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Gonzalez JM, Aranda B. Microbial Growth under Limiting Conditions-Future Perspectives. Microorganisms 2023; 11:1641. [PMID: 37512814 PMCID: PMC10383181 DOI: 10.3390/microorganisms11071641] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/02/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Microorganisms rule the functioning of our planet and each one of the individual macroscopic living creature. Nevertheless, microbial activity and growth status have always been challenging tasks to determine both in situ and in vivo. Microbial activity is generally related to growth, and the growth rate is a result of the availability of nutrients under adequate or adverse conditions faced by microbial cells in a changing environment. Most studies on microorganisms have been carried out under optimum or near-optimum growth conditions, but scarce information is available about microorganisms at slow-growing states (i.e., near-zero growth and maintenance metabolism). This study aims to better understand microorganisms under growth-limiting conditions. This is expected to provide new perspectives on the functions and relevance of the microbial world. This is because (i) microorganisms in nature frequently face conditions of severe growth limitation, (ii) microorganisms activate singular pathways (mostly genes remaining to be functionally annotated), resulting in a broad range of secondary metabolites, and (iii) the response of microorganisms to slow-growth conditions remains to be understood, including persistence strategies, gene expression, and cell differentiation both within clonal populations and due to the complexity of the environment.
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Affiliation(s)
- Juan M Gonzalez
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas, IRNAS-CSIC, E-41012 Sevilla, Spain
| | - Beatriz Aranda
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas, IRNAS-CSIC, E-41012 Sevilla, Spain
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2
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Bossé JT, Li Y, Cohen LM, Stegger M, Angen Ø, Lacouture S, Gottschalk M, Lei L, Koene M, Kuhnert P, Bandara AB, Inzana TJ, Holden MTG, Harris D, Oshota O, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR, On Behalf Of The BRaDP T Consortium. Complete genome for Actinobacillus pleuropneumoniae serovar 8 reference strain 405: comparative analysis with draft genomes for different laboratory stock cultures indicates little genetic variation. Microb Genom 2021; 7. [PMID: 34818145 PMCID: PMC8743550 DOI: 10.1099/mgen.0.000687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report here the complete genome sequence of the widely studied Actinobacillus pleuropneumoniae serovar 8 reference strain 405, generated using the Pacific Biosciences (PacBio) RS II platform. Furthermore, we compared draft sequences generated by Illumina sequencing of six stocks of this strain, including the same original stock used to generate the PacBio sequence, held in different countries and found little genetic variation, with only three SNPs identified, all within the degS gene. However, sequences of two small plasmids, pARD3079 and p405tetH, detected by Illumina sequencing of the draft genomes were not identified in the PacBio sequence of the reference strain.
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Affiliation(s)
- Janine T Bossé
- Section of Paediatric Infectious Diseases, Department of Infectious Diseases, Imperial College London, London, UK
| | - Yanwen Li
- Section of Paediatric Infectious Diseases, Department of Infectious Diseases, Imperial College London, London, UK
| | - Liza Miriam Cohen
- Department of Production Animal Clinical Sciences Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Øystein Angen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sonia Lacouture
- Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculté de Médecine Vétérinaire, Université de Montréal, Québec, Canada
| | - Marcelo Gottschalk
- Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculté de Médecine Vétérinaire, Université de Montréal, Québec, Canada
| | - Liancheng Lei
- College of Veterinary Medicine, Jilin University, Changchun, P.R China
| | - Miriam Koene
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, Universität Bern, Bern, Switzerland
| | - Aloka B Bandara
- Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, USA
| | - Thomas J Inzana
- Present address: College of Veterinary Medicine, Long Island University, Brookville, USA.,Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, USA
| | - Matthew T G Holden
- Present address: School of Medicine, University of St Andrews, St Andrews, UK.,The Wellcome Trust Sanger Institute, Cambridge, UK
| | - David Harris
- The Wellcome Trust Sanger Institute, Cambridge, UK
| | - Olusegun Oshota
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Brendan W Wren
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Andrew N Rycroft
- Department of Pathology and Pathogen Biology, The Royal Veterinary College, Hatfield, UK
| | - Paul R Langford
- Section of Paediatric Infectious Diseases, Department of Infectious Diseases, Imperial College London, London, UK
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Pell LG, Horne RG, Huntley S, Rahman H, Kar S, Islam MS, Evans KC, Saha SK, Campigotto A, Morris SK, Roth DE, Sherman PM. Antimicrobial susceptibilities and comparative whole genome analysis of two isolates of the probiotic bacterium Lactiplantibacillus plantarum, strain ATCC 202195. Sci Rep 2021; 11:15893. [PMID: 34354117 PMCID: PMC8342526 DOI: 10.1038/s41598-021-94997-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 07/13/2021] [Indexed: 12/24/2022] Open
Abstract
A synbiotic containing Lactiplantibacillus plantarum [American Type Culture Collection (ATCC) strain identifier 202195] and fructooligosaccharide was reported to reduce the risk of sepsis in young infants in rural India. Here, the whole genome of two isolates of L. plantarum ATCC 202195, which were deposited to the ATCC approximately 20 years apart, were sequenced and analyzed to verify their taxonomic and strain-level identities, identify potential antimicrobial resistant genes and virulence factors, and identify genetic characteristics that may explain the observed clinical effects of L. plantarum ATCC 202195. Minimum inhibitory concentrations for selected antimicrobial agents were determined using broth dilution and gradient strip diffusion techniques. The two L. plantarum ATCC 202195 isolates were genetically identical with only three high-quality single nucleotides polymorphisms identified, and with an average nucleotide identity of 99.99%. In contrast to previously published reports, this study determined that each isolate contained two putative plasmids. No concerning acquired or transferable antimicrobial resistance genes or virulence factors were identified. Both isolates were sensitive to several clinically important antibiotics including penicillin, ampicillin and gentamicin, but resistant to vancomycin. Genes involved in stress response, cellular adhesion, carbohydrate metabolism and vitamin biosynthesis are consistent with features of probiotic organisms.
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Affiliation(s)
- Lisa G Pell
- Centre for Global Child Health, Hospital for Sick Children, Toronto, ON, Canada
| | - Rachael G Horne
- Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Stuart Huntley
- International Flavors & Fragrances Inc., Madison, WI, USA
| | | | - Sanchita Kar
- Child Health Research Foundation, Dhaka, Bangladesh
| | | | - Kara C Evans
- International Flavors & Fragrances Inc., Madison, WI, USA
| | - Samir K Saha
- Child Health Research Foundation, Dhaka, Bangladesh
| | - Aaron Campigotto
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Microbiology, Hospital for Sick Children, Toronto, ON, Canada
| | - Shaun K Morris
- Centre for Global Child Health, Hospital for Sick Children, Toronto, ON, Canada
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Division of Infectious Diseases, Hospital for Sick Children, Toronto, ON, Canada
| | - Daniel E Roth
- Centre for Global Child Health, Hospital for Sick Children, Toronto, ON, Canada.
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
- Paediatric Medicine and Child Health Evaluative Sciences, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada.
| | - Philip M Sherman
- Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada.
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
- Gastroenterology, Hepatology and Nutrition, Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada.
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Laws M, Hind C, Rahman KM, Sutton JM, Wand ME. Whole Genome Sequencing of Staphylococcus aureus SA-1199B Reveals Previously Unreported Mutations. Int J Antimicrob Agents 2020; 57:106225. [PMID: 33189889 DOI: 10.1016/j.ijantimicag.2020.106225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/15/2020] [Accepted: 11/01/2020] [Indexed: 10/23/2022]
Affiliation(s)
- Mark Laws
- Institute of Pharmaceutical Sciences, School of Cancer and Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Charlotte Hind
- Public Health England, National Infection Service, Research and Development Institute, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Khondaker Miraz Rahman
- Institute of Pharmaceutical Sciences, School of Cancer and Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - J Mark Sutton
- Public Health England, National Infection Service, Research and Development Institute, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Matthew E Wand
- Public Health England, National Infection Service, Research and Development Institute, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK.
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Gonzalez JM, Puerta-Fernández E, Santana MM, Rekadwad B. On a Non-Discrete Concept of Prokaryotic Species. Microorganisms 2020; 8:microorganisms8111723. [PMID: 33158054 PMCID: PMC7692863 DOI: 10.3390/microorganisms8111723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 01/09/2023] Open
Abstract
The taxonomic concept of species has received continuous attention. A microbial species as a discrete box contains a limited number of highly similar microorganisms assigned to that taxon, following a polyphasic approach. In the 21st Century, with the advancements of sequencing technologies and genomics, the existence of a huge prokaryotic diversity has become well known. At present, the prokaryotic species might no longer have to be understood as discrete values (such as 1 or 2, by homology to Natural numbers); rather, it is expected that some microorganisms could be potentially distributed (according to their genome features and phenotypes) in between others (such as decimal numbers between 1 and 2; real numbers). We propose a continuous species concept for microorganisms, which adapts to the current knowledge on the huge diversity, variability and heterogeneity existing among bacteria and archaea. Likely, this concept could be extended to eukaryotic microorganisms. The continuous species concept considers a species to be delimited by the distance between a range of variable features following a Gaussian-type distribution around a reference organism (i.e., its type strain). Some potential pros and cons of a continuous concept are commented on, offering novel perspectives on our understanding of the highly diversified prokaryotic world, thus promoting discussion and further investigation in the field.
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Affiliation(s)
- Juan M. Gonzalez
- Instituto de Recursos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas, IRNAS-CSIC, Avda. Reina Mercedes 10, 41012 Sevilla, Spain;
- Correspondence: ; Tel.: +34-95-462-4711
| | - Elena Puerta-Fernández
- Instituto de Recursos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas, IRNAS-CSIC, Avda. Reina Mercedes 10, 41012 Sevilla, Spain;
| | - Margarida M. Santana
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Edifício C2, Campo Grande, 1749-016 Lisboa, Portugal;
| | - Bhagwan Rekadwad
- National Centre for Microbial Resource, National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Ganeshkhind Road, Maharashtra State, Pune 411007, India;
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Sakurai K, Yuasa M, Ohji S, Hosoyama A, Sato M, Fujita N, Kawasaki H. Gene Mutations in Ganoderma lucidum During Long-Term Preservation by Repeated Subculturing. Biopreserv Biobank 2019; 17:395-400. [PMID: 30938541 DOI: 10.1089/bio.2018.0149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Subculturing is frequently used for the preservation of basidiomycetes. In this study, to assess and verify the risks of repeated subculturing on the long-term preservation of strains of culture collections, we performed single nucleotide polymorphism (SNP) analysis in genes encoding enzymes of the mevalonate pathway, 1,3-β-glucan synthesis, lignin degradation, and the tricarboxylic acid (TCA) cycle of mycelia before and after preserving for a 4-year period by the subculturing 30 times every 45 days of Ganoderma lucidum NBRC 8346. As a result of analyzing 60 genes of the strain, SNPs were found in 18 genes, and 14 of them were found in the exon region. Nonsynonymous coding SNPs were found in two genes (atoB_2, hmgr) encoding enzymes of mevalonate pathway and five genes (lcc1_9, lcc1_11, lcc1_13, dslcc6, aa5_1_9) encoding enzymes of lignin degradation after subculturing of G. lucidum NBRC 8346.
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Affiliation(s)
- Kenta Sakurai
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Tokyo, Japan
| | - Munemitsu Yuasa
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Tokyo, Japan
| | - Syoko Ohji
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Tokyo, Japan
| | - Akira Hosoyama
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Tokyo, Japan
| | - Masanori Sato
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Tokyo, Japan
| | - Nobuyuki Fujita
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Tokyo, Japan
| | - Hiroko Kawasaki
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Tokyo, Japan
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Washetine K, Heeke S, Ribeyre C, Bourreau C, Normand C, Blons H, Laurent-Puig P, Mulot C, Clermont D, David M, Clément B, Dagher G, Hofman P. DNAshell Protects DNA Stored at Room Temperature for Downstream Next-Generation Sequencing Studies. Biopreserv Biobank 2019; 17:352-354. [PMID: 30912674 DOI: 10.1089/bio.2018.0129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Kevin Washetine
- 1Laboratoire de Pathologie Clinique et Experimentale, Biobanque BB-0033-00025, FHU OncoAge, Université Côte d'Azur, Nice, France
| | - Simon Heeke
- 1Laboratoire de Pathologie Clinique et Experimentale, Biobanque BB-0033-00025, FHU OncoAge, Université Côte d'Azur, Nice, France
| | - Camille Ribeyre
- 1Laboratoire de Pathologie Clinique et Experimentale, Biobanque BB-0033-00025, FHU OncoAge, Université Côte d'Azur, Nice, France
| | - Camille Bourreau
- 2Collection de l'Institut Pasteur (CIP), CRB EPIGENETEC, INSERM UMR-S1147, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Corinne Normand
- 2Collection de l'Institut Pasteur (CIP), CRB EPIGENETEC, INSERM UMR-S1147, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Hélène Blons
- 2Collection de l'Institut Pasteur (CIP), CRB EPIGENETEC, INSERM UMR-S1147, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Pierre Laurent-Puig
- 2Collection de l'Institut Pasteur (CIP), CRB EPIGENETEC, INSERM UMR-S1147, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Claire Mulot
- 2Collection de l'Institut Pasteur (CIP), CRB EPIGENETEC, INSERM UMR-S1147, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | | | | | - Bruno Clément
- 5INSERM, INRA, University of Rennes, NuMeCan, CRB Santé, CHU Rennes, France
| | | | - Paul Hofman
- 1Laboratoire de Pathologie Clinique et Experimentale, Biobanque BB-0033-00025, FHU OncoAge, Université Côte d'Azur, Nice, France
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