph A. DeGiorgis
- Department of Biology, Providence College, Providence, Rhode Island, USA
- Whitman Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Kathleen Cornely
- Department of Chemistry and Biochemistry, Providence College, Providence, Rhode Island, USA
| |
Collapse
|
41
|
Torkashvand N, Kamyab H, Shahverdi AR, Khoshayand MR, Sepehrizadeh Z. Isolation, characterization, and genome analysis of a broad host range Salmonella phage vB_SenS_TUMS_E4: a candidate bacteriophage for biocontrol. Vet Res Commun 2023; 47:1493-1503. [PMID: 37097546 DOI: 10.1007/s11259-023-10105-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/14/2023] [Indexed: 04/26/2023]
Abstract
Salmonella enteritidis is one of the most important foodborne pathogens that cause numerous outbreaks worldwide. Some strains of Salmonella have become progressively resistant to antibiotics, so they could represent a critical threat to public health and have led to the use of alternative therapeutic approaches like phage therapy. In this study, a lytic phage, vB_SenS_TUMS_E4 (E4), was isolated from poultry effluent and characterized to evaluate its potential and efficacy for bio-controlling S. enteritidis in foods. Transmission electron microscopy revealed that E4 has a siphovirus morphotype, with an isometric head and non-contractile tail. Determining the host range showed that this phage can effectively infect different motile as well as non-motile Salmonella enterica serovars. The biological characteristics of E4 showed that it has a short latent period of about 15 min and a large burst size of 287 PFU/cell, and is also significantly stable in a broad range of pHs and temperatures. The E4 whole genome contains 43,018 bp and encodes 60 coding sequences (CDSs) but no tRNA genes. Bioinformatics analysis revealed that the genome of E4 lacks any genes related to lysogeny behavior, antibiotic resistance, toxins, or virulence factors. The efficacy of phage E4 as a bio-control agent was assessed in various foodstuffs inoculated with S. enteritidis at 4°C and 25°C, and the resulting data indicated that it could eradicate S. enteritidis after a very short time of 15 min. The findings of the present study showed that E4 is a hopeful candidate as a bio-control agent against S. enteritidis and has the potential to be used in various foodstuffs.
Collapse
Affiliation(s)
- Narges Torkashvand
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, PO Box 14155-6451, Iran
| | - Haniyeh Kamyab
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, PO Box 14155-6451, Iran
| | - Ahmad Reza Shahverdi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, PO Box 14155-6451, Iran
| | - Mohammad Reza Khoshayand
- Department of Food and Drug Control, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Zargham Sepehrizadeh
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, PO Box 14155-6451, Iran.
| |
Collapse
|
42
|
Wetzel KS, Illouz M, Abad L, Aull HG, Russell DA, Garlena RA, Cristinziano M, Malmsheimer S, Chalut C, Hatfull GF, Kremer L. Therapeutically useful mycobacteriophages BPs and Muddy require trehalose polyphleates. Nat Microbiol 2023; 8:1717-1731. [PMID: 37644325 PMCID: PMC10465359 DOI: 10.1038/s41564-023-01451-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/17/2023] [Indexed: 08/31/2023]
Abstract
Mycobacteriophages show promise as therapeutic agents for non-tuberculous mycobacterium infections. However, little is known about phage recognition of Mycobacterium cell surfaces or mechanisms of phage resistance. We show here that trehalose polyphleates (TPPs)-high-molecular-weight, surface-exposed glycolipids found in some mycobacterial species-are required for infection of Mycobacterium abscessus and Mycobacterium smegmatis by clinically useful phages BPs and Muddy. TPP loss leads to defects in adsorption and infection and confers resistance. Transposon mutagenesis shows that TPP disruption is the primary mechanism for phage resistance. Spontaneous phage resistance occurs through TPP loss by mutation, and some M. abscessus clinical isolates are naturally phage-insensitive due to TPP synthesis gene mutations. Both BPs and Muddy become TPP-independent through single amino acid substitutions in their tail spike proteins, and M. abscessus mutants resistant to TPP-independent phages reveal additional resistance mechanisms. Clinical use of BPs and Muddy TPP-independent mutants should preempt phage resistance caused by TPP loss.
Collapse
Affiliation(s)
- Katherine S Wetzel
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Morgane Illouz
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Lawrence Abad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Haley G Aull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Madison Cristinziano
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Silke Malmsheimer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Christian Chalut
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France.
- INSERM, IRIM, Montpellier, France.
| |
Collapse
|
43
|
Sultan-Alolama MI, Amin A, Vijayan R, El-Tarabily KA. Isolation, Characterization, and Comparative Genomic Analysis of Bacteriophage Ec_MI-02 from Pigeon Feces Infecting Escherichia coli O157:H7. Int J Mol Sci 2023; 24:ijms24119506. [PMID: 37298457 DOI: 10.3390/ijms24119506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
The most significant serotype of Shiga-toxigenic Escherichia coli that causes foodborne illnesses is Escherichia coli O157:H7. Elimination of E. coli O157:H7 during food processing and storage is a possible solution. Bacteriophages have a significant impact on bacterial populations in nature due to their ability to lyse their bacterial host. In the current study, a virulent bacteriophage, Ec_MI-02, was isolated from the feces of a wild pigeon in the United Arab Emirates (UAE) for potential future use as a bio-preservative or in phage therapy. Using a spot test and an efficiency of plating analysis, Ec_MI-02 was found to infect in addition to the propagation host, E. coli O157:H7 NCTC 12900, five different serotypes of E. coli O157:H7 (three clinical samples from infected patients, one from contaminated green salad, and one from contaminated ground beef). Based on morphology and genome analysis, Ec_MI-02 belongs to the genus Tequatrovirus under the order Caudovirales. The adsorption rate constant (K) of Ec_MI-02 was found to be 1.55 × 10-8 mL/min. The latent period was 50 min with a burst size of almost 10 plaque forming units (pfu)/host cell in the one-step growth curve when the phage Ec_MI-02 was cultivated using the propagation host E. coli O157:H7 NCTC 12900. Ec_MI-02 was found to be stable at a wide range of pH, temperature, and commonly used laboratory disinfectants. Its genome is 165,454 bp long with a GC content of 35.5% and encodes 266 protein coding genes. Ec_MI-02 has genes encoding for rI, rII, and rIII lysis inhibition proteins, which supports the observation of delayed lysis in the one-step growth curve. The current study provides additional evidence that wild birds could also be a good natural reservoir for bacteriophages that do not carry antibiotic resistance genes and could be good candidates for phage therapy. In addition, studying the genetic makeup of bacteriophages that infect human pathogens is crucial for ensuring their safe usage in the food industry.
Collapse
Affiliation(s)
- Mohamad Ismail Sultan-Alolama
- Zayed Complex for Herbal Research and Traditional Medicine, Research and Innovation Center, Department of Health, Abu Dhabi 5674, United Arab Emirates
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Amr Amin
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- The Big Data Analytics Center, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain P.O. Box 17666, United Arab Emirates
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Harry Butler Institute, Murdoch University, Murdoch, WA 6150, Australia
| |
Collapse
|
44
|
Anderman E, Dini T, Eldbah K, Frino T, Milavec J, Sayed A, Profrock V, Virtue R, Qyshkollari T, Harrison M. Genome Sequence of Gordonia terrae Phage APunk. Microbiol Resour Announc 2023;:e0122022. [PMID: 36877085 DOI: 10.1128/mra.01220-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
Gordonia phage APunk was isolated from soil collected in Grand Rapids (MI, USA) using Gordonia terrae 3612. The genome of APunk is 59,154 bp long, has a 67.7% GC content, and contains 32 protein-coding genes. Based on its gene content similarity to actinobacteriophages, APunk is assigned to phage cluster DE4.
Collapse
|
45
|
Mastropaolo MD, Fallest-Strobl PC, Sequira DM, Campbell DD, Negro CJ, Tuang KS, Sigmund-Hamre IM, Womack CL, Mansbridge T, Metzler AL, Sasher EG, Collins C, Crowley NK, Dower VR, Bates M, Bjorkelo C, Johnson H, Salvitti LR; Neumann University Phage Discovery Group. Genome Sequences of Five Microbacterium foliorum Phages, GaeCeo, NeumannU, Eightball, Chivey, and Hiddenleaf. Microbiol Resour Announc 2023;:e0110622. [PMID: 36861977 DOI: 10.1128/mra.01106-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Five siphoviruses were isolated from soil in southeastern Pennsylvania using Microbacterium foliorum. Bacteriophages NeumannU and Eightball have 25 predicted genes, Chivey and Hiddenleaf have 87 genes, and GaeCeo has 60 genes. Based on gene content similarity to sequenced actinobacteriophages, these five phages are distributed across clusters EA, EE, and EF.
Collapse
|
46
|
Kornienko M, Bespiatykh D, Malakhova M, Gorodnichev R, Kuptsov N, Shitikov E. PCR Assay for Rapid Taxonomic Differentiation of Virulent Staphylococcus aureus and Klebsiella pneumoniae Bacteriophages. Int J Mol Sci 2023; 24. [PMID: 36901913 DOI: 10.3390/ijms24054483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
Phage therapy is now seen as a promising way to overcome the current global crisis in the spread of multidrug-resistant bacteria. However, phages are highly strain-specific, and in most cases one will have to isolate a new phage or search for a phage suitable for a therapeutic application in existing libraries. At an early stage of the isolation process, rapid screening techniques are needed to identify and type potential virulent phages. Here, we propose a simple PCR approach to differentiate between two families of virulent Staphylococcus phages (Herelleviridae and Rountreeviridae) and eleven genera of virulent Klebsiella phages (Przondovirus, Taipeivirus, Drulisvirus, Webervirus, Jiaodavirus, Sugarlandvirus, Slopekvirus, Jedunavirus, Marfavirus, Mydovirus and Yonseivirus). This assay includes a thorough search of a dataset comprising S. aureus (n = 269) and K. pneumoniae (n = 480) phage genomes available in the NCBI RefSeq/GenBank database for specific genes that are highly conserved at the taxonomic group level. The selected primers showed high sensitivity and specificity for both isolated DNA and crude phage lysates, which permits circumventing DNA purification protocols. Our approach can be extended and applied to any group of phages, given the large number of available genomes in the databases.
Collapse
|
47
|
Dulberger CL, Guerrero-Bustamante CA, Owen SV, Wilson S, Wuo MG, Garlena RA, Serpa LA, Russell DA, Zhu J, Braunecker BJ, Squyres GR, Baym M, Kiessling LL, Garner EC, Rubin EJ, Hatfull GF. Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection. Nat Microbiol 2023; 8:695-710. [PMID: 36823286 PMCID: PMC10066036 DOI: 10.1038/s41564-023-01333-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/23/2023] [Indexed: 02/25/2023]
Abstract
Mycobacteriophages are a diverse group of viruses infecting Mycobacterium with substantial therapeutic potential. However, as this potential becomes realized, the molecular details of phage infection and mechanisms of resistance remain ill-defined. Here we use live-cell fluorescence microscopy to visualize the spatiotemporal dynamics of mycobacteriophage infection in single cells and populations, showing that infection is dependent on the host nucleoid-associated Lsr2 protein. Mycobacteriophages preferentially adsorb at Mycobacterium smegmatis sites of new cell wall synthesis and following DNA injection, Lsr2 reorganizes away from host replication foci to establish zones of phage DNA replication (ZOPR). Cells lacking Lsr2 proceed through to cell lysis when infected but fail to generate consecutive phage bursts that trigger epidemic spread of phage particles to neighbouring cells. Many mycobacteriophages code for their own Lsr2-related proteins, and although their roles are unknown, they do not rescue the loss of host Lsr2.
Collapse
Affiliation(s)
- Charles L Dulberger
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | | | - Siân V Owen
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sean Wilson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Michael G Wuo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lexi A Serpa
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Junhao Zhu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ben J Braunecker
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Georgia R Squyres
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Michael Baym
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
| |
Collapse
|
48
|
Zuberi YA, Diaz-Sanchez A, Gutierrez J, Jakubowski SJ, Saha S. Isolation and Annotation of Xitlalli, a Cluster EK1 Actinobacteriophage Isolated Using Microbacterium foliorum. Microbiol Resour Announc 2023; 12:e0127022. [PMID: 36696397 DOI: 10.1128/mra.01270-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Xitlalli is an actinobacteriophage that was isolated from soil using Microbacterium foliorum. Based on gene content similarity to phages in the Actinobacteriophage Database, Xitlalli is assigned to cluster EK1. The genome is 53,929 bp long and contains 52 protein-coding genes, of which 26% could be assigned functions.
Collapse
|
49
|
Milhaven M, Cai L, Cherian S, Johnson K, Salas Perez K, Blanco M, Garg A, Lobatos J, Mitra C, Strasser M, Harms R, Pfeifer SP. Complete Genome Sequence of the Microbacterium Bacteriophage Chako. Microbiol Resour Announc 2023; 12:e0125122. [PMID: 36645290 DOI: 10.1128/mra.01251-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We characterized the complete genome sequence of Chako, an obligate lytic bacteriophage with siphovirus morphology from subcluster EA1 that infects Microbacterium foliorum NRRL B-24224. Its 41.6-kb genome contains 62 putative protein-coding genes and is highly similar to that of bacteriophage HanSolo (99.26% nucleotide identity).
Collapse
|
50
|
Amarh ED, Dedrick RM, Garlena RA, Russell DA, Gauthier CH, Aull HG, Abad L, Jacobs-Sera D, Akusobi C, Rubin EJ, Hatfull GF. Unusual prophages in Mycobacterium abscessus genomes and strain variations in phage susceptibilities. PLoS One 2023; 18:e0281769. [PMID: 36795728 DOI: 10.1371/journal.pone.0281769] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/31/2023] [Indexed: 02/17/2023] Open
Abstract
Mycobacterium abscessus infections are relatively common in patients with cystic fibrosis and are clinically challenging, with frequent intrinsic resistance to antibiotics. Therapeutic treatment with bacteriophages offers some promise but faces many challenges including substantial variation in phage susceptibilities among clinical isolates, and the need to personalize therapies for individual patients. Many strains are not susceptible to any phages or are not efficiently killed by lytic phages, including all smooth colony morphotype strains tested to-date. Here, we analyze a set of new M. abscessus isolates for the genomic relationships, prophage content, spontaneous phage release, and phage susceptibilities. We find that prophages are common in these M. abscessus genomes, but some have unusual arrangements, including tandemly integrated prophages, internal duplications, and they participate in active exchange of polymorphic toxin-immunity cassettes secreted by ESX systems. Relatively few strains are efficiently infected by any mycobacteriophages, and the infection patterns do not reflect the overall phylogenetic relationships of the strains. Characterization of these strains and their phage susceptibility profiles will help to advance the broader application of phage therapies for NTM infections.
Collapse
|