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Archive

August 2019; Volume 8,Issue 32

Genome Sequences

  • Complete Genome Sequence of <em>Agrococcus</em> sp. Strain SGAir0287, Isolated from Tropical Air Collected in Singapore
    Genome Sequences
    Complete Genome Sequence of Agrococcus sp. Strain SGAir0287, Isolated from Tropical Air Collected in Singapore

    Agrococcus sp. strain SGAir0287 was isolated from tropical air samples collected in Singapore. Assembled using single-molecule real-time (SMRT) sequencing and MiSeq reads, the genome consists of one circular chromosome of 3,084,767 bp. The entire genome has 2,870 protein-coding genes, 45 tRNAs, and 3 rRNAs.

    Kenny J. X. Lau, Ana Carolina M. Junqueira, Akira Uchida, Rikky W. Purbojati, James N. I. Houghton, Caroline Chénard, Anthony Wong, Sandra Kolundžija, Megan E. Clare, Kavita K. Kushwaha, Alexander Putra, Nicolas E. Gaultier, Cassie E. Heinle, Balakrishnan N. V. Premkrishnan, Vineeth Kodengil Vettah, Daniela I. Drautz-Moses, Stephan C. Schuster
    8 Aug 2019
  • Genome Sequences of Two <span class="named-content genus-species" id="named-content-1">Azospirillum</span> sp. Strains, TSA2S and TSH100, Plant Growth-Promoting Rhizobacteria with N<sub>2</sub>O Mitigation Abilities
    Genome Sequences
    Genome Sequences of Two Azospirillum sp. Strains, TSA2S and TSH100, Plant Growth-Promoting Rhizobacteria with N2O Mitigation Abilities

    Azospirillum sp. strains TSA2S and TSH100 are plant growth-promoting rhizobacteria with the capacity to mitigate N2O from agricultural soil. They were isolated from the rhizosphere of paddy soil in Tokyo, Japan. Here, we present the genome sequences of these two strains.

    Nan Gao, Weishou Shen, Tomoyasu Nishizawa, Kazuo Isobe, Yong Guo, Hanjie Ying, Keishi Senoo
    8 Aug 2019
  • Draft Genome Sequence of <em>Massilia</em> sp. Strain MC02, Isolated from a Sandy Loam Maize Soil
    Genome Sequences
    Draft Genome Sequence of Massilia sp. Strain MC02, Isolated from a Sandy Loam Maize Soil

    From farmed corn soil in California, we isolated and sequenced a new member of the genus Massilia, Massilia sp. strain MC02. Massilia sp. MC02 has an assembled draft genome of 5,023,356 bp with a total of 4,790 protein-encoding genes and 3,028 predicted proteins, 47 tRNA genes, and 2 rRNA operons.

    Rachel Raths, Vincent Peta, Heike Bücking
    8 Aug 2019
  • Complete Genome Sequence of Enterotoxigenic <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Podophage LL11
    Genome Sequences
    Complete Genome Sequence of Enterotoxigenic Escherichia coli Podophage LL11

    Enterotoxigenic Escherichia coli (ETEC) is an opportunistic pathogen that commonly causes foodborne illness. Study of bacteriophages against this pathogen could be useful to develop alternative treatment approaches. Here, we present the complete genome sequence of LL11, a T7-like podophage that infects ETEC.

    Matthew Theodore, Lauren Lessor, Chandler O’Leary, Rohit Kongari, Jason Gill, Mei Liu
    8 Aug 2019
  • Genome Sequence of a T4-like Phage, <em>Escherichia</em> Phage vB_EcoM-Sa45lw, Infecting Shiga Toxin-Producing <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Strains
    Genome Sequences
    Genome Sequence of a T4-like Phage, Escherichia Phage vB_EcoM-Sa45lw, Infecting Shiga Toxin-Producing Escherichia coli Strains

    Escherichia phage vB_EcoM-Sa45lw, a new member of the T4-like phages, was isolated from surface water in a produce-growing area. The phage, containing double-stranded DNA with a genome size of 167,353 bp and 282 predicted open reading frames (ORFs), is able to infect generic Escherichia coli and Shiga toxin-producing...

    Yen-Te Liao, Yujie Zhang, Alexandra Salvador, Vivian C. H. Wu
    8 Aug 2019
  • Complete Genome Sequences of <span class="named-content genus-species" id="named-content-1">Streptomyces lividans</span> Bacteriophages Satis and JustBecause
    Genome Sequences
    Complete Genome Sequences of Streptomyces lividans Bacteriophages Satis and JustBecause

    We present here the complete genomes of two Streptomyces bacteriophages, Satis and JustBecause. Both phages were isolated directly from soil samples collected in St. Louis, MO, and present with an unusual prolate head morphology and large genome lengths of over 180 kb.

    Kelly Hartigan, John Hudson Alarcon, Andrew Cao, Yongzhen Chen, Nicole Curnutt, Brooke Felsheim, Saransh Gothi, Lucia Grandison, Matthew McDermut, Kaeli-Skye Spight, Xuejing Xu, Kathleen Weston-Hafer, Christopher Shaffer
    8 Aug 2019
  • Draft Genome Sequence of Manganese-Oxidizing Bacterium <span class="named-content genus-species" id="named-content-1">Massilia</span> sp. Strain Mn16-1_5, Isolated from Serpentine Soil in Taitung, Taiwan
    Genome Sequences
    Draft Genome Sequence of Manganese-Oxidizing Bacterium Massilia sp. Strain Mn16-1_5, Isolated from Serpentine Soil in Taitung, Taiwan

    Massilia sp. strain Mn16-1_5 was isolated from serpentine soil. This strain is able to oxidize manganese and has the potential for bioremediation of chromium. Here, we present a 5.53-Mb draft genome sequence of this strain with a G+C content of 64.8% that might provide more information for species delineation and oxidase genes in this strain.

    Sheng-Chung Chen, Chuen-Huey Chiu, Pin-Tzu Chiu, Yo-Chia Chen, Yong-Hong Lin, Chiu-Chung Young, Juei-Yu Chiu
    8 Aug 2019
  • Draft Genome Sequence of <em>Brevundimonas</em> sp. Strain T2.26MG-97, Isolated from a Rock Core Sample from 492.6 Meters Deep on the Subsurface of the Iberian Pyrite Belt
    Genome Sequences
    Draft Genome Sequence of Brevundimonas sp. Strain T2.26MG-97, Isolated from a Rock Core Sample from 492.6 Meters Deep on the Subsurface of the Iberian Pyrite Belt

    The draft genome of Brevundimonas sp. strain T2.26MG-97, isolated at a depth of 492.6 m in the subsurface of the Iberian Pyrite Belt, is reported here. It consists of 262 scaffolds with a total genome length of 3.68 Mbp, where 3,549 coding DNA sequences have been annotated.

    E. Rodríguez-Robles, J. M. Martínez, T. Leandro, R. Amils
    8 Aug 2019
  • First Whole-Genome Sequence of a Highly Resistant <span class="named-content genus-species" id="named-content-1">Klebsiella pneumoniae</span> Sequence Type 14 Strain Isolated from Sudan
    Genome Sequences
    First Whole-Genome Sequence of a Highly Resistant Klebsiella pneumoniae Sequence Type 14 Strain Isolated from Sudan

    Klebsiella pneumoniae is an opportunistic pathogen that accounts for a significant proportion of hospital-acquired infections and is a leading cause of nosocomial outbreaks. Here, we describe the genomic sequence of a highly resistant K. pneumoniae sequence type 14 (ST14) strain isolated from Sudan...

    Sofia B. Mohamed, Sumaya Kambal, Abdalla Munir, Nusiba Abdalla, Mohamed Hassan, Ahmed Hamad, Sara Mohammed, Fatima Ahmed, Omnia Hamid, Arshad Ismail, Mushal Allam
    8 Aug 2019
  • Complete Genome Sequence and Methylome Analysis of <span class="named-content genus-species" id="named-content-1">Thermoactinomyces vulgaris</span> 2H
    Genome Sequences
    Complete Genome Sequence and Methylome Analysis of Thermoactinomyces vulgaris 2H

    Here, we report the complete genome sequence and full methylome analysis of a newly isolated, aerobic, thermophilic, Gram-positive actinomycete, a strain of Thermoactinomyces vulgaris designated strain 2H.

    Houda Mankai, Brian P. Anton, Victoria Wu, Tamas Vincze, Richard J. Roberts, Ferid Limam, Alexey Fomenkov
    8 Aug 2019
  • Whole-Genome Sequencing of Four <em>Campylobacter</em> Strains Isolated from Gull Excreta Collected from Hobie Beach (Oxnard, CA, USA)
    Genome Sequences
    Whole-Genome Sequencing of Four Campylobacter Strains Isolated from Gull Excreta Collected from Hobie Beach (Oxnard, CA, USA)

    Campylobacter spp. are commensal organisms in avian species and are one of the leading causes of bacterial foodborne human diarrheal disease worldwide. We report the draft genome sequences of Campylobacter volucris, C. lari, and...

    Vicente Gomez-Alvarez, Nicholas J. Ashbolt, John F. Griffith, Jorge Santo Domingo, Jingrang Lu
    8 Aug 2019
  • Draft Genome Sequence of <em>Massilia</em> sp. Strain ONC3, a Novel Bacterial Species of the <em>Oxalobacteraceae</em> Family Isolated from Garden Soil
    Genome Sequences
    Draft Genome Sequence of Massilia sp. Strain ONC3, a Novel Bacterial Species of the Oxalobacteraceae Family Isolated from Garden Soil

    From garden soil, we isolated and sequenced Massilia sp. strain ONC3, a new member of the Oxalobacteraceae within the Massilia genus. Sequence analysis showed an assembled genome size of 5,622,601 bp, with a predicted total of 5,104 protein-coding sequences, 3,194 functionally assigned...

    Vincent Peta, Rachel Raths, Heike Bücking
    8 Aug 2019
  • Draft Genome Sequences of Potentially Pathogenic <span class="named-content genus-species" id="named-content-1">Clostridium perfringens</span> Strains from Environmental Surface Water in the North West Province of South Africa
    Genome Sequences
    Draft Genome Sequences of Potentially Pathogenic Clostridium perfringens Strains from Environmental Surface Water in the North West Province of South Africa

    Surface water systems in South Africa are experiencing a major decline in quality due to various anthropogenic factors. This poses a possible health risk for humans. Here, we present the draft genome sequences of three Clostridium perfringens isolates obtained from a fecally polluted river system in the North West province of South Africa.

    Johannes Cornelius Jacobus Fourie, Tomasz J. Sanko, Cornelius Carlos Bezuidenhout, Charlotte Mienie, Rasheed Adegbola Adeleke
    8 Aug 2019
  • Complete Genome Sequence of <em>Caloramator</em> sp. Strain E03, a Novel Ethanologenic, Thermophilic, Obligately Anaerobic Bacterium
    Genome Sequences
    Complete Genome Sequence of Caloramator sp. Strain E03, a Novel Ethanologenic, Thermophilic, Obligately Anaerobic Bacterium

    Here, we report the complete genome sequence of Caloramator sp. strain E03, an anaerobic thermophile that was isolated from a hot spring within the Rabbit Creek area of Yellowstone National Park. The assembly contains a single 2,984,770-bp contig with a G+C content of 31.3% and is predicted to encode 2,678 proteins.

    E. Anne Hatmaker, Dawn M. Klingeman, Roman K. Martin, Adam M. Guss, James G. Elkins
    8 Aug 2019
  • Complete Genome Sequences of Three Star-Shaped Bacteria, <span class="named-content genus-species" id="named-content-1">Stella humosa</span>, <span class="named-content genus-species" id="named-content-2">Stella vacuolata</span>, and <span class="named-content genus-species" id="named-content-3">Stella</span> Species ATCC 35155
    Genome Sequences
    Complete Genome Sequences of Three Star-Shaped Bacteria, Stella humosa, Stella vacuolata, and Stella Species ATCC 35155

    Stella species are unique star-shaped alphaproteobacteria found in various environments. We report the complete genome sequences of three Stella strains, Stella humosa ATCC 43930, Stella vacuolata ATCC 43931, and ...

    Atsushi Shibai, Tomoya Maeda, Masako Kawada, Hazuki Kotani, Natsue Sakata, Chikara Furusawa
    8 Aug 2019
  • Draft Genome Sequence of <em>Duganella</em> sp. Strain DN04, Isolated from Cultivated Soil
    Genome Sequences
    Draft Genome Sequence of Duganella sp. Strain DN04, Isolated from Cultivated Soil

    Here, we sequenced Duganella sp. strain DN04, a novel species within the genus Duganella that was isolated from a maize field in North Carolina. The assembled draft genome size is 6,562,230 bp, with a total of 6,039 protein coding sequences and 3,889 functionally assigned genes, including genes putatively involved in the colonization of plants.

    ...
    Rachel Raths, Vincent Peta, Heike Bücking
    8 Aug 2019
  • Complete Genome Sequence of <em>Nissabacter</em> sp. Strain SGAir0207, Isolated from an Air Sample Collected in Singapore
    Genome Sequences
    Complete Genome Sequence of Nissabacter sp. Strain SGAir0207, Isolated from an Air Sample Collected in Singapore

    Nissabacter sp. strain SGAir0207 was isolated from a tropical air sample collected in Singapore. Its genome was assembled using a hybrid approach with long and short reads, resulting in one chromosome of 3.9 Mb and 7 plasmids. The complete genome consists of 4,403 protein-coding, 84 tRNA, and 22 rRNA genes.

    Nicolas E. Gaultier, Ana Carolina M. Junqueira, Akira Uchida, Rikky W. Purbojati, James N. I. Houghton, Caroline Chénard, Anthony Wong, Sandra Kolundžija, Megan E. Clare, Kavita K. Kushwaha, Alexander Putra, Carmon Kee, Balakrishnan N. V. Premkrishnan, Cassie E. Heinle, Serene B. Y. Lim, Vineeth Kodengil Vettath, Daniela I. Drautz-Moses, Stephan C. Schuster
    8 Aug 2019
  • Complete Genome Sequences of Cluster F Mycobacteriophages EleanorGeorge, Mattes, and Spikelee
    Genome Sequences
    Complete Genome Sequences of Cluster F Mycobacteriophages EleanorGeorge, Mattes, and Spikelee

    EleanorGeorge, Mattes, and Spikelee are mycobacteriophages isolated from different soil samples using Mycobacterium smegmatis mc2155 as the host. Each was obtained using direct isolation techniques, purified, and then sequenced. Based on sequence similarity, all three belong to the F1 subcluster and are temperate phages.

    Christina Jacob, Yunia Alvarez, Cynthia Castro, Katherine Clarke, Linda Dantico, Bernadette J. Connors
    8 Aug 2019
  • Full Chloroplast Genome Sequence of the Economically Important Dietary Supplement and Spice <em>Curcuma longa</em>
    Genome Sequences
    Full Chloroplast Genome Sequence of the Economically Important Dietary Supplement and Spice Curcuma longa

    Curcuma longa L. is a native species of Asia that is commonly known as turmeric. It is a spice also used in traditional medicine to treat a wide range of illnesses. Here, we present the fully annotated chloroplast genome of Curcuma longa.

    Amanda M. Windsor, Brittany M. Ott, Ning Zhang, Jun Wen, Erica Hsu, Sara M. Handy
    8 Aug 2019
  • Whole-Genome Sequence of <span class="named-content genus-species" id="named-content-1">Acinetobacter baumannii</span> Strain NUBRI-A, Isolated from a Hospitalized Patient in Khartoum, Sudan
    Genome Sequences
    Whole-Genome Sequence of Acinetobacter baumannii Strain NUBRI-A, Isolated from a Hospitalized Patient in Khartoum, Sudan

    Acinetobacter baumannii has emerged as an important pathogen leading to multiple nosocomial outbreaks. Here, we describe the genomic sequence of a multidrug-resistant Acinetobacter baumannii sequence type 164 (ST164) isolate from a hospital patient in Sudan. To our knowledge, this is the first...

    Sofia B. Mohamed, Mohamed Hassan, Abdalla Munir, Sumaya Kambal, Nusiba I. Abdalla, Ahmed Hamad, Sara Mohammed, Fatima Ahmed, Omnia Hamid, Arshad Ismail, Mushal Allam
    8 Aug 2019
  • Complete Genome Sequence of <em>Brachybacterium</em> sp. Strain SGAir0954, Isolated from Singapore Air
    Genome Sequences
    Complete Genome Sequence of Brachybacterium sp. Strain SGAir0954, Isolated from Singapore Air

    Brachybacterium sp. strain SGAir0954 was isolated from tropical air collected in Singapore, and its genome was sequenced and assembled using long reads generated by single-molecule real-time (SMRT) sequencing. The complete genome has a size of 3.41 Mb and consists of 2,955 protein coding genes, 50 tRNAs, and 9 rRNAs.

    Phu Pwint Thin Hlaing, Ana Carolina M. Junqueira, Akira Uchida, Rikky W. Purbojati, James N. I. Houghton, Caroline Chénard, Anthony Wong, Megan E. Clare, Kavita K. Kushwaha, Alexander Putra, Carmon Kee, Nicolas E. Gaultier, Balakrishnan N. V. Premkrishnan, Cassie E. Heinle, Serene B. Y. Lim, Vineeth Kodengil Vettah, Daniela I. Drautz-Moses, Stephan C. Schuster
    8 Aug 2019

Amplicon Sequence Collections

  • 16S rRNA Gene Amplicon Sequence Data from Chicken Cecal Feces from Vietnam and Thailand
    Amplicon Sequence Collections
    16S rRNA Gene Amplicon Sequence Data from Chicken Cecal Feces from Vietnam and Thailand

    Here, we report 16S rRNA amplicon sequence data from chicken cecal feces from Vietnam and Thailand. Lachnospiraceae, Ruminococcaceae, and Bacteroidaceae were dominant in cecal feces microbiota.

    Nachiko Takeshita, Hyunjung Kim, Kringkrai Witoonsatian, Mari Tohya, Tấn Hùng Võ, Nuchjaree Boonyong, Thị Phương Bình Nguyễn, Ichiro Nakagawa, Nattakan Meekhanon, Ngọc Hải Nguyễn, Tsutomu Sekizaki
    8 Aug 2019

Protocols and Workflows

  • octoFLU: Automated Classification for the Evolutionary Origin of Influenza A Virus Gene Sequences Detected in U.S. Swine
    Protocols and Workflows
    octoFLU: Automated Classification for the Evolutionary Origin of Influenza A Virus Gene Sequences Detected in U.S. Swine

    The diversity of the 8 genes of influenza A viruses (IAV) in swine reflects introductions from nonswine hosts and subsequent antigenic drift and shift. Here, we curated a data set and present a pipeline that assigns evolutionary lineage and genetic clade to query gene segments.

    Jennifer Chang, Tavis K. Anderson, Michael A. Zeller, Phillip C. Gauger, Amy L. Vincent
    8 Aug 2019

Author Corrections

  • Correction for Kee et al., “Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Pseudomonas stutzeri</span> Strain SGAir0442, Isolated from Singapore Air Samples”
    Author Correction
    Correction for Kee et al., “Complete Genome Sequence of Pseudomonas stutzeri Strain SGAir0442, Isolated from Singapore Air Samples”
    Carmon Kee, Ana Carolina M. Junqueira, Akira Uchida, Rikky W. Purbojati, James N. I. Houghton, Caroline Chénard, Anthony Wong, Sandra Kolundžija, Megan E. Clare, Kavita K. Kushwaha, Deepa Panicker, Alexander Putra, Nicolas E. Gaultier, Balakrishnan N. V. Premkrishnan, Cassie E. Heinle, Vineeth Kodengil Vettath, Daniela I. Drautz-Moses, Stephan C. Schuster
    8 Aug 2019
  • Correction for Vettath et al., “Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Acinetobacter indicus</span> Strain SGAir0564 Isolated from Tropical Air Collected in Singapore”
    Author Correction
    Correction for Vettath et al., “Complete Genome Sequence of Acinetobacter indicus Strain SGAir0564 Isolated from Tropical Air Collected in Singapore”
    Vineeth Kodengil Vettath, Ana Carolina M. Junqueira, Akira Uchida, Rikky W. Purbojati, James N. I. Houghton, Caroline Chénard, Daniela I. Drautz-Moses, Anthony Wong, Sandra Kolundžija, Megan E. Clare, Kavita K. Kushwaha, Deepa Panicker, Alexander Putra, Nicolas E. Gaultier, Cassie E. Heinle, Balakrishnan N. V. Premkrishnan, Stephan C. Schuster
    8 Aug 2019
  • Correction for Heinle et al., “Complete Genome Sequence of <span class="named-content genus-species" id="named-content-1">Lelliottia nimipressuralis</span> Strain SGAir0187, Isolated from Tropical Air Collected in Singapore”
    Author Correction
    Correction for Heinle et al., “Complete Genome Sequence of Lelliottia nimipressuralis Strain SGAir0187, Isolated from Tropical Air Collected in Singapore”
    Cassie E. Heinle, Ana Carolina M. Junqueira, Akira Uchida, Rikky W. Purbojati, James N. I. Houghton, Caroline Chénard, Daniela I. Drautz-Moses, Anthony Wong, Sandra Kolundžija, Megan E. Clare, Kavita K. Kushwaha, Deepa Panicker, Alexander Putra, Nicolas E. Gaultier, Balakrishnan N. V. Premkrishnan, Vineeth Kodengil Vettath, Stephan C. Schuster
    8 Aug 2019
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Microbiology Resource Announcements: 8 (32)

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