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Alexyuk M, Bogoyavlenskiy A, Moldakhanov Y, Akanova K, Manakbayeva A, Alexyuk P. Draft genome sequence data of methicillin-resistant Staphylococcus aureus, strain 4233. Data Brief 2024; 54:110492. [PMID: 38799713 PMCID: PMC11127097 DOI: 10.1016/j.dib.2024.110492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024] Open
Abstract
Staphylococcus aureus is a conditionally pathogenic microorganism and one of the main causative agents of antibiotic resistant nosocomial infections. In immunocompromised people, S. aureus infection can cause folliculitis, furuncles, impetigo, osteomyelitis, septic arthritis, sepsis, endocarditis, pneumonia and meningitis. In the presented work, sequencing of a methicillin-resistant S. aureus, strain 4233, was performed on the Illumina MiSeq platform, followed by bioinformatics processing and gene annotation using SPAdes, RAST and CARD programs and databases. The submitted genome is a total of 2,790,390 bp long and contains 2759 genes, including 82 RNA genes. 33 % of the genes are functionally significant and represent 25 functional groups. Fourteen genes encoding resistance factors to 14 different types of antibacterial drugs were predicted. The information provided on the genome of S. aureus, strain 4233 will be of value in investigating the evolution and formation of antibiotic-resistant forms of S. aureus.
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Affiliation(s)
- Madina Alexyuk
- Research and Production Center for Microbiology and Virology, Bogenbay batyr. Str., 105, Almaty 050010, Kazakhstan
| | - Andrey Bogoyavlenskiy
- Research and Production Center for Microbiology and Virology, Bogenbay batyr. Str., 105, Almaty 050010, Kazakhstan
| | - Yergali Moldakhanov
- Research and Production Center for Microbiology and Virology, Bogenbay batyr. Str., 105, Almaty 050010, Kazakhstan
| | - Kuralay Akanova
- Research and Production Center for Microbiology and Virology, Bogenbay batyr. Str., 105, Almaty 050010, Kazakhstan
| | - Adolat Manakbayeva
- Research and Production Center for Microbiology and Virology, Bogenbay batyr. Str., 105, Almaty 050010, Kazakhstan
| | - Pavel Alexyuk
- Research and Production Center for Microbiology and Virology, Bogenbay batyr. Str., 105, Almaty 050010, Kazakhstan
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2
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Elrashedy A, Nayel M, Salama A, Zaghawa A, Abdelsalam NR, Hasan ME. Phylogenetic Analysis and Comparative Genomics of Brucella abortus and Brucella melitensis Strains in Egypt. J Mol Evol 2024:10.1007/s00239-024-10173-0. [PMID: 38809331 DOI: 10.1007/s00239-024-10173-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024]
Abstract
Brucellosis is a notifiable disease induced by a facultative intracellular Brucella pathogen. In this study, eight Brucella abortus and eighteen Brucella melitensis strains from Egypt were annotated and compared with RB51 and REV1 vaccines respectively. RAST toolkit in the BV-BRC server was used for annotation, revealing genome length of 3,250,377 bp and 3,285,803 bp, 3289 and 3323 CDS, 48 and 49 tRNA genes, the same number of rRNA (3) genes, 583 and 586 hypothetical proteins, 2697 and 2726 functional proteins for B. abortus and B. melitensis respectively. B. abortus strains exhibit a similar number of candidate genes, while B. melitensis strains showed some differences, especially in the SRR19520422 Faiyum strain. Also, B. melitensis clarified differences in antimicrobial resistance genes (KatG, FabL, MtrA, MtrB, OxyR, and VanO-type) in SRR19520319 Faiyum and (Erm C and Tet K) in SRR19520422 Faiyum strain. Additionally, the whole genome phylogeny analysis proved that all B. abortus strains were related to vaccinated animals and all B. melitensis strains of Menoufia clustered together and closely related to Gharbia, Dameitta, and Kafr Elshiek. The Bowtie2 tool identified 338 (eight B. abortus) and 4271 (eighteen B. melitensis) single nucleotide polymorphisms (SNPs) along the genomes. These variants had been annotated according to type and impact. Moreover, thirty candidate genes were predicted and submitted at GenBank (24 in B. abortus) and (6 in B. melitensis). This study contributes significant insights into genetic variation, virulence factors, and vaccine-related associations of Brucella pathogens, enhancing our knowledge of brucellosis epidemiology and evolution in Egypt.
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Affiliation(s)
- Alyaa Elrashedy
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt.
| | - Mohamed Nayel
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Akram Salama
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Ahmed Zaghawa
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Nader R Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, 21531, Egypt
| | - Mohamed E Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
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3
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Xue L, Guo Y, Tang F, Chen S, Liao F, Li D. Complete genome sequence of Pseudomonas aeruginosa L3, a bacterium with Mn(II) oxidative property isolated from heavy metal-contaminated soils. Microbiol Resour Announc 2024:e0002624. [PMID: 38809065 DOI: 10.1128/mra.00026-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/10/2024] [Indexed: 05/30/2024] Open
Abstract
Pseudomonas aeruginosa L3, isolated from heavy metal-contaminated soils, possesses the ability of Mn(II) oxidation. To further enhance the understanding of genes involved in Mn(II) oxidation, the complete genome of this strain was sequenced and annotated, which has a total size of 6.39 Mb with a G + C content of 66.39%.
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Affiliation(s)
- Lan Xue
- School of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China
| | - Yueshuai Guo
- School of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China
| | - Fengzhen Tang
- School of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China
| | - Sha Chen
- School of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China
- Zhuzhou City Joint Laboratory of Environmental Microbiology and Plant Resources Utilization, Hunan University of Technology, Zhuzhou, China
- Hunan Provincial Engineering Research Center of Lily Germplasm Resource Innovation and Deep Processing, Hunan University of Technology, Zhuzhou, China
| | - Fengfeng Liao
- School of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China
| | - Ding Li
- School of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China
- Zhuzhou City Joint Laboratory of Environmental Microbiology and Plant Resources Utilization, Hunan University of Technology, Zhuzhou, China
- Hunan Provincial Engineering Research Center of Lily Germplasm Resource Innovation and Deep Processing, Hunan University of Technology, Zhuzhou, China
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4
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Ishizawa H, Tada M, Tashiro Y, Kuroda M, Inoue D, Dohra H, Futamata H, Ike M. Complete genome sequences of six duckweed-associated bacterial strains for studying community assembly in synthetic plant microbiome. Microbiol Resour Announc 2024; 13:e0128023. [PMID: 38426728 PMCID: PMC11008219 DOI: 10.1128/mra.01280-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Abstract
We report the complete genome sequences of six bacterial strains isolated from a floating macrophyte, duckweed. These six strains, representing the six dominant families of the natural duckweed microbiome, establish a simple model ecosystem when inoculated onto sterilized duckweed. Their genomes would provide insights into community assembly in plant microbiome.
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Affiliation(s)
- Hidehiro Ishizawa
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Minami Tada
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Yosuke Tashiro
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Masashi Kuroda
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
- Faculty of Social and Environmental Studies, Tokoha University, Shizuoka, Japan
| | - Daisuke Inoue
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Hideo Dohra
- Research Institute of Green Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hiroyuki Futamata
- Research Institute of Green Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Michihiko Ike
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
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Moriuchi R, Sano R, Fujii S, Suzuki Y, Makita M, Kawashima Y, Shirakawa T, Shindo R, Shinkai T, Miura K, Hirose M, Nakajima M, Kurokawa A, Chetia R, Hirokawa C, Suzuki T, Ito Y, Murano H, Dohra H, Ogawa N, Kanesaki Y. Complete genome sequence of Paraburkholderia sp. strain 22B1P capable of utilizing 3-chlorobenzoate as a carbon source. Microbiol Resour Announc 2024; 13:e0123523. [PMID: 38488372 PMCID: PMC11008179 DOI: 10.1128/mra.01235-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024] Open
Abstract
Paraburkholderia sp. strain 22B1P utilizes 3-chlorobenzoate as a carbon source. Complete genome sequencing of strain 22B1P revealed two chromosomes and two plasmids. The genes involved in the conversion of 3-chlorobenzoate to 3-chlorocatechol and those involved in the conversion of 3-chlorocatechol to 3-oxoadipate were located on chromosomes 2 and 1, respectively.
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Affiliation(s)
- Ryota Moriuchi
- Shizuoka Instrumental Analysis Center, Shizuoka University, Suruga-ku, Shizuoka, Japan
- Division of Technical Service, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Rion Sano
- Shizuoka Prefectural Fujinomiya-Kita High School, Fujinomiya, Shizuoka, Japan
| | - Shuma Fujii
- OISCA Hamamatsu Kokusai High School, Hamamatsu, Shizuoka, Japan
| | - Yuito Suzuki
- Shizuoka Prefectural Shimada Senior High School, Shimada, Shizuoka, Japan
| | - Miyune Makita
- Shizuoka Prefectural Shimada Senior High School, Shimada, Shizuoka, Japan
| | - Yo Kawashima
- Hamamatsu Gakugei High School, Hamamatsu, Shizuoka, Japan
| | | | - Renki Shindo
- Shizuoka Prefectural Shizuoka Higashi High School, Aoi-ku, Shizuoka, Japan
| | - Tatsumi Shinkai
- Shizuoka Prefectural Shizuoka Higashi High School, Aoi-ku, Shizuoka, Japan
| | - Kaede Miura
- Fuji Sacred Heart School, Susono, Shizuoka, Japan
| | - Moka Hirose
- Fuji Sacred Heart School, Susono, Shizuoka, Japan
| | - Momiji Nakajima
- Faculty of Agriculture, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Asahi Kurokawa
- Faculty of Agriculture, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Rituparna Chetia
- Graduate School of Integrated Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Chiharu Hirokawa
- Shizuoka Instrumental Analysis Center, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Tomoko Suzuki
- Shizuoka Instrumental Analysis Center, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Yukiko Ito
- Division of Technical Service, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Hiroki Murano
- Division of Technical Service, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Hideo Dohra
- Shizuoka Instrumental Analysis Center, Shizuoka University, Suruga-ku, Shizuoka, Japan
- Graduate School of Integrated Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Naoto Ogawa
- Faculty of Agriculture, Shizuoka University, Suruga-ku, Shizuoka, Japan
- Graduate School of Integrated Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Yu Kanesaki
- Shizuoka Instrumental Analysis Center, Shizuoka University, Suruga-ku, Shizuoka, Japan
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6
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Hoffman T, Kinne J, Cho KH. Pro-SMP finder-A systematic approach for discovering small membrane proteins in prokaryotes. PLoS One 2024; 19:e0299169. [PMID: 38422081 PMCID: PMC10903887 DOI: 10.1371/journal.pone.0299169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Prokaryotic chromosomes contain numerous small open reading frames (ORFs) of less than 200 bases. Since high-throughput proteomics methods often miss proteins containing fewer than 60 amino acids, it is difficult to decern if they encode proteins. Recent studies have revealed that many small proteins are membrane proteins with a single membrane-anchoring α-helix. As membrane anchoring or transmembrane motifs are accurately identifiable with high confidence using computational algorithms like Phobius and TMHMM, small membrane proteins (SMPS) can be predicted with high accuracy. This study employed a systematic approach, utilizing well-verified algorithms such as Orfipy, Phobius, and Blast to identify SMPs in prokaryotic organisms. Our main search parameters targeted candidate SMPs with an open reading frame between 60-180 nucleotides, a membrane-anchoring or transmembrane region 15 and 30 amino acids long, and sequence conservation among other microorganisms. Our findings indicate that each prokaryote possesses many SMPs, with some identified in the intergenic regions of currently annotated chromosomes. More extensively studied microorganisms, such as Escherichia coli and Bacillus subtilis, have more SMPs identified in their genomes compared to less studied microorganisms, suggesting the possibility of undiscovered SMPs in less studied microorganisms. In this study, we describe the common SMPs identified across various microorganisms and explore their biological roles. We have also developed a software pipeline and an accompanying online interface for discovering SMPs (http://cs.indstate.edu/pro-smp-finder). This resource aims to assist researchers in identifying new SMPs encoded in microbial genomes of interest.
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Affiliation(s)
- Tara Hoffman
- Department of Math and Computer Science, Indiana State University, Terre Haute, Indiana, United States of America
| | - Jeff Kinne
- Department of Math and Computer Science, Indiana State University, Terre Haute, Indiana, United States of America
| | - Kyu Hong Cho
- Department of Biology, Indiana State University, Terre Haute, Indiana, United States of America
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7
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Breton S. Comparative mitogenomics of Brachiopods reveals conservatism in articulate species and unusualness in inarticulate species. Mol Biol Rep 2024; 51:298. [PMID: 38341808 DOI: 10.1007/s11033-024-09270-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/18/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND Brachiopods are a phylum of marine invertebrates with over 10,000 fossil species. Today, there are fewer than 500 extant species assigned to the class Articulata or Inarticulata and for which knowledge of evolutionary genetics and genomics is still poor. Until now, complete mitogenome sequences of two inarticulate species and four articulate species were available. METHODS AND RESULTS The complete mitogenome of the inarticulate brachiopod species Lingula reevii (20,778 bp) was obtained by using next generation sequencing. It contains 12 protein-coding genes (the annotation of atp8 is unsure), two ribosomal RNA genes, 26 transfer RNA genes, and one supernumerary ORF that is also conserved in the inarticulate species Lingula anatina. It is hypothesized that this ORF could represent a Lingula-specific mtORFan gene (without obvious homology to other genes). Comparative mitogenomics indicate the mitochondrial gene order of L. reevii is unique among brachiopods, and that compared to articulate species, inarticulate species exhibit massive mitogenome rearrangements, deviant ATP8 protein sequences and supernumerary ORFs, possibly representing species- or lineage-specific mtORFan genes. CONCLUSION The results of this study enrich genetics knowledge of extant brachiopods, which may eventually help to test hypotheses about their decline.
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Affiliation(s)
- Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada.
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8
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Kim J, Herrera C, Aung WY, Gonzales Boyles GP, Chavez C, Cibulka M, Foley E, Guerra J, Kumar DBM, Levrant W, Lim L, Llanes J, O'Brien ZK, Pagaduan A, Richardson JA, Rosales K, Schrecengost J, Shin T, Strong-Lundquist G, Tat W, Vanderford F, Vrinceanu I, Wang V, Yang S, Strong C, Tsourkas PK, Regner K. Complete genome sequences of cluster F1 and cluster B1 Mycobacterium smegmatis phages Karhdo and Basato. Microbiol Resour Announc 2024; 13:e0093823. [PMID: 38051075 DOI: 10.1128/mra.00938-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/14/2023] [Indexed: 12/07/2023] Open
Abstract
We present the complete genome sequences of Mycobacterium smegmatis phages Karhdo and Basato, isolated in Clark County, Nevada. The phages were isolated and annotated by students enrolled in undergraduate research courses over two semesters at the University of Nevada, Las Vegas.
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Affiliation(s)
- Jireh Kim
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Carlos Herrera
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Wai Yan Aung
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | | | - Carmina Chavez
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Mona Cibulka
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Emma Foley
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Jose Guerra
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | | | - Willow Levrant
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Lewis Lim
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Jose Llanes
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | | | - Art Pagaduan
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | | | - Khristian Rosales
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | | | - Tommy Shin
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | | | - Winnie Tat
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Fritz Vanderford
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | | | - Vicky Wang
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Stephanie Yang
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Christy Strong
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
| | - Philippos K Tsourkas
- School of Medicine and Public Health, University of Wisconsin , Madison, Wisconsin, USA
| | - Kurt Regner
- School of Life Sciences, University of Nevada , Las Vegas, Nevada, USA
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9
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Xu Y, Wang W, Su W, Wang M, Xu H, Zhang X, Li L. A widespread single amino acid mutation in AcrA reduces tigecycline susceptibility in Klebsiella pneumoniae. Microbiol Spectr 2024; 12:e0203023. [PMID: 38032193 PMCID: PMC10782974 DOI: 10.1128/spectrum.02030-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Tigecycline, a glycecycline antibiotic with broad-spectrum activity against almost all Gram-positive and Gram-negative bacteria, is a highly concerned "last-resort" antibiotic. In addition to plasmid-hosted mobile tet(X) conferring high-level resistance to tigecycline, there are many reports suggesting increased expression of AcrAB-TolC efflux pump leads to tigecycline non-susceptibility. However, the role of mutations in AcrAB-TolC on tigecycline resistance has not been identified. This study reports a novel T188A mutation of the AcrA subunit of AcrAB-TolC complex in a clinical tigecycline-resistant Klebsiella pneumoniae strain and reveals the role of AcrA mutation on tigecycline resistance in K. pneumoniae. High prevalence of A188 type AcrA in hypervirulent multidrug-resistant K. pneumoniae indicates that mutations of the AcrAB-TolC complex may play a larger role in determining bacterial pathogenesis and antibiotic susceptibility than previously expected.
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Affiliation(s)
- Yingchao Xu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Wenjia Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Wenya Su
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Mingyu Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Hai Xu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Xuhua Zhang
- Laboratory Medicine Center, The Second Hospital of Shandong University, Jinan, China
| | - Ling Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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10
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Haft DH, Badretdin A, Coulouris G, DiCuccio M, Durkin A, Jovenitti E, Li W, Mersha M, O’Neill K, Virothaisakun J, Thibaud-Nissen F. RefSeq and the prokaryotic genome annotation pipeline in the age of metagenomes. Nucleic Acids Res 2024; 52:D762-D769. [PMID: 37962425 PMCID: PMC10767926 DOI: 10.1093/nar/gkad988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) contains over 315 000 bacterial and archaeal genomes and 236 million proteins with up-to-date and consistent annotation. In the past 3 years, we have expanded the diversity of the RefSeq collection by including the best quality metagenome-assembled genomes (MAGs) submitted to INSDC (DDBJ, ENA and GenBank), while maintaining its quality by adding validation checks. Assemblies are now more stringently evaluated for contamination and for completeness of annotation prior to acceptance into RefSeq. MAGs now account for over 17000 assemblies in RefSeq, split over 165 orders and 362 families. Changes in the Prokaryotic Genome Annotation Pipeline (PGAP), which is used to annotate nearly all RefSeq assemblies include better detection of protein-coding genes. Nearly 83% of RefSeq proteins are now named by a curated Protein Family Model, a 4.7% increase in the past three years ago. In addition to literature citations, Enzyme Commission numbers, and gene symbols, Gene Ontology terms are now assigned to 48% of RefSeq proteins, allowing for easier multi-genome comparison. RefSeq is found at https://www.ncbi.nlm.nih.gov/refseq/. PGAP is available as a stand-alone tool able to produce GenBank-ready files at https://github.com/ncbi/pgap.
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Affiliation(s)
- Daniel H Haft
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Azat Badretdin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - George Coulouris
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Michael DiCuccio
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - A Scott Durkin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eric Jovenitti
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Wenjun Li
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Megdelawit Mersha
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kathleen R O’Neill
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Joel Virothaisakun
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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11
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Altae-Tran H, Kannan S, Suberski AJ, Mears KS, Demircioglu FE, Moeller L, Kocalar S, Oshiro R, Makarova KS, Macrae RK, Koonin EV, Zhang F. Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering. Science 2023; 382:eadi1910. [PMID: 37995242 PMCID: PMC10910872 DOI: 10.1126/science.adi1910] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 09/28/2023] [Indexed: 11/25/2023]
Abstract
Microbial systems underpin many biotechnologies, including CRISPR, but the exponential growth of sequence databases makes it difficult to find previously unidentified systems. In this work, we develop the fast locality-sensitive hashing-based clustering (FLSHclust) algorithm, which performs deep clustering on massive datasets in linearithmic time. We incorporated FLSHclust into a CRISPR discovery pipeline and identified 188 previously unreported CRISPR-linked gene modules, revealing many additional biochemical functions coupled to adaptive immunity. We experimentally characterized three HNH nuclease-containing CRISPR systems, including the first type IV system with a specified interference mechanism, and engineered them for genome editing. We also identified and characterized a candidate type VII system, which we show acts on RNA. This work opens new avenues for harnessing CRISPR and for the broader exploration of the vast functional diversity of microbial proteins.
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Affiliation(s)
- Han Altae-Tran
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Soumya Kannan
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Anthony J. Suberski
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Kepler S. Mears
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - F. Esra Demircioglu
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Lukas Moeller
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Selin Kocalar
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Rachel Oshiro
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD 20894, USA
| | - Rhiannon K. Macrae
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD 20894, USA
| | - Feng Zhang
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
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12
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Guliayeva D, Akhremchuk A, Sikolenko M, Evdokimova O, Valentovich L, Sidarenka A. Roseateles amylovorans sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 2023; 73. [PMID: 37917535 DOI: 10.1099/ijsem.0.006133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
A Gram-stain-negative, rod-shaped, amylolytic bacterial strain, designated as bsSlp3-1T, was isolated from the Slepian water system, a freshwater reservoir. Strain bsSlp3-1T was found to be aerobic, oxidase-positive and catalase-negative, grew at 5-37 °C (optimum, 28 °C), pH 5.0-9.5 (optimum, pH 7.0) and low NaCl concentration (up to 1.0 %). Comparative analysis of 16S rRNA gene sequence similarity revealed that strain bsSlp3-1T clustered with Roseateles species and is closely related to Roseateles depolymerans KCTC 42856T (98.7 %) and Roseateles terrae CCUG 52222T (98.6 %). Whole-genome comparisons using average nucleotide identity and digital DNA-DNA hybridization values suggested that strain bsSlp3-1T represents a novel species within the genus Roseateles and is most closely related to Roseateles aquatilis CCUG 48205T (81.2 and 25.6 %, respectively). The genome of strain bsSlp3-1T consisted of a single circular chromosome with size 6 289 366 bp and DNA G+C content of 66.8 mol%. The predominant cellular fatty acids of bsSlp3-1T were cis-9-hexadecanoic and hexadecenoic acids. According to the data obtained in this work, strain bsSlp3-1T represents a novel Roseateles species for which the name Roseateles amylovorans sp. nov. is proposed. The type strain is bsSlp3-1T (=BIM B-1768T=NBIMCC 9098T=VKM B-3671T).
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Affiliation(s)
- Darya Guliayeva
- The Institute of Microbiology of the National Academy of Sciences of Belarus, Kuprevich Str., 2, 220084, Minsk, Belarus
| | - Artur Akhremchuk
- The Institute of Microbiology of the National Academy of Sciences of Belarus, Kuprevich Str., 2, 220084, Minsk, Belarus
| | - Maxim Sikolenko
- The Institute of Microbiology of the National Academy of Sciences of Belarus, Kuprevich Str., 2, 220084, Minsk, Belarus
| | - Olesya Evdokimova
- The Institute of Microbiology of the National Academy of Sciences of Belarus, Kuprevich Str., 2, 220084, Minsk, Belarus
| | - Leonid Valentovich
- The Institute of Microbiology of the National Academy of Sciences of Belarus, Kuprevich Str., 2, 220084, Minsk, Belarus
| | - Anastasiya Sidarenka
- The Institute of Microbiology of the National Academy of Sciences of Belarus, Kuprevich Str., 2, 220084, Minsk, Belarus
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13
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Sali O, Patel DM, Ortega MC, Han S, Esperanza Gonzales HG, Haneefzai OS, Herrera C, Kim J, Knoles B, Lopez A, Richardson JA, Roach DA, Vergonia-Fehlman M, Vincent J, Yim SH, Cutter LIC, Strong C, Tsourkas PK, Regner K. Complete genome sequences of cluster G1 and cluster K4 Mycobacterium smegmatis phages omnicritical and Barkley26. Microbiol Resour Announc 2023; 12:e0027423. [PMID: 37671868 PMCID: PMC10586113 DOI: 10.1128/mra.00274-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/26/2023] [Indexed: 09/07/2023] Open
Abstract
We present the complete genome sequence of two Actinobacteriophages, OmniCritical and Barkley26, isolated in Clark County, NV. Over two semesters, The University of Nevada, Las Vegas (UNLV) students isolated and purified phages and manually annotated the genomes. The courses follow the HHMI Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Sciences (SEA-PHAGES) curricula.
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Affiliation(s)
- Ojas Sali
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Dave M. Patel
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | | | - Sydnee Han
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | | | | | - Carlos Herrera
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Jireh Kim
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Brooke Knoles
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Abigail Lopez
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | | | | | | | - Jessica Vincent
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Sang Ho Yim
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Leo I. C. Cutter
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Christy Strong
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
| | - Philippos K. Tsourkas
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Kurt Regner
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
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14
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Zhao L, Yang C, Chen M, Zhang J, Kong M, Dong L, Gong J, Yang J, Pu J, Lu S, Jin D, Liu L, Wang S, Xu J. Marnyiella aurantia, gen. nov., sp. nov., a novel bacterial species of the family Weeksellaceae that could produce flexirubin type pigments. Int J Syst Evol Microbiol 2023; 73. [PMID: 37906507 DOI: 10.1099/ijsem.0.006020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023] Open
Abstract
Two Gram-stain-negative, non-spore-forming, rod-shaped, and obligately aerobic bacteria, designated strains CX-624T and cx-311, were isolated from soil samples in Qinghai Province, China. The two strains grew best at 28 °C on the plate with Tryptone soya agar (TSA). Cells formed circular, convex, translucent, smooth, and orange colonies with approximately 1.0 mm diameter after 2 days of incubation on TSA at 28 °C. The strains were oxidase-negative and catalase-positive. The predominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0, and major polar lipids included phosphatidylethanolamine, an unidentified aminophospholipid, four unidentified lipids and an aminolipid. MK-6 was the sole menaquinone in strain CX-624T. Comparative analysis of the nearly full-length 16S rRNA gene sequences showed strains CX-624T and cx-311 were member of the family Weeksellaceae, with the highest similarity to Kaistella haifensis H38T (96.66 %), Epilithonimonas pallida DSM 18015T (96.59 %), and Chryseobacterium gambrini DSM 18014T (96.53 %). Both phylogenetic analysis of the 16S rRNA gene and 177 core genes revealed that strains CX-624T and cx-311 formed an independent clade. Average nucleotide identity values (< 72.64 %), average amino-acid identity values (<72.61 %) and digital DNA-DNA hybridization (< 21.10 %) indicated that the strains CX-624T and cx-311 should constitute a novel genus. The DNA G+C contents of strains CX-624T and cx-311 were 43.0 mol% and 42.7 mol%. According to the data obtained in this study, strain CX-624T represents a novel species belonging to a novel genus of the Weeksellaceae, for which the name Marnyiella aurantia gen. nov., sp. nov. is proposed. The type strain is CX-624T (=GDMCC 1.1714T = JCM 33925T).
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Affiliation(s)
- Lijun Zhao
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Caixin Yang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Mengshan Chen
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jing Zhang
- Marine College, Shandong University, Weihai, PR China
| | - Mimi Kong
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Lingzhi Dong
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jian Gong
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Suping Wang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
| | - Jianguo Xu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Institute of Public Health, Nankai University, Tianjin 300350, PR China
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15
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Arikawa K, Hosokawa M. Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics. Comput Struct Biotechnol J 2023; 21:4508-4518. [PMID: 37771751 PMCID: PMC10523443 DOI: 10.1016/j.csbj.2023.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/10/2023] [Accepted: 09/10/2023] [Indexed: 09/30/2023] Open
Abstract
Owing to the ineffectiveness of traditional culture techniques for the vast majority of microbial species, culture-independent analyses utilizing next-generation sequencing and bioinformatics have become essential for gaining insight into microbial ecology and function. This mini-review focuses on two essential methods for obtaining genetic information from uncultured prokaryotes, metagenomics and single-cell genomics. We analyzed the registration status of uncultured prokaryotic genome data from major public databases and assessed the advantages and limitations of both the methods. Metagenomics generates a significant quantity of sequence data and multiple prokaryotic genomes using straightforward experimental procedures. However, in ecosystems with high microbial diversity, such as soil, most genes are presented as brief, disconnected contigs, and lack association of highly conserved genes and mobile genetic elements with individual species genomes. Although technically more challenging, single-cell genomics offers valuable insights into complex ecosystems by providing strain-resolved genomes, addressing issues in metagenomics. Recent technological advancements, such as long-read sequencing, machine learning algorithms, and in silico protein structure prediction, in combination with vast genomic data, have the potential to overcome the current technical challenges and facilitate a deeper understanding of uncultured microbial ecosystems and microbial dark matter genes and proteins. In light of this, it is imperative that continued innovation in both methods and technologies take place to create high-quality reference genome databases that will support future microbial research and industrial applications.
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Affiliation(s)
- Koji Arikawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
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16
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Horsfield ST, Tonkin-Hill G, Croucher NJ, Lees JA. Accurate and fast graph-based pangenome annotation and clustering with ggCaller. Genome Res 2023; 33:1622-1637. [PMID: 37620118 PMCID: PMC10620059 DOI: 10.1101/gr.277733.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023]
Abstract
Bacterial genomes differ in both gene content and sequence mutations, which underlie extensive phenotypic diversity, including variation in susceptibility to antimicrobials or vaccine-induced immunity. To identify and quantify important variants, all genes within a population must be predicted, functionally annotated, and clustered, representing the "pangenome." Despite the volume of genome data available, gene prediction and annotation are currently conducted in isolation on individual genomes, which is computationally inefficient and frequently inconsistent across genomes. Here, we introduce the open-source software graph-gene-caller (ggCaller). ggCaller combines gene prediction, functional annotation, and clustering into a single workflow using population-wide de Bruijn graphs, removing redundancy in gene annotation and resulting in more accurate gene predictions and orthologue clustering. We applied ggCaller to simulated and real-world bacterial data sets containing hundreds or thousands of genomes, comparing it to current state-of-the-art tools. ggCaller has considerable speed-ups with equivalent or greater accuracy, particularly with data sets containing complex sources of error, such as assembly contamination or fragmentation. ggCaller is also an important extension to bacterial genome-wide association studies, enabling querying of annotated graphs for functional analyses. We highlight this application by functionally annotating DNA sequences with significant associations to tetracycline and macrolide resistance in Streptococcus pneumoniae, identifying key resistance determinants that were missed when using only a single reference genome. ggCaller is a novel bacterial genome analysis tool with applications in bacterial evolution and epidemiology.
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Affiliation(s)
- Samuel T Horsfield
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London W12 0BZ, United Kingdom;
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Gerry Tonkin-Hill
- Department of Biostatistics, University of Oslo, Blindern, 0372 Oslo, Norway
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London W12 0BZ, United Kingdom
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London W12 0BZ, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
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17
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Riley R, Bowers RM, Camargo AP, Campbell A, Egan R, Eloe-Fadrosh EA, Foster B, Hofmeyr S, Huntemann M, Kellom M, Kimbrel JA, Oliker L, Yelick K, Pett-Ridge J, Salamov A, Varghese NJ, Clum A. Terabase-Scale Coassembly of a Tropical Soil Microbiome. Microbiol Spectr 2023; 11:e0020023. [PMID: 37310219 PMCID: PMC10434106 DOI: 10.1128/spectrum.00200-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/24/2023] [Indexed: 06/14/2023] Open
Abstract
Petabases of environmental metagenomic data are publicly available, presenting an opportunity to characterize complex environments and discover novel lineages of life. Metagenome coassembly, in which many metagenomic samples from an environment are simultaneously analyzed to infer the underlying genomes' sequences, is an essential tool for achieving this goal. We applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 terabases (Tbp) of metagenome data from a tropical soil in the Luquillo Experimental Forest (LEF), Puerto Rico. The resulting coassembly yielded 39 high-quality (>90% complete, <5% contaminated, with predicted 23S, 16S, and 5S rRNA genes and ≥18 tRNAs) metagenome-assembled genomes (MAGs), including two from the candidate phylum Eremiobacterota. Another 268 medium-quality (≥50% complete, <10% contaminated) MAGs were extracted, including the candidate phyla Dependentiae, Dormibacterota, and Methylomirabilota. In total, 307 medium- or higher-quality MAGs were assigned to 23 phyla, compared to 294 MAGs assigned to nine phyla in the same samples individually assembled. The low-quality (<50% complete, <10% contaminated) MAGs from the coassembly revealed a 49% complete rare biosphere microbe from the candidate phylum FCPU426 among other low-abundance microbes, an 81% complete fungal genome from the phylum Ascomycota, and 30 partial eukaryotic MAGs with ≥10% completeness, possibly representing protist lineages. A total of 22,254 viruses, many of them low abundance, were identified. Estimation of metagenome coverage and diversity indicates that we may have characterized ≥87.5% of the sequence diversity in this humid tropical soil and indicates the value of future terabase-scale sequencing and coassembly of complex environments. IMPORTANCE Petabases of reads are being produced by environmental metagenome sequencing. An essential step in analyzing these data is metagenome assembly, the computational reconstruction of genome sequences from microbial communities. "Coassembly" of metagenomic sequence data, in which multiple samples are assembled together, enables more complete detection of microbial genomes in an environment than "multiassembly," in which samples are assembled individually. To demonstrate the potential for coassembling terabases of metagenome data to drive biological discovery, we applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 Tbp of reads from a humid tropical soil environment. The resulting coassembly, its functional annotation, and analysis are presented here. The coassembly yielded more, and phylogenetically more diverse, microbial, eukaryotic, and viral genomes than the multiassembly of the same data. Our resource may facilitate the discovery of novel microbial biology in tropical soils and demonstrates the value of terabase-scale metagenome sequencing.
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Affiliation(s)
- Robert Riley
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Robert M. Bowers
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Antonio Pedro Camargo
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Ashley Campbell
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Rob Egan
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | | | - Brian Foster
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Steven Hofmeyr
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Marcel Huntemann
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Matthew Kellom
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Jeffrey A. Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Leonid Oliker
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Katherine Yelick
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, California, USA
| | - Asaf Salamov
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Neha J. Varghese
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Alicia Clum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
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18
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Pérez-Quintero AL, Rodriguez-R LM, Cuesta-Morrondo S, Hakalová E, Betancurt-Anzola D, Valera LCC, Cardenas LAC, Matiz-Céron L, Jacobs JM, Roman-Reyna V, Muñoz AR, Giraldo AJB, Koebnik R. Comparative Genomics Identifies Conserved and Variable TAL Effectors in African Strains of the Cotton Pathogen Xanthomonas citri pv. malvacearum. PHYTOPATHOLOGY 2023; 113:1387-1393. [PMID: 37081724 DOI: 10.1094/phyto-12-22-0477-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Strains of Xanthomonas citri pv. malvacearum cause bacterial blight of cotton, a potentially serious threat to cotton production worldwide, including in sub-Saharan countries. Development of disease symptoms, such as water soaking, has been linked to the activity of a class of type 3 effectors, called transcription activator-like (TAL) effectors, which induce susceptibility genes in the host's cells. To gain further insight into the global diversity of the pathogen, to elucidate their repertoires of TAL effector genes, and to better understand the evolution of these genes in the cotton-pathogenic xanthomonads, we sequenced the genomes of three African strains of X. citri pv. malvacearum using nanopore technology. We show that the cotton-pathogenic pathovar of X. citri is a monophyletic lineage containing at least three distinct genetic subclades, which appear to be mirrored by their repertoires of TAL effectors. We observed an atypical level of TAL effector gene pseudogenization, which might be related to resistance genes that are deployed to control the disease. Our work thus contributes to a better understanding of the conservation and importance of TAL effectors in the interaction with the host plant, which can inform strategies for improving resistance against bacterial blight in cotton.
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Affiliation(s)
- Alvaro L Pérez-Quintero
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Sara Cuesta-Morrondo
- Departamento de Protección Vegetal, Laboratorio Bacteriología, Centro Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), 28040, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | | | - Daniela Betancurt-Anzola
- Universidad de Los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura Carolina Camelo Valera
- Universidad de Los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Luis Alberto Chica Cardenas
- Universidad de Los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Luisa Matiz-Céron
- Universidad de Los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, U.S.A
| | - Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, OH, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, U.S.A
| | - Alejandro Reyes Muñoz
- Universidad de Los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | | | - Ralf Koebnik
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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19
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Arnold ND, Garbe D, Brück TB. Isolation, biochemical characterization, and genome sequencing of two high-quality genomes of a novel chitinolytic Jeongeupia species. Microbiologyopen 2023; 12:e1372. [PMID: 37642486 PMCID: PMC10404844 DOI: 10.1002/mbo3.1372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
Chitin is the second most abundant polysaccharide worldwide as part of arthropods' exoskeletons and fungal cell walls. Low concentrations in soils and sediments indicate rapid decomposition through chitinolytic organisms in terrestrial and aquatic ecosystems. The enacting enzymes, so-called chitinases, and their products, chitooligosaccharides, exhibit promising characteristics with applications ranging from crop protection to cosmetics, medical, textile, and wastewater industries. Exploring novel chitinolytic organisms is crucial to expand the enzymatical toolkit for biotechnological chitin utilization and to deepen our understanding of diverse catalytic mechanisms. In this study, we present two long-read sequencing-based genomes of highly similar Jeongeupia species, which have been screened, isolated, and biochemically characterized from chitin-amended soil samples. Through metabolic characterization, whole-genome alignments, and phylogenetic analysis, we could demonstrate how the investigated strains differ from the taxonomically closest strain Jeongeupia naejangsanensis BIO-TAS4-2T (DSM 24253). In silico analysis and sequence alignment revealed a multitude of highly conserved chitinolytic enzymes in the investigated Jeongeupia genomes. Based on these results, we suggest that the two strains represent a novel species within the genus of Jeongeupia, which may be useful for environmentally friendly N-acetylglucosamine production from crustacean shell or fungal biomass waste or as a crop protection agent.
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Affiliation(s)
- Nathanael D. Arnold
- Department of ChemistryWerner‐Siemens Chair for Synthetic Biotechnology (WSSB), TUM School of Natural Sciences, Technical University of MunichGarchingGermany
| | - Daniel Garbe
- Department of ChemistryWerner‐Siemens Chair for Synthetic Biotechnology (WSSB), TUM School of Natural Sciences, Technical University of MunichGarchingGermany
| | - Thomas B. Brück
- Department of ChemistryWerner‐Siemens Chair for Synthetic Biotechnology (WSSB), TUM School of Natural Sciences, Technical University of MunichGarchingGermany
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20
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Li F, Zhao W, Zhu P, Li Z, Song J, Zhu J, Gao H. Moraxella nasibovis sp. nov., Isolated from a Cow with Respiratory Disease. Curr Microbiol 2023; 80:305. [PMID: 37493823 DOI: 10.1007/s00284-023-03415-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023]
Abstract
Strain ZY190618T, isolated from the nasal cavity of a cow with respiratory disease, was subjected to taxonomic characterization. Cells of the strain were Gram-stain-negative, aerobic and coccus-shaped. Phylogenetic analysis based on 16 S rRNA gene sequences indicated that the strain belonged to the genus Moraxella with the highest similarity of 98.1% to Moraxella nasovis CCUG 75922T. Phylogenomic analysis based on 810 single-copy genes revealed that the strain was a member of the genus Moraxella and formed a deep and separated clade within the genus. The strain showed the highest orthologous average nucleotide identity (OrthoANI) value of 77.1% with Moraxella ovis CCUG 354T and digital DNA-DNA hybridization (dDDH) value of 24.7% with Moraxella equi NCTC 11012T, respectively. The DNA G + C content was 46.5 mol%. The strain optimally grew at 37 °C (temperature range, 24-42 °C), at pH 8.0 (pH range, 6.0-9.0) and with 1.5% (w/v) NaCl (NaCl range, 0.5-3.0%). The strain contained C18:1 ω9c as the sole predominant fatty acid (> 5 %) and CoQ-8 as the major respiratory quinone. The major polar lipids included phosphatidylglycerol, phosphatidylethanolamine, cardiolipin, monolysocardiolipin and hemibismonoacylglycerophosphate. Based on these data, strain ZY190618T clearly represents a novel species in the genus Moraxella, for which the name Moraxella nasibovis sp. nov. (The type strain ZY190618T = CCUG 75921T = CCTCC AB 2021472T) is proposed.
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Affiliation(s)
- Fuxiang Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Wenhua Zhao
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Pei Zhu
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Zhanhong Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Jianling Song
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Jianbo Zhu
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China
| | - Huafeng Gao
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, 650224, People's Republic of China.
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21
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Nikaidou Y, Guo Y, Taguchi M, Chohnan S, Nishizawa T, Kurusu Y. Complete genome sequence of Pseudoalteromonas sp. PS1M3, a psychrotrophic bacterium isolated from deep-sea sediment off the Boso Peninsula, Japan Trench. Mar Genomics 2023; 69:101028. [PMID: 37100529 DOI: 10.1016/j.margen.2023.101028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023]
Abstract
Herein, we report the complete genome sequence of Pseudoalteromonas sp. PS1M3 (= NCBI 87791), which is a psychrotrophic bacterium that inhabits in seabed off the Boso Peninsula, Japan Trench. Analysis of the genomic sequence revealed that PS1M3 possesses 2 circular chromosomal DNAs and 2 circular plasmid DNAs. The genome of PS1M3 had a total size of 4,351,630 bp, an average GC content of 39.9%, and contained a total of 3811 predicted protein coding sequences, 28 rRNAs, and 100 tRNAs. The Kyoto Encyclopedia of Genes and Genomes (KEGG) was utilized to annotate the genes and KofamKOALA within KEGG assigned a gene cluster involved in glycogen biosynthesis and metabolic pathways with regard to heavy metal resistance (copper; cop and mercury; mer), indicating that PS1M3 can potentially use a stored glycogen as an energy source under oligotrophic environment and cope with multi-heavy metal contamination. To assess available genome relatedness indices, whole-genome average nucleotide identity analysis was examined using the complete genome sequences of Pseudoalteromonas spp., showing that 67.29-97.40% sequence similarity with PS1M3. This study may be useful in understanding the roles of a psychrotrophic Pseudoalteromonas in cold deep-sea sediment adaptation mechanisms.
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22
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Lin X, Hu T, Chen J, Liang H, Zhou J, Wu Z, Ye C, Jin X, Xu X, Zhang W, Jing X, Yang T, Wang J, Yang H, Kristiansen K, Xiao L, Zou Y. The genomic landscape of reference genomes of cultivated human gut bacteria. Nat Commun 2023; 14:1663. [PMID: 36966151 PMCID: PMC10039858 DOI: 10.1038/s41467-023-37396-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/14/2023] [Indexed: 03/27/2023] Open
Abstract
Culture-independent metagenomic studies have revolutionized our understanding of the gut microbiota. However, the lack of full genomes from cultured species is still a limitation for in-depth studies of the gut microbiota. Here we present a substantially expanded version of our Cultivated Genome Reference (CGR), termed CGR2, providing 3324 high-quality draft genomes from isolates selected from a large-scale cultivation of bacterial isolates from fecal samples of healthy Chinese individuals. The CGR2 classifies 527 species (179 previously unidentified species) from 8 phyla, and uncovers a genomic and functional diversity of Collinsella aerofaciens. The CGR2 genomes match 126 metagenome-assembled genomes without cultured representatives in the Unified Human Gastrointestinal Genome (UHGG) collection and harbor 3767 unidentified secondary metabolite biosynthetic gene clusters, providing a source of natural compounds with pharmaceutical potentials. We uncover accurate phage-bacterium linkages providing information on the evolutionary characteristics of interaction between bacteriophages and bacteria at the strain level.
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Affiliation(s)
- Xiaoqian Lin
- BGI-Shenzhen, Shenzhen, 518083, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | | | - Jianwei Chen
- BGI-Shenzhen, Shenzhen, 518083, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | | | - Jianwei Zhou
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China
| | - Zhinan Wu
- BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Ye
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Xiaohuan Jing
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Tao Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, 518083, China.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- PREDICT, Center for Molecular Prediction of Inflammatory Bowel Disease, Faculty of Medicine, Aalborg University, 2450, Copenhagen, Denmark.
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen, 518083, China.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China.
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China.
| | - Yuanqiang Zou
- BGI-Shenzhen, Shenzhen, 518083, China.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China.
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23
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Near-Complete Whole-Genome Sequence of Paenibacillus sp. nov. Strain J5C2022, a Sucretolerant and Endospore-Forming Bacterium Isolated from Highly Concentrated Sugar Brine. Microbiol Resour Announc 2023; 12:e0105522. [PMID: 36877039 PMCID: PMC10112168 DOI: 10.1128/mra.01055-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
Here, we present a 7.62-Mbp genome sequence of Paenibacillus sp. nov. strain J5C2022, a Gram-positive facultatively anaerobic bacterium that was isolated from 4-month-old fruit pickle brine and sequenced using the Illumina platform.
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24
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Whole-Genome Sequence of a Stenotrophomonas maltophilia Isolate from Tap Water in an Intensive Care Unit. Microbiol Resour Announc 2023; 12:e0099522. [PMID: 36633414 PMCID: PMC9933727 DOI: 10.1128/mra.00995-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Here, we present a 4,508,936-bp complete genome sequence of Stenotrophomonas maltophilia strain HW002Y, which was isolated from the tap water in an intensive care unit at Sultan Ahmad Shah Medical Centre at the International Islamic University of Malaysia (Kuantan, Pahang, Malaysia). Sequencing was performed using a Nanopore Flongle flow cell.
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25
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Friedrich I, Neubauer H, Kuritsyn A, Bodenberger B, Tskhay F, Hartmann S, Poehlein A, Bömeke M, Hoppert M, Schneider D, Hertel R, Daniel R. Brevundimonas and Serratia as host systems for assessing associated environmental viromes and phage diversity by complementary approaches. Front Microbiol 2023; 14:1095850. [PMID: 37025643 PMCID: PMC10070969 DOI: 10.3389/fmicb.2023.1095850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/23/2023] [Indexed: 04/08/2023] Open
Abstract
Focusing on visible plaques for phage isolation leaves the question if we miss the diversity of non-plaque forming phages. We addressed this question through direct plaque-based isolation by employing the new hosts Brevundimonas pondensis LVF1 and Serratia marcescens LVF3 dsDNA, ssDNA, dsRNA, and ssRNA host-associated metavirome analysis. Of the 25 distinctive dsDNA phage isolates, 14 were associated with Brevundimonas and 11 with Serratia. TEM analysis revealed that 6 were myoviruses, 18 siphoviruses and 1 podovirus, while phages infecting Brevundimonas belonged all to siphoviruses. The associated viromes suggested a higher phage diversity in summer than in winter, and dsDNA phages were the dominant group. Isolation of vB_SmaP-Kaonashi was possible after investigating the viromes associated with Serratia, demonstrating the great potential of accompanying host-associated metavirome analysis. The ssDNA virome analysis showed that the B. pondensis LVF1 host is associated with Microviridae and Inoviridae phages, although none of them were isolated. The results demonstrated that the classical isolation technique is not exhausted, leading to the isolation of new dsDNA phages. It can be further improved by combination with metavirome techniques, which revealed further diversity.
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Affiliation(s)
- Ines Friedrich
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Hannes Neubauer
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Alisa Kuritsyn
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Bernhard Bodenberger
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Faina Tskhay
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Sara Hartmann
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Mechthild Bömeke
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Michael Hoppert
- General Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Robert Hertel
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
- FG Synthetic Microbiology, Institute of Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
- *Correspondence: Rolf Daniel,
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26
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Baltoumas FA, Karatzas E, Paez-Espino D, Venetsianou NK, Aplakidou E, Oulas A, Finn RD, Ovchinnikov S, Pafilis E, Kyrpides NC, Pavlopoulos GA. Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters. FRONTIERS IN BIOINFORMATICS 2023; 3:1157956. [PMID: 36959975 PMCID: PMC10029925 DOI: 10.3389/fbinf.2023.1157956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
Metagenomics has enabled accessing the genetic repertoire of natural microbial communities. Metagenome shotgun sequencing has become the method of choice for studying and classifying microorganisms from various environments. To this end, several methods have been developed to process and analyze the sequence data from raw reads to end-products such as predicted protein sequences or families. In this article, we provide a thorough review to simplify such processes and discuss the alternative methodologies that can be followed in order to explore biodiversity at the protein family level. We provide details for analysis tools and we comment on their scalability as well as their advantages and disadvantages. Finally, we report the available data repositories and recommend various approaches for protein family annotation related to phylogenetic distribution, structure prediction and metadata enrichment.
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Affiliation(s)
- Fotis A. Baltoumas
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
- *Correspondence: Fotis A. Baltoumas, ; Nikos C. Kyrpides, ; Georgios A. Pavlopoulos,
| | - Evangelos Karatzas
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
| | - David Paez-Espino
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States
| | - Nefeli K. Venetsianou
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
| | - Eleni Aplakidou
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
| | - Anastasis Oulas
- The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Robert D. Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - Sergey Ovchinnikov
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, United States
| | - Evangelos Pafilis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - Nikos C. Kyrpides
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States
- *Correspondence: Fotis A. Baltoumas, ; Nikos C. Kyrpides, ; Georgios A. Pavlopoulos,
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
- Center of New Biotechnologies and Precision Medicine, Department of Medicine, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
- Hellenic Army Academy, Vari, Greece
- *Correspondence: Fotis A. Baltoumas, ; Nikos C. Kyrpides, ; Georgios A. Pavlopoulos,
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27
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Jia K, Peng Y, Chen X, Jian H, Jin M, Yi Z, Su M, Dong X, Yi M. A Novel Inovirus Reprograms Metabolism and Motility of Marine Alteromonas. Microbiol Spectr 2022; 10:e0338822. [PMID: 36301121 PMCID: PMC9769780 DOI: 10.1128/spectrum.03388-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/09/2022] [Indexed: 01/10/2023] Open
Abstract
Members from the Inoviridae family with striking features are widespread, highly diverse, and ecologically pervasive across multiple hosts and environments. However, a small number of inoviruses have been isolated and studied. Here, a filamentous phage infecting Alteromonas abrolhosensis, designated ϕAFP1, was isolated from the South China Sea and represented a novel genus of Inoviridae. ϕAFP1 consisted of a single-stranded DNA genome (5986 bp), encoding eight putative ORFs. Comparative analyses revealed ϕAFP1 could be regarded as genetic mosaics having homologous sequences with Ralstonia and Stenotrophomonas phages. The temporal transcriptome analysis of A. abrolhosensis to ϕAFP1 infection revealed that 7.78% of the host genes were differentially expressed. The genes involved in translation processes, ribosome pathways, and degradation of multiple amino acid pathways at the plateau period were upregulated, while host material catabolic and bacterial motility-related genes were downregulated, indicating that ϕAFP1 might hijack the energy of the host for the synthesis of phage proteins. ϕAFP1 exerted step-by-step control on host genes through the appropriate level of utilizing host resources. Our study provided novel information for a better understanding of filamentous phage characteristics and phage-host interactions. IMPORTANCE Alteromonas is widely distributed and plays a vital role in biogeochemical in marine environments. However, little information about Alteromonas phages is available. Here, we isolated and characterized the biological characteristics and genome sequence of a novel inovirus infecting Alteromonas abrolhosensis, designated ϕAFP1, representing a novel viral genus of Inoviridae. We then presented a comprehensive view of the ϕAFP1 phage-Alteromonas abrolhosensis interactions, elucidating reprogramed host metabolism and motility. Our study provided novel information for better comprehension of filamentous phage characteristics and phage-host interactions.
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Affiliation(s)
- Kuntong Jia
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Yongyi Peng
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Xueji Chen
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Min Jin
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Zhiwei Yi
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Ming Su
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Meisheng Yi
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
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28
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Complete Genome Sequences of Two Predatory Bacterial Strains,
Bacteriovorax
sp. HI3 and
Myxococcus
sp. MH1, Isolated from a Freshwater Pond. Microbiol Resour Announc 2022; 11:e0114622. [DOI: 10.1128/mra.01146-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We report the complete genome sequences of two predatory bacterial strains,
Bacteriovorax
sp. HI3 and
Myxococcus
sp. MH1, which were isolated from a freshwater pond. These two strains are grouped with the
Bdellovibrio
and like organisms and myxobacteria, respectively. Their genomes expand our knowledge of the characteristics of predatory bacteria.
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Li T, Yin Y. Critical assessment of pan-genomic analysis of metagenome-assembled genomes. Brief Bioinform 2022; 23:6702672. [PMID: 36124775 PMCID: PMC9677465 DOI: 10.1093/bib/bbac413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 12/30/2022] Open
Abstract
Pan-genome analyses of metagenome-assembled genomes (MAGs) may suffer from the known issues with MAGs: fragmentation, incompleteness and contamination. Here, we conducted a critical assessment of pan-genomics of MAGs, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs. We found that incompleteness led to significant core gene (CG) loss. The CG loss remained when using different pan-genome analysis tools (Roary, BPGA, Anvi'o) and when using a mixture of MAGs and complete genomes. Contamination had little effect on core genome size (except for Roary due to in its gene clustering issue) but had major influence on accessory genomes. Importantly, the CG loss was partially alleviated by lowering the CG threshold and using gene prediction algorithms that consider fragmented genes, but to a less degree when incompleteness was higher than 5%. The CG loss also led to incorrect pan-genome functional predictions and inaccurate phylogenetic trees. Our main findings were supported by a study of real MAG-isolate genome data. We conclude that lowering CG threshold and predicting genes in metagenome mode (as Anvi'o does with Prodigal) are necessary in pan-genome analysis of MAGs. Development of new pan-genome analysis tools specifically for MAGs are needed in future studies.
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Affiliation(s)
- Tang Li
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE, 68508, USA
| | - Yanbin Yin
- Corresponding author. Yanbin Yin, Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE 68508, USA. Tel.: +1-402-472-4303; E-mail:
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30
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Complete Genome Sequence of Rhodococcus qingshengii N9T-4. Microbiol Resour Announc 2022; 11:e0089122. [DOI: 10.1128/mra.00891-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Rhodococcus qingshengii
N9T-4 can grow on media without added carbon sources. Here, we report the complete nucleotide sequence of the N9T-4 genome, consisting of a chromosome (6,439,972 bp), a linear plasmid (pN9T4-1 [565,206 bp]), and two circular plasmids (pN9T-4-2 [99,662 bp] and pN9T-4-3 [30,419 bp]).
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31
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Seong HJ, Roux S, Hwang CY, Sul WJ. Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics. MICROBIOME 2022; 10:157. [PMID: 36167684 PMCID: PMC9516812 DOI: 10.1186/s40168-022-01340-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 07/28/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life. RESULTS We reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark. CONCLUSIONS Overall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome. Video Abstract.
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Affiliation(s)
- Hoon Je Seong
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Chung Yeon Hwang
- School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
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32
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Clavijo F, Barrera C, Benčič A, Croce V, Jacobs JM, Bernal AJ, Koebnik R, Roman-Reyna V. Complete Genome Sequence Resource for Xanthomonas translucens pv. undulosa MAI5034, a Wheat Pathogen from Uruguay. PHYTOPATHOLOGY 2022; 112:2036-2039. [PMID: 35559654 DOI: 10.1094/phyto-01-22-0025-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Felipe Clavijo
- Laboratorio de Microbiología Molecular, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Claudia Barrera
- Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - Aleksander Benčič
- National Institute of Biology, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Valentina Croce
- Laboratorio de Microbiología Molecular, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, U.S.A
| | - Adriana J Bernal
- Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - Ralf Koebnik
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, OH, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, U.S.A
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33
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Near-Complete Whole-Genome Sequencing of Two Burkholderia pseudomallei Strains Harbouring Novel Molecular Class D Beta-Lactamase Genes, Isolated from Malaysia. Microbiol Resour Announc 2022; 11:e0046822. [PMID: 36043870 PMCID: PMC9583775 DOI: 10.1128/mra.00468-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we present two 7.1- and 7.3-bp near-complete genome sequences of Burkholderia pseudomallei strains of HTAA077 and HRPB058, isolated from a pus culture from a confirmed melioidosis patient at Hospital Tengku Ampuan Afzan, Kuantan, Malaysia, and from blood culture from a patient at Hospital Raja Permaisuri Bainun, Ipoh, Malaysia, using a Nanopore MinION instrument.
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34
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Complete Genome Sequence of a Psychrophilic Bacterium,
Pseudoalteromonas
sp. Strain APM04, Isolated from the Seafloor of the South Mariana Trough, Pacific Ocean. Microbiol Resour Announc 2022; 11:e0037422. [PMID: 35894625 PMCID: PMC9387264 DOI: 10.1128/mra.00374-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete genome sequence of Pseudoalteromonas sp. strain APM04, which is a psychrophilic bacterium that inhabits the seabed of the South Mariana Trough, Pacific Ocean, was determined to characterize the genetic features associated with evolution in extremophilic and oligotrophic deep seawater.
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35
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Nitrogen Fixation Activity and Genome Analysis of a Moderately Haloalkaliphilic Anoxygenic Phototrophic Bacterium Rhodovulum tesquicola. Microorganisms 2022; 10:microorganisms10081615. [PMID: 36014033 PMCID: PMC9412634 DOI: 10.3390/microorganisms10081615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
The genome of the moderately haloalkaliphilic diazotrophic anoxygenic phototrophic bacterium Rhodovulum tesquicola A-36sT isolated from an alkaline lake was analyzed and compared to the genomes of the closest species Rhodovulum steppense A-20sT and Rhodovulum strictum DSM 11289T. The genomic features of three organisms are quite similar, reflecting their ecological and physiological role of facultative photoheterotrophs. Nevertheless, the nitrogenase activity of the pure cultures of the studied bacteria differed significantly: the highest rate (4066 nmoles C2H2/mg of dry weight per hour) was demonstrated by Rhodovulum strictum while the rates in Rhodovulum tesquicola and Rhodovulum steppense were an order of magnitude lower (278 and 523 nmoles C2H2/mg of dry weight per hour, respectively). This difference can be attributed to the presence of an additional nitrogenase operon found exclusively in R. strictum and to the structural variation in nitrogenase operon in R. tesquicola.
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36
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Genomic, Metabolic, and Immunological Characterization of GMP-Grade Mycobacterium phlei. Microbiol Spectr 2022; 10:e0007022. [PMID: 35727046 PMCID: PMC9430659 DOI: 10.1128/spectrum.00070-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium phlei (M. phlei) is an understudied microbe with medical values as an immunomodulating agent. Here, we establish an industrial strain of M. phlei, CUD, and characterize its genomic, metabolic, and immunological profiles. The established strain has been stably passed for more than a decade, indicated by next-generation sequencing of its 5.3 Mb genome. We show that the intramuscular inoculation of heat-inactivated CUD in immunocompetent mice is well tolerated, and can mount immunological responses. Immunophenotyping demonstrates induced innate and adaptive immune responses in peripheral blood, spleen, and inguinal lymph nodes of CUD-treated mice. Using GC-TOF-MS, we find that the metabolomic profiles of different batches are highly concordant. These results demonstrate a highly reproducible production of M. phlei under GMP conditions. IMPORTANCE Heat-inactivated M. phlei demonstrates promising efficacy to treat BCG-unresponsive non-muscle-invasive bladder cancer patients in clinical trials. However, lack of GMP-grade heat-inactivated M. phlei hampers further clinical investigations. Here, we described a GMP-grade, heat-inactivated M. phlei product, and presented initial characterization of its safety and immunomodulating properties. This product will serve as a starting point for further preclinical studies as well as clinical trials such as in combination with immune checkpoint inhibitors to treat bladder cancer.
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37
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Kim YT, Kim CH, Kwon JG, Cho JH, Shin YS, Kim HB, Lee JH. In vivo Trial of Bifidobacterium longum Revealed the Complex Network Correlations Between Gut Microbiota and Health Promotional Effects. Front Microbiol 2022; 13:886934. [PMID: 35783421 PMCID: PMC9247516 DOI: 10.3389/fmicb.2022.886934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Abstract
Complete genome sequence analysis of Bifidobacterium longum subsp. longum BCBL-583 isolated from a Korean female fecal sample showed no virulence factor or antibiotic resistance gene, suggesting human safety. In addition, this strain has oxygen and heat tolerance genes for food processing, and cholesterol reduction and mucin adhesion-related genes were also found. For in vivo evaluations, a high fat diet (HFD) mouse model was used, showing that BCBL-583 administration to the model (HFD-583) reduced the total cholesterol and LDL-cholesterol in the blood and decreased pro-inflammatory cytokines but increased anti-inflammatory cytokines, substantiating its cholesterol reduction and anti-inflammation activities. Subsequent microbiome analysis of the fecal samples from the HFD mouse model revealed that BCBL-583 administration changed the composition of gut microbiota. After 9 weeks feeding of bifidobacteria, Firmicutes, Actinobacteria, and Bacteroidetes increased, but Proteobacteria maintained in the HFD mouse models. Further comparative species-level compositional analysis revealed the inhibitions of cholesterol reduction-related Eubacterium coprostanoligenes and obesity-related Lactococcus by the supplementation of B. longum BCBL-583, suggesting its possible cholesterol reduction and anti-obesity activities. The correlation analysis of HFD-583 between the gut microbiota compositional change and cholesterol/immune response showed that Verrucomicrobia, Firmicutes, Actinobacteria, and Bacteroidetes may play an important role in cholesterol reduction and anti-inflammation. However, correlation analysis of Proteobacteria showed the reverse correlation in HFD-583. Interestingly, the correlation analysis of B. longum ATCC 15707 administration to HFD model showed similar patterns of cholesterol but different in immune response patterns. Therefore, this correlation analysis suggests that the microbial composition and inflammatory cytokine/total-cholesterol may be closely related in the administration of BCBL-583 in the HFD mice group. Consequently, BCBL-583 could be a good probiotic strain for gut health promotion through gut microbiota modulation.
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Affiliation(s)
- You-Tae Kim
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Science, Seoul National University, Seoul, South Korea
| | - Chul-Hong Kim
- Department of Food Science and Biotechnology, Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
- Food Research Center, Binggrae Co., Ltd., Namyangju, South Korea
| | - Joon-Gi Kwon
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Science, Seoul National University, Seoul, South Korea
| | - Jae Hyoung Cho
- Department of Animal Resources Science, Dankook University, Cheonan, South Korea
| | - Young-Sup Shin
- Food Research Center, Binggrae Co., Ltd., Namyangju, South Korea
| | - Hyeun Bum Kim
- Department of Animal Resources Science, Dankook University, Cheonan, South Korea
- Hyeun Bum Kim,
| | - Ju-Hoon Lee
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Science, Seoul National University, Seoul, South Korea
- *Correspondence: Ju-Hoon Lee,
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38
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Marciano DC, Wang C, Hsu TK, Bourquard T, Atri B, Nehring RB, Abel NS, Bowling EA, Chen TJ, Lurie PD, Katsonis P, Rosenberg SM, Herman C, Lichtarge O. Evolutionary action of mutations reveals antimicrobial resistance genes in Escherichia coli. Nat Commun 2022; 13:3189. [PMID: 35680894 PMCID: PMC9184624 DOI: 10.1038/s41467-022-30889-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/24/2022] [Indexed: 11/08/2022] Open
Abstract
Since antibiotic development lags, we search for potential drug targets through directed evolution experiments. A challenge is that many resistance genes hide in a noisy mutational background as mutator clones emerge in the adaptive population. Here, to overcome this noise, we quantify the impact of mutations through evolutionary action (EA). After sequencing ciprofloxacin or colistin resistance strains grown under different mutational regimes, we find that an elevated sum of the evolutionary action of mutations in a gene identifies known resistance drivers. This EA integration approach also suggests new antibiotic resistance genes which are then shown to provide a fitness advantage in competition experiments. Moreover, EA integration analysis of clinical and environmental isolates of antibiotic resistant of E. coli identifies gene drivers of resistance where a standard approach fails. Together these results inform the genetic basis of de novo colistin resistance and support the robust discovery of phenotype-driving genes via the evolutionary action of genetic perturbations in fitness landscapes.
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Affiliation(s)
- David C Marciano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Chen Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Teng-Kuei Hsu
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Thomas Bourquard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Benu Atri
- Structural and Computational Biology & Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, 77030, USA
- Clara Analytics Inc., 451 El Camino Real #201, Santa Clara, CA, 95050, USA
| | - Ralf B Nehring
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nicholas S Abel
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elizabeth A Bowling
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Taylor J Chen
- Integrative Molecular & Biomedical Biosciences Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pamela D Lurie
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular & Biomedical Biosciences Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Structural and Computational Biology & Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, 77030, USA.
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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39
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Li T, Li Y, Ma X, Dan X, Huang X, Li Q, Lei S, Zhang Z, Huang S, Jiang W, Yu Y, He YQ. Comparative Genomic Analysis of Two Xanthomonas oryzae pv. oryzae Strains Isolated From Low Land and High Mountain Paddies in Guangxi, China. Front Microbiol 2022; 13:867633. [PMID: 35572630 PMCID: PMC9096941 DOI: 10.3389/fmicb.2022.867633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/15/2022] [Indexed: 11/22/2022] Open
Abstract
Xanthomonas oryzae pv. textitoryzae (Xoo) is a causal agent of rice bacterial leaf blight (BLB), the major rice disease, which is seriously constraining rice production in Asia. The interaction between Xoo and rice is in a dynamic process, essentially the co-evolution. Tracking the occurrence of plant diseases and identifying the epidemic pathogens in time are critical to assessing the epidemic disease status and understanding the pathogen evolution. In 2020, the occurrences of rice BLB were spotted in many places of Guangxi, the major rice growing region in China. Two of the 2020-epidemic Xoo strains, namely, GXO20-01 and GXO20-06, were isolated from low land and high mountain paddies in Guangxi, respectively, and were demonstrated to be race R8 of Chinese Xoo strains, but with significantly different virulence on certain susceptible varieties of rice. The HiFi PacBio sequencing revealed that GXO20-01 and GXO20-06 share the highly syntenic genome structures and the major genome contents, but only differ in <10 genes, including one gene encoding for transcription activator-like effector (TALE). A phylogenomic analysis grouped GXO20-01 and GXO20-06 into the PX-A lineage, stood close to PXO563 and PXO71 strains, but stood away from the other Chinese Xoo strains; for example, the JL25 and YC11. A comparative genomic analysis revealed that the major pathogenicity/virulence genes are conserved in two, newly isolated Xoo strains and the other Xoo strains in PX-A lineage, including the majority genes for the TALomes. The genomic differences between the Xoo strains were pinpointed to a few tal genes, which were variable in both their numbers and sequences, even between GXO20-01 and GXO20-06, the two 2020-epidemic Xoo strains. The study further revealed the instability and variability of tal genes in Xoo and highlighted the utility of HiFi long-read sequencing in TALE analysis and pathogen tracking.
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Affiliation(s)
- Tianjiao Li
- College of Agriculture, Guangxi University, Nanning, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource and College of Life Science and Technology, Nanning, China
| | - Yiming Li
- College of Agriculture, Guangxi University, Nanning, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource and College of Life Science and Technology, Nanning, China
| | - Xiuguo Ma
- College of Agriculture, Guangxi University, Nanning, China
| | - Xue Dan
- College of Agriculture, Guangxi University, Nanning, China
| | - Xianjiao Huang
- College of Agriculture, Guangxi University, Nanning, China
| | - Qinying Li
- Napo Agricultural and Rural Bureau, Napo County, Baise, China
| | - Shimin Lei
- College of Agriculture, Guangxi University, Nanning, China
| | - Zhengchun Zhang
- New Rural Development Institute of Guangxi University, Nanning, China
| | - Sheng Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource and College of Life Science and Technology, Nanning, China
| | - Wei Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource and College of Life Science and Technology, Nanning, China
| | - Yanhua Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource and College of Life Science and Technology, Nanning, China
| | - Yong-Qiang He
- College of Agriculture, Guangxi University, Nanning, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource and College of Life Science and Technology, Nanning, China
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40
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Smith C, Canestrari JG, Wang AJ, Champion MM, Derbyshire KM, Gray TA, Wade JT. Pervasive translation in Mycobacterium tuberculosis. eLife 2022; 11:e73980. [PMID: 35343439 PMCID: PMC9094748 DOI: 10.7554/elife.73980] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Most bacterial ORFs are identified by automated prediction algorithms. However, these algorithms often fail to identify ORFs lacking canonical features such as a length of >50 codons or the presence of an upstream Shine-Dalgarno sequence. Here, we use ribosome profiling approaches to identify actively translated ORFs in Mycobacterium tuberculosis. Most of the ORFs we identify have not been previously described, indicating that the M. tuberculosis transcriptome is pervasively translated. The newly described ORFs are predominantly short, with many encoding proteins of ≤50 amino acids. Codon usage of the newly discovered ORFs suggests that most have not been subject to purifying selection, and hence are unlikely to contribute to cell fitness. Nevertheless, we identify 90 new ORFs (median length of 52 codons) that bear the hallmarks of purifying selection. Thus, our data suggest that pervasive translation of short ORFs in Mycobacterium tuberculosis serves as a rich source for the evolution of new functional proteins.
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Affiliation(s)
- Carol Smith
- Wadsworth Center, Division of Genetics, New York State Department of HealthAlbanyUnited States
| | - Jill G Canestrari
- Wadsworth Center, Division of Genetics, New York State Department of HealthAlbanyUnited States
| | - Archer J Wang
- Wadsworth Center, Division of Genetics, New York State Department of HealthAlbanyUnited States
| | - Matthew M Champion
- Department of Chemistry and Biochemistry, University of Notre DameNotre DameUnited States
| | - Keith M Derbyshire
- Wadsworth Center, Division of Genetics, New York State Department of HealthAlbanyUnited States
- Department of Biomedical Sciences, School of Public Health, University at AlbanyNew YorkUnited States
| | - Todd A Gray
- Wadsworth Center, Division of Genetics, New York State Department of HealthAlbanyUnited States
- Department of Biomedical Sciences, School of Public Health, University at AlbanyNew YorkUnited States
| | - Joseph T Wade
- Wadsworth Center, Division of Genetics, New York State Department of HealthAlbanyUnited States
- Department of Biomedical Sciences, School of Public Health, University at AlbanyNew YorkUnited States
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41
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Topaz N, Tsang R, Deghmane AE, Claus H, Lâm TT, Litt D, Bajanca-Lavado MP, Pérez-Vázquez M, Vestrheim D, Giufrè M, Van Der Ende A, Gaillot O, Kuch A, McElligott M, Taha MK, Wang X. Phylogenetic Structure and Comparative Genomics of Multi-National Invasive Haemophilus influenzae Serotype a Isolates. Front Microbiol 2022; 13:856884. [PMID: 35401483 PMCID: PMC8988223 DOI: 10.3389/fmicb.2022.856884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
Recent reports have indicated a rise of invasive disease caused by Haemophilus influenzae serotype a (Hia) in North America and some European countries. The whole-genome sequences for a total of 410 invasive Hia isolates were obtained from 12 countries spanning the years of 1998 to 2019 and underwent phylogenetic and comparative genomic analysis in order to characterize the major strains causing disease and the genetic variation present among factors contributing to virulence and antimicrobial resistance. Among 410 isolate sequences received, 408 passed our quality control and underwent genomic analysis. Phylogenetic analysis revealed that the Hia isolates formed four genetically distinct clades: clade 1 (n = 336), clade 2 (n = 13), clade 3 (n = 3) and clade 4 (n = 56). A low diversity subclade 1.1 was found in clade 1 and contained almost exclusively North American isolates. The predominant sequence types in the Hia collection were ST-56 (n = 125), ST-23 (n = 98) and ST-576 (n = 51), which belonged to clade 1, and ST-62 (n = 54), which belonged to clade 4. Clades 1 and 4 contained predominantly North American isolates, and clades 2 and 3 predominantly contained European isolates. Evidence of the presence of capsule duplication was detected in clade 1 and 2 isolates. Seven of the virulence genes involved in endotoxin biosynthesis were absent from all Hia isolates. In general, the presence of known factors contributing to β-lactam antibiotic resistance was low among Hia isolates. Further tests for virulence and antibiotic susceptibility would be required to determine the impact of these variations among the isolates.
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Affiliation(s)
- Nadav Topaz
- Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Raymond Tsang
- Vaccine Preventable Bacterial Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Ala-Eddine Deghmane
- Centre National de Référence des Méningocoques, Institut Pasteur, Paris, France
| | - Heike Claus
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Thiên-Trí Lâm
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - David Litt
- Respiratory and Vaccine Preventable Bacterial Reference Unit, Public Health England, London, United Kingdom
| | - Maria Paula Bajanca-Lavado
- Haemophilus Influenzae Reference Laboratory, Department of Infectious Disease, National Institute of Health, Lisbon, Portugal
| | - María Pérez-Vázquez
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Didrik Vestrheim
- Norwegian Institute of Public Health, Division of Infection Control and Environmental Health, Oslo, Norway
| | - Maria Giufrè
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Arie Van Der Ende
- Department of Medical Microbiology and Infection Prevention and the Netherlands Reference Laboratory for Bacterial Meningitis, University of Amsterdam, Amsterdam, Netherlands
| | - Olivier Gaillot
- Service de Bactériologie-Hygiène, CHU Lille, Lille, France
- CNRS, INSERM, U1019-UMR 8204, Center for Infection and Immunity, CHU Lille, Lille, France
| | - Alicja Kuch
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Martha McElligott
- Irish Meningitis and Sepsis Reference Laboratory, Children’s Health Ireland at Temple Street, Dublin, Ireland
| | - Muhamed-Kheir Taha
- Centre National de Référence des Méningocoques, Institut Pasteur, Paris, France
| | - Xin Wang
- Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
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A Novel and Ubiquitous Marine Methylophage Provides Insights into Viral-Host Coevolution and Possible Host-Range Expansion in Streamlined Marine Heterotrophic Bacteria. Appl Environ Microbiol 2022; 88:e0025522. [PMID: 35311512 PMCID: PMC9004378 DOI: 10.1128/aem.00255-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The methylotrophic OM43 clade are Gammaproteobacteria that comprise some of the smallest free-living cells known and have highly streamlined genomes. OM43 represents an important microbial link between marine primary production and remineralization of carbon back to the atmosphere. Bacteriophages shape microbial communities and are major drivers of mortality and global marine biogeochemistry. Recent cultivation efforts have brought the first viruses infecting members of the OM43 clade into culture. Here, we characterize a novel myophage infecting OM43 called Melnitz. Melnitz was isolated independently from water samples from a subtropical ocean gyre (Sargasso Sea) and temperate coastal (Western English Channel) systems. Metagenomic recruitment from global ocean viromes confirmed that Melnitz is globally ubiquitous, congruent with patterns of host abundance. Bacteria with streamlined genomes such as OM43 and the globally dominant SAR11 clade use riboswitches as an efficient method to regulate metabolism. Melnitz encodes a two-piece tmRNA (ssrA), controlled by a glutamine riboswitch, providing evidence that riboswitch use also occurs for regulation during phage infection of streamlined heterotrophs. Virally encoded tRNAs and ssrA found in Melnitz were phylogenetically more closely related to those found within the alphaproteobacterial SAR11 clade and their associated myophages than those within their gammaproteobacterial hosts. This suggests the possibility of an ancestral host transition event between SAR11 and OM43. Melnitz and a related myophage that infects SAR11 were unable to infect hosts of the SAR11 and OM43, respectively, suggesting host transition rather than a broadening of host range. IMPORTANCE Isolation and cultivation of viruses are the foundations on which the mechanistic understanding of virus-host interactions and parameterization of bioinformatic tools for viral ecology are based. This study isolated and characterized the first myophage known to infect the OM43 clade, expanding our knowledge of this understudied group of microbes. The nearly identical genomes of four strains of Melnitz isolated from different marine provinces and the global abundance estimations from metagenomic data suggest that this viral population is globally ubiquitous. Genome analysis revealed several unusual features in Melnitz and related genomes recovered from viromes, such as a curli operon and virally encoded tmRNA controlled by a glutamine riboswitch, neither of which are found in the host. Further phylogenetic analysis of shared genes indicates that this group of viruses infecting the gammaproteobacterial OM43 shares a recent common ancestor with viruses infecting the abundant alphaproteobacterial SAR11 clade. Host ranges are affected by compatible cell surface receptors, successful circumvention of superinfection exclusion systems, and the presence of required accessory proteins, which typically limits phages to singular narrow groups of closely related bacterial hosts. This study provides intriguing evidence that for streamlined heterotrophic bacteria, virus-host transitioning may not be necessarily restricted to phylogenetically related hosts but is a function of shared physical and biochemical properties of the cell.
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Li Y, Dan X, Li T, Wu Q, Wang Z, Xu L, Ma X, Bie F, Lei S, Huang S, Jiang W, He YQ. Complete Genome Resource of a Commonly Used Laboratory Substrain of Xanthomonas oryzae pv. oryzae PXO99 A. PLANT DISEASE 2022; 106:1045-1048. [PMID: 35259005 DOI: 10.1094/pdis-10-21-2176-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Yiming Li
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Xue Dan
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Tianjiao Li
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Qiaozhi Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Zihao Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Lidan Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Xiuguo Ma
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Fengzhi Bie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Shimin Lei
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Sheng Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Wei Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Yong-Qiang He
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and College of Life Science and Technology, 100 Daxue Road, Nanning, Guangxi 530004, China
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Complete Genome Sequence of Xanthomonas campestris pv.
campestris
SB80, a Race 4 Strain Isolated from White Head Cabbage in Turkey. Microbiol Resour Announc 2022; 11:e0002222. [PMID: 35191748 PMCID: PMC8928781 DOI: 10.1128/mra.00022-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Here, we report the complete genome sequence of the race 4 strain Xanthomonas campestris pv. campestris SB80, which was isolated from a symptomatic white head cabbage leaf in Samsun Province, Turkey, in 2019. The genome consists of a circular chromosome (5,129,762 bp) with a G+C content of 64.98%, for which 4,159 putative protein-coding genes, 2 rRNA operons, 54 tRNAs, and 86 noncoding RNAs (ncRNAs) were predicted.
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Gemayel K, Lomsadze A, Borodovsky M. StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes. FRONTIERS IN BIOINFORMATICS 2021; 1:704157. [PMID: 36303749 PMCID: PMC9581028 DOI: 10.3389/fbinf.2021.704157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 11/04/2021] [Indexed: 12/31/2022] Open
Abstract
State-of-the-art algorithms of ab initio gene prediction for prokaryotic genomes were shown to be sufficiently accurate. A pair of algorithms would agree on predictions of gene 3'ends. Nonetheless, predictions of gene starts would not match for 15-25% of genes in a genome. This discrepancy is a serious issue that is difficult to be resolved due to the absence of sufficiently large sets of genes with experimentally verified starts. We have introduced StartLink that infers gene starts from conservation patterns revealed by multiple alignments of homologous nucleotide sequences. We also have introduced StartLink+ combining both ab initio and alignment-based methods. The ability of StartLink to predict the start of a given gene is restricted by the availability of homologs in a database. We observed that StartLink made predictions for 85% of genes per genome on average. The StartLink+ accuracy was shown to be 98-99% on the sets of genes with experimentally verified starts. In comparison with database annotations, we observed that the annotated gene starts deviated from the StartLink+ predictions for ∼5% of genes in AT-rich genomes and for 10-15% of genes in GC-rich genomes on average. The use of StartLink+ has a potential to significantly improve gene start annotation in genomic databases.
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Affiliation(s)
- Karl Gemayel
- School of Computational Science and Engineering, Georgia Tech, Atlanta, GA, United States
| | - Alexandre Lomsadze
- Wallace H Coulter Department of Biomedical Engineering, Georgia Tech and Emory University, Atlanta, GA, United States
| | - Mark Borodovsky
- School of Computational Science and Engineering, Georgia Tech, Atlanta, GA, United States
- Wallace H Coulter Department of Biomedical Engineering, Georgia Tech and Emory University, Atlanta, GA, United States
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russia
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46
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Draft Genome Sequence of Lactiplantibacillus plantarum NMZ-1139, Isolated from Whisky Mash. Microbiol Resour Announc 2021; 10:e0100821. [PMID: 34881979 PMCID: PMC8656376 DOI: 10.1128/mra.01008-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactiplantibacillus plantarum NMZ-1139 was isolated from whisky mash and applied to sour beer production. Here, we report the draft genome sequence of L. plantarum NMZ-1139, which contains 3,117 protein-coding sequences, including genes associated with hop resistance, such as horA and hitA.
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Dimonaco NJ, Aubrey W, Kenobi K, Clare A, Creevey CJ. No one tool to rule them all: prokaryotic gene prediction tool annotations are highly dependent on the organism of study. Bioinformatics 2021; 38:1198-1207. [PMID: 34875010 PMCID: PMC8825762 DOI: 10.1093/bioinformatics/btab827] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 11/13/2021] [Accepted: 12/02/2021] [Indexed: 01/06/2023] Open
Abstract
MOTIVATION The biases in CoDing Sequence (CDS) prediction tools, which have been based on historic genomic annotations from model organisms, impact our understanding of novel genomes and metagenomes. This hinders the discovery of new genomic information as it results in predictions being biased towards existing knowledge. To date, users have lacked a systematic and replicable approach to identify the strengths and weaknesses of any CDS prediction tool and allow them to choose the right tool for their analysis. RESULTS We present an evaluation framework (ORForise) based on a comprehensive set of 12 primary and 60 secondary metrics that facilitate the assessment of the performance of CDS prediction tools. This makes it possible to identify which performs better for specific use-cases. We use this to assess 15 ab initio- and model-based tools representing those most widely used (historically and currently) to generate the knowledge in genomic databases. We find that the performance of any tool is dependent on the genome being analysed, and no individual tool ranked as the most accurate across all genomes or metrics analysed. Even the top-ranked tools produced conflicting gene collections, which could not be resolved by aggregation. The ORForise evaluation framework provides users with a replicable, data-led approach to make informed tool choices for novel genome annotations and for refining historical annotations. AVAILABILITY AND IMPLEMENTATION Code and datasets for reproduction and customisation are available at https://github.com/NickJD/ORForise. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nicholas J Dimonaco
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3PD, UK,To whom correspondence should be addressed.
| | - Wayne Aubrey
- Department of Computer Science, Aberystwyth University, Aberystwyth SY23 3DB, UK
| | - Kim Kenobi
- Department of Mathematics, Aberystwyth University, Aberystwyth SY23 3BZ, UK
| | - Amanda Clare
- Department of Computer Science, Aberystwyth University, Aberystwyth SY23 3DB, UK
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Lazeroff M, Ryder G, Harris SL, Tsourkas PK. Phage Commander, an Application for Rapid Gene Identification in Bacteriophage Genomes Using Multiple Programs. PHAGE 2021; 2:204-213. [PMID: 36147516 PMCID: PMC9041506 DOI: 10.1089/phage.2020.0044] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Matt Lazeroff
- Department of Computer Science, and University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Geordie Ryder
- Department of Electrical and Computer Engineering, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Sarah L. Harris
- Department of Electrical and Computer Engineering, University of Nevada Las Vegas, Las Vegas, Nevada, USA
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Huang CJ, Wu TL, Zheng PX, Ou JY, Ni HF, Lin YC. Comparative Genomic Analysis Uncovered Evolution of Pathogenicity Factors, Horizontal Gene Transfer Events, and Heavy Metal Resistance Traits in Citrus Canker Bacterium Xanthomonas citri subsp. citri. Front Microbiol 2021; 12:731711. [PMID: 34557177 PMCID: PMC8453159 DOI: 10.3389/fmicb.2021.731711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/18/2021] [Indexed: 12/30/2022] Open
Abstract
Background: Worldwide citrus production is severely threatened by Asiatic citrus canker which is caused by the proteobacterium Xanthomonas citri subsp. citri. Foliar sprays of copper-based bactericides are frequently used to control plant bacterial diseases. Despite the sequencing of many X. citri strains, the genome diversity and distribution of genes responsible for metal resistance in X. citri subsp. citri strains from orchards with different management practices in Taiwan are not well understood. Results: The genomes of three X. citri subsp. citri strains including one copper-resistant strain collected from farms with different management regimes in Taiwan were sequenced by Illumina and Nanopore sequencing and assembled into complete circular chromosomes and plasmids. CRISPR spoligotyping and phylogenomic analysis indicated that the three strains were located in the same phylogenetic lineages and shared ∼3,000 core-genes with published X. citri subsp. citri strains. These strains differed mainly in the CRISPR repeats and pathogenicity-related plasmid-borne transcription activator-like effector (TALE)-encoding pthA genes. The copper-resistant strain has a unique, large copper resistance plasmid due to an unusual ∼40 kbp inverted repeat. Each repeat contains a complete set of the gene cluster responsible for copper and heavy metal resistance. Conversely, the copper sensitive strains carry no metal resistance genes in the plasmid. Through comparative analysis, the origin and evolution of the metal resistance clusters was resolved. Conclusion: Chromosomes remained constant among three strains collected in Taiwan, but plasmids likely played an important role in maintaining pathogenicity and developing bacterial fitness in the field. The evolution of pathogenicity factors and horizontal gene transfer events were observed in the three strains. These data suggest that agricultural management practices could be a potential trigger for the evolution of citrus canker pathogens. The decrease in the number of CRISPR repeats and pthA genes might be the result of adaptation to a less stressful environment. The metal resistance genes in the copper resistant X. citri strain likely originated from the Mauritian strain not the local copper-resistant X. euvesicatoria strain. This study highlights the importance of plasmids as 'vehicles' for exchanging genetic elements between plant pathogenic bacteria and contributing to bacterial adaptation to the environment.
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Affiliation(s)
- Chien-Jui Huang
- Department of Plant Medicine, National Chiayi University, Chiayi, Taiwan
| | - Ting-Li Wu
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Po-Xing Zheng
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Jheng-Yang Ou
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Hui-Fang Ni
- Department of Plant Protection, Chiayi Agricultural Experiment Station, Taiwan Agricultural Research Institute, Chiayi, Taiwan
| | - Yao-Cheng Lin
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
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Marsh JI, Hu H, Gill M, Batley J, Edwards D. Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1677-1690. [PMID: 33852055 DOI: 10.1007/s00122-021-03820-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/18/2021] [Indexed: 05/05/2023]
Abstract
Safeguarding crop yields in a changing climate requires bioinformatics advances in harnessing data from vast phenomics and genomics datasets to translate research findings into climate smart crops in the field. Climate change and an additional 3 billion mouths to feed by 2050 raise serious concerns over global food security. Crop breeding and land management strategies will need to evolve to maximize the utilization of finite resources in coming years. High-throughput phenotyping and genomics technologies are providing researchers with the information required to guide and inform the breeding of climate smart crops adapted to the environment. Bioinformatics has a fundamental role to play in integrating and exploiting this fast accumulating wealth of data, through association studies to detect genomic targets underlying key adaptive climate-resilient traits. These data provide tools for breeders to tailor crops to their environment and can be introduced using advanced selection or genome editing methods. To effectively translate research into the field, genomic and phenomic information will need to be integrated into comprehensive clade-specific databases and platforms alongside accessible tools that can be used by breeders to inform the selection of climate adaptive traits. Here we discuss the role of bioinformatics in extracting, analysing, integrating and managing genomic and phenomic data to improve climate resilience in crops, including current, emerging and potential approaches, applications and bottlenecks in the research and breeding pipeline.
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Affiliation(s)
- Jacob I Marsh
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia
| | - Haifei Hu
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia
| | - Mitchell Gill
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia.
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