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Archive

October 2019; Volume 8,Issue 40

Genome Sequences

  • Complete Genome Sequence of <em>Cycloclasticus</em> sp. Strain PY97N, Which Includes Two Heavy Metal Resistance Genomic Islands
    Genome Sequences
    Complete Genome Sequence of Cycloclasticus sp. Strain PY97N, Which Includes Two Heavy Metal Resistance Genomic Islands

    We present the complete genome sequence of fluoranthene-consuming Cycloclasticus sp. strain PY97N. This strain has one circular chromosome with a G+C content of 42.06%. Moreover, two genomic islands were identified as putative conjugative elements. These genomic details are expected to inform our understanding of the remarkable catabolic capacities of organisms of the...

    Zhisong Cui, Veronika Kivenson, Na Liu, Angela Xu, Xiao Luan, Wei Gao, Blair Paul, David L. Valentine
    3 Oct 2019
  • Complete Genome Sequence of <em>Rhodococcus</em> sp. Strain SGAir0479, Isolated from Indoor Air Collected in Singapore
    Genome Sequences
    Complete Genome Sequence of Rhodococcus sp. Strain SGAir0479, Isolated from Indoor Air Collected in Singapore

    The complete genome sequence of Rhodococcus sp. strain SGAir0479 is presented here. This organism was isolated from an air sample collected in an indoor location in Singapore. The consensus assembly generated one chromosome of 4.86 Mb (G+C content of 69.8%) and one plasmid of 104,493 bp.

    Elaine L. Oliveira, Daniela I. Drautz-Moses, Akira Uchida, Rikky W. Purbojati, Anthony Wong, Kavita K. Kushwaha, Alexander Putra, Ngu War Aung, Balakrishnan N. V. Premkrishnan, Cassie E. Heinle, Vineeth Kodengil Vettath, Ana Carolina M. Junqueira, Stephan C. Schuster
    3 Oct 2019
  • Complete Genome Sequence of a Quorum-Sensing Bacterium, <em>Oceanicola</em> sp. Strain D3, Isolated from a Microplastic Surface in Coastal Water of Qingdao, China
    Genome Sequences
    Complete Genome Sequence of a Quorum-Sensing Bacterium, Oceanicola sp. Strain D3, Isolated from a Microplastic Surface in Coastal Water of Qingdao, China

    Oceanicola sp. strain D3 was isolated from the plastisphere of polyvinyl chloride (PVC) in coastal water of Qingdao, China. Here, we present the complete genome sequence of strain D3, which consists of a chromosome of 3,926,685 bp with a G+C content of 64.49% and 4,964 coding DNA sequences. This is the first report of a quorum-sensing (QS) system in an Oceanicola...

    Qian Li, Xiyuan Xu, Changfei He, Li Zheng, Wei Gao, Chengjun Sun, Jingxi Li, Fenglei Gao
    3 Oct 2019
  • Genome Sequence of “<em>Candidatus</em> Nitrosocosmicus franklandus” C13, a Terrestrial Ammonia-Oxidizing Archaeon
    Genome Sequences
    Genome Sequence of “Candidatus Nitrosocosmicus franklandus” C13, a Terrestrial Ammonia-Oxidizing Archaeon

    “Candidatus Nitrosocosmicus franklandus” C13 is an ammonia-oxidizing archaeon (AOA) isolated from soil. Its complete genome is 2.84 Mb and possesses predicted AOA metabolic pathways for energy generation and carbon dioxide fixation but no typical surface layer (S-layer) proteins, only one ammonium transporter, and divergent A-type ATP synthase genes.

    Graeme W. Nicol, Linda Hink, Cécile Gubry-Rangin, James I. Prosser, Laura E. Lehtovirta-Morley
    3 Oct 2019
  • Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Mycoplasma bovis</span> Strain KG4397, Isolated from Cattle in Japan
    Genome Sequences
    Complete Genome Sequence of Mycoplasma bovis Strain KG4397, Isolated from Cattle in Japan

    Mycoplasma bovis is a major bacterial pathogen that causes pneumonia, mastitis, and arthritis in cattle. In this study, we performed whole-genome sequencing of an M. bovis strain isolated in Japan for the first time and announce the complete genome sequence of strain KG4397, which caused respiratory...

    Misako Morimoto, Tsuyoshi Kenri, Takashi Ohmori, Kaho Teshima, Kazumoto Shibuya, Chihiro Sasakawa, Masato Suzuki
    3 Oct 2019
  • Complete Genome Sequence of an Enterohemorrhagic <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> O111:H8 Strain Recovered from a Large Outbreak in Japan Associated with Consumption of Raw Beef
    Genome Sequences
    Complete Genome Sequence of an Enterohemorrhagic Escherichia coli O111:H8 Strain Recovered from a Large Outbreak in Japan Associated with Consumption of Raw Beef

    We present the complete genome sequence of an enterohemorrhagic Escherichia coli O111:H8 strain. This strain was isolated from a hemolytic-uremic syndrome patient and was responsible for a large outbreak associated with the consumption of raw beef in 2011.

    Tsuyoshi Sekizuka, Kenichi Lee, Keiko Kimata, Junko Isobe, Makoto Kuroda, Sunao Iyoda, Makoto Ohnishi, Tetsutaro Sata, Masanori Watahiki
    3 Oct 2019
  • Whole-Genome Sequencing of <em>Mycobacterium tilburgii</em> Strain MEPHI
    Genome Sequences
    Whole-Genome Sequencing of Mycobacterium tilburgii Strain MEPHI

    Mycobacterium tilburgii is a fastidious mycobacterium which has previously been reported to cause severe disseminated infections. Genome sequencing of the M. tilburgii MEPHI clinical isolate yielded 3.14 Mb, with 66.3% GC content, and confirmed phylogenetic placement within the Mycobacterium...

    Jamal Saad, Michel Drancourt, Margaret M. Hannan, Patrick J. Stapleton, Simon Grandjean Lapierre
    3 Oct 2019
  • Complete Genome Sequence of Bacteriophage Finny, Isolated from a <span class="named-content genus-species" id="named-content-1">Microbacterium foliorum</span> Culture
    Genome Sequences
    Complete Genome Sequence of Bacteriophage Finny, Isolated from a Microbacterium foliorum Culture

    Actinobacteriophage Finny contains a circularly permuted 40,313-bp double-stranded DNA genome with 63 predicted protein-coding genes. Finny was directly isolated from a soil sample collected in New Braunfels, Texas, that was incubated with Microbacterium foliorum SEA B-24224. Finny is closely related to bacteriophages MCubed, Andromedas, ColaCorta, Eleri, and Sansa....

    Tiffany Lee, Michaela Aguirre, Shey Andrews, Kayla Bahr, Abigail Ballard, Matthew Bristerpostma, Faith Cox, Leah Dowell, David Kiker, Tiffany Lujan, Stacy Luka, Abbigal Ramirez, Rheaven Sandoval, Kenneth Underhill, Haze Murphy, Cecilia Cabrera, Dustin Edwards
    3 Oct 2019
  • Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Siphophage Snoke
    Genome Sequences
    Complete Genome Sequence of Escherichia coli Siphophage Snoke

    Escherichia coli is a Gram-negative bacterium often found in animal intestinal tracts. Here, we present the genome of the Guernseyvirinae-like E. coli 4s siphophage Snoke. The 44.4-kb genome contains 81 protein-coding genes, for which 33 functions were predicted. The capsid morphogenesis...

    James E. Corban, Jacob Gramer, Russell Moreland, Mei Liu, Jolene Ramsey
    3 Oct 2019
  • Draft Genome Sequences of <span class="named-content genus-species" id="named-content-1">Enterococcus faecalis</span> Strains Isolated from Healthy Japanese Individuals
    Genome Sequences
    Draft Genome Sequences of Enterococcus faecalis Strains Isolated from Healthy Japanese Individuals

    Enterococcus faecalis is a common commensal of the intestines of humans and other mammals but is also a frequent cause of serious ailments. Here, we report 14 draft genome sequences of strains of Enterococcus faecalis, a normal inhabitant and Gram-positive bacterium that was isolated from 7 healthy...

    Kazuki Tanaka, Tsubasa Watabe, Kumiko Kato, Tomoya Tsukimi, Mitsuhiko P. Sato, Toshitaka Odamaki, Masaru Tomita, Shinji Fukuda
    3 Oct 2019
  • Whole-Genome Sequencing of a <em>Mycobacterium orygis</em> Strain Isolated from Cattle in Chennai, India
    Genome Sequences
    Whole-Genome Sequencing of a Mycobacterium orygis Strain Isolated from Cattle in Chennai, India

    Here, we report the isolation of Mycobacterium orygis from dairy cattle in Chennai, India. Spoligotyping assigned the isolate to spoligotype 587 (ST587), which belongs to M. orygis. This species was confirmed as M. orygis using whole-genome sequencing.

    Ahmed Kabir Refaya, Narender Kumar, Dhinakar Raj, Maroudam Veerasamy, Subramanyam Balaji, Sivakumar Shanmugam, Ananthi Rajendran, Srikanth Prasad Tripathy, Soumya Swaminathan, Sharon J. Peacock, Kannan Palaniyandi
    3 Oct 2019
  • Coding-Complete Genome Sequence of a Pollen-Associated Virus Belonging to the <em>Secoviridae</em> Family Recovered from a Japanese Apricot (<em>Prunus mume</em>) Metagenome Data Set
    Genome Sequences
    Coding-Complete Genome Sequence of a Pollen-Associated Virus Belonging to the Secoviridae Family Recovered from a Japanese Apricot (Prunus mume) Metagenome Data Set

    We report the coding-complete genome sequence of Japanese apricot pollen-associated secovirus 1 (JAPSV1), a virus belonging to the Secoviridae family, recovered from Japanese apricot (Prunus mume) pollen that is closely related to Peach leaf pitting-associated virus (PLPAV). This discovery adds to the number of known pollen-associated...

    Andrea M. Fetters, Paul G. Cantalupo, Tia-Lynn Ashman, James M. Pipas
    3 Oct 2019
  • Draft Genome Sequences of Three Isolates of <em>Coniothyrium glycines</em>, Causal Agent of Red Leaf Blotch of Soybean
    Genome Sequences
    Draft Genome Sequences of Three Isolates of Coniothyrium glycines, Causal Agent of Red Leaf Blotch of Soybean

    Coniothyrium glycines, the causal agent of red leaf blotch in soybeans, is considered a high-consequence biological agent. With limited genomic information known, there are no molecular genotyping or detection methods available. We report the draft genome sequences of three C. glycines isolates, greatly enhancing our knowledge of this species.

    ...
    Trenna Blagden, Andres Espindola, Kitty Cardwell, Alejandro Ortega-Beltran, Ranajit Bandyopadhyay
    3 Oct 2019
  • Complete Genome Sequence of an Adenovirus-1 Isolate from an African Pygmy Hedgehog (<em>Atelerix albiventris</em>) Exhibiting Respiratory Symptoms in Japan
    Genome Sequences
    Complete Genome Sequence of an Adenovirus-1 Isolate from an African Pygmy Hedgehog (Atelerix albiventris) Exhibiting Respiratory Symptoms in Japan

    This study reports the complete genome sequence of an African pygmy hedgehog adenovirus-1 isolate from an African pygmy hedgehog which displayed respiratory symptoms that included nasal discharge, sniffling, coughing, and respiratory distress. The viral genome is 31,764 bp long and shows four deletion sites compared to that of skunk adenovirus-1.

    Hiroo Madarame, Jumpei Uchiyama, Kenichi Tamukai, Yukie Katayama, Nanako Osawa, Kaoru Suzuki, Tetsuya Mizutani, Hideharu Ochiai
    3 Oct 2019
  • Draft Genome Sequences of Five <em>Proteobacteria</em> Isolated from Lechuguilla Cave, New Mexico, USA, and Insights into Taxonomy and Quorum Sensing
    Genome Sequences
    Draft Genome Sequences of Five Proteobacteria Isolated from Lechuguilla Cave, New Mexico, USA, and Insights into Taxonomy and Quorum Sensing

    Genomic resources remain scarce for bacteria isolated from oligotrophic caves. We sequenced the genomes of five Proteobacteria isolated from Lechuguilla Cave in New Mexico. Genome-based phylogeny indicates that each strain belongs to a distinct genus. Two Rhizobiaceae isolates possess genomic potential for the biosynthesis of acyl-homoserine lactone.

    Han Ming Gan, Peter C. Wengert, Hazel A. Barton, André O. Hudson, Michael A. Savka
    3 Oct 2019
  • Draft Genome Sequence of <span class="named-content genus-species" id="named-content-1">Kytococcus schroeteri</span> Strain H01, Isolated from Human Skin
    Genome Sequences
    Draft Genome Sequence of Kytococcus schroeteri Strain H01, Isolated from Human Skin

    Kytococcus schroeteri strain H01 was isolated from the skin of a healthy volunteer who underwent erythromycin treatment for a skin disorder 1 year prior. The draft genome consists of 2.38 Mb, a G+C content of 73.06%, and 2,221 protein coding sequences. This is the first genome characterization of a K....

    Amine M. Boukerb, Magalie Robert, Nataliya A. Teteneva, Natalia D. Danilova, Marina V. Zhurina, Sergey V. Mart’yanov, Vladimir K. Plakunov, Marc G. J. Feuilloley, Andrei V. Gannesen
    3 Oct 2019
  • Complete Coding Sequence of <em>Andean Potato Mottle Virus</em> from a 40-Year-Old Sample from Peru
    Genome Sequences
    Complete Coding Sequence of Andean Potato Mottle Virus from a 40-Year-Old Sample from Peru

    A complete coding sequence of the type strain of Andean potato mottle virus from Peru (isolate Lm) was obtained. Comparison of its RNA1 and RNA2 sequences with variants of this virus isolated in Brazil revealed RNA1 and RNA2 nucleotide identities of 81 to 83% and 70 to 71%, respectively.

    Ian P. Adams, Cesar Fribourg, Adrian Fox, Neil Boonham, Roger A. C. Jones
    3 Oct 2019
  • Draft Genome Sequence of <em>Brevibacillus</em> sp. Strain LEMMJ03, Isolated from an Antarctic Volcano
    Genome Sequences
    Draft Genome Sequence of Brevibacillus sp. Strain LEMMJ03, Isolated from an Antarctic Volcano

    Here, we announce the draft genome sequence of Brevibacillus sp. strain LEMMJ03, isolated from Whalers Bay sediment (Deception Island, Antarctica). In total, 4,500 coding sequences (CDS), among those 102 coding for tRNAs and 5 for noncoding RNAs (ncRNAs), were predicted from the 4.64-Mb genome. Predicted functions were for bacteriocin and degradation of aromatic...

    Júnia Schultz, René Kallies, Ulisses Nunes da Rocha, Alexandre Soares Rosado
    3 Oct 2019
  • Complete Genome Sequence of a <span class="named-content genus-species" id="named-content-1">Papio anubis</span> Simian Foamy Provirus
    Genome Sequences
    Complete Genome Sequence of a Papio anubis Simian Foamy Provirus

    The full-length sequence of a Papio anubis simian foamy provirus was obtained by using PCR followed by Sanger sequencing. This simian foamy virus from a P. anubis animal (SFVp.anubis) is 13,393 bp long. Like other proviruses, the genome of SFVp.anubis is organized with long terminal repeats (LTRs),...

    Brice Jegado, Renaud Mahieux
    3 Oct 2019
  • Draft Genome Sequence of Methicillin-Resistant <span class="named-content genus-species" id="named-content-1">Staphylococcus aureus</span> Strain AW7, Isolated from a Patient with Bacteremia
    Genome Sequences
    Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus Strain AW7, Isolated from a Patient with Bacteremia

    Methicillin-resistant Staphylococcus aureus (MRSA) strain AW7 is a commonly used challenge strain in experimental models of MRSA infection. Here, we report its draft genome sequence.

    David R. Cameron, Alban Ramette, Josef Prazak, José Entenza, Matthias Haenggi, Yok-Ai Que, Grégory Resch
    3 Oct 2019
  • Draft Genome Sequence of <span class="named-content genus-species" id="named-content-1">Microbacterium</span> sp. Gd 4-13, Isolated from Gydanskiy Peninsula Permafrost Sediments of Marine Origin
    Genome Sequences
    Draft Genome Sequence of Microbacterium sp. Gd 4-13, Isolated from Gydanskiy Peninsula Permafrost Sediments of Marine Origin

    Here, we report the draft genome sequence of Microbacterium sp. strain Gd 4-13, isolated from late Pleistocene permafrost of marine origin located on the Gydanskiy Peninsula. Genome sequence analysis was performed to understand strain survivability mechanisms under permafrost conditions and to expand biotechnology applications.

    Elena V. Spirina, Konstantin V. Kuleshov, Alfiya K. Yunusova, Tatiana A. Vishnivetskaya, Elizaveta M. Rivkina
    3 Oct 2019
  • Genome Sequences of Three <em>Lactobacillus</em> Species Strains of the Stomach of the White-Footed Deermouse (<span class="named-content genus-species" id="named-content-1">Peromyscus leucopus</span>)
    Genome Sequences
    Genome Sequences of Three Lactobacillus Species Strains of the Stomach of the White-Footed Deermouse (Peromyscus leucopus)

    Three colony types of Lactobacillus were isolated from the stomach of LL colony stock Peromyscus leucopus deermice, a reservoir for several human zoonoses. Genome sequences revealed two isolates to be new strains of Lactobacillus animalis and...

    Khalil Bassam, Ana Milovic, Alan G. Barbour
    3 Oct 2019
  • Complete Genome Sequence of Potential Deoxynivalenol-Degrading Bacterium <span class="named-content genus-species" id="named-content-1">Youhaiella tibetensis</span> Type Strain F4
    Genome Sequences
    Complete Genome Sequence of Potential Deoxynivalenol-Degrading Bacterium Youhaiella tibetensis Type Strain F4

    Here, we report the first complete genome sequence of the potential deoxynivalenol-degrading strain Youhaiella tibetensis F4T (China General Microbiological Culture Collection Center [CGMCC] 1.12719T). To the best of our knowledge, this is also the first announcement of the complete genome sequence of a Youhaiella species.

    ...
    Yang Wang, Songxue Wang
    3 Oct 2019
  • Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Vibrio natriegens</span> Phage Phriendly
    Genome Sequences
    Complete Genome Sequence of Vibrio natriegens Phage Phriendly

    Vibrio natriegens is a fast-growing marine bacterium of interest for biotechnology applications. Here, we describe the isolation and genome annotation of V. natriegens podophage Phriendly. Among the 72 predicted coding genes and 1 tRNA, Phriendly’s 50,218-bp genome has low sequence identity to known phages.

    James Clark, Adey Awah, Russell Moreland, Mei Liu, Jason J. Gill, Jolene Ramsey
    3 Oct 2019
  • Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Siphophage Shashou
    Genome Sequences
    Complete Genome Sequence of Escherichia coli Siphophage Shashou

    Here, we announce the genome of the Escherichia coli 4s siphophage Shashou, which presents similarity to members of the Guernseyvirinae subfamily. Shashou is predicted to use a headful packaging mechanism for its 44,155-bp genome and to encode 77 proteins.

    Tyler Higbee, Shih-Hung Yang, Russell Moreland, Mei Liu, Jolene Ramsey
    3 Oct 2019
  • Complete Genome Sequence of Multidrug-Resistant <span class="named-content genus-species" id="named-content-1">Salmonella enterica</span> Serovar I 4,[5],12:i:− 2015 U.S. Pork Outbreak Isolate USDA15WA-1
    Genome Sequences
    Complete Genome Sequence of Multidrug-Resistant Salmonella enterica Serovar I 4,[5],12:i:− 2015 U.S. Pork Outbreak Isolate USDA15WA-1

    The genome of a multidrug-resistant (MDR) Salmonella enterica subsp. enterica serovar I 4,[5],12:i:− isolate from the 2015 U.S. pork outbreak was sequenced. The complete nucleotide sequence of USDA15WA-1 is 5,031,277 bp, including Salmonella genomic island 4 encoding tolerance to multiple...

    Bradley L. Bearson, Julian M. Trachsel, Devin B. Holman, Brian W. Brunelle, Sathesh K. Sivasankaran, Mustafa Simmons, Jamie Wasilenko, Glenn Tillman, John J. Johnston, Shawn M. D. Bearson
    3 Oct 2019
  • Whole-Genome Sequence of High-Risk Clone Sequence Type 111 of <span class="named-content genus-species" id="named-content-1">Pseudomonas aeruginosa</span> Strain NUBRI-P, Isolated from a Wounded Sudanese Patient
    Genome Sequences
    Whole-Genome Sequence of High-Risk Clone Sequence Type 111 of Pseudomonas aeruginosa Strain NUBRI-P, Isolated from a Wounded Sudanese Patient

    Pseudomonas aeruginosa is a common nosocomial pathogen often associated with a high mortality rate in vulnerable populations. Here, we describe the genomic sequence of a pan-resistant, high-risk clone of P. aeruginosa sequence type 111 (ST111) isolated from a hospital patient in Sudan.

    ...
    Sofia B. Mohamed, Sumaya Kambal, Abdalla Munir, Nusiba I. Abdalla, Ahmed Hamad, Sara E. Mohammed, Fatima E. Ahmed, Omnia Hamid, Mohamed M. Hassan, Arshad Ismail, Mushal Allam
    3 Oct 2019
  • Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Staphylococcus aureus</span> Myophage Maine
    Genome Sequences
    Complete Genome Sequence of Staphylococcus aureus Myophage Maine

    Multidrug-resistant strains of Staphylococcus aureus cause serious human disease worldwide. Bacteriophages offer a promising alternative to traditional antibiotics. Here, we announce the 141,712-bp genome of S. aureus phage Maine. A myophage with 9,019-bp predicted terminal repeats and high...

    Russell Moreland, Abby Korn, Heather Newkirk, Mei Liu, Jason J. Gill, Jesse Cahill, Jolene Ramsey
    3 Oct 2019

Omics Data Sets

  • Coastal Ocean Metagenomes and Curated Metagenome-Assembled Genomes from Marsh Landing, Sapelo Island (Georgia, USA)
    Omics Data Sets
    Coastal Ocean Metagenomes and Curated Metagenome-Assembled Genomes from Marsh Landing, Sapelo Island (Georgia, USA)

    Microbes play a dominant role in the biogeochemistry of coastal waters, which receive organic matter from diverse sources. We present metagenomes and 45 metagenome-assembled genomes (MAGs) from Sapelo Island, Georgia, to further understand coastal microbial populations.

    Julian Damashek, Christian F. Edwardson, Bradley B. Tolar, Scott M. Gifford, Mary Ann Moran, James T. Hollibaugh
    3 Oct 2019

Author Correction

  • Correction for Israeli et al., “Draft Genome Sequence of a Rare Israeli Clinical Isolate of <span class="named-content genus-species" id="named-content-1">Burkholderia pseudomallei</span>”
    Author Correction
    Correction for Israeli et al., “Draft Genome Sequence of a Rare Israeli Clinical Isolate of Burkholderia pseudomallei”
    Ofir Israeli, Inbar Cohen-Gihon, Tal Brosh-Nissimov, Shay Weiss, Anat Zvi, Adi Beth-Din, Ohad Shifman, Ma’ayan Israeli, Uri Elia, Shirley Lazar, Erez Bar-Haim, Ofer Cohen, Theodor Chitlaru
    3 Oct 2019
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