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Archive

January 2019; Volume 8,Issue 3

Genome Sequences

  • Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Nocardia farcinica</span> W6977<sup>T</sup> Obtained by Combining Illumina and PacBio Reads
    Genome Sequences
    Complete Genome Sequence of Nocardia farcinica W6977T Obtained by Combining Illumina and PacBio Reads

    The complete genome sequence of the Nocardia farcinica type strain was obtained by combining Illumina HiSeq and PacBio reads, producing a single 6.29-Mb chromosome and 2 circular plasmids. Bioinformatic analysis identified 5,991 coding sequences, including putative genes for virulence, microbial resistance, transposons, and biosynthesis gene clusters.

    ...
    Christopher A. Gulvik, Robert A. Arthur, Ben W. Humrighouse, Dhwani Batra, Lori A. Rowe, Brent A. Lasker, John R. McQuiston
    17 Jan 2019
  • Draft Genome Sequence of <span class="named-content genus-species" id="named-content-1">Lactobacillus reuteri</span> Strain LR CGMCC 11154, Isolated from the Feces of Healthy Weaned Piglets
    Genome Sequences
    Draft Genome Sequence of Lactobacillus reuteri Strain LR CGMCC 11154, Isolated from the Feces of Healthy Weaned Piglets

    Lactobacillus reuteri strain LR CGMCC 11154, which was isolated from the feces of healthy weaned piglets, was experimentally proven to be a probiotic bacterium. The whole genome was sequenced on the Illumina Miseq platform to obtain the draft genome, which consists of 120 contigs totaling 1.9 Mbp encoding 1,854 genes.

    Ting Yu, Xi Yang, Zhilin Wang, Cui Zhu, Jinlong Bei, Li Wang, Wenhua Liu, Qingfeng Zhu, Zongyong Jiang, Zhuang Chen
    17 Jan 2019
  • Draft Genome Sequence of <span class="named-content genus-species" id="named-content-1">Streptomyces spongiicola</span> Strain 531S, an Actinobacterium Isolated from Marine Sediment
    Genome Sequences
    Draft Genome Sequence of Streptomyces spongiicola Strain 531S, an Actinobacterium Isolated from Marine Sediment

    Streptomyces spongiicola strain 531S (NBRC 113560) was isolated from marine sediment on a beach on Sesoko Island (Okinawa, Japan). We report here the draft genome sequence of S. spongiicola 531S, in which 24 potential secondary metabolite gene clusters were predicted with antiSMASH.

    ...
    Hideo Dohra, Issara Kaweewan, Beatriz E. Casareto, Yoshimi Suzuki, Shinya Kodani
    17 Jan 2019
  • Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> O157:H7 Phage PhiG17
    Genome Sequences
    Complete Genome Sequence of Escherichia coli O157:H7 Phage PhiG17

    Here, we announce the complete genome sequence of bacteriophage PhiG17, which is virulent to Escherichia coli O157:H7 strains and was isolated from cattle feces in the North West province of South Africa. This report presents the major genetic features of the phage PhiG17 based on its whole-genome sequence.

    Muyiwa A. Akindolire, Bukola R. Aremu, Collins N. Ateba
    17 Jan 2019
  • A Hybrid Sequencing Approach Completes the Genome Sequence of <span class="named-content genus-species" id="named-content-1">Thermoanaerobacter ethanolicus</span> JW 200
    Genome Sequences
    A Hybrid Sequencing Approach Completes the Genome Sequence of Thermoanaerobacter ethanolicus JW 200

    Thermoanaerobacter ethanolicus JW 200 has been identified as a potential sustainable biofuel producer due to its ability to readily ferment carbohydrates to ethanol. A hybrid sequencing approach, combining Oxford Nanopore and Illumina DNA sequence reads, was applied to produce a single contiguous genome sequence of 2,911,280 bp.

    Richard K. Tennant, Monica L. Ayine, Ann L. Power, James A. Gilman, Mark Hewlett, Paul B. C. James, Chloe Singleton, David A. Parker, John Love
    17 Jan 2019
  • Genome Sequence of <span class="named-content genus-species" id="named-content-1">Providencia rettgeri</span> NVIT03, Isolated from <span class="named-content genus-species" id="named-content-2">Nasonia vitripennis</span>
    Genome Sequences
    Genome Sequence of Providencia rettgeri NVIT03, Isolated from Nasonia vitripennis

    Providencia rettgeri is a common insect-associated Gram-negative bacterium. Here, we present the draft genome sequence of P. rettgeri NVIT03, the most common bacterial symbiont of the insect hymenopteran model Nasonia vitripennis...

    Guan-Hong Wang, Robert M. Brucker
    17 Jan 2019
  • First Detection and Genome Sequence of Senecavirus A in Vietnam
    Genome Sequences
    First Detection and Genome Sequence of Senecavirus A in Vietnam

    In 2018, senecavirus A was detected for the first time in Vietnam. This report contains the first complete genome of a senecavirus A isolate collected from pigs in Kon Tum Province, Vietnam.

    Jonathan Arzt, Miranda R. Bertram, Le T. Vu, Steven J. Pauszek, Ethan J. Hartwig, George R. Smoliga, Rachel Palinski, Carolina Stenfeldt, Ian H. Fish, Bui H. Hoang, Nguyen T. Phuong, Vo V. Hung, Pham P. Vu, Nguyen K. Dung, Pham V. Dong, Nguyen N. Tien, Do H. Dung
    17 Jan 2019
  • Whole-Genome Sequences of <span class="named-content genus-species" id="named-content-1">Ralstonia solanacearum</span> Strains P816, P822, and P824, Emerging Pathogens of Blueberry in Florida
    Genome Sequences
    Whole-Genome Sequences of Ralstonia solanacearum Strains P816, P822, and P824, Emerging Pathogens of Blueberry in Florida

    Ralstonia solanacearum is the causal agent of bacterial wilt in numerous species of plants. Here, we report the whole-genome sequence of three phylogenetically diverse R. solanacearum strains, P816, P822, and P824, reported for the first time as causal agents of an emerging blueberry disease in...

    Ana Maria Bocsanczy, Andres S. Espindola, David J. Norman
    17 Jan 2019
  • Complete Genome Sequence of Mobuck Virus Isolated from a Florida White-Tailed Deer (<span class="named-content genus-species" id="named-content-1">Odocoileus virginianus</span>)
    Genome Sequences
    Complete Genome Sequence of Mobuck Virus Isolated from a Florida White-Tailed Deer (Odocoileus virginianus)

    Here, we report the complete genome sequence of mobuck virus isolated from a Florida white-tailed deer (Odocoileus virginianus) in 2017. This is the second report of mobuck virus in the United States and expands the known geographic range of this novel orbivirus into Florida.

    Mohammad Shamim Ahasan, Juan M. Campos Krauer, Kuttichantran Subramaniam, John A. Lednicky, Julia C. Loeb, Katherine A. Sayler, Samantha M. Wisely, Thomas B. Waltzek
    17 Jan 2019
  • Genome Sequences of Antigenically Distinct Serotype O Foot-and-Mouth Disease Viruses from Pakistan
    Genome Sequences
    Genome Sequences of Antigenically Distinct Serotype O Foot-and-Mouth Disease Viruses from Pakistan

    The genome sequences of three serotype O foot-and-mouth disease viruses (FMDVs) isolated from outbreaks in Pakistan in 2016 and 2017 are described. Despite all three isolates being classified in the same FMDV genetic sublineage, two of them displayed a distinct antigenic phenotype against commonly used vaccine strains.

    Katarzyna Bachanek-Bankowska, Jemma Wadsworth, Elisabeth Henry, Anna B. Ludi, Abdelghani Bin-Tarif, Bob Statham, Donald P. King, Muhammad Afzal, Manzoor Hussain, Shumaila Manzoor, Muhammad Abubakar, Nick J. Knowles
    17 Jan 2019
  • Draft Whole-Genome Sequence of a “<em>Candidatus</em> Liberibacter asiaticus” Strain from Yunnan, China
    Genome Sequences
    Draft Whole-Genome Sequence of a “Candidatus Liberibacter asiaticus” Strain from Yunnan, China

    The draft genome sequence of “Candidatus Liberibacter asiaticus” strain YNJS7C, isolated from a navel orange tree in Yunnan Province, China, is presented here. The YNJS7C strain has a genome size of 1,258,986 bp, with a G+C content of 36.6%, 1,174 predicted open reading frames, and 53 RNA genes.

    Yanling Chen, Tao Li, Zheng Zheng, Meirong Xu, Xiaoling Deng
    17 Jan 2019
  • Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Vibrio mediterranei</span> 117-T6, a Potentially Pathogenic Bacterium Isolated from the Conchocelis of <span class="named-content genus-species" id="named-content-2">Pyropia</span> spp.
    Genome Sequences
    Complete Genome Sequence of Vibrio mediterranei 117-T6, a Potentially Pathogenic Bacterium Isolated from the Conchocelis of Pyropia spp.

    Vibrio mediterranei is a Gram-negative bacterium of the family Vibrionaceae. Vibrio mediterranei...

    Qiqin Liu (刘棋琴), Mengya Xu (徐梦雅), Yingyun He (何应芸), Zhen Tao (陶震), Rui Yang (杨锐), Haimin Chen (陈海敏)
    17 Jan 2019
  • Draft Genome Sequence of <span class="named-content genus-species" id="named-content-1">Bacillus coagulans</span> ZB29, a Commercial Probiotic Strain
    Genome Sequences
    Draft Genome Sequence of Bacillus coagulans ZB29, a Commercial Probiotic Strain

    Bacillus coagulans ZB29, isolated from milk, is a safe strain already available on market shelves and characterized by certified beneficial effects. Here, we report the 3,646,473-bp genome sequence of this bacterium, its sequence assembly, and its annotations.

    Darshana Chauhan, Yama Patel, Jayraj A. Doshi, Rashesh D. Doshi, Anjali Bose
    17 Jan 2019
  • Genome Sequence of a Classical Swine Fever Virus of Subgenotype 2.1, Isolated from a Pig in Japan in 2018
    Genome Sequences
    Genome Sequence of a Classical Swine Fever Virus of Subgenotype 2.1, Isolated from a Pig in Japan in 2018

    In 2018, classical swine fever virus (CSFV) was detected in Japan. Here, we report the whole-genome sequence of CSFV/JPN/1/2018.

    Tatsuya Nishi, Ken-ichiro Kameyama, Tomoko Kato, Katsuhiko Fukai
    17 Jan 2019
  • Draft Genome Sequence of <span class="named-content genus-species" id="named-content-1">Bacillus velezensis</span> CE2, Which Genetically Encodes a Novel Multicomponent Lantibiotic
    Genome Sequences
    Draft Genome Sequence of Bacillus velezensis CE2, Which Genetically Encodes a Novel Multicomponent Lantibiotic

    Bacillus velezensis CE2 produces potent antimicrobial compound(s). The draft genome sequence of the strain reported here is 4.1 Mb with a G+C content of 46.1%.

    Emily Campbell, Michelle Gerst, B. Carol Huang, Nguyet Kong, Bart C. Weimer, Ahmed E. Yousef
    17 Jan 2019
  • Complete Genome Sequence of <em>Bradyrhizobium</em> sp. Strain ORS3257, an Efficient Nitrogen-Fixing Bacterium Isolated from Cowpea in Senegal
    Genome Sequences
    Complete Genome Sequence of Bradyrhizobium sp. Strain ORS3257, an Efficient Nitrogen-Fixing Bacterium Isolated from Cowpea in Senegal

    Here, we report the complete genome sequence of Bradyrhizobium sp. strain ORS3257, which forms efficient symbioses with cowpea, peanut, or groundnut.

    Antoine Le Quéré, Djamel Gully, Albin Teulet, Elisabeth Navarro, Daniel Gargani, Joël Fardoux, Stéphane Cruveiller, Marc Neyra, Eric Giraud, Tatiana Krasova Wade
    17 Jan 2019
  • High-Quality Draft Genome Sequence of <span class="named-content genus-species" id="named-content-1">Pseudomonas reidholzensis</span> Strain CCOS 865<sup>T</sup>
    Genome Sequences
    High-Quality Draft Genome Sequence of Pseudomonas reidholzensis Strain CCOS 865T

    We have sequenced and assembled the genome of Pseudomonas reidholzensis CCOS 865T, which was isolated in 2014 from forest soil. Members of the genus Pseudomonas play important roles in environmental systems and are utilized in many biotechnological processes.

    Dominik Rutz, David Frasson, Martin Sievers, Jochen Blom, Fabio Rezzonico, Joël F. Pothier, Theo H. M. Smits
    17 Jan 2019
  • Closed Genome Sequence of <span class="named-content genus-species" id="named-content-1">Bacillus paralicheniformis</span> Strain CBMAI 1303, a Bacterium Applied for Phytopathogen Biocontrol
    Genome Sequences
    Closed Genome Sequence of Bacillus paralicheniformis Strain CBMAI 1303, a Bacterium Applied for Phytopathogen Biocontrol

    We report the complete genome sequence and annotation of Bacillus paralicheniformis strain CBMAI 1303, a bacterium applied for phytopathogen biocontrol.

    Victor Satler Pylro, Armando Cavalcante Franco Dias, Fernando Dini Andreote, Alessandro de Mello Varani, Laura Rabelo Leite, Cristiane Cipolla Fasanella Andreote, Eduardo Roberto de Almeida Bernardo, Thales Facanali Martins
    17 Jan 2019
  • Whole-Genome Sequences of <span class="named-content genus-species" id="named-content-1">Staphylococcus aureus</span> Isolates from Cystic Fibrosis Lung Infections
    Genome Sequences
    Whole-Genome Sequences of Staphylococcus aureus Isolates from Cystic Fibrosis Lung Infections

    Staphylococcus aureus is an early colonizer in the lungs of individuals with cystic fibrosis (CF), but surprisingly, only a limited number of genomes from CF-associated S. aureus isolates have been sequenced. Here, we present the whole-genome sequences of 65...

    Eryn E. Bernardy, Robert A. Petit, III, Abraham G. Moller, Jennifer A. Blumenthal, Alexander J. McAdam, Gregory P. Priebe, Aroon T. Chande, Lavanya Rishishwar, I. King Jordan, Timothy D. Read, Joanna B. Goldberg
    17 Jan 2019
  • Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Lactococcus lactis</span> subsp. <span class="named-content genus-species" id="named-content-2">cremoris</span> 3107, Host for the Model Lactococcal P335 Bacteriophage TP901-1
    Genome Sequences
    Complete Genome Sequence of Lactococcus lactis subsp. cremoris 3107, Host for the Model Lactococcal P335 Bacteriophage TP901-1

    The complete genome sequence of Lactococcus lactis subsp. cremoris 3107, a dairy starter strain and a host for the model lactococcal P335 bacteriophage TP901-1, is reported here.

    Andrea Erazo Garzon, Jennifer Mahony, Francesca Bottacini, Philip Kelleher, Douwe van Sinderen
    17 Jan 2019
  • Complete Genome Sequences of Two <span class="named-content genus-species" id="named-content-1">Megasphaera elsdenii</span> Strains, NCIMB 702410 and ATCC 25940
    Genome Sequences
    Complete Genome Sequences of Two Megasphaera elsdenii Strains, NCIMB 702410 and ATCC 25940

    Here, we report the complete genome sequences of two Megasphaera elsdenii strains, ATCC 25940 and NCIMB 702410. M. elsdenii is an anaerobic bacterium capable of producing butanoate and hexanoate and is a member of the Negativicutes...

    E. Anne Hatmaker, Dawn M. Klingeman, Kaela B. O’Dell, Lauren A. Riley, Beth Papanek, Adam M. Guss
    17 Jan 2019
  • Genome Sequencing of an <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Sequence Type 617 Strain Isolated from Beach Ghost Shrimp (<span class="named-content genus-species" id="named-content-2">Callichirus m</span><span class="named-content genus-species" id="named-content-3">ajor</span>) from a Heavily Polluted Ecosystem Reveals a Wider Resistome against Heavy Metals and Antibiotics
    Genome Sequences
    Genome Sequencing of an Escherichia coli Sequence Type 617 Strain Isolated from Beach Ghost Shrimp (Callichirus major) from a Heavily Polluted Ecosystem Reveals a Wider Resistome against Heavy Metals and Antibiotics

    Here, we present the draft genome sequence of a multidrug-resistant (MDR) Escherichia coli strain belonging to sequence type 617 (ST617), isolated from beach ghost shrimp from polluted coastal waters in Brazil. These data provide valuable information for comparative genomic analysis, related to the dissemination of MDR...

    Daniel F. Monte, Fábio P. Sellera, Miriam R. Fernandes, Quézia Moura, Mariza Landgraf, Nilton Lincopan
    17 Jan 2019
  • Draft Genome Sequences of <span class="named-content genus-species" id="named-content-1">Legionella taurinensis</span> Recovered from a Hot Water System in Austria, 2018
    Genome Sequences
    Draft Genome Sequences of Legionella taurinensis Recovered from a Hot Water System in Austria, 2018

    Members of the genus Legionella are widespread in natural water sources. This is the first report on the draft genome sequences of Legionella taurinensis in Austria.

    Ali Chakeri, Franz Allerberger, Michael Kundi, Anna Stöger, Sonja Rehak, Werner Ruppitsch, Daniela Schmid
    17 Jan 2019
  • Whole-Genome Sequences of <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Isolates from Cocoa Beans Imported from Bolivia
    Genome Sequences
    Whole-Genome Sequences of Escherichia coli Isolates from Cocoa Beans Imported from Bolivia

    Four Escherichia coli isolates were obtained from a batch of cocoa beans imported from Bolivia. The cocoa beans were rejected by a U.S.

    Hephzibah Nwanosike, Taejung Chung, Lingzi Xiaoli, Megan Condello, Edward G. Dudley, Jasna Kovac
    17 Jan 2019
  • Draft Genome Sequences of Four <span class="named-content genus-species" id="named-content-1">Rhodobacter sphaeroides</span> Strains Isolated from a Marine Ecosystem
    Genome Sequences
    Draft Genome Sequences of Four Rhodobacter sphaeroides Strains Isolated from a Marine Ecosystem

    Rhodobacter sphaeroides is an alphaproteobacterium found in freshwater and marine ecosystems. To better understand the metabolic diversity within this species, we isolated and sequenced four R. sphaeroides isolates obtained from Trunk River in Woods Hole, Massachusetts.

    Michael S. Guzman, Arpita Bose
    17 Jan 2019
  • Complete Genome Sequence of an Alphabaculovirus from the Southern Armyworm, <em>Spodoptera eridania</em>
    Genome Sequences
    Complete Genome Sequence of an Alphabaculovirus from the Southern Armyworm, Spodoptera eridania

    We report the complete genome sequence of a baculovirus from the moth Spodoptera eridania, the southern armyworm. The genome sequence is 149,090 bp and exhibits the greatest degree of sequence similarity with genomes from alphabaculoviruses isolated from other moths of the genus Spodoptera.

    Robert L. Harrison, Daniel L. Rowley
    17 Jan 2019
  • Draft Genome Sequence of <em>Serratia</em> sp. 1D1416
    Genome Sequences
    Draft Genome Sequence of Serratia sp. 1D1416

    This work reports the draft genome of Serratia sp. 1D1416. The assembled genome contains a 5,552,016-bp circular chromosome.

    Diaa Alabed, Naxin Huo, Yong Gu, Kent F. McCue, James G. Thomson
    17 Jan 2019
  • Draft Genome Sequences of Eight <em>Vibrio</em> sp. Clinical Isolates from across the United States That Form a Basal Sister Clade to <span class="named-content genus-species" id="named-content-1">Vibrio cholerae</span>
    Genome Sequences
    Draft Genome Sequences of Eight Vibrio sp. Clinical Isolates from across the United States That Form a Basal Sister Clade to Vibrio cholerae

    We sequenced the genomes of eight isolates from various regions of the United States. These isolates form a monophyletic cluster clearly related to but distinct from Vibrio cholerae.

    Kevin Liang, Mohammad Tarequl Islam, Nora Hussain, Nathan S. Winkjer, Monica S. Im, Lori A. Rowe, Cheryl L. Tarr, Yan Boucher
    17 Jan 2019
  • Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Phascolarctobacterium faecium</span> JCM 30894, a Succinate-Utilizing Bacterium Isolated from Human Feces
    Genome Sequences
    Complete Genome Sequence of Phascolarctobacterium faecium JCM 30894, a Succinate-Utilizing Bacterium Isolated from Human Feces

    Phascolarctobacterium faecium is an anaerobic microbe known as a member of the human gut microbiome. Here, we report the complete genome sequence of Phascolarctobacterium faecium JCM 30894 and the elucidation of the mechanism for utilization of succinate by this bacterium based on the genome...

    Yusuke Ogata, Wataru Suda, Nao Ikeyama, Masahira Hattori, Moriya Ohkuma, Mitsuo Sakamoto
    17 Jan 2019

Amplicon Sequence Collections

  • Prokaryotic Community Structure of Long-Term Fertilization Field Andisols in Central Japan
    Amplicon Sequence Collections
    Prokaryotic Community Structure of Long-Term Fertilization Field Andisols in Central Japan

    Long-term fertilization experiments are a useful way to elucidate the impacts of fertilization on soil ecosystems. Here, we report the prokaryotic community structure in experimental field soil after 80 years of successive fertilization.

    Kazumori Mise, Hitoshi Moro, Takashi Kunito, Keishi Senoo, Shigeto Otsuka
    17 Jan 2019
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Microbiology Resource Announcements: 8 (3)

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volume 8, issue 3
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