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Suzuki M, Hashimoto Y, Hirabayashi A, Yahara K, Yoshida M, Fukano H, Hoshino Y, Shibayama K, Tomita H. Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing. Methods Mol Biol 2023; 2632:227-246. [PMID: 36781732 DOI: 10.1007/978-1-0716-2996-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Antimicrobial-resistant (AMR) bacterial infections caused by clinically important bacteria, including ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) and mycobacteria (Mycobacterium tuberculosis and nontuberculous mycobacteria), have become a global public health threat. Their epidemic and pandemic clones often accumulate useful accessory genes in their genomes, such as AMR genes (ARGs) and virulence factor genes (VFGs). This process is facilitated by horizontal gene transfer among microbial communities via mobile genetic elements (MGEs), such as plasmids and phages. Nanopore long-read sequencing allows easy and inexpensive analysis of complex bacterial genome structures, although some aspects of sequencing data calculation and genome analysis methods are not systematically understood. Here we describe the latest and most recommended experimental and bioinformatics methods available for the construction of complete bacterial genomes from nanopore sequencing data and the detection and classification of genotypes of bacterial chromosomes, ARGs, VFGs, plasmids, and other MGEs based on their genomic sequences for genomic epidemiological analysis of AMR bacteria.
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Affiliation(s)
- Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan.
| | - Yusuke Hashimoto
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Aki Hirabayashi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mitsunori Yoshida
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hanako Fukano
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Keigo Shibayama
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Japan.,Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, Maebashi, Japan
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2
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Takahashi M, Shinohara S, Hamada M, Tamura T, Dohra H, Kodani S, Nakagawa Y, Kokubo S, Hayakawa M, Yamamura H. Streptomyces pacificus sp. nov., a novel spongiicolazolicin-producing actinomycete isolated from a coastal sediment. J Antibiot (Tokyo) 2023; 76:93-100. [PMID: 36564595 DOI: 10.1038/s41429-022-00589-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
A polyphasic approach was used to determine the taxonomic position of a marine actinomycete, designated isolate CWH03T, which we previously reported to produce new linear azole-containing peptides spongiicolazolicins A and B. Strain CWH03T is mesophilic, neutrophilic, and halotolerant streptomycete that forms spiral spore chains on aerial mycelium. Comparative 16S rRNA gene sequencing showed that CWH03T was most closely related to Streptomyces tirandamycinicus HNM0039T (99.7%), Streptomyces spongiicola HNM0071T (99.4%), 'Streptomyces marianii' ICN19T (99.1%) and Streptomyces wuyuanensis CGMCC4.7042T (99.0%). The phylogenetic tree prepared using the 16S rRNA gene, as well as the phylogenomic tree using the genome BLAST distance phylogeny method and 81 core housekeeping genes, respectively, showed that the closest relative of strain CWH03T was S. spongiicola HNM0071T. The average nucleotide identity and digital DNA-DNA hybridization values between strains CWH03T and S. spongiicola HNM0071T were 91.46% and 44.2%, respectively, which were below the thresholds of 96% and 70% for prokaryotic conspecific assignation. The G+C content of the genomic DNA of strain CWH03T was 72.3%. Whole-cell hydrolysates of strain CWH03T contained LL-diaminopimelic acid. The predominant menaquinone was MK-9(H8) (88.3%), and the major fatty acids were iso-C16:0 (28.4%), anteiso-C15:0 (15.0%) and iso-C15:0 (12.9%). The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. Based on data obtained from phenotypic, phylogenetic, genomic, and chemotaxonomic analyses, strain CWH03T represents a novel species of the genus Streptomyces, for which the proposed name is Streptomyces pacificus sp. nov. The type strain is CWH03T ( = NBRC 114659T = TBRC 15780T).
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Affiliation(s)
- Miku Takahashi
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan
| | - Shoya Shinohara
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Hideo Dohra
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Academic Institute, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Youji Nakagawa
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan
| | - Susumu Kokubo
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan
| | - Masayuki Hayakawa
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan
- Yamanashi Prefectural University, Iida-5-11-1, Kofu, 400-0035, Japan
| | - Hideki Yamamura
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan.
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Ito Z, Koido S, Kato K, Odamaki T, Horiuchi S, Akasu T, Saruta M, Hata T, Kumagai Y, Fujioka S, Misawa T, Xiao JZ, Sato N, Ohkusa T. Dysbiosis of the Fecal and Biliary Microbiota in Biliary Tract Cancer. Cancers (Basel) 2022; 14:5379. [PMID: 36358797 PMCID: PMC9653963 DOI: 10.3390/cancers14215379] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 09/29/2023] Open
Abstract
Characteristic bile duct and gut microbiota have been identified in patients with chronic biliary tract disease. This study aimed to characterize the fecal and bile microbiota in biliary tract cancer (BTC) patients and their relationship. Patients with BTC (n = 30) and benign biliary disease (BBD) without cholangitis (n = 11) were included. Ten healthy, age-matched subjects were also recruited for fecal microbiota comparison. The fecal and bile duct microbiotas were analyzed by sequencing the 16S rRNA gene V3-V4 region. Live bacteria were obtained in the bile from three BTC patients by culture, and metagenomics-based identification was performed. Linear discriminant analysis effect size showed a higher Enterobacteriaceae abundance and a lower Clostridia abundance, including that of Faecalibacterium and Coprococcus, in the BTC patients than in the other subjects. Ten of 17 operational taxonomic units (OTUs) assigned to Enterobacteriaceae in the bile were matched with the OTUs found in the BTC subject fecal samples. Furthermore, a bile-isolated strain possessed the carcinogenic bacterial colipolyketide synthase-encoding gene. Enterobacteriaceae was enriched in the BTC feces, and more than half of Enterobacteriaceae in the bile matched that in the feces at the OTU level. Our data suggests that fecal microbiota dysbiosis may contribute to BTC onset.
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Affiliation(s)
- Zensho Ito
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, The Jikei University School of Medicine, Kashiwa Hospital, Kashiwa City 277-8567, Chiba, Japan
- Institute of Clinical Medicine and Research, The Jikei University School of Medicine, Kashiwa City 277-8567, Chiba, Japan
| | - Shigeo Koido
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, The Jikei University School of Medicine, Kashiwa Hospital, Kashiwa City 277-8567, Chiba, Japan
- Institute of Clinical Medicine and Research, The Jikei University School of Medicine, Kashiwa City 277-8567, Chiba, Japan
| | - Kumiko Kato
- Gut Microbiota Department, Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., Higashihara 252-8583, Zama, Japan
| | - Toshitaka Odamaki
- Gut Microbiota Department, Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., Higashihara 252-8583, Zama, Japan
| | - Sankichi Horiuchi
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, The Jikei University School of Medicine, Kashiwa Hospital, Kashiwa City 277-8567, Chiba, Japan
- Institute of Clinical Medicine and Research, The Jikei University School of Medicine, Kashiwa City 277-8567, Chiba, Japan
| | - Takafumi Akasu
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, The Jikei University School of Medicine, Kashiwa Hospital, Kashiwa City 277-8567, Chiba, Japan
| | - Masayuki Saruta
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, The Jikei University School of Medicine, Tokyo 105-8471, Japan
| | - Taigo Hata
- Department of Surgery, The Jikei University School of Medicine, Kashiwa Hospital, Kashiwa City 277-8567, Chiba, Japan
| | - Yu Kumagai
- Department of Surgery, The Jikei University School of Medicine, Kashiwa Hospital, Kashiwa City 277-8567, Chiba, Japan
| | - Shuichi Fujioka
- Department of Surgery, The Jikei University School of Medicine, Kashiwa Hospital, Kashiwa City 277-8567, Chiba, Japan
| | - Takeyuki Misawa
- Department of Surgery, The Jikei University School of Medicine, Kashiwa Hospital, Kashiwa City 277-8567, Chiba, Japan
| | - Jin-zhong Xiao
- Gut Microbiota Department, Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., Higashihara 252-8583, Zama, Japan
| | - Nobuhiro Sato
- Department of Microbiota Research, Juntendo University Graduate School of Medicine, 3-3-1 Hongo, Tokyo 113-0033, Japan
| | - Toshifumi Ohkusa
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, The Jikei University School of Medicine, Kashiwa Hospital, Kashiwa City 277-8567, Chiba, Japan
- Department of Microbiota Research, Juntendo University Graduate School of Medicine, 3-3-1 Hongo, Tokyo 113-0033, Japan
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Turner D, Adriaenssens EM, Tolstoy I, Kropinski AM. Phage Annotation Guide: Guidelines for Assembly and High-Quality Annotation. PHAGE (NEW ROCHELLE, N.Y.) 2021; 2:170-182. [PMID: 35083439 PMCID: PMC8785237 DOI: 10.1089/phage.2021.0013] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
All sequencing projects of bacteriophages (phages) should seek to report an accurate and comprehensive annotation of their genomes. This article defines 14 questions for those new to phage genomics that should be addressed before submitting a genome sequence to the International Nucleotide Sequence Database Collaboration or writing a publication.
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Affiliation(s)
- Dann Turner
- Department of Applied Sciences, Faculty of Health and Applied Sciences, University of the West of England, Bristol, United Kingdom
| | | | - Igor Tolstoy
- Viral Resources, National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, Maryland, USA
| | - Andrew M. Kropinski
- Department of Food Science, and University of Guelph, Guelph, Ontario, Canada
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
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Okido T, Kodama Y, Mashima J, Kosuge T, Fujisawa T, Ogasawara O. DNA Data Bank of Japan (DDBJ) update report 2021. Nucleic Acids Res 2021; 50:D102-D105. [PMID: 34751405 PMCID: PMC8689959 DOI: 10.1093/nar/gkab995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 11/29/2022] Open
Abstract
The Bioinformation and DDBJ (DNA Data Bank of Japan) Center (DDBJ Center; https://www.ddbj.nig.ac.jp) operates archival databases that collect nucleotide sequences, study and sample information, and distribute them without access restriction to progress life science research as a member of the International Nucleotide Sequence Database Collaboration (INSDC), in collaboration with the National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute. Besides the INSDC databases, the DDBJ Center also provides the Genomic Expression Archive for functional genomics data and the Japanese Genotype-phenotype Archive for human data requiring controlled access. Additionally, the DDBJ Center started a new public repository, MetaboBank, for experimental raw data and metadata from metabolomics research in October 2020. In response to the COVID-19 pandemic, the DDBJ Center openly shares SARS-CoV-2 genome sequences in collaboration with Shizuoka Prefecture and Keio University. The operation of DDBJ is based on the National Institute of Genetics (NIG) supercomputer, which is open for large-scale sequence data analysis for life science researchers. This paper reports recent updates on the archival databases and the services of DDBJ.
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Affiliation(s)
- Toshihisa Okido
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yuichi Kodama
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jun Mashima
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takehide Kosuge
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takatomo Fujisawa
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Osamu Ogasawara
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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Ecale Zhou CL, Kimbrel J, Edwards R, McNair K, Souza BA, Malfatti S. MultiPhATE2: code for functional annotation and comparison of phage genomes. G3 (BETHESDA, MD.) 2021; 11:jkab074. [PMID: 33734357 PMCID: PMC8104953 DOI: 10.1093/g3journal/jkab074] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/25/2021] [Indexed: 11/12/2022]
Abstract
To address a need for improved tools for annotation and comparative genomics of bacteriophage genomes, we developed multiPhATE2. As an extension of multiPhATE, a functional annotation code released previously, multiPhATE2 performs gene finding using multiple algorithms, compares the results of the algorithms, performs functional annotation of coding sequences, and incorporates additional search algorithms and databases to extend the search space of the original code. MultiPhATE2 performs gene matching among sets of closely related bacteriophage genomes, and uses multiprocessing to speed computations. MultiPhATE2 can be re-started at multiple points within the workflow to allow the user to examine intermediate results and adjust the subsequent computations accordingly. In addition, multiPhATE2 accommodates custom gene calls and sequence databases, again adding flexibility. MultiPhATE2 was implemented in Python 3.7 and runs as a command-line code under Linux or MAC operating systems. Full documentation is provided as a README file and a Wiki website.
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Affiliation(s)
- Carol L Ecale Zhou
- Global Security Computing Applications, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Jeffrey Kimbrel
- Biosciences & Biotechnology Research Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Robert Edwards
- Computational Sciences Research Center, San Diego State University, San Diego, CA 92182, USA
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
- Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
- College of Science and Engineering, Flinders University, Bedford Park, SA 5048, Australia
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA 92182, USA
| | - Brian A Souza
- Biosciences & Biotechnology Research Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Stephanie Malfatti
- Biosciences & Biotechnology Research Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
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Fukuda A, Kodama Y, Mashima J, Fujisawa T, Ogasawara O. DDBJ update: streamlining submission and access of human data. Nucleic Acids Res 2021; 49:D71-D75. [PMID: 33156332 PMCID: PMC7779041 DOI: 10.1093/nar/gkaa982] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 01/25/2023] Open
Abstract
The Bioinformation and DDBJ Center (DDBJ Center, https://www.ddbj.nig.ac.jp) provides databases that capture, preserve and disseminate diverse biological data to support research in the life sciences. This center collects nucleotide sequences with annotations, raw sequencing data, and alignment information from high-throughput sequencing platforms, and study and sample information, in collaboration with the National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI). This collaborative framework is known as the International Nucleotide Sequence Database Collaboration (INSDC). In collaboration with the National Bioscience Database Center (NBDC), the DDBJ Center also provides a controlled-access database, the Japanese Genotype–phenotype Archive (JGA), which archives and distributes human genotype and phenotype data, requiring authorized access. The NBDC formulates guidelines and policies for sharing human data and reviews data submission and use applications. To streamline all of the processes at NBDC and JGA, we have integrated the two systems by introducing a unified login platform with a group structure in September 2020. In addition to the public databases, the DDBJ Center provides a computer resource, the NIG supercomputer, for domestic researchers to analyze large-scale genomic data. This report describes updates to the services of the DDBJ Center, focusing on the NBDC and JGA system enhancements.
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Affiliation(s)
- Asami Fukuda
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yuichi Kodama
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jun Mashima
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takatomo Fujisawa
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Osamu Ogasawara
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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