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Asgharzadeh Kangachar S, Logel DY, Trofimova E, Zhu HX, Zaugg J, Schembri MA, Weynberg KD, Jaschke PR. Discovery and characterisation of new phage targeting uropathogenic Escherichia coli. Virology 2024; 597:110148. [PMID: 38941748 DOI: 10.1016/j.virol.2024.110148] [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] [Received: 01/31/2024] [Revised: 06/02/2024] [Accepted: 06/18/2024] [Indexed: 06/30/2024]
Abstract
Antimicrobial resistance is an escalating threat with few new therapeutic options in the pipeline. Urinary tract infections (UTIs) are one of the most prevalent bacterial infections globally and are prone to becoming recurrent and antibiotic resistant. We discovered and characterized six novel Autographiviridae and Guernseyvirinae bacterial viruses (phage) against uropathogenic Escherichia coli (UPEC), a leading cause of UTIs. The phage genomes were between 39,471 bp - 45,233 bp, with 45.0%-51.0% GC%, and 57-84 predicted coding sequences per genome. We show that tail fiber domain structure, predicted host capsule type, and host antiphage repertoire correlate with phage host range. In vitro characterisation of phage cocktails showed synergistic improvement against a mixed UPEC strain population and when sequentially dosed. Together, these phage are a new set extending available treatments for UTI from UPEC, and phage vM_EcoM_SHAK9454 represents a promising candidate for further improvement through engineering.
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Affiliation(s)
- Shahla Asgharzadeh Kangachar
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Dominic Y Logel
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Ellina Trofimova
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Hannah X Zhu
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Julian Zaugg
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Mark A Schembri
- Institute for Molecular Bioscience (IMB), University of Queensland, Brisbane, Queensland, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Karen D Weynberg
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Paul R Jaschke
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia.
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Xu Y, Liu B, Jiao N, Liu J, Chen F. New evidence supports the prophage origin of RcGTA. Appl Environ Microbiol 2024:e0043424. [PMID: 39189727 DOI: 10.1128/aem.00434-24] [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: 03/06/2024] [Accepted: 08/11/2024] [Indexed: 08/28/2024] Open
Abstract
Gene transfer agents (GTAs) are phage-like entities that package and transfer random host genome fragments between prokaryotes. RcGTA, produced by Rhodobacter capsulatus, is hypothesized to originate from a prophage ancestor. Most of the evidence supporting this hypothesis came from the finding of RcGTA-like genes in phages. More than 75% of the RcGTA genes have a phage homolog. However, only a few RcGTA homologs have been identified in a (pro)phage genome, leaving the hypothesis that GTAs evolved from prophages through gene loss with only weak evidence. We herein report the discovery of an inducible prophage (vB_MseS-P1) from a Mesorhizobium sediminum strain that contains the largest number (12) of RcGTA homologs found in a phage genome to date. We also identified three putative prophages and two prophage remnants harboring 12-14 RcGTA homologs in a Methylobacterium nodulans strain. The protein remote homology detection also revealed more RcGTA homologs from other phages than we previously thought. Moreover, the head-tail gene architecture of these newly discovered prophage-related elements closely resembles that of RcGTA. Furthermore, vB_MseS-P1 virions have structural proteins similar to RcGTA particles. Close phylogenetic relationships between certain prophage genes and RcGTA-like genes in Alphaproteobacteria further support the shared ancestry between RcGTA and prophages. Our findings provide new relatively direct evidence of the origin of RcGTA from a prophage progenitor.IMPORTANCEGTAs are important genetic elements in certain groups of bacteria and contribute to the genetic diversification, evolution, and ecological adaptation of bacteria. RcGTA, a common type of GTA, is known to package and transfer random fragments of the bacterial genome to recipient cells. However, the origin of RcGTA is still elusive. It has been hypothesized that RcGTA evolved from a prophage ancestor through gene loss. However, the few RcGTA homologs identified in a (pro)phage genome leave the hypothesis lacking direct evidence. This study uncovers the presence of a large number of RcGTA homologs in an inducible prophage and several putative prophages. The similar head-tail gene architecture and structural protein compositions of these newly discovered prophage-related elements and RcGTA further demonstrate an unprecedentedly observed close evolutionary relationship between prophages and RcGTA. Together, our findings provide more direct evidence supporting the origin of RcGTA from prophage.
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Affiliation(s)
- Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Qingdao Key Laboratory of Ocean Carbon Sequestration and Negative Emission Technology, Shandong University, Qingdao, China
| | - Binbin Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Nianzhi Jiao
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Qingdao Key Laboratory of Ocean Carbon Sequestration and Negative Emission Technology, Shandong University, Qingdao, China
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Qingdao Key Laboratory of Ocean Carbon Sequestration and Negative Emission Technology, Shandong University, Qingdao, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
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Singh A, T V A, Singh S, Saxena AK, Nain L. Application of fungal inoculants enhances colonization of secondary bacterial degraders during in situ paddy straw degradation: a genomic insights into cross-domain synergism. Int Microbiol 2024:10.1007/s10123-024-00570-2. [PMID: 39138687 DOI: 10.1007/s10123-024-00570-2] [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: 01/31/2024] [Revised: 06/01/2024] [Accepted: 08/01/2024] [Indexed: 08/15/2024]
Abstract
Rice cultivation generates huge amounts of on farm residues especially under mechanical harvesting. Paddy straw being recalcitrant hinders sowing of upcoming rabi crops like wheat and mustard. Non-environmental sustainable practice of on-farm burning of the paddy residues is being popularly followed for quick disposal of the agro-residues and land preparation. However, conservation agriculture involving in situ residue incorporation can be a sustainable option to utilize the residues for improvement of soil biological health. However, low temperature coupled with poor nitrogen status of soil reduces the decomposition rate of residues that may lead to nitrogen immobilization and hindrance in land preparation. In this direction, ecological impact of two approaches viz priming with urea and copiotrophic fungus-based bioformulation (CFB) consisting of Coprinopsis cinerea LA2 and Cyathus stercoreus ITCC3745 was studied for in situ degradation of residues. Succession of bacterial diversity was deciphered through high throughput whole metagenomic sequencing along with studies on dynamics of soil microbial enzymes. Treatments receiving CFB (T1) and urea (T2) when compared with bulk soil (absolute control) showed an increase in richness of the microbial diversity as compared to control straw retained treatment control (T3). The β diversity indices also indicated sufficient group variations among the treatments receiving CFB and urea as compared to only straw retained treatment and bulk soil. Priming of paddy straw with CFB and urea also induced significant rewiring of the bacterial co-occurrence networks. Quantification of soil ligno-cellulolytic activity as well as abundance of carbohydrate active enzymes (CAZy) genes indicated high activities of hydrolytic enzymes in CFB primed straw retention treatment as compared to urea primed straw retention treatment. The genomic insights on effectiveness of copiotrophic fungus bioformulation for in situ degradation of paddy straw will further help in developing strategies for management of crop residues in eco-friendly manner.
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Affiliation(s)
- Arjun Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, Kushmaur, UP, India
- ICAR-Central Soil Salinity Research Institute, RRS Lucknow, Lucknow, UP, India
| | - Abiraami T V
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | - Surender Singh
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana, India.
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, Kushmaur, UP, India
| | - Lata Nain
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Lehikoinen J, Nurmi K, Ainola M, Clancy J, Nieminen JK, Jansson L, Vauhkonen H, Vaheri A, Smura T, Laakso SM, Eklund KK, Tienari PJ. Epstein-Barr Virus in the Cerebrospinal Fluid and Blood Compartments of Patients With Multiple Sclerosis and Controls. NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2024; 11:e200226. [PMID: 38608226 PMCID: PMC11087029 DOI: 10.1212/nxi.0000000000200226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/24/2024] [Indexed: 04/14/2024]
Abstract
BACKGROUND AND OBJECTIVES Epstein-Barr virus (EBV) infection is a major risk factor of multiple sclerosis (MS). We examined the presence of EBV DNA in the CSF and blood of patients with MS and controls. We analyzed whether EBV DNA is more common in the CSF of patients with MS than in controls and estimated the proportions of EBV-positive B cells in the CSF and blood. METHODS CSF supernatants and cells were collected at diagnostic lumbar punctures from 45 patients with MS and 45 HLA-DR15 matched controls with other conditions, all participants were EBV seropositive. Cellular DNA was amplified by Phi polymerase targeting both host and viral DNA, and representative samples were obtained in 28 cases and 28 controls. Nonamplified DNA from CSF cells (14 cases, 14 controls) and blood B cells (10 cases, 10 controls) were analyzed in a subset of participants. Multiple droplet digital PCR (ddPCR) runs were performed per sample to assess the cumulative EBV positivity rate. To detect viral RNA as a sign of activation, RNA sequencing was performed in blood CD4-positive, CD8-positive, and CD19-positive cells from 21 patients with MS and 3 controls. RESULTS One of the 45 patients with MS and none of the 45 controls were positive for EBV DNA in CSF supernatants (1 mL). CSF cellular DNA was analyzed in 8 independent ddPCRs: EBV DNA was detected at least once in 18 (64%) of the 28 patients with MS and in 15 (54%) of the 28 controls (p = 0.59, Fisher test). The cumulative EBV positivity increased steadily up to 59% in the successive ddPCRs, suggesting that all individuals would have reached EBV positivity in the CSF cells, if more DNA would have been analyzed. The estimated proportion of EBV-positive B cells was >1/10,000 in both the CSF and blood. We did not detect viral RNA, except from endogenous retroviruses, in the blood lymphocyte subpopulations. DISCUSSION EBV-DNA is equally detectable in the CSF cells of both patients with MS and controls with ddPCR, and the probabilistic approach indicates that the true positivity rate approaches 100% in EBV-positive individuals. The proportion of EBV-positive B cells seems higher than previously estimated.
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Affiliation(s)
- Joonas Lehikoinen
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Katariina Nurmi
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Mari Ainola
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Jonna Clancy
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Janne K Nieminen
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Lilja Jansson
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Hanna Vauhkonen
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Antti Vaheri
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Teemu Smura
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Sini M Laakso
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Kari K Eklund
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
| | - Pentti J Tienari
- From the Translational Immunology Research Program (J.L., K.N., M.A., J.K.N., L.J., S.M.L., K.K.E., P.J.T.), University of Helsinki; Departments of Neurology (J.L., J.K.N., L.J., S.M.L., P.J.T.), Neurocenter, and Rheumatology (K.N., M.A., K.K.E.), Helsinki University Hospital; Research and Development (J.C.), Finnish Red Cross Blood Service, Helsinki; and Department of Virology (H.V., A.V., T.S.), Medicum, University of Helsinki, Finland
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Wienhausen G, Moraru C, Bruns S, Tran DQ, Sultana S, Wilkes H, Dlugosch L, Azam F, Simon M. Ligand cross-feeding resolves bacterial vitamin B 12 auxotrophies. Nature 2024; 629:886-892. [PMID: 38720071 DOI: 10.1038/s41586-024-07396-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 04/08/2024] [Indexed: 05/24/2024]
Abstract
Cobalamin (vitamin B12, herein referred to as B12) is an essential cofactor for most marine prokaryotes and eukaryotes1,2. Synthesized by a limited number of prokaryotes, its scarcity affects microbial interactions and community dynamics2-4. Here we show that two bacterial B12 auxotrophs can salvage different B12 building blocks and cooperate to synthesize B12. A Colwellia sp. synthesizes and releases the activated lower ligand α-ribazole, which is used by another B12 auxotroph, a Roseovarius sp., to produce the corrin ring and synthesize B12. Release of B12 by Roseovarius sp. happens only in co-culture with Colwellia sp. and only coincidently with the induction of a prophage encoded in Roseovarius sp. Subsequent growth of Colwellia sp. in these conditions may be due to the provision of B12 by lysed cells of Roseovarius sp. Further evidence is required to support a causative role for prophage induction in the release of B12. These complex microbial interactions of ligand cross-feeding and joint B12 biosynthesis seem to be widespread in marine pelagic ecosystems. In the western and northern tropical Atlantic Ocean, bacteria predicted to be capable of salvaging cobinamide and synthesizing only the activated lower ligand outnumber B12 producers. These findings add new players to our understanding of B12 supply to auxotrophic microorganisms in the ocean and possibly in other ecosystems.
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Affiliation(s)
- Gerrit Wienhausen
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany.
- Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA, USA.
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Stefan Bruns
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Den Quoc Tran
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Sabiha Sultana
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Heinz Wilkes
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Leon Dlugosch
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Farooq Azam
- Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany.
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany.
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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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7
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Sawada H, Someya N, Morohoshi T, Ono M, Satou M. Pectobacterium araliae sp. nov., a pathogen causing bacterial soft rot of Japanese angelica tree in Japan. Int J Syst Evol Microbiol 2024; 74. [PMID: 38625720 DOI: 10.1099/ijsem.0.006326] [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: 04/17/2024] Open
Abstract
Phytopathogenic bacteria (MAFF 302110T and MAFF 302107) were isolated from lesions on Japanese angelica trees affected by bacterial soft rot in Yamanashi Prefecture, Japan. The strains were Gram-reaction-negative, facultatively anaerobic, motile with peritrichous flagella, rod-shaped, and non-spore-forming. The genomic DNA G+C content was 51.1 mol % and the predominant cellular fatty acids included summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 2 (comprising any combination of C12 : 0 aldehyde, an unknown fatty acid with an equivalent chain length of 10.928, C16 : 1 iso I, and C14 : 0 3OH), and C12 : 0. Phylogenetic analyses based on 16S rRNA and gyrB gene sequences, along with phylogenomic analysis utilizing whole-genome sequences, consistently placed these strains within the genus Pectobacterium. However, their phylogenetic positions did not align with any known species within the genus. Comparative studies involving average nucleotide identity and digital DNA-DNA hybridization with the closely related species indicated values below the thresholds employed for the prokaryotic species delineation (95-96 % and 70 %, respectively), with the highest values observed for Pectobacterium polonicum DPMP315T (92.10 and 47.1 %, respectively). Phenotypic characteristics, cellular fatty acid composition, and a repertoire of secretion systems could differentiate the strains from their closest relatives. The phenotypic, chemotaxonomic, and genotypic data obtained in this study show that MAFF 302110T/MAFF 302107 represent a novel species of the genus Pectobacterium, for which we propose the name Pectobacterium araliae sp. nov., designating MAFF 302110T (=ICMP 25161T) as the type strain.
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Affiliation(s)
- Hiroyuki Sawada
- Research Center of Genetic Resources, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Nobutaka Someya
- Institute for Plant Protection, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Tomohiro Morohoshi
- Graduate School of Regional Development and Creativity, Utsunomiya University, 7-1-2 Yoto, Utsunomiya, Tochigi 321-8585, Japan
| | - Mitsuaki Ono
- Yamanashi Agritechnology Center (retired), 1100 Shimoimai, Kai, Yamanashi 400-0105, Japan
| | - Mamoru Satou
- Research Center of Genetic Resources, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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8
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Do HE, Ha YB, Kim JS, Suh MK, Kim HS, Eom MK, Lee JH, Park SH, Kang SW, Lee DH, Yoon H, Lee JH, Lee JS. Phocaeicola acetigenes sp. nov., producing acetic acid and iso-butyric acid, isolated faeces from a healthy human. Antonie Van Leeuwenhoek 2024; 117:30. [PMID: 38302626 DOI: 10.1007/s10482-024-01930-8] [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: 08/14/2023] [Accepted: 01/20/2024] [Indexed: 02/03/2024]
Abstract
An obligately anaerobic, non-motile, Gram-stain-negative, and rod-shaped strain KGMB11183T was isolated from the feces of healthy Koreans. The growth of strain KGMB11183T occurred at 30-45 °C (optimum 37 °C), at pH 6-9 (optimum pH 7), and in the presence of 0-0.5% NaCl (optimum 0%). Strain KGMB11183T showed 16S rRNA gene sequence similarities of 95.4% and 94.2% to the closest recognized species, Phocaeicola plebeius M12T, and Phocaeicola faecicola AGMB03916T. Phylogenetic analysis showed that strain KGMB11183T is a member of the genus Phocaeiocla. The major end products of fermentation are acetic acid and isobutyric acid. The major cellular fatty acids (> 10%) of this isolate were C18:1 cis 9, anteiso-C15:0, and summed feature 11 (iso-C17:0 3-OH and/or C18:2 DMA). The assembled draft genome sequences of strain KGMB11183T consisted of 3,215,271 bp with a DNA G + C content of 41.4%. According to genomic analysis, strain KGMB11183T has a number of genes that produce acetic acid. The genome of strain KGMB11183T encoded the starch utilization system (Sus) operon, SusCDEF suggesting that strain uses many complex polysaccharides that cannot be digested by humans. Based on the physiological, chemotaxonomic, phenotypic, and phylogenetic data, strain KGMB11183T is regarded a novel species of the genus Phocaeicola. The type strain is KGMB11183T (= KCTC 25284T = JCM 35696T).
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Affiliation(s)
- Hyo Eun Do
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
- Department of Oriental Medicine Resources, Jeonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do, 54596, Republic of Korea
| | - Young Bong Ha
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Ji-Sun Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Min Kuk Suh
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
- Department of Lifestyle Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do, 54596, Republic of Korea
| | - Han Sol Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
- Department of Lifestyle Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do, 54596, Republic of Korea
| | - Mi Kyung Eom
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Se Won Kang
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Dong Ho Lee
- Seoul National University Bundang Hospital, 82 Gumi-ro, 173 Beon-Gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Hyuk Yoon
- Seoul National University Bundang Hospital, 82 Gumi-ro, 173 Beon-Gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Je Hee Lee
- CJ Bioscience, Inc., 14 Sejong-Daero, Jung-gu, Seoul, 04527, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea.
- University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
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9
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Manohar P, Young R. Complete genomic analysis of Escherichia phage Mangalyan infecting Escherichia fergusonii. Microbiol Resour Announc 2024; 13:e0096323. [PMID: 38088570 PMCID: PMC10793314 DOI: 10.1128/mra.00963-23] [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: 10/11/2023] [Accepted: 11/09/2023] [Indexed: 01/18/2024] Open
Abstract
Escherichia fergusonii is a rarely isolated opportunistic pathogen in animals and humans. Here, we present the annotated genome sequence of Escherichia phage Mangalyan, a T4-like bacteriophage infecting E. fergusonii isolated from chickens. Phage Mangalyan has a genome length of 140,513 bp and belongs to the Vequintavirinae family.
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Affiliation(s)
- Prasanth Manohar
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M AgriLife Research, Texas A&M University, College Station, Texas, USA
| | - Ry Young
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M AgriLife Research, Texas A&M University, College Station, Texas, USA
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10
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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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11
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Rondel F, Farooq H, Hosseini R, Grinshpon M, Zelikovsky A. EMPathways2: Estimation of Enzyme Expression and Metabolic Pathway Activity Using RNA-Seq Reads. Methods Mol Biol 2024; 2812:39-46. [PMID: 39068356 DOI: 10.1007/978-1-0716-3886-6_3] [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: 07/30/2024]
Abstract
In this chapter, we outline an approach to analyzing metatranscriptomic data, focusing on the assessment of differential enzyme expression and metabolic pathway activities using a novel bioinformatics software tool, EMPathways2. The analysis pipeline commences with raw data originating from a sequencer and concludes with an output of enzyme expressions and an estimate of metabolic pathway activities. The initial step involves aligning specific transcriptomes assembled from RNA-Seq data using Bowtie2 and acquiring gene expression data with IsoEM2. Subsequently, the pipeline proceeds to quality assessment and preprocessing of the input data, ensuring accurate estimates of enzymes and their differential regulation. Upon completion of the preprocessing stage, EMPathways2 is employed to decipher the intricate relationships between genes, enzymes, and pathways. An online repository containing sample data has been made available, alongside custom Python scripts designed to modify the output of the programs within the pipeline for diverse downstream analyses. This chapter highlights the technical aspects and practical applications of using EMPathways2, which facilitates the advancement of transcriptome data analysis and contributes to a deeper understanding of the complex regulatory mechanisms underlying living systems.
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Affiliation(s)
- Filipp Rondel
- Department of Computer Science, Georgia State University, Atlanta, GA, USA
| | - Hafsa Farooq
- Department of Computer Science, Georgia State University, Atlanta, GA, USA
| | - Roya Hosseini
- Department of Computer Science, Georgia State University, Atlanta, GA, USA
| | - Mark Grinshpon
- Department of Mathematics and Statistics, Georgia State University, Atlanta, GA, USA
| | - Alex Zelikovsky
- Department of Computer Science, Georgia State University, Atlanta, GA, USA.
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12
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Kubo Y, Tanizaki Y, Hira D, Nakayama Y, Kadooka C, Oka T. Complete genome sequence of Bacillus subtilis subsp. natto NARUSE using PacBio sequencing. Microbiol Resour Announc 2023; 12:e0057823. [PMID: 37982649 PMCID: PMC10720478 DOI: 10.1128/mra.00578-23] [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: 07/05/2023] [Accepted: 10/19/2023] [Indexed: 11/21/2023] Open
Abstract
We report the complete genome sequence of Bacillus subtilis subsp. natto NARUSE, which has been traditionally employed for fermenting soybeans in Japan. The genome was sequenced using the PacBio system, yielding a sequence, yielding a sequence length of 4,148,793 nucleotides for the circular chromosome and 62,770 nucleotides for the plasmid.
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Affiliation(s)
- Yukie Kubo
- Kyushu Soy Food Co., Ltd., Kumamoto, Japan
- Marukin Foods Co., Ltd., Kumamoto, Japan
| | - Yoshiyuki Tanizaki
- Kyushu Soy Food Co., Ltd., Kumamoto, Japan
- Marukin Foods Co., Ltd., Kumamoto, Japan
| | - Daisuke Hira
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, Kumamoto, Japan
| | - Yasumune Nakayama
- Division of Applied Microbial Technology, Graduate School of Engineering, Sojo University, Kumamoto, Japan
| | - Chihiro Kadooka
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, Kumamoto, Japan
- Division of Applied Microbial Technology, Graduate School of Engineering, Sojo University, Kumamoto, Japan
| | - Takuji Oka
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, Kumamoto, Japan
- Division of Applied Microbial Technology, Graduate School of Engineering, Sojo University, Kumamoto, Japan
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13
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Hamese S, Mugwanda K, Takundwa M, Prinsloo E, Thimiri Govinda Raj DB. Recent advances in genome annotation and synthetic biology for the development of microbial chassis. J Genet Eng Biotechnol 2023; 21:156. [PMID: 38038785 PMCID: PMC10692039 DOI: 10.1186/s43141-023-00598-3] [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: 04/11/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023]
Abstract
This article provides an overview of microbial host selection, synthetic biology, genome annotation, metabolic modeling, and computational methods for predicting gene essentiality for developing a microbial chassis. This article focuses on lactic acid bacteria (LAB) as a microbial chassis and strategies for genome annotation of the LAB genome. As a case study, Lactococcus lactis is chosen based on its well-established therapeutic applications such as probiotics and oral vaccine development. In this article, we have delineated the strategies for genome annotations of lactic acid bacteria. These strategies also provide insights into streamlining genome reduction without compromising the functionality of the chassis and the potential for minimal genome chassis development. These insights underscore the potential for the development of efficient and sustainable synthetic biology systems using streamlined microbial chassis with minimal genomes.
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Affiliation(s)
- Saltiel Hamese
- Synthetic Nanobiotechnology and Biomachines Group, Centre for Synthetic Biology and Precision Medicine, Next Generation Health Cluster, CSIR Pretoria, South Africa
- Biotechnology Innovation Centre, Rhodes University, PO Box 94, Makhanda, 6140, South Africa
| | - Kanganwiro Mugwanda
- Synthetic Nanobiotechnology and Biomachines Group, Centre for Synthetic Biology and Precision Medicine, Next Generation Health Cluster, CSIR Pretoria, South Africa
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Mutsa Takundwa
- Synthetic Nanobiotechnology and Biomachines Group, Centre for Synthetic Biology and Precision Medicine, Next Generation Health Cluster, CSIR Pretoria, South Africa
| | - Earl Prinsloo
- Biotechnology Innovation Centre, Rhodes University, PO Box 94, Makhanda, 6140, South Africa
| | - Deepak B Thimiri Govinda Raj
- Synthetic Nanobiotechnology and Biomachines Group, Centre for Synthetic Biology and Precision Medicine, Next Generation Health Cluster, CSIR Pretoria, South Africa.
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14
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Dixit S, Sahoo K, Gaur M, Subudhi E. Investigating microbiome and transcriptome data to uncover the key microbial community involved in lignocellulose degradation within the Deulajhari hot spring consortium. Data Brief 2023; 51:109648. [PMID: 37840989 PMCID: PMC10570936 DOI: 10.1016/j.dib.2023.109648] [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: 06/27/2023] [Revised: 09/11/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023] Open
Abstract
Geothermally heated spring water contaminated with decomposed leaf biomass creates unique hot spring ecosystems that support the recycling of diverse nutrients and harbor microbial consortia capable of degrading lignocellulose. We present microbiome and transcriptome data from the bacterial consortium of Deulajhari hot springs, characterized by a temperature of approximately 58 °C and surrounded by a dense population of pandanus plants in Angul, Odisha, India. Metagenomics and metatranscriptomics datasets were generated by extracting total DNA and RNA from the consortium sample of hotspring sediment, followed by shotgun sequencing using the Illumina HiSeq 2500 platform. The metagenomics dataset produced approximately 38,694 contigs, while the metatranscriptomics dataset yielded 9226 contigs, resulting in a total nucleotide size of 89,857,616 and 15,541,403 bps, respectively. Analysis using MEGAN6 against the NCBI "taxonomy" database revealed the presence of 18 and 12 phyla, including candidate phyla, in respective datasets. Proteobacteria exhibited the highest relative abundance in the metagenomics dataset, while Firmicutes was highly abundant in the metatranscriptomics dataset. At the genus level, a total of 92 and 25 genera were predicted in both datasets, with lignocellulose degrading Meiothermus being highly abundant in both metagenomics and metatranscriptomics datasets. We also observed that the unknown bacteria and unidentified sequences were found in significant proportion in the metatranscriptomics dataset. We assembled and functionally annotated approximately 23,960 contigs using the Prokka pipeline. Among the SEED category, the most expressed and annotated microbial genes fall under the unknown category as well as Biotin synthesis and their utilization. Furthermore, some of these genes were implicated in the degradation of aromatic amino acids, D-mannitol, and D-mannose. These findings contribute to our understanding of how the composition and abundance of bacterial communities facilitate lignocellulose degradation in extreme environments and biofuel generation.
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Affiliation(s)
- Sangita Dixit
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, India
| | - Kalpana Sahoo
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, India
| | - Mahendra Gaur
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, India
| | - Enketeswara Subudhi
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, India
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15
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Yao G, Le T, Korn AM, Peterson HN, Liu M, Gonzalez CF, Gill JJ. Phage Milagro: a platform for engineering a broad host range virulent phage for Burkholderia. J Virol 2023; 97:e0085023. [PMID: 37943040 PMCID: PMC10688314 DOI: 10.1128/jvi.00850-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/21/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE Burkholderia infections are a significant concern in people with CF and other immunocompromising disorders, and are difficult to treat with conventional antibiotics due to their inherent drug resistance. Bacteriophages, or bacterial viruses, are now seen as a potential alternative therapy for these infections, but most of the naturally occurring phages are temperate and have narrow host ranges, which limit their utility as therapeutics. Here we describe the temperate Burkholderia phage Milagro and our efforts to engineer this phage into a potential therapeutic by expanding the phage host range and selecting for phage mutants that are strictly virulent. This approach may be used to generate new therapeutic agents for treating intractable infections in CF patients.
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Affiliation(s)
- Guichun Yao
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Tram Le
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Abby M. Korn
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Hannah N. Peterson
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Mei Liu
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Carlos F. Gonzalez
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Jason J. Gill
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
- Department of Animal Science, Texas A&M University, College Station, Texas, USA
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16
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Liu Y, Meng X, Zheng H, Cai L, Wei S, He M, He J, Hao Y, Ge C, Liu J, Chen F, Xu Y. A novel long-tailed myovirus represents a new T4-like cyanophage cluster. Front Microbiol 2023; 14:1293846. [PMID: 38029084 PMCID: PMC10665884 DOI: 10.3389/fmicb.2023.1293846] [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: 09/13/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Cyanophages affect the abundance, diversity, metabolism, and evolution of picocyanobacteria in marine ecosystems. Here we report an estuarine Synechococcus phage, S-CREM2, which represents a novel viral genus and leads to the establishment of a new T4-like cyanophage clade named cluster C. S-CREM2 possesses the longest tail (~418 nm) among isolated cyanomyoviruses and encodes six tail-related proteins that are exclusively homologous to those predicted in the cluster C cyanophages. Furthermore, S-CREM2 may carry three regulatory proteins in the virion, which may play a crucial role in optimizing the host intracellular environment for viral replication at the initial stage of infection. The cluster C cyanophages lack auxiliary metabolic genes (AMGs) that are commonly found in cyanophages of the T4-like clusters A and B and encode unique AMGs like an S-type phycobilin lyase gene. A variation in the composition of tRNA and cis-regulatory RNA genes was observed between the marine and freshwater phage strains in cluster C, reflecting their different modes of coping with hosts and habitats. The cluster C cyanophages are widespread in estuarine and coastal regions and exhibit equivalent or even higher relative abundance compared to those of clusters A and B cyanophages in certain estuarine regions. The isolation of cyanophage S-CREM2 provides new insights into the phage-host interactions mediated by both newly discovered AMGs and virion-associated proteins and emphasizes the ecological significance of cluster C cyanophages in estuarine environments.
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Affiliation(s)
- Yuanfang Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xue Meng
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Hongrui Zheng
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Shuzhen Wei
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Minglu He
- School of Information Science and Engineering, Shandong University, Qingdao, China
| | - Jiale He
- School of Life Science, Shandong University, Qingdao, China
| | - Yue Hao
- School of Life Science, Shandong University, Qingdao, China
| | - Chang Ge
- School of Life Science, Shandong University, Qingdao, China
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, United States
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
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17
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Vik D, Bolduc B, Roux S, Sun CL, Pratama AA, Krupovic M, Sullivan MB. MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets. ISME COMMUNICATIONS 2023; 3:87. [PMID: 37620369 PMCID: PMC10449787 DOI: 10.1038/s43705-023-00295-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/04/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
Our knowledge of viral sequence space has exploded with advancing sequencing technologies and large-scale sampling and analytical efforts. Though archaea are important and abundant prokaryotes in many systems, our knowledge of archaeal viruses outside of extreme environments is limited. This largely stems from the lack of a robust, high-throughput, and systematic way to distinguish between bacterial and archaeal viruses in datasets of curated viruses. Here we upgrade our prior text-based tool (MArVD) via training and testing a random forest machine learning algorithm against a newly curated dataset of archaeal viruses. After optimization, MArVD2 presented a significant improvement over its predecessor in terms of scalability, usability, and flexibility, and will allow user-defined custom training datasets as archaeal virus discovery progresses. Benchmarking showed that a model trained with viral sequences from the hypersaline, marine, and hot spring environments correctly classified 85% of the archaeal viruses with a false detection rate below 2% using a random forest prediction threshold of 80% in a separate benchmarking dataset from the same habitats.
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Affiliation(s)
- Dean Vik
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA.
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christine L Sun
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Akbar Adjie Pratama
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, Paris, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA.
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA.
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18
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Schwarz JC, Chan BK, Turner PE, Burmeister AR. Complete Genome Assembly and Annotation of Escherichia coli Bacteriophage 107. Microbiol Resour Announc 2023:e0010623. [PMID: 37191527 DOI: 10.1128/mra.00106-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
We present the annotated genome sequence of Escherichia coli bacteriophage 107, a T4-like bacteriophage. Phage 107 has a genome length of 167,509 bp and 287 predicted genes.
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Affiliation(s)
- Joshua C Schwarz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Center for Phage Biology and Therapy, Yale University, New Haven, Connecticut, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA
- Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, USA
- Center for Phage Biology and Therapy, Yale University, New Haven, Connecticut, USA
| | - Alita R Burmeister
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA
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19
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Tokuda R, Iwabuchi N, Kitazawa Y, Nijo T, Suzuki M, Maejima K, Oshima K, Namba S, Yamaji Y. Potential mobile units drive the horizontal transfer of phytoplasma effector phyllogen genes. Front Genet 2023; 14:1132432. [PMID: 37252660 PMCID: PMC10210161 DOI: 10.3389/fgene.2023.1132432] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/03/2023] [Indexed: 05/31/2023] Open
Abstract
Phytoplasmas are obligate intracellular plant pathogenic bacteria that can induce phyllody, which is a type of abnormal floral organ development. Phytoplasmas possess phyllogens, which are effector proteins that cause phyllody in plants. Phylogenetic comparisons of phyllogen and 16S rRNA genes have suggested that phyllogen genes undergo horizontal transfer between phytoplasma species and strains. However, the mechanisms and evolutionary implications of this horizontal gene transfer are unclear. Here, we analyzed synteny in phyllogen flanking genomic regions from 17 phytoplasma strains that were related to six 'Candidatus' species, including three strains newly sequenced in this study. Many of the phyllogens were flanked by multicopy genes within potential mobile units (PMUs), which are putative transposable elements found in phytoplasmas. The multicopy genes exhibited two distinct patterns of synteny that correlated with the linked phyllogens. The low level of sequence identities and partial truncations found among these phyllogen flanking genes indicate that the PMU sequences are deteriorating, whereas the highly conserved sequences and functions (e.g., inducing phyllody) of the phyllogens suggest that the latter are important for phytoplasma fitness. Furthermore, although their phyllogens were similar, PMUs in strains related to 'Ca. P. asteris' were often located in different regions of the genome. These findings strongly indicate that PMUs drive the horizontal transfer of phyllogens among phytoplasma species and strains. These insights improve our understanding of how symptom-determinant genes have been shared among phytoplasmas.
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Affiliation(s)
- Ryosuke Tokuda
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Nozomu Iwabuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yugo Kitazawa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takamichi Nijo
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masato Suzuki
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kensaku Maejima
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kenro Oshima
- Faculty of Bioscience and Applied Chemistry, Hosei University, Tokyo, Japan
| | - Shigetou Namba
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yasuyuki Yamaji
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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20
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Shen K, Din AU, Sinha B, Zhou Y, Qian F, Shen B. Translational informatics for human microbiota: data resources, models and applications. Brief Bioinform 2023; 24:7152256. [PMID: 37141135 DOI: 10.1093/bib/bbad168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
With the rapid development of human intestinal microbiology and diverse microbiome-related studies and investigations, a large amount of data have been generated and accumulated. Meanwhile, different computational and bioinformatics models have been developed for pattern recognition and knowledge discovery using these data. Given the heterogeneity of these resources and models, we aimed to provide a landscape of the data resources, a comparison of the computational models and a summary of the translational informatics applied to microbiota data. We first review the existing databases, knowledge bases, knowledge graphs and standardizations of microbiome data. Then, the high-throughput sequencing techniques for the microbiome and the informatics tools for their analyses are compared. Finally, translational informatics for the microbiome, including biomarker discovery, personalized treatment and smart healthcare for complex diseases, are discussed.
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Affiliation(s)
- Ke Shen
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Ahmad Ud Din
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Baivab Sinha
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Yi Zhou
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Fuliang Qian
- Center for Systems Biology, Suzhou Medical College of Soochow University, Suzhou 215123, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Suzhou 215123, China
| | - Bairong Shen
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
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21
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Duncan A, Barry K, Daum C, Eloe-Fadrosh E, Roux S, Schmidt K, Tringe SG, Valentin KU, Varghese N, Salamov A, Grigoriev IV, Leggett RM, Moulton V, Mock T. Dataset of 143 metagenome-assembled genomes from the Arctic and Atlantic Oceans, including 21 for eukaryotic organisms. Data Brief 2023; 47:108990. [PMID: 36879606 PMCID: PMC9984783 DOI: 10.1016/j.dib.2023.108990] [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: 08/19/2022] [Revised: 01/18/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
This article presents metagenome-assembled genomes (MAGs) for both eukaryotic and prokaryotic organisms originating from the Arctic and Atlantic oceans, along with gene prediction and functional annotation for MAGs from both domains. Eleven samples from the chlorophyll-a maximum layer of the surface ocean were collected during two cruises in 2012; six from the Arctic in June-July on ARK-XXVII/1 (PS80), and five from the Atlantic in November on ANT-XXIX/1 (PS81). Sequencing and assembly was carried out by the Joint Genome Institute (JGI), who provide annotation of the assembled sequences, and 122 MAGs for prokaryotic organisms. A subsequent binning process identified 21 MAGs for eukaryotic organisms, mostly identified as Mamiellophyceae or Bacillariophyceae. The data for each MAG includes sequences in FASTA format, and tables of functional annotation of genes. For eukaryotic MAGs, transcript and protein sequences for predicted genes are available. A spreadsheet is provided summarising quality measures and taxonomic classifications for each MAG. These data provide draft genomes for uncultured marine microbes, including some of the first MAGs for polar eukaryotes, and can provide reference genetic data for these environments, or used in genomics-based comparison between environments.
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Affiliation(s)
- Anthony Duncan
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR47TJ, UK
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Chris Daum
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Emiley Eloe-Fadrosh
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Simon Roux
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Katrin Schmidt
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR47TJ, UK
| | - Susannah G Tringe
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Klaus U Valentin
- Alfred-Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Neha Varghese
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | | | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR47TJ, UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR47TJ, UK
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22
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Thippabhotla S, Liu B, Podgorny A, Yooseph S, Yang Y, Zhang J, Zhong C. Integrated de novo gene prediction and peptide assembly of metagenomic sequencing data. NAR Genom Bioinform 2023; 5:lqad023. [PMID: 36915411 PMCID: PMC10006731 DOI: 10.1093/nargab/lqad023] [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: 09/22/2021] [Revised: 12/03/2022] [Accepted: 02/18/2023] [Indexed: 03/16/2023] Open
Abstract
Metagenomics is the study of all genomic content contained in given microbial communities. Metagenomic functional analysis aims to quantify protein families and reconstruct metabolic pathways from the metagenome. It plays a central role in understanding the interaction between the microbial community and its host or environment. De novo functional analysis, which allows the discovery of novel protein families, remains challenging for high-complexity communities. There are currently three main approaches for recovering novel genes or proteins: de novo nucleotide assembly, gene calling and peptide assembly. Unfortunately, their information dependency has been overlooked, and each has been formulated as an independent problem. In this work, we develop a sophisticated workflow called integrated Metagenomic Protein Predictor (iMPP), which leverages the information dependencies for better de novo functional analysis. iMPP contains three novel modules: a hybrid assembly graph generation module, a graph-based gene calling module, and a peptide assembly-based refinement module. iMPP significantly improved the existing gene calling sensitivity on unassembled metagenomic reads, achieving a 92-97% recall rate at a high precision level (>85%). iMPP further allowed for more sensitive and accurate peptide assembly, recovering more reference proteins and delivering more hypothetical protein sequences. The high performance of iMPP can provide a more comprehensive and unbiased view of the microbial communities under investigation. iMPP is freely available from https://github.com/Sirisha-t/iMPP.
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Affiliation(s)
- Sirisha Thippabhotla
- Department of Electrical Engineering and Computer Science, The University of Kansas, Lawrence, KS 66045, USA
| | - Ben Liu
- Department of Electrical Engineering and Computer Science, The University of Kansas, Lawrence, KS 66045, USA
| | - Adam Podgorny
- Center for Computational Biology, The University of Kansas, Lawrence, KS 66045, USA
| | - Shibu Yooseph
- Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA
| | - Youngik Yang
- National Marine Biodiversity Institute of Korea, 101-75, Jangsan-ro, Janghang-eup, Seochun-gun, Chungchungnam-do, 33662, South Korea
| | - Jun Zhang
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA.,Department of Cancer Biology, University of Kansas Cancer Center; Kansas City, KS 66160, USA
| | - Cuncong Zhong
- Department of Electrical Engineering and Computer Science, The University of Kansas, Lawrence, KS 66045, USA
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23
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Tada Y, Marumoto K, Iwamoto Y, Takeda K, Sakugawa H. Distribution and phylogeny of mercury methylation, demethylation, and reduction genes in the Seto Inland Sea of Japan. MARINE POLLUTION BULLETIN 2023; 186:114381. [PMID: 36459771 DOI: 10.1016/j.marpolbul.2022.114381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Mercury (Hg) adversely affects human and environmental health. To evaluate the mercury (Hg) speciation (methylation, demethylation, and reduction) of microorganisms in coastal seawater, we analyzed the microbial functional gene sets involved in Hg methylation (hgcA and hgcB), demethylation (merB), and reduction (merA) using a metagenomic approach in the eastern and western parts (the Kii and Bungo channels, respectively) of the Seto Inland Sea (SIS) of Japan. We determined the concentration of dissolved total mercury (dTHg) and methylated mercury (dMeHg) in seawater. The metagenomic analysis detected hgcAB, merA, and merB in both channels, whereas the phylogenies of these genes differed between them. A correlation between Hg concentration (both dTHg and dMeHg) and the relative abundance of each gene was not observed. Our data suggests that microbial Hg methylation and demethylation could occur in the SIS and there could be a distinct microbial Hg speciation process between the Kii and Bungo channels.
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Affiliation(s)
- Yuya Tada
- National Institute for Minamata Disease, Department of Environment and Public Health, Kumamoto, Japan.
| | - Kohji Marumoto
- National Institute for Minamata Disease, Department of Environment and Public Health, Kumamoto, Japan
| | - Yoko Iwamoto
- Hiroshima University, Graduate School of Integrated Sciences for Life, Hiroshima, Japan
| | - Kazuhiko Takeda
- Hiroshima University, Graduate School of Integrated Sciences for Life, Hiroshima, Japan
| | - Hiroshi Sakugawa
- Hiroshima University, Graduate School of Integrated Sciences for Life, Hiroshima, Japan
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24
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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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25
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Naligama KN, Halmillawewa AP. Pectobacterium carotovorum Phage vB_PcaM_P7_Pc Is a New Member of the Genus Certrevirus. Microbiol Spectr 2022; 10:e0312622. [PMID: 36346243 PMCID: PMC9769974 DOI: 10.1128/spectrum.03126-22] [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: 08/12/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022] Open
Abstract
Pectobacterium carotovorum is an economically important phytopathogen and has been identified as the major causative agent of bacterial soft rot in carrots. Control of this phytopathogen is vital to minimizing carrot harvest losses. As fully efficient control measures to successfully avoid the disease are unavailable, the phage-mediated biocontrol of the pathogen has recently gained scientific attention. In this study, we present a comprehensive characterization of the P. carotovorum phage vB_PcaM_P7_Pc (abbreviated as P7_Pc) that was isolated from infected carrot samples with characteristic soft rot symptoms, which were obtained from storage facilities at market places in Gampaha District, Sri Lanka. P7_Pc is a myovirus, and it exhibits growth characteristics of an exclusively lytic life cycle. It showed visible lysis against four of the tested P. carotovorum strains and one Pectobacterium aroidearum strain. This phage also showed a longer latent period (125 min) than other related phages; however, this did not affect its high phage titter (>1010 PFU/mL). The final assembled genome of P7_Pc is 147,299 bp in length with a G+C content of 50.34%. Of the 298 predicted open reading frames (ORFs) of the genome of P7_Pc, putative functions were assigned to 53 ORFs. Seven tRNA-coding genes were predicted in the genome, while the genome lacked any major genes coding for lysogeny-related products, confirming its virulent nature. The P7_Pc genome shares 96.12% and 95.74% average nucleotide identities with Cronobacter phages CR8 and PBES02, respectively. Phylogenetic and phylogenomic analyses of the genome revealed that P7_Pc clusters well within the clade with the members representing the genus Certrevirus. Currently, there are only 4 characterized Pectobacterium phages (P. atrosepticum phages phiTE and CB7 and Pectobacterium phages DU_PP_I and DU_PP_IV) that are classified under the genus, making the phage P7_Pc the first reported member of the genus isolated using the host bacterium P. carotovorum. The results of this study provide a detailed characterization of the phage P7_Pc, enabling its careful classification into the genus Certrevirus. The knowledge gathered on the phage based on the shared biology of the genus will further aid in the future selection of phage P7_Pc as a biocontrol agent. IMPORTANCE Bacterial soft rot disease, caused by Pectobacterium spp., can lead to significant losses in carrot yields. As current control measures involving the use of chemicals or antibiotics are not recommended in many countries, bacteriophage-mediated biocontrol strategies are being explored for the successful control of these phytopathogens. The successful implementation of such biocontrol strategies relies heavily upon the proper understanding of the growth characteristics and genomic properties of the phage. Further, the selection of taxonomically different phages for the formulation of phage cocktails in biocontrol applications is critical to combat potential bacterial resistance development. This study was conducted to carefully characterize and resolve the phylogenetic placement of the P. carotovorum phage vB_PcaM_P7_Pc by using its biological and genomic properties. Phage P7_Pc has a myovirus morphotype with an exclusively lytic life cycle, and the absence of genes related to lysogeny, toxin production, and antibiotic resistance in its genome confirmed its suitability to be used in environmental applications. Furthermore, P7_Pc is classified under the genus Certrevirus, making it the first reported phage of the genus of the host species, P. carotovorum.
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Affiliation(s)
- Kishani N. Naligama
- Department of Microbiology, Faculty of Science, University of Kelaniya, Kelaniya, Sri Lanka
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26
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Pillay S, Calderón-Franco D, Urhan A, Abeel T. Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings. Front Microbiol 2022; 13:1066995. [PMID: 36532424 PMCID: PMC9755710 DOI: 10.3389/fmicb.2022.1066995] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/09/2022] [Indexed: 08/12/2023] Open
Abstract
The success of antibiotics as a therapeutic agent has led to their ineffectiveness. The continuous use and misuse in clinical and non-clinical areas have led to the emergence and spread of antibiotic-resistant bacteria and its genetic determinants. This is a multi-dimensional problem that has now become a global health crisis. Antibiotic resistance research has primarily focused on the clinical healthcare sectors while overlooking the non-clinical sectors. The increasing antibiotic usage in the environment - including animals, plants, soil, and water - are drivers of antibiotic resistance and function as a transmission route for antibiotic resistant pathogens and is a source for resistance genes. These natural compartments are interconnected with each other and humans, allowing the spread of antibiotic resistance via horizontal gene transfer between commensal and pathogenic bacteria. Identifying and understanding genetic exchange within and between natural compartments can provide insight into the transmission, dissemination, and emergence mechanisms. The development of high-throughput DNA sequencing technologies has made antibiotic resistance research more accessible and feasible. In particular, the combination of metagenomics and powerful bioinformatic tools and platforms have facilitated the identification of microbial communities and has allowed access to genomic data by bypassing the need for isolating and culturing microorganisms. This review aimed to reflect on the different sequencing techniques, metagenomic approaches, and bioinformatics tools and pipelines with their respective advantages and limitations for antibiotic resistance research. These approaches can provide insight into resistance mechanisms, the microbial population, emerging pathogens, resistance genes, and their dissemination. This information can influence policies, develop preventative measures and alleviate the burden caused by antibiotic resistance.
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Affiliation(s)
- Stephanie Pillay
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
| | | | - Aysun Urhan
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
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27
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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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28
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Zhang L, Wang X, Hua X, Yu Y, Leptihn S, Loh B. Therapeutic evaluation of the Acinetobacter baumannii phage Phab24 for clinical use. Virus Res 2022; 320:198889. [PMID: 35970267 DOI: 10.1016/j.virusres.2022.198889] [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] [Received: 06/20/2022] [Revised: 08/03/2022] [Accepted: 08/11/2022] [Indexed: 11/23/2022]
Abstract
Phages have shown to be effective in treating bacterial infections. However, when evaluating the therapeutic potential of novel phage isolates which have the ability to infect and kill a pathogen, it is important to include parameters such as stability (crucial for storage and delivery), infection dynamics in vitro and in vivo (for efficacy and dosing), and an in-depth genome analysis (to exclude the presence of virulence or lysogeny genes), among others. In this study, we characterized bacteriophage Phab24, which infects a colistin-resistant strain of the notorious nosocomial pathogen Acinetobacter baumannii. Our study is crucial for the use of Phab24 in therapy, while also advancing our understanding of phage predation.
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Affiliation(s)
- Liwei Zhang
- Zhejiang University-University of Edinburgh (ZJU-UoE) Institute, Zhejiang University, International Campus, Haining, Zhejiang, China
| | - Xiaoqing Wang
- School of Medicine, Lishui University, Lishui, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Sebastian Leptihn
- Zhejiang University-University of Edinburgh (ZJU-UoE) Institute, Zhejiang University, International Campus, Haining, Zhejiang, China; Department of Infectious Diseases, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; University of Edinburgh Medical School, Biomedical Sciences, College of Medicine & Veterinary Medicine, The University of Edinburgh, 1 George Square, Edinburgh EH8 9JZ, United Kingdom.
| | - Belinda Loh
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, Leipzig 04103, Germany.
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29
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Gendre J, Ansaldi M, Olivenza DR, Denis Y, Casadesús J, Ginet N. Genetic Mining of Newly Isolated Salmophages for Phage Therapy. Int J Mol Sci 2022; 23:8917. [PMID: 36012174 PMCID: PMC9409062 DOI: 10.3390/ijms23168917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/29/2022] [Accepted: 08/07/2022] [Indexed: 11/16/2022] Open
Abstract
Salmonella enterica, a Gram-negative zoonotic bacterium, is mainly a food-borne pathogen and the main cause of diarrhea in humans worldwide. The main reservoirs are found in poultry farms, but they are also found in wild birds. The development of antibiotic resistance in S. enterica species raises concerns about the future of efficient therapies against this pathogen and revives the interest in bacteriophages as a useful therapy against bacterial infections. Here, we aimed to decipher and functionally annotate 10 new Salmonella phage genomes isolated in Spain in the light of phage therapy. We designed a bioinformatic pipeline using available building blocks to de novo assemble genomes and perform syntaxic annotation. We then used genome-wide analyses for taxonomic annotation enabled by vContact2 and VICTOR. We were also particularly interested in improving functional annotation using remote homologies detection and comparisons with the recently published phage-specific PHROG protein database. Finally, we searched for useful functions for phage therapy, such as systems encoded by the phage to circumvent cellular defenses with a particular focus on anti-CRISPR proteins. We, thus, were able to genetically characterize nine virulent phages and one temperate phage and identify putative functions relevant to the formulation of phage cocktails for Salmonella biocontrol.
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Affiliation(s)
- Julia Gendre
- Laboratoire de Chimie Bactérienne, (UMR7283)-CNRS/Aix-Marseille Université, 13009 Marseille, France
| | - Mireille Ansaldi
- Laboratoire de Chimie Bactérienne, (UMR7283)-CNRS/Aix-Marseille Université, 13009 Marseille, France
| | - David R. Olivenza
- Departamento de Genética, Facultad de Biologia, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Yann Denis
- Institut de Microbiologie de la Méditerranée, (FR3479)-CNRS/Aix-Marseille Université, 13009 Marseille, France
| | - Josep Casadesús
- Departamento de Genética, Facultad de Biologia, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Nicolas Ginet
- Laboratoire de Chimie Bactérienne, (UMR7283)-CNRS/Aix-Marseille Université, 13009 Marseille, France
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30
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Zucker F, Bischoff V, Olo Ndela E, Heyerhoff B, Poehlein A, Freese HM, Roux S, Simon M, Enault F, Moraru C. New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria. Virus Evol 2022; 8:veac070. [PMID: 36533142 PMCID: PMC9753089 DOI: 10.1093/ve/veac070] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/24/2022] [Accepted: 07/28/2022] [Indexed: 10/01/2023] Open
Abstract
The Microviridae family represents one of the major clades of single-stranded DNA (ssDNA) phages. Their cultivated members are lytic and infect Proteobacteria, Bacteroidetes, and Chlamydiae. Prophages have been predicted in the genomes from Bacteroidales, Hyphomicrobiales, and Enterobacteriaceae and cluster within the 'Alpavirinae', 'Amoyvirinae', and Gokushovirinae. We have isolated 'Ascunsovirus oldenburgi' ICBM5, a novel phage distantly related to known Microviridae. It infects Sulfitobacter dubius SH24-1b and uses both a lytic and a carrier-state life strategy. Using ICBM5 proteins as a query, we uncovered in publicly available resources sixty-five new Microviridae prophages and episomes in bacterial genomes and retrieved forty-seven environmental viral genomes (EVGs) from various viromes. Genome clustering based on protein content and phylogenetic analysis showed that ICBM5, together with Rhizobium phages, new prophages, episomes, and EVGs cluster within two new phylogenetic clades, here tentatively assigned the rank of subfamily and named 'Tainavirinae' and 'Occultatumvirinae'. They both infect Rhodobacterales. Occultatumviruses also infect Hyphomicrobiales, including nitrogen-fixing endosymbionts from cosmopolitan legumes. A biogeographical assessment showed that tainaviruses and occultatumviruses are spread worldwide, in terrestrial and marine environments. The new phage isolated here sheds light onto new and diverse branches of the Microviridae tree, suggesting that much of the ssDNA phage diversity remains in the dark.
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Affiliation(s)
- Falk Zucker
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Vera Bischoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Eric Olo Ndela
- Laboratoire Microorganismes: Genome Environment (LMGE), Université Clermont Auvergne, CNRS, 1 Imp. Amélie Murat, Aubière 63170, Frankreich
| | - Benedikt Heyerhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August-University Göttingen, Institute of Microbiology and Genetics, Grisebachstr. 8, Göttingen D-37077, Germany
| | - Heike M Freese
- Leibniz-Institut DSMZ, Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7 B, Braunschweig D-38124, Germany
| | - Simon Roux
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA 94720, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Francois Enault
- Laboratoire Microorganismes: Genome Environment (LMGE), Université Clermont Auvergne, CNRS, 1 Imp. Amélie Murat, Aubière 63170, Frankreich
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
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31
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Yanagisawa M, Asamizu S, Satoh K, Oono Y, Onaka H. Effects of carbon ion beam-induced mutagenesis for the screening of RED production-deficient mutants of Streptomyces coelicolor JCM4020. PLoS One 2022; 17:e0270379. [PMID: 35834474 PMCID: PMC9282665 DOI: 10.1371/journal.pone.0270379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/08/2022] [Indexed: 12/22/2022] Open
Abstract
Streptomyces lividans TK23 interacts with mycolic acid-containing bacteria (MACB), such as Tsukamurella pulmonis TP-B0596, and this direct cell contact activates its secondary metabolism (e.g., the production of undecylprodigiosin: RED). Here, we employed carbon (12C5+) ion beam-induced mutagenesis to investigate the signature of induced point mutations and further identify the gene(s) responsible for the production of secondary metabolites induced by T. pulmonis. We irradiated spores of the Streptomyces coelicolor strain JCM4020 with carbon ions to generate a mutant library. We screened the RED production-deficient mutants of S. coelicolor by mixing them with T. pulmonis TP-B0596 on agar plates, identifying the red/white phenotype of the growing colonies. Through this process, we selected 59 RED-deficient mutants from around 152,000 tested spores. We resequenced the genomes of 16 mutants and identified 44 point mutations, which revealed the signatures induced by 12C5+-irradiation. Via gene complementation experiments, we also revealed that two genes-glutamate synthase (gltB) and elongation factor G (fusA)-are responsible for the reduced production of RED.
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Affiliation(s)
- Masaomi Yanagisawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Shumpei Asamizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo, Tokyo, Japan
- * E-mail: (SA); (HO)
| | - Katsuya Satoh
- Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute, Quantum Beam Science Research Directorate, National Institutes for Quantum Science and Technology, Takasaki, Gunma, Japan
| | - Yutaka Oono
- Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute, Quantum Beam Science Research Directorate, National Institutes for Quantum Science and Technology, Takasaki, Gunma, Japan
| | - Hiroyasu Onaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo, Tokyo, Japan
- * E-mail: (SA); (HO)
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32
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In-Depth Analysis of an Obligate Anaerobe Paraclostridium bifermentans Isolated from Uterus of Bubalus bubalis. Animals (Basel) 2022; 12:ani12141765. [PMID: 35883312 PMCID: PMC9311886 DOI: 10.3390/ani12141765] [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: 03/23/2022] [Revised: 05/12/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Non-specific uterine infections in bovine (uterine line inflammation) are a significant issue for the dairy industry. These infections are responsible for significant financial losses all over the world. Paraclostridium bifermentans is an obligate anaerobe, gram-positive rod-shaped bacteria belonging to the Clostridia class and the Peptostreptococcaceae family produces endospores. This bacterium has the ability to infiltrate bovine uterine endometrial epithelial cells and cause infection in the endometrium epithelial cells. Our study found that an examination of a buffalo uterus with yellowish purulent discharge reported the presence of pathogenic bacteria Paraclostridium bifermentans, where its genomic characterization, substrate utilization, and antibiotic susceptibility potentiality was studied. This discovery indicates the presence of virulence genes as well as pathogenic features. This is the first report of P. bifermentans from the bovine uterus environment. Abstract Chronic non-specific contamination of the reproductive tract in animals is a major issue during early postpartum, natural coitus, or artificial insemination. Uterine infection is one of the major concerns reducing fertility, production loss, and early culling of the animals. Therefore, the aim of this study was to identify any novel bacterium if present in the uterine environment of Bubalus bubalis causing infections. A strictly anaerobic bacterial strain designated as Paraclostridium bifermentans GBRC was isolated and characterized. Bacterium was found to be Gram positive moderate rod with motility. The optimum growth was observed at 40 ± 2 °C. The pathogenic characteristics of the GBRC strain, such as hemolysis, gelatin hydrolysis, and the production of volatile sulfur compounds, were similar to those seen in the epithelial layer invading pathogenic strains. Assembled genome size was 3.6 MB, with 78 contigs, and a G + C content of 28.10%. Furthermore, the whole genome sequence analysis confirmed the presence of genes encoding virulence factors and provided genomic insights on adaptation of the strain in the uterine environment. Based on the phenotypic and genetic differences with phylogenetic relatives, strain GBRC is proposed to represent a first reported species of the genus Paraclostridium with potential pathogenic character, from the buffalo uterine environment. This study analysis of the GBRC strain serves as a key reference point for the investigation of potential pathogenic strains that may cause endometritis and metritis in bovine.
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Syberg-Olsen MJ, Garber AI, Keeling PJ, McCutcheon JP, Husnik F. Pseudofinder: detection of pseudogenes in prokaryotic genomes. Mol Biol Evol 2022; 39:6633826. [PMID: 35801562 PMCID: PMC9336565 DOI: 10.1093/molbev/msac153] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Prokaryotic genomes are usually densely packed with intact and functional genes. However, in certain contexts, such as after recent ecological shifts or extreme population bottlenecks, broken and nonfunctional gene fragments can quickly accumulate and form a substantial fraction of the genome. Identification of these broken genes, called pseudogenes, is a critical step for understanding the evolutionary forces acting upon, and the functional potential encoded within, prokaryotic genomes. Here, we present Pseudofinder, an open-source software dedicated to pseudogene identification and analysis in bacterial and archaeal genomes. We demonstrate that Pseudofinder’s multi-pronged, reference-based approach can detect a wide variety of pseudogenes, including those that are highly degraded and typically missed by gene-calling pipelines, as well newly formed pseudogenes containing only one or a few inactivating mutations. Additionally, Pseudofinder can detect genes that lack inactivating substitutions but experiencing relaxed selection. Implementation of Pseudofinder in annotation pipelines will allow more precise estimations of the functional potential of sequenced microbes, while also generating new hypotheses related to the evolutionary dynamics of bacterial and archaeal genomes.
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Affiliation(s)
| | - Arkadiy I Garber
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - John P McCutcheon
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA.,Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, Maryland, USA
| | - Filip Husnik
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Okinawa Institute of Science and Technology, Okinawa, Japan
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Truong Nguyen PT, Culverwell CL, Suvanto MT, Korhonen EM, Uusitalo R, Vapalahti O, Smura T, Huhtamo E. Characterisation of the RNA Virome of Nine Ochlerotatus Species in Finland. Viruses 2022; 14:1489. [PMID: 35891469 PMCID: PMC9324324 DOI: 10.3390/v14071489] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/19/2022] [Accepted: 06/19/2022] [Indexed: 02/01/2023] Open
Abstract
RNA viromes of nine commonly encountered Ochlerotatus mosquito species collected around Finland in 2015 and 2017 were studied using next-generation sequencing. Mosquito homogenates were sequenced from 91 pools comprising 16-60 morphologically identified adult females of Oc. cantans, Oc. caspius, Oc. communis, Oc. diantaeus, Oc. excrucians, Oc. hexodontus, Oc. intrudens, Oc. pullatus and Oc. punctor/punctodes. In total 514 viral Reverse dependent RNA polymerase (RdRp) sequences of 159 virus species were recovered, belonging to 25 families or equivalent rank, as follows: Aliusviridae, Aspiviridae, Botybirnavirus, Chrysoviridae, Chuviridae, Endornaviridae, Flaviviridae, Iflaviridae, Negevirus, Partitiviridae, Permutotetraviridae, Phasmaviridae, Phenuiviridae, Picornaviridae, Qinviridae, Quenyavirus, Rhabdoviridae, Sedoreoviridae, Solemoviridae, Spinareoviridae, Togaviridae, Totiviridae, Virgaviridae, Xinmoviridae and Yueviridae. Of these, 147 are tentatively novel viruses. One sequence of Sindbis virus, which causes Pogosta disease in humans, was detected from Oc. communis from Pohjois-Karjala. This study greatly increases the number of mosquito-associated viruses known from Finland and presents the northern-most mosquito-associated viruses in Europe to date.
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Affiliation(s)
- Phuoc T. Truong Nguyen
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
| | - C. Lorna Culverwell
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
- The Natural History Museum, Cromwell Road, South Kensington, London SW5 7BD, UK
| | - Maija T. Suvanto
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin Katu 2, P.O. Box 66, FI-00014 Helsinki, Finland
| | - Essi M. Korhonen
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin Katu 2, P.O. Box 66, FI-00014 Helsinki, Finland
| | - Ruut Uusitalo
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin Katu 2, P.O. Box 66, FI-00014 Helsinki, Finland
- Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Gustaf Hällströmin Katu 2, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin Katu 2, P.O. Box 66, FI-00014 Helsinki, Finland
- Virology and Immunology, Diagnostic Center, HUSLAB, Helsinki University Hospital, FI-00029 Helsinki, Finland
| | - Teemu Smura
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
| | - Eili Huhtamo
- Department of Virology, Medicum, University of Helsinki, Haartmaninkatu 3, FI-00290 Helsinki, Finland; (C.L.C.); (M.T.S.); (E.M.K.); (R.U.); (O.V.); (T.S.); (E.H.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin Katu 2, P.O. Box 66, FI-00014 Helsinki, Finland
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Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy. Nat Commun 2022; 13:3776. [PMID: 35773283 PMCID: PMC9247103 DOI: 10.1038/s41467-022-31455-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 06/17/2022] [Indexed: 12/12/2022] Open
Abstract
In 2016, a 68-year-old patient with a disseminated multidrug-resistant Acinetobacter baumannii infection was successfully treated using lytic bacteriophages. Here we report the genomes of the nine phages used for treatment and three strains of A. baumannii isolated prior to and during treatment. The phages used in the initial treatment are related, T4-like myophages. Analysis of 19 A. baumannii isolates collected before and during phage treatment shows that resistance to the T4-like phages appeared two days following the start of treatment. We generate complete genomic sequences for three A. baumannii strains (TP1, TP2 and TP3) collected before and during treatment, supporting a clonal relationship. Furthermore, we use strain TP1 to select for increased resistance to five of the phages in vitro, and identify mutations that are also found in phage-insensitive isolates TP2 and TP3 (which evolved in vivo during phage treatment). These results support that in vitro investigations can produce results that are relevant to the in vivo environment.
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Van der Jeugt F, Maertens R, Steyaert A, Verschaffelt P, De Tender C, Dawyndt P, Mesuere B. UMGAP: the Unipept MetaGenomics Analysis Pipeline. BMC Genomics 2022; 23:433. [PMID: 35689184 PMCID: PMC9188040 DOI: 10.1186/s12864-022-08542-4] [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: 02/06/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Background Shotgun metagenomics yields ever richer and larger data volumes on the complex communities living in diverse environments. Extracting deep insights from the raw reads heavily depends on the availability of fast, accurate and user-friendly biodiversity analysis tools. Results Because environmental samples may contain strains and species that are not covered in reference databases and because protein sequences are more conserved than the genes encoding them, we explore the alternative route of taxonomic profiling based on protein coding regions translated from the shotgun metagenomics reads, instead of directly processing the DNA reads. We therefore developed the Unipept MetaGenomics Analysis Pipeline (UMGAP), a highly versatile suite of open source tools that are implemented in Rust and support parallelization to achieve optimal performance. Six preconfigured pipelines with different performance trade-offs were carefully selected, and benchmarked against a selection of state-of-the-art shotgun metagenomics taxonomic profiling tools. Conclusions UMGAP’s protein space detour for taxonomic profiling makes it competitive with state-of-the-art shotgun metagenomics tools. Despite our design choices of an extra protein translation step, a broad spectrum index that can identify both archaea, bacteria, eukaryotes and viruses, and a highly configurable non-monolithic design, UMGAP achieves low runtime, manageable memory footprint and high accuracy. Its interactive visualizations allow for easy exploration and comparison of complex communities. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-022-08542-4).
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Affiliation(s)
- Felix Van der Jeugt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.
| | - Rien Maertens
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Aranka Steyaert
- Department of Information Technology, IDLab, imec, Ghent, Belgium
| | - Pieter Verschaffelt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Caroline De Tender
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Ghent, Belgium
| | - Peter Dawyndt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Bart Mesuere
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
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37
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Van der Jeugt F, Dawyndt P, Mesuere B. FragGeneScanRs: faster gene prediction for short reads. BMC Bioinformatics 2022; 23:198. [PMID: 35643462 PMCID: PMC9148508 DOI: 10.1186/s12859-022-04736-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/17/2022] [Indexed: 11/16/2022] Open
Abstract
Background FragGeneScan is currently the most accurate and popular tool for gene prediction in short and error-prone reads, but its execution speed is insufficient for use on larger data sets. The parallelization which should have addressed this is inefficient. Its alternative implementation FragGeneScan+ is faster, but introduced a number of bugs related to memory management, race conditions and even output accuracy. Results This paper introduces FragGeneScanRs, a faster Rust implementation of the FragGeneScan gene prediction model. Its command line interface is backward compatible and adds extra features for more flexible usage. Its output is equivalent to the original FragGeneScan implementation. Conclusions Compared to the current C implementation, shotgun metagenomic reads are processed up to 22 times faster using a single thread, with better scaling for multithreaded execution. The Rust code of FragGeneScanRs is freely available from GitHub under the GPL-3.0 license with instructions for installation, usage and other documentation (https://github.com/unipept/FragGeneScanRs). Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04736-5.
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Johny TK, Puthusseri RM, Saidumohamed BE, Sheela UB, Puthusseri SP, Sasidharan RS, Bhat SG. Appraisal of cytotoxicity and acrylamide mitigation potential of L-asparaginase SlpA from fish gut microbiome. Appl Microbiol Biotechnol 2022; 106:3583-3598. [PMID: 35579684 DOI: 10.1007/s00253-022-11954-7] [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: 12/18/2021] [Revised: 04/27/2022] [Accepted: 05/03/2022] [Indexed: 11/29/2022]
Abstract
L-asparaginase catalyzes the hydrolysis of L-asparagine to L-aspartic acid and ammonia. It has application in the treatment of acute lymphoblastic leukemia in children, as well as in other malignancies, in addition to its role as a food processing aid for the mitigation of acrylamide formation in the baking industry. Its use in cancer chemotherapy is limited due to problems such as its intrinsic glutaminase activity and associated side effects, leading to an increased interest in the search for novel L-asparaginases without L-glutaminase activity. This study reports the cloning and expression of an L-asparaginase contig obtained from whole metagenome shotgun sequencing of Sardinella longiceps gut microbiota. Purified recombinant glutaminase-free L-asparaginase SlpA was a 74 kDa homodimer, with maximal activity at pH 8 and 30 °C. Km and Vmax of SlpA were determined to be 3.008 mM and 0.014 mM/min, respectively. SlpA displayed cytotoxic activity against K-562 (chronic myeloid leukemia) and MCF-7 (breast cancer) cell lines with IC50 values of 0.3443 and 2.692 U/mL, respectively. SlpA did not show any cytotoxic activity against normal lymphocytes and was proved to be hemocompatible. Pre-treatment of biscuit and bread dough with different concentrations of SlpA resulted in a clear, dose-dependent reduction of acrylamide formation during baking. KEY POINTS: • Cloned and expressed L-asparaginase (SlpA) from fish gut microbiota • Purified SlpA displayed good cytotoxicity against K-562 and MCF-7 cell lines • SlpA addition caused a significant reduction of acrylamide formation during baking.
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Affiliation(s)
- Tina Kollannoor Johny
- Department of Biotechnology, Cochin University of Science and Technology, Cochin, Kerala, 682022, India
| | - Rinu Madhu Puthusseri
- Department of Biotechnology, Cochin University of Science and Technology, Cochin, Kerala, 682022, India
| | | | | | - Saipriya Parol Puthusseri
- Department of Biotechnology, Cochin University of Science and Technology, Cochin, Kerala, 682022, India
| | - Raghul Subin Sasidharan
- Department of Zoology, Government College Kariavattom, University of Kerala, Thiruvananthapuram, Kerala, 695581, India
| | - Sarita Ganapathy Bhat
- Department of Biotechnology, Cochin University of Science and Technology, Cochin, Kerala, 682022, India.
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Complete Genome Sequence of Stenotrophomonas maltophilia Phage Philippe. Microbiol Resour Announc 2022; 11:e0012522. [PMID: 35510862 PMCID: PMC9202365 DOI: 10.1128/mra.00125-22] [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
Stenotrophomonas maltophilia is emerging as an opportunistic multidrug-resistant pathogen. S. maltophilia podophage Philippe has a 74,717-bp genome which is related broadly to the N4-like phage group, including Stenotrophomonas phage Pokken. The low sequence identity to other described phages suggests that Philippe is an unclassified member of the N4-like subfamily Rothmandenesvirinae.
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40
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Complete Genome Sequence of Stenotrophomonas maltophilia Siphophage Siara. Microbiol Resour Announc 2022; 11:e0017722. [PMID: 35499340 PMCID: PMC9119069 DOI: 10.1128/mra.00177-22] [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
Stenotrophomonas maltophilia is associated with an increasing incidence of nosocomial infections. Here, we describe the isolation and genome annotation of S. maltophilia siphophage Siara. Its 61,427-bp genome is currently related only to one phage in the NCBI database, namely, S. maltophilia phage Salva, and is not related to any prophages.
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Zheng X, Jahn MT, Sun M, Friman VP, Balcazar JL, Wang J, Shi Y, Gong X, Hu F, Zhu YG. Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes. THE ISME JOURNAL 2022; 16:1397-1408. [PMID: 35039616 PMCID: PMC9038774 DOI: 10.1038/s41396-022-01188-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 12/29/2021] [Accepted: 01/06/2022] [Indexed: 12/13/2022]
Abstract
Viruses significantly influence local and global biogeochemical cycles and help bacteria to survive in different environments by encoding various auxiliary metabolic genes (AMGs) associated with energy acquisition, stress tolerance and degradation of xenobiotics. Here we studied whether bacterial (dsDNA) virus encoded AMGs are enriched in organochlorine pesticide (OCP) contaminated soil in China and if viral AMGs include genes linked to OCP biodegradation. Using metagenomics, we found that OCP-contaminated soils displayed a lower bacterial, but higher diversity of viruses that harbored a higher relative abundance of AMGs linked to pesticide degradation and metabolism. Furthermore, the diversity and relative abundance of AMGs significantly increased along with the severity of pesticide contamination, and several biodegradation genes were identified bioinformatically in viral metagenomes. Functional assays were conducted to experimentally demonstrate that virus-encoded L-2-haloacid dehalogenase gene (L-DEX) is responsible for the degradation of L-2-haloacid pesticide precursors, improving bacterial growth at sub-inhibitory pesticide concentrations. Taken together, these results demonstrate that virus-encoded AMGs are linked to bacterial metabolism and biodegradation, being more abundant and diverse in soils contaminated with pesticides. Moreover, our findings highlight the importance of virus-encoded accessory genes for bacterial ecology in stressful environments, providing a novel avenue for using viruses in the bioremediation of contaminated soils.
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Affiliation(s)
- Xiaoxuan Zheng
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Martin T Jahn
- Departments of Biochemistry, Zoology and Chemistry, University of Oxford, Oxford, OX1 3SZ, United Kingdom
| | - Mingming Sun
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
- Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing, 210095, China.
| | - Ville-Petri Friman
- University of York, Department of Biology, Wentworth Way, York, Y010 5DD, United Kingdom.
| | - Jose Luis Balcazar
- Catalan Institute for Water Research (ICRA), Girona, 17003, Spain
- University of Girona, Girona, 17004, Spain
| | - Jinfeng Wang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008, China
| | - Xin Gong
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yong-Guan Zhu
- Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian, 100085, Beijing, China
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Duncan A, Barry K, Daum C, Eloe-Fadrosh E, Roux S, Schmidt K, Tringe SG, Valentin KU, Varghese N, Salamov A, Grigoriev IV, Leggett RM, Moulton V, Mock T. Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans. MICROBIOME 2022; 10:67. [PMID: 35484634 PMCID: PMC9047304 DOI: 10.1186/s40168-022-01254-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Phytoplankton communities significantly contribute to global biogeochemical cycles of elements and underpin marine food webs. Although their uncultured genomic diversity has been estimated by planetary-scale metagenome sequencing and subsequent reconstruction of metagenome-assembled genomes (MAGs), this approach has yet to be applied for complex phytoplankton microbiomes from polar and non-polar oceans consisting of microbial eukaryotes and their associated prokaryotes. RESULTS Here, we have assembled MAGs from chlorophyll a maximum layers in the surface of the Arctic and Atlantic Oceans enriched for species associations (microbiomes) with a focus on pico- and nanophytoplankton and their associated heterotrophic prokaryotes. From 679 Gbp and estimated 50 million genes in total, we recovered 143 MAGs of medium to high quality. Although there was a strict demarcation between Arctic and Atlantic MAGs, adjacent sampling stations in each ocean had 51-88% MAGs in common with most species associations between Prasinophytes and Proteobacteria. Phylogenetic placement revealed eukaryotic MAGs to be more diverse in the Arctic whereas prokaryotic MAGs were more diverse in the Atlantic Ocean. Approximately 70% of protein families were shared between Arctic and Atlantic MAGs for both prokaryotes and eukaryotes. However, eukaryotic MAGs had more protein families unique to the Arctic whereas prokaryotic MAGs had more families unique to the Atlantic. CONCLUSION Our study provides a genomic context to complex phytoplankton microbiomes to reveal that their community structure was likely driven by significant differences in environmental conditions between the polar Arctic and warm surface waters of the tropical and subtropical Atlantic Ocean. Video Abstract.
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Affiliation(s)
- Anthony Duncan
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR47TJ, UK
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Chris Daum
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Emiley Eloe-Fadrosh
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Simon Roux
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Katrin Schmidt
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR47TJ, UK
| | - Susannah G Tringe
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Klaus U Valentin
- Alfred-Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Neha Varghese
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | | | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR47TJ, UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR47TJ, UK.
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Abstract
Stenotrophomonas maltophilia is an opportunistic bacterium that is commonly associated with respiratory infections in immunocompromised patients, including cystic fibrosis patients. In this report, we introduce the complete genome sequence of S. maltophilia podophage Pepon, which is a T7-like phage closely related to the previously reported phage Ponderosa.
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44
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Keown RA, Dums JT, Brumm PJ, MacDonald J, Mead DA, Ferrell BD, Moore RM, Harrison AO, Polson SW, Wommack KE. Novel Viral DNA Polymerases From Metagenomes Suggest Genomic Sources of Strand-Displacing Biochemical Phenotypes. Front Microbiol 2022; 13:858366. [PMID: 35531281 PMCID: PMC9069017 DOI: 10.3389/fmicb.2022.858366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/08/2022] [Indexed: 01/21/2023] Open
Abstract
Viruses are the most abundant and diverse biological entities on the planet and constitute a significant proportion of Earth's genetic diversity. Most of this diversity is not represented by isolated viral-host systems and has only been observed through sequencing of viral metagenomes (viromes) from environmental samples. Viromes provide snapshots of viral genetic potential, and a wealth of information on viral community ecology. These data also provide opportunities for exploring the biochemistry of novel viral enzymes. The in vitro biochemical characteristics of novel viral DNA polymerases were explored, testing hypothesized differences in polymerase biochemistry according to protein sequence phylogeny. Forty-eight viral DNA Polymerase I (PolA) proteins from estuarine viromes, hot spring metagenomes, and reference viruses, encompassing a broad representation of currently known diversity, were synthesized, expressed, and purified. Novel functionality was shown in multiple PolAs. Intriguingly, some of the estuarine viral polymerases demonstrated moderate to strong innate DNA strand displacement activity at high enzyme concentration. Strand-displacing polymerases have important technological applications where isothermal reactions are desirable. Bioinformatic investigation of genes neighboring these strand displacing polymerases found associations with SNF2 helicase-associated proteins. The specific function of SNF2 family enzymes is unknown for prokaryotes and viruses. In eukaryotes, SNF2 enzymes have chromatin remodeling functions but do not separate nucleic acid strands. This suggests the strand separation function may be fulfilled by the DNA polymerase for viruses carrying SNF2 helicase-associated proteins. Biochemical data elucidated from this study expands understanding of the biology and ecological behavior of unknown viruses. Moreover, given the numerous biotechnological applications of viral DNA polymerases, novel viral polymerases discovered within viromes may be a rich source of biological material for further in vitro DNA amplification advancements.
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Affiliation(s)
- Rachel A. Keown
- Department of Biological Sciences, College of Arts and Sciences, University of Delaware, Newark, DE, United States
| | - Jacob T. Dums
- Biotechnology Program, North Carolina State University, Raleigh, NC, United States
| | | | | | - David A. Mead
- Varigen Biosciences Corporation, Middleton, WI, United States
| | - Barbra D. Ferrell
- Department of Plant and Soil Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark, DE, United States
| | - Ryan M. Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States
| | - Amelia O. Harrison
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States
| | - Shawn W. Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States
- Department of Computer and Information Sciences, College of Arts and Sciences, University of Delaware, Newark, DE, United States
| | - K. Eric Wommack
- Department of Plant and Soil Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark, DE, United States
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Complete Genome Sequence of Alcaligenes faecalis Phage Piluca. Microbiol Resour Announc 2022; 11:e0012422. [PMID: 35289650 PMCID: PMC9022569 DOI: 10.1128/mra.00124-22] [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: 11/30/2022] Open
Abstract
Alcaligenes faecalis is an opportunistic pathogen exhibiting drug resistance. Here, the 35,451-bp genome of A. faecalis phage Piluca is described. Piluca is not closely related to any isolated phages in the NCBI database. Piluca possesses genes encoding CI-like and Cro-like repressors and a tyrosine integrase, suggesting its temperate lifestyle.
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46
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Complete Genome Sequence of Enterococcus faecalis Siphophage Sigurd. Microbiol Resour Announc 2022; 11:e0012322. [PMID: 35343805 PMCID: PMC9022519 DOI: 10.1128/mra.00123-22] [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
Enterococcus faecalis is associated with antibiotic-resistant infections, and this study presents E. faecalis siphophage Sigurd. The 41,811-bp Sigurd genome is divided into two arms defined by long convergent predicted transcription units that are separated by a bidirectional rho-independent terminator. Sigurd has a small terminase that is closely related to Bacillus subtilis cos phage phi105.
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47
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Complete Genome Sequences of Lambdoid Phages 21, 434, and 434B and Several Lambda Hybrids. Microbiol Resour Announc 2022; 11:e0012022. [PMID: 35412353 PMCID: PMC9119081 DOI: 10.1128/mra.00120-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Recombinational hybrids between phage λ and its relatives were instrumental in the beginnings of molecular biology. Here, we report the complete genome sequences of lambdoid phages 21 and 434 and three of their λ hybrids. In addition, we describe 434B, where the entire lysis gene region was replaced by cryptic prophage sequences.
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48
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Complete Genome Sequence of Stenotrophomonas maltophilia Podophage Paxi. Microbiol Resour Announc 2022; 11:e0017922. [PMID: 35377170 PMCID: PMC9022576 DOI: 10.1128/mra.00179-22] [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: 11/25/2022] Open
Abstract
Stenotrophomonas maltophilia is a multidrug-resistant nosocomial pathogen that can cause life-threatening infections among immunocompromised populations. This report presents the complete 74,962-bp genome of S. maltophilia podophage Paxi, an N4-like phage sharing 85.3% nucleotide similarity to S. maltophilia podophage Pokken.
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49
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Sharma N, Kumari R, Thakur M, Rai AK, Singh SP. Molecular dissemination of emerging antibiotic, biocide, and metal co-resistomes in the Himalayan hot springs. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 307:114569. [PMID: 35091250 DOI: 10.1016/j.jenvman.2022.114569] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/11/2022] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Growing resistance among microbial communities against antimicrobial compounds, especially antibiotics, is a significant threat to living beings. With increasing antibiotic resistance in human pathogens, it is necessary to examine the habitats having community interests. In the present study, a metagenomic approach has been employed to understand the causes, dissemination, and effects of antibiotic, metal, and biocide resistomes on the microbial ecology of three hot springs, Borong, Lingdem, and Yumthang, located at different altitudes of the Sikkim Himalaya. The taxonomic assessment of these hot springs depicted the predominance of mesophilic organisms, mainly belonging to the phylum Proteobacteria. The enriched microbial metabolism assosiated with energy, cellular processes, adaptation to diverse environments, and defence were deciphered in the metagenomes. The genes representing resistance to semisynthetic antibiotics, e.g., aminoglycosides, fluoroquinolones, fosfomycin, vancomycin, trimethoprim, tetracycline, streptomycin, beta-lactams, multidrug resistance, and biocides such as triclosan, hydrogen peroxide, acriflavin, were abundantly present. Various genes attributing resistance to copper, arsenic, iron, and mercury in metal resistome were detected. Relative abundance, correlation, and genome mapping of metagenome-assembled genomes indicated the co-evolution of antibiotic and metal resistance in predicted novel species belonging to Vogesella, Thiobacillus, and Tepidimona genera. The metagenomic findings were further validated with isolation of microbial cultures, exhibiting resistance against antibiotics and heavy metals, from the hot spring water samples. The study furthers our understanding about the molecular basis of co-resistomes in the ceological niches and their possible impact on the environment.
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Affiliation(s)
- Nitish Sharma
- Center of Innovative and Applied Bioprocessing, SAS Nagar, Mohali, India; Department of Biotechnology, Panjab University, Chandigarh, India
| | - Reena Kumari
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India
| | - Monika Thakur
- Center of Innovative and Applied Bioprocessing, SAS Nagar, Mohali, India; Department of Biotechnology, Panjab University, Chandigarh, India
| | - Amit K Rai
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India.
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing, SAS Nagar, Mohali, India.
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50
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Complete Genome Sequence of Burkholderia cenocepacia Phage Paku. Microbiol Resour Announc 2022; 11:e0122021. [PMID: 35343779 PMCID: PMC9022590 DOI: 10.1128/mra.01220-21] [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: 11/23/2022] Open
Abstract
Burkholderia cenocepacia is able to cause infections in cystic fibrosis patients. B. cenocepacia phage Paku has a 42,727-bp genome sharing a phiKMV-like genome arrangement. T7-like tail components were identified in parallel with a tyrosine integrase, suggesting that Paku might exhibit a temperate lifestyle, an atypical feature for an Autographiviridae phage.
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