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Kim SO, Kim MJ, Choi NY, Kim JH, Oh MS, Lee CH, Park SA. Psychophysiological and Metabolomics Responses of Adults during Horticultural Activities Using Soil Inoculated with Streptomyces rimosus: A Pilot Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:12901. [PMID: 36232200 PMCID: PMC9564959 DOI: 10.3390/ijerph191912901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/04/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
This study compared the physiological effects at a metabolomics level with autonomic nervous system responses in adults during soil mixing activities, based on the presence or absence of Streptomyces rimosus in the soil. Thirty adult participants performed soil mixing activities for 5 min using sterilized soil with culture media and Streptomyces rimosus, respectively. Blood samples were drawn twice from each participant after each activity. Electroencephalograms were measured during the activity. Serum metabolites underwent metabolite profiling by gas chromatography, followed by multivariate analyses. Serum brain-derived neurotrophic factor and C-reactive protein levels were measured by Enzyme-Linked Immunosorbent Assay. Soil-emitted volatile organic compounds were identified via solid-phase microextraction and gas chromatography-mass spectroscopy, followed by multivariate analyses. The volatile compound analysis revealed that the terpenoid and benzoid compounds, geosmin, and 2-methylisoborneol were greater in soil with Streptomyces rimosus. Serum metabolomics revealed that the treatment group (soil inoculated with Streptomyces rimosus) possessed relatively higher levels of serotonin compared to the control group (soil mixed with culture media), and serum C-reactive protein levels were significantly lower in the treatment group. In the treatment group, the electroencephalogram revealed that alpha band activity of the occipital lobe increased. This study concludes that Streptomyces rimosus soil contact can positively affect human metabolic and autonomic reactions. Therefore, this pilot study confirmed the possible role of soil microorganisms in horticultural activities for psychophysiological effects in humans.
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Affiliation(s)
- Seon-Ok Kim
- Department of Bio and Healing Convergence, Graduate School, Konkuk University, Seoul 05029, Korea
| | - Min Ji Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Na-Yoon Choi
- Department of Bio and Healing Convergence, Graduate School, Konkuk University, Seoul 05029, Korea
| | - Jin Hee Kim
- Department of Biomedical and Pharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul 02447, Korea
| | - Myung Sook Oh
- Department of Biomedical and Pharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul 02447, Korea
| | - Choong Hwan Lee
- MetaMass Corp., Seoul 05029, Korea
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Sin-Ae Park
- Department of Bio and Healing Convergence, Graduate School, Konkuk University, Seoul 05029, Korea
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
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2
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Li Y, Lee SR, Han EJ, Seyedsayamdost MR. Momomycin, an Antiproliferative Cryptic Metabolite from the Oxytetracycline Producer Streptomyces rimosus. Angew Chem Int Ed Engl 2022; 61:e202208573. [PMID: 35903822 PMCID: PMC9489664 DOI: 10.1002/anie.202208573] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Indexed: 08/27/2023]
Abstract
Natural products provide an important source of pharmaceuticals and chemical tools. Traditionally, assessment of unexplored microbial phyla has led to new natural products. However, with every new microbe, the number of orphan biosynthetic gene clusters (BGC) grows. As such, the more difficult proposition is finding new molecules from well-studied strains. Herein, we targeted Streptomyces rimosus, the widely-used oxytetracycline producer, for the discovery of new natural products. Using MALDI-MS-guided high-throughput elicitor screening (HiTES), we mapped the global secondary metabolome of S. rimosus and structurally characterized products of three cryptic BGCs, including momomycin, an unusual cyclic peptide natural product with backbone modifications and several non-canonical amino acids. We elucidated important aspects of its biosynthesis and evaluated its bioactivity. Our studies showcase HiTES as an effective approach for unearthing new chemical matter from "drained" strains.
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Affiliation(s)
- Yuchen Li
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
| | - Seoung Rak Lee
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
| | - Esther J. Han
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544 (USA)
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544 (USA)
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3
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Zarei S, Taghavi SM, Rahimi T, Mafakheri H, Potnis N, Koebnik R, Fischer-Le Saux M, Pothier JF, Palacio Bielsa A, Cubero J, Portier P, Jacques MA, Osdaghi E. Taxonomic Refinement of Xanthomonas arboricola. PHYTOPATHOLOGY 2022; 112:1630-1639. [PMID: 35196068 DOI: 10.1094/phyto-12-21-0519-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Xanthomonas arboricola comprises a number of economically important fruit tree pathogens classified within different pathovars. Dozens of nonpathogenic and taxonomically unvalidated strains are also designated as X. arboricola, leading to a complicated taxonomic status in the species. In this study, we have evaluated the whole-genome resources of all available Xanthomonas spp. strains designated as X. arboricola in the public databases to refine the members of the species based on DNA similarity indexes and core genome-based phylogeny. Our results show that, of the nine validly described pathovars within X. arboricola, pathotype strains of seven pathovars are taxonomically genuine, belonging to the core clade of the species regardless of their pathogenicity on the host of isolation (thus the validity of pathovar status). However, strains of X. arboricola pv. guizotiae and X. arboricola pv. populi do not belong to X. arboricola because of the low DNA similarities between the type strain of the species and the pathotype strains of these two pathovars. Thus, we propose to elevate the two pathovars to the rank of a species as X. guizotiae sp. nov. with the type strain CFBP 7408T and X. populina sp. nov. with the type strain CFBP 3123T. In addition, other mislabeled strains of X. arboricola were scattered within Xanthomonas spp. that belong to previously described species or represent novel species that await formal description.
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Affiliation(s)
- Sadegh Zarei
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Touraj Rahimi
- Department of Agronomy and Plant Breeding, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Hamzeh Mafakheri
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, U.S.A
| | - Ralf Koebnik
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | - Joël F Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Ana Palacio Bielsa
- Departamento de Protección Vegetal, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Jaime Cubero
- Departamento de Protección Vegetal, Centro Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
| | - Perrine Portier
- Institut Agro, Université de Angers, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, Angers, France
| | - Marie-Agnes Jacques
- Institut Agro, Université de Angers, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, Angers, France
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
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Li Y, Lee SR, Han EJ, Seyedsayamdost MR. Momomycin, an Antiproliferative Cryptic Metabolite from the Oxytetracycline Producer Streptomyces rimosus. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yuchen Li
- Princeton University Chemistry UNITED STATES
| | | | | | - Mohammad R. Seyedsayamdost
- Princeton University Chemistry Washington UniversityFrick Chemistry Lab, Room 333 08544 Princeton UNITED STATES
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Reference-Grade Genome and Large Linear Plasmid of Streptomyces rimosus: Pushing the Limits of Nanopore Sequencing. Microbiol Spectr 2022; 10:e0243421. [PMID: 35377231 PMCID: PMC9045324 DOI: 10.1128/spectrum.02434-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptomyces rimosus ATCC 10970 is the parental strain of industrial strains used for the commercial production of the important antibiotic oxytetracycline. As an actinobacterium with a large linear chromosome containing numerous long repeat regions, high GC content, and a single giant linear plasmid (GLP), these genomes are challenging to assemble. Here, we apply a hybrid sequencing approach relying on the combination of short- and long-read next-generation sequencing platforms and whole-genome restriction analysis by using pulsed-field gel electrophoresis (PFGE) to produce a high-quality reference genome for this biotechnologically important bacterium. By using PFGE to separate and isolate plasmid DNA from chromosomal DNA, we successfully sequenced the GLP using Nanopore data alone. Using this approach, we compared the sequence of GLP in the parent strain ATCC 10970 with those found in two semi-industrial progenitor strains, R6-500 and M4018. Sequencing of the GLP of these three S. rimosus strains shed light on several rearrangements accompanied by transposase genes, suggesting that transposases play an important role in plasmid and genome plasticity in S. rimosus. The polished annotation of secondary metabolite biosynthetic pathways compared to metabolite analysis in the ATCC 10970 strain also refined our knowledge of the secondary metabolite arsenal of these strains. The proposed methodology is highly applicable to a variety of sequencing projects, as evidenced by the reliable assemblies obtained. IMPORTANCE The genomes of Streptomyces species are difficult to assemble due to long repeats, extrachromosomal elements (giant linear plasmids [GLPs]), rearrangements, and high GC content. To improve the quality of the S. rimosus ATCC 10970 genome, producer of oxytetracycline, we validated the assembly of GLPs by applying a new approach to combine pulsed-field gel electrophoresis separation and GLP isolation and sequenced the isolated GLP with Oxford Nanopore technology. By examining the sequenced plasmids of ATCC 10970 and two industrial progenitor strains, R6-500 and M4018, we identified large GLP rearrangements. Analysis of the assembled plasmid sequences shed light on the role of transposases in genome plasticity of this species. The new methodological approach developed for Nanopore sequencing is highly applicable to a variety of sequencing projects. In addition, we present the annotated reference genome sequence of ATCC 10970 with a detailed analysis of the biosynthetic gene clusters.
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Re-classification of Streptomyces venezuelae strains and mining secondary metabolite biosynthetic gene clusters. iScience 2021; 24:103410. [PMID: 34877485 PMCID: PMC8627960 DOI: 10.1016/j.isci.2021.103410] [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: 07/07/2021] [Revised: 09/05/2021] [Accepted: 11/04/2021] [Indexed: 11/20/2022] Open
Abstract
Streptomyces species have attracted considerable interest as a reservoir of medically important secondary metabolites, which are even diverse and different between strains. Here, we reassess ten Streptomyces venezuelae strains by presenting the highly resolved classification, using 16S rRNA sequencing, MALDI-TOF MS protein profiling, and whole-genome sequencing. The results revealed that seven of the ten strains were misclassified as S. venezuelae species. Secondary metabolite biosynthetic gene cluster (smBGC) mining and targeted LC-MS/MS based metabolite screening of S. venezuelae and misclassified strains identified in total 59 secondary metabolites production. In addition, a comparison of pyrrolamide-type antibiotic BGCs of four misclassified strains, followed by functional genomics, revealed that athv28 is critical in the synthesis of the anthelvencin precursor, 5-amino-3,4-dihydro-2H-pyrrole-2-carboxylate (ADPC). Our findings illustrate the importance of the accurate classification and better utilization of misclassified Streptomyces strains to discover smBGCs and their secondary metabolite products.
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Algora-Gallardo L, Schniete JK, Mark DR, Hunter IS, Herron PR. Bilateral symmetry of linear streptomycete chromosomes. Microb Genom 2021; 7. [PMID: 34779763 PMCID: PMC8743542 DOI: 10.1099/mgen.0.000692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Here, we characterize an uncommon set of telomeres from Streptomyces rimosus ATCC 10970, the parental strain of a lineage of one of the earliest-discovered antibiotic producers. Following the closure of its genome sequence, we compared unusual telomeres from this organism with the other five classes of replicon ends found amongst streptomycetes. Closed replicons of streptomycete chromosomes were organized with respect to their phylogeny and physical orientation, which demonstrated that different telomeres were not associated with particular clades and are likely shared amongst different strains by plasmid-driven horizontal gene transfer. Furthermore, we identified a ~50 kb origin island with conserved synteny that is located at the core of all streptomycete chromosomes and forms an axis around which symmetrical chromosome inversions can take place. Despite this chromosomal bilateral symmetry, a bias in parS sites to the right of oriC is maintained across the family Streptomycetaceae and suggests that the formation of ParB/parS nucleoprotein complexes on the right replichore is a conserved feature in streptomycetes. Consequently, our studies reveal novel features of linear bacterial replicons that, through their manipulation, may lead to improvements in growth and productivity of this important industrial group of bacteria.
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Affiliation(s)
- Lis Algora-Gallardo
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Jana K Schniete
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK.,Department of Biology, Edge Hill University, Ormskirk L39 4QP, UK
| | - David R Mark
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Iain S Hunter
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Paul R Herron
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
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Caicedo-Montoya C, Manzo-Ruiz M, Ríos-Estepa R. Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds. Front Microbiol 2021; 12:677558. [PMID: 34659136 PMCID: PMC8510958 DOI: 10.3389/fmicb.2021.677558] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/30/2021] [Indexed: 01/07/2023] Open
Abstract
Species of the genus Streptomyces are known for their ability to produce multiple secondary metabolites; their genomes have been extensively explored to discover new bioactive compounds. The richness of genomic data currently available allows filtering for high quality genomes, which in turn permits reliable comparative genomics studies and an improved prediction of biosynthetic gene clusters (BGCs) through genome mining approaches. In this work, we used 121 genome sequences of the genus Streptomyces in a comparative genomics study with the aim of estimating the genomic diversity by protein domains content, sequence similarity of proteins and conservation of Intergenic Regions (IGRs). We also searched for BGCs but prioritizing those with potential antibiotic activity. Our analysis revealed that the pan-genome of the genus Streptomyces is clearly open, with a high quantity of unique gene families across the different species and that the IGRs are rarely conserved. We also described the phylogenetic relationships of the analyzed genomes using multiple markers, obtaining a trustworthy tree whose relationships were further validated by Average Nucleotide Identity (ANI) calculations. Finally, 33 biosynthetic gene clusters were detected to have potential antibiotic activity and a predicted mode of action, which might serve up as a guide to formulation of related experimental studies.
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Affiliation(s)
- Carlos Caicedo-Montoya
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Medellín, Colombia
| | - Monserrat Manzo-Ruiz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Rigoberto Ríos-Estepa
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Medellín, Colombia
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Tenebro CP, Trono DJVL, Vicera CVB, Sabido EM, Ysulat JA, Macaspac AJM, Tampus KA, Fabrigar TAP, Saludes JP, Dalisay DS. Multiple strain analysis of Streptomyces species from Philippine marine sediments reveals intraspecies heterogeneity in antibiotic activities. Sci Rep 2021; 11:17544. [PMID: 34475427 PMCID: PMC8413401 DOI: 10.1038/s41598-021-96886-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/10/2021] [Indexed: 12/17/2022] Open
Abstract
The marine ecosystem has become the hotspot for finding antibiotic-producing actinomycetes across the globe. Although marine-derived actinomycetes display strain-level genomic and chemodiversity, it is unclear whether functional traits, i.e., antibiotic activity, vary in near-identical Streptomyces species. Here, we report culture-dependent isolation, antibiotic activity, phylogeny, biodiversity, abundance, and distribution of Streptomyces isolated from marine sediments across the west-central Philippines. Out of 2212 marine sediment-derived actinomycete strains isolated from 11 geographical sites, 92 strains exhibited antibacterial activities against multidrug-resistant Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli. The 16S rRNA and rpoB gene sequence analyses confirmed that antibiotic-producing strains belong to the genus Streptomyces, highlighting Streptomyces parvulus as the most dominant species and three possible new species. Antibiotic-producing Streptomyces strains were highly diverse in Southern Antique, and species diversity increase with marine sediment depth. Multiple strains with near-identical 16S rRNA and rpoB gene sequences displayed varying strength of antibiotic activities. The genotyping of PKS and NRPS genes revealed that closely related antibiotic-producing strains have similar BGC domains supported by their close phylogenetic proximity. These findings collectively suggest Streptomyces' intraspecies adaptive characteristics in distinct ecological niches that resulted in outcompeting other bacteria through differential antibiotic production.
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Affiliation(s)
- Chuckcris P Tenebro
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, 5000, Iloilo City, Philippines
| | - Dana Joanne Von L Trono
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, 5000, Iloilo City, Philippines
| | - Carmela Vannette B Vicera
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, 5000, Iloilo City, Philippines
| | - Edna M Sabido
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, 5000, Iloilo City, Philippines
| | - Jovito A Ysulat
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, 5000, Iloilo City, Philippines
| | - Aaron Joseph M Macaspac
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, 5000, Iloilo City, Philippines
| | - Kimberly A Tampus
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, 5000, Iloilo City, Philippines
| | - Trisha Alexis P Fabrigar
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, 5000, Iloilo City, Philippines
| | - Jonel P Saludes
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, 5000, Iloilo City, Philippines.,Department of Chemistry, College of Liberal Arts, Sciences, and Education, University of San Agustin, 5000, Iloilo City, Philippines.,Balik Scientist Program, Department of Science and Technology, Philippine Council for Health Research and Development (PCHRD), 1631, Bicutan, Taguig City, Philippines
| | - Doralyn S Dalisay
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, 5000, Iloilo City, Philippines. .,Department of Biology, College of Liberal Arts, Sciences, and Education, University of San Agustin, 5000, Iloilo City, Philippines. .,Balik Scientist Program, Department of Science and Technology, Philippine Council for Health Research and Development (PCHRD), 1631, Bicutan, Taguig City, Philippines.
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Sabido EM, Tenebro CP, Trono DJVL, Vicera CVB, Leonida SFL, Maybay JJWB, Reyes-Salarda R, Amago DS, Aguadera AMV, Octaviano MC, Saludes JP, Dalisay DS. Insights into the Variation in Bioactivities of Closely Related Streptomyces Strains from Marine Sediments of the Visayan Sea against ESKAPE and Ovarian Cancer. Mar Drugs 2021; 19:md19080441. [PMID: 34436280 PMCID: PMC8399204 DOI: 10.3390/md19080441] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/27/2021] [Accepted: 07/27/2021] [Indexed: 12/25/2022] Open
Abstract
Marine sediments host diverse actinomycetes that serve as a source of new natural products to combat infectious diseases and cancer. Here, we report the biodiversity, bioactivities against ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) and ovarian cancer, and metabolites variation among culturable actinomycetes isolated from the marine sediments of Visayan Sea, Philippines. We identified 15 Streptomyces species based on a 16S rRNA gene sequence analysis. The crude extracts of 10 Streptomyces species have inhibited the growth of ESKAPE pathogens with minimum inhibitory concentration (MIC) values ranging from 0.312 mg/mL to 20 mg/mL depending on the strain and pathogens targeted. Additionally, ten crude extracts have antiproliferative activity against A2780 human ovarian carcinoma at 2 mg/mL. To highlight, we observed that four phylogenetically identical Streptomyces albogriseolus strains demonstrated variation in antibiotic and anticancer activities. These strains harbored type I and II polyketide synthase (PKS) and non-ribosomal synthetase (NRPS) genes in their genomes, implying that their bioactivity is independent of the polymerase chain reaction (PCR)-detected bio-synthetic gene clusters (BGCs) in this study. Metabolite profiling revealed that the taxonomically identical strains produced core and strain-specific metabolites. Thus, the chemical diversity among these strains influences the variation observed in their biological activities. This study expanded our knowledge on the potential of marine-derived Streptomyces residing from the unexplored regions of the Visayan Sea as a source of small molecules against ESKAPE pathogens and cancer. It also highlights that Streptomyces species strains produce unique strain-specific secondary metabolites; thus, offering new chemical space for natural product discovery.
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Affiliation(s)
- Edna M. Sabido
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City 5000, Philippines; (E.M.S.); (S.F.L.L.); (J.J.W.B.M.); (D.S.A.); (A.M.V.A.); (M.C.O.)
| | - Chuckcris P. Tenebro
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, Iloilo City 5000, Philippines; (C.P.T.); (D.J.V.L.T.); (C.V.B.V.); (R.R.-S.)
| | - Dana Joanne Von L. Trono
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, Iloilo City 5000, Philippines; (C.P.T.); (D.J.V.L.T.); (C.V.B.V.); (R.R.-S.)
| | - Carmela Vannette B. Vicera
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, Iloilo City 5000, Philippines; (C.P.T.); (D.J.V.L.T.); (C.V.B.V.); (R.R.-S.)
| | - Sheeny Fane L. Leonida
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City 5000, Philippines; (E.M.S.); (S.F.L.L.); (J.J.W.B.M.); (D.S.A.); (A.M.V.A.); (M.C.O.)
| | - Jose Jeffrey Wayne B. Maybay
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City 5000, Philippines; (E.M.S.); (S.F.L.L.); (J.J.W.B.M.); (D.S.A.); (A.M.V.A.); (M.C.O.)
| | - Rikka Reyes-Salarda
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, Iloilo City 5000, Philippines; (C.P.T.); (D.J.V.L.T.); (C.V.B.V.); (R.R.-S.)
- Department of Biology, College of Liberal Arts, Sciences, and Education, University of San Agustin, Iloilo City 5000, Philippines
| | - Diana S. Amago
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City 5000, Philippines; (E.M.S.); (S.F.L.L.); (J.J.W.B.M.); (D.S.A.); (A.M.V.A.); (M.C.O.)
| | - Angelica Marie V. Aguadera
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City 5000, Philippines; (E.M.S.); (S.F.L.L.); (J.J.W.B.M.); (D.S.A.); (A.M.V.A.); (M.C.O.)
| | - May C. Octaviano
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City 5000, Philippines; (E.M.S.); (S.F.L.L.); (J.J.W.B.M.); (D.S.A.); (A.M.V.A.); (M.C.O.)
| | - Jonel P. Saludes
- Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City 5000, Philippines; (E.M.S.); (S.F.L.L.); (J.J.W.B.M.); (D.S.A.); (A.M.V.A.); (M.C.O.)
- Department of Chemistry, College of Liberal Arts, Sciences, and Education, University of San Agustin, Iloilo City 5000, Philippines
- Tuklas Lunas Development Center, University of San Agustin, Iloilo City 5000, Philippines
- Balik Scientist Program, Department of Science and Technology, Philippine Council for Health Research and Development (PCHRD), Bicutan, Taguig City 1631, Philippines
- Correspondence: (J.P.S.); (D.S.D.); Tel.: +63-33-503-6887 (J.P.S.); +63-33-501-0350 (D.S.D.)
| | - Doralyn S. Dalisay
- Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, Iloilo City 5000, Philippines; (C.P.T.); (D.J.V.L.T.); (C.V.B.V.); (R.R.-S.)
- Department of Biology, College of Liberal Arts, Sciences, and Education, University of San Agustin, Iloilo City 5000, Philippines
- Tuklas Lunas Development Center, University of San Agustin, Iloilo City 5000, Philippines
- Balik Scientist Program, Department of Science and Technology, Philippine Council for Health Research and Development (PCHRD), Bicutan, Taguig City 1631, Philippines
- Correspondence: (J.P.S.); (D.S.D.); Tel.: +63-33-503-6887 (J.P.S.); +63-33-501-0350 (D.S.D.)
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Park CJ, Caimi NA, Buecher DC, Valdez EW, Northup DE, Andam CP. Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA. BMC Genomics 2021; 22:247. [PMID: 33827425 PMCID: PMC8028829 DOI: 10.1186/s12864-021-07546-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/19/2021] [Indexed: 11/10/2022] Open
Abstract
Background Antibiotic-producing Streptomyces bacteria are ubiquitous in nature, yet most studies of its diversity have focused on free-living strains inhabiting diverse soil environments and those in symbiotic relationship with invertebrates. Results We studied the draft genomes of 73 Streptomyces isolates sampled from the skin (wing and tail membranes) and fur surfaces of bats collected in Arizona and New Mexico. We uncovered large genomic variation and biosynthetic potential, even among closely related strains. The isolates, which were initially identified as three distinct species based on sequence variation in the 16S rRNA locus, could be distinguished as 41 different species based on genome-wide average nucleotide identity. Of the 32 biosynthetic gene cluster (BGC) classes detected, non-ribosomal peptide synthetases, siderophores, and terpenes were present in all genomes. On average, Streptomyces genomes carried 14 distinct classes of BGCs (range = 9–20). Results also revealed large inter- and intra-species variation in gene content (single nucleotide polymorphisms, accessory genes and singletons) and BGCs, further contributing to the overall genetic diversity present in bat-associated Streptomyces. Finally, we show that genome-wide recombination has partly contributed to the large genomic variation among strains of the same species. Conclusions Our study provides an initial genomic assessment of bat-associated Streptomyces that will be critical to prioritizing those strains with the greatest ability to produce novel antibiotics. It also highlights the need to recognize within-species variation as an important factor in genetic manipulation studies, diversity estimates and drug discovery efforts in Streptomyces. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07546-w.
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Affiliation(s)
- Cooper J Park
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Nicole A Caimi
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | | | - Ernest W Valdez
- Department of Biology, University of New Mexico, Albuquerque, NM, USA.,U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
| | - Diana E Northup
- Department of Biology, University of New Mexico, Albuquerque, NM, USA.
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.
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12
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Matarrita-Carranza B, Murillo-Cruz C, Avendaño R, Ríos MI, Chavarría M, Gómez-Calvo ML, Tamayo-Castillo G, Araya JJ, Pinto-Tomás AA. Streptomyces sp. M54: an actinobacteria associated with a neotropical social wasp with high potential for antibiotic production. Antonie van Leeuwenhoek 2021; 114:379-398. [PMID: 33587228 DOI: 10.1007/s10482-021-01520-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/17/2021] [Indexed: 11/28/2022]
Abstract
Streptomyces symbionts in insects have shown to be a valuable source of new antibiotics. Here, we report the genome sequence and the potential for antibiotic production of "Streptomyces sp. M54", an Actinobacteria associated with the eusocial wasp, Polybia plebeja. The Streptomyces sp. M54 genome is composed of a chromosome (7.96 Mb), and a plasmid (1.91 Kb) and harbors 30 biosynthetic gene clusters for secondary metabolites, of which only one third has been previously characterized. Growth inhibition bioassays show that this bacterium produces antimicrobial compounds that are active against Hirsutella citriformis, a natural fungal enemy of its host, and the human pathogens Staphylococcus aureus and Candida albicans. Analyses through TLC-bioautography, LC-MS/MS and NMR allowed the identification of five macrocyclic ionophore antibiotics, with previously reported antibacterial, antitumor and antiviral properties. Phylogenetic analyses placed Streptomyces sp. M54 in a clade of other host-associated strains taxonomically related to Streptomyces griseus. Pangenomic and ANI analyses confirm the identity of one of its closest relatives as Streptomyces sp. LaPpAH-199, a strain isolated from an ant-plant symbiosis in Africa. In summary, our results suggest an insect-microbe association in distant geographic areas and showcase the potential of Streptomyces sp. M54 and related strains for the discovery of novel antibiotics.
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Affiliation(s)
| | - Catalina Murillo-Cruz
- Centro de Investigación en Estructuras Microscópicas (CIEMic), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica
| | - María Isabel Ríos
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica.,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - María Luisa Gómez-Calvo
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Giselle Tamayo-Castillo
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Juan J Araya
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Adrián A Pinto-Tomás
- Centro de Investigación en Estructuras Microscópicas (CIEMic), Universidad de Costa Rica, 11501-2060, San José, Costa Rica. .,Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, 11501-2060, San José, Costa Rica. .,Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.
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13
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Świecimska M, Golińska P, Nouioui I, Wypij M, Rai M, Sangal V, Goodfellow M. Streptomyces alkaliterrae sp. nov., isolated from an alkaline soil, and emended descriptions of Streptomyces alkaliphilus, Streptomyces calidiresistens and Streptomyces durbertensis. Syst Appl Microbiol 2020; 43:126153. [PMID: 33161356 DOI: 10.1016/j.syapm.2020.126153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/10/2020] [Accepted: 10/16/2020] [Indexed: 12/15/2022]
Abstract
A polyphasic study was undertaken to establish the taxonomic position of six representative streptomycetes isolated from an alkaline soil adjacent to a meteoric alkaline soda lake in India. Chemotaxonomic, cultural and morphological properties of the isolates were consistent with their classification in the genus Streptomyces. The isolates formed extensively branched substrate mycelia and aerial hyphae that differentiated in straight chains of spores with smooth surfaces. They contained LL-diaminopimelic acid in the wall peptidoglycan, produced either hexa- or octa-hydrogenated menaquinones with nine isoprene units, major amounts of saturated, iso- and anteiso- fatty acids and phosphatidylethanolamine as the characteristic polar lipid. The isolates grew well at 30 °C, pH 9 and in the presence of 3 to 5% (w/v) sodium chloride. Isolates OF1T, OF3 and OF8 formed a distinct clade within the Streptomyces 16S rRNA gene tree sharing relatively high sequence similarities with the type strains of Streptomyces durbertensis (99.3%), Streptomyces palmae (98.1%) and Streptomyces xinghaiensis (98.3%), but can be distinguished from them using combinations of phenotypic properties. A phylogenomic tree based on draft genome sequences of the isolates and S. durbertensis DSM 104538T confirmed the phylogenetic relationships. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values calculated from the whole genome sequences of isolate OF1T and S. durbertensis DSM 104538T were low at 92.0% and 45.2%, respectively, indicating that they belong to different genomic species. Consequently, on the basis of the genomic, phylogenetic and associated phenotypic data it is proposed that isolates OF1T, OF3 and OF8 be assigned to the genus Streptomyces as Streptomyces alkaliterrae sp. nov. with strain OF1T (NCIMB 15195T =PCM 3001T) as the type strain. Isolates IF11, IF17 and IF19, and S. alkaliphilus DSM 42118T were shown to belong to the same taxospecies and together with S. calidiresistens DSM 42108T comprised a well supported clade in the Streptomyces 16S rRNA gene tree. Isolate IF17 and S. alkaliphilus DSM 42118T formed a well-supported clade in the phylogenomic tree, had almost identical digital G + C similarity values, produced long straight chains of smooth-surfaced spores and shared ANI and dDDH values (98.0 and 79.6%, respectively) consistent with their assignment to the same genomic species. In light of all of the data isolates IF11, IF17 and IF19 should be seen as authentic stains of S. alkalihilus. Data acquired in the present study have also been used to emend the descriptions of S. alkaliphilus, S. calidiresistens and S. durbertensis. The genomes of isolates IF17, and OF1T, OF3 and OF8 contain relatively high numbers of biosynthetic gene clusters some of which were discontinously distributed indicating ones predicted to express for novel specialised metabolites.
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Affiliation(s)
- Magdalena Świecimska
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87 100 Torun, Poland
| | - Patrycja Golińska
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87 100 Torun, Poland.
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom; Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Magdalena Wypij
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87 100 Torun, Poland
| | - Mahendra Rai
- Nanobiotechnology Laboratory, Department of Biotechnology, SGB Amravati University, Amravati-444602, Maharashtra, India
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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On the Risks of Phylogeny-Based Strain Prioritization for Drug Discovery: Streptomyces lunaelactis as a Case Study. Biomolecules 2020; 10:biom10071027. [PMID: 32664387 PMCID: PMC7408125 DOI: 10.3390/biom10071027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/11/2022] Open
Abstract
Strain prioritization for drug discovery aims at excluding redundant strains of a collection in order to limit the repetitive identification of the same molecules. In this work, we wanted to estimate what can be unexploited in terms of the amount, diversity, and novelty of compounds if the search is focused on only one single representative strain of a species, taking Streptomyces lunaelactis as a model. For this purpose, we selected 18 S. lunaelactis strains taxonomically clustered with the archetype strain S. lunaelactis MM109T. Genome mining of all S. lunaelactis isolated from the same cave revealed that 54% of the 42 biosynthetic gene clusters (BGCs) are strain specific, and five BGCs are not present in the reference strain MM109T. In addition, even when a BGC is conserved in all strains such as the bag/fev cluster involved in bagremycin and ferroverdin production, the compounds produced highly differ between the strains and previously unreported compounds are not produced by the archetype MM109T. Moreover, metabolomic pattern analysis uncovered important profile heterogeneity, confirming that identical BGC predisposition between two strains does not automatically imply chemical uniformity. In conclusion, trying to avoid strain redundancy based on phylogeny and genome mining information alone can compromise the discovery of new natural products and might prevent the exploitation of the best naturally engineered producers of specific molecules.
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15
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Komaki H, Hosoyama A, Igarashi Y, Tamura T. Streptomyces lydicamycinicus sp. nov. and Its Secondary Metabolite Biosynthetic Gene Clusters for Polyketide and Nonribosomal Peptide Compounds. Microorganisms 2020; 8:microorganisms8030370. [PMID: 32155704 PMCID: PMC7143880 DOI: 10.3390/microorganisms8030370] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/21/2020] [Accepted: 03/02/2020] [Indexed: 11/17/2022] Open
Abstract
(1) Background: Streptomyces sp. TP-A0598 derived from seawater produces lydicamycin and its congeners. We aimed to investigate its taxonomic status; (2) Methods: A polyphasic approach and whole genome analysis are employed; (3) Results: Strain TP-A0598 contained ll-diaminopimelic acid, glutamic acid, glycine, and alanine in its peptidoglycan. The predominant menaquinones were MK-9(H6) and MK-9(H8), and the major fatty acids were C16:0, iso-C15:0, iso-C16:0, and anteiso-C15:0. Streptomyces sp. TP-A0598 showed a 16S rDNA sequence similarity value of 99.93% (1 nucleottide difference) to Streptomyces angustmyceticus NRRL B-2347T. The digital DNA–DNA hybridisation value between Streptomyces sp. TP-A0598 and its closely related type strains was 25%–46%. Differences in phenotypic characteristics between Streptomyces sp. TP-A0598 and its phylogenetically closest relative, S. angustmyceticus NBRC 3934T, suggested strain TP-A0598 to be a novel species. Streptomyces sp. TP-A0598 and S. angustmyceticus NBRC 3934T harboured nine and 13 biosynthetic gene clusters for polyketides and nonribosomal peptides, respectively, among which only five clusters were shared between them, whereas the others are specific for each strain; and (4) Conclusions: For strain TP-A0598, the name Streptomyces lydicamycinicus sp. nov. is proposed; the type strain is TP-A0598T (=NBRC 110027T).
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Affiliation(s)
- Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan; (A.H.); (T.T.)
- Correspondence: ; Tel.: +81-438-20-5764
| | - Akira Hosoyama
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan; (A.H.); (T.T.)
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan;
| | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan; (A.H.); (T.T.)
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16
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Bull AT, Goodfellow M. Dark, rare and inspirational microbial matter in the extremobiosphere: 16 000 m of bioprospecting campaigns. MICROBIOLOGY-SGM 2020; 165:1252-1264. [PMID: 31184575 DOI: 10.1099/mic.0.000822] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The rationale of our bioprospecting campaigns is that the extremobiosphere, particularly the deep sea and hyper-arid deserts, harbours undiscovered biodiversity that is likely to express novel chemistry and biocatalysts thereby providing opportunities for therapeutic drug and industrial process development. We have focused on actinobacteria because of their frequent role as keystone species in soil ecosystems and their unrivalled track record as a source of bioactive compounds. Population numbers and diversity of actinobacteria in the extremobiosphere are traditionally considered to be low, although they often comprise the dominant bacterial biota. Recent metagenomic evaluation of 'the uncultured microbial majority' has now revealed enormous taxonomic diversity among 'dark' and 'rare' actinobacteria in samples as diverse as sediments from the depths of the Mariana Trench and soils from the heights of the Central Andes. The application of innovative culture and screening options that emphasize rigorous dereplication at each stage of the analysis, and strain prioritization to identify 'gifted' organisms, have been deployed to detect and characterize bioactive hit compounds and sought-after catalysts from this hitherto untapped resource. The rewards include first-in-a-class chemical entities with novel modes of action, as well as a growing microbial seed bank that represents a potentially enormous source of biotechnological and therapeutic innovation.
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Affiliation(s)
- Alan T Bull
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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17
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Abstract
S. enterica is a major foodborne pathogen, which can be transmitted via several distinct routes from animals and environmental sources to human hosts. Multiple subspecies and serotypes of S. enterica exhibit considerable differences in virulence, host specificity, and colonization. This study provides detailed insights into the dynamics of recombination and its contributions to S. enterica subspecies evolution. Widespread recombination within the species means that new adaptations arising in one lineage can be rapidly transferred to another lineage. We therefore predict that recombination has been an important factor in the emergence of several major disease-causing strains from diverse genomic backgrounds and their ability to adapt to disparate environments. Salmonella is responsible for many nontyphoidal foodborne infections and enteric (typhoid) fever in humans. Of the two Salmonella species, Salmonella enterica is highly diverse and includes 10 known subspecies and approximately 2,600 serotypes. Understanding the evolutionary processes that generate the tremendous diversity in Salmonella is important in reducing and controlling the incidence of disease outbreaks and the emergence of virulent strains. In this study, we aim to elucidate the impact of homologous recombination in the diversification of S. enterica subspecies. Using a data set of previously published 926 Salmonella genomes representing the 10 S. enterica subspecies and Salmonella bongori, we calculated a genus-wide pan-genome composed of 84,041 genes and the S. enterica pan-genome of 81,371 genes. The size of the accessory genomes varies between 12,429 genes in S. enterica subsp. arizonae (subsp. IIIa) to 33,257 genes in S. enterica subsp. enterica (subsp. I). A total of 12,136 genes in the Salmonella pan-genome show evidence of recombination, representing 14.44% of the pan-genome. We identified genomic hot spots of recombination that include genes associated with flagellin and the synthesis of methionine and thiamine pyrophosphate, which are known to influence host adaptation and virulence. Last, we uncovered within-species heterogeneity in rates of recombination and preferential genetic exchange between certain donor and recipient strains. Frequent but biased recombination within a bacterial species may suggest that lineages vary in their response to environmental selection pressure. Certain lineages, such as the more uncommon non-enterica subspecies (non-S. enterica subsp. enterica), may also act as a major reservoir of genetic diversity for the wider population. IMPORTANCES. enterica is a major foodborne pathogen, which can be transmitted via several distinct routes from animals and environmental sources to human hosts. Multiple subspecies and serotypes of S. enterica exhibit considerable differences in virulence, host specificity, and colonization. This study provides detailed insights into the dynamics of recombination and its contributions to S. enterica subspecies evolution. Widespread recombination within the species means that new adaptations arising in one lineage can be rapidly transferred to another lineage. We therefore predict that recombination has been an important factor in the emergence of several major disease-causing strains from diverse genomic backgrounds and their ability to adapt to disparate environments.
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18
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Lee IPA, Andam CP. Pan-genome diversification and recombination in Cronobacter sakazakii, an opportunistic pathogen in neonates, and insights to its xerotolerant lifestyle. BMC Microbiol 2019; 19:306. [PMID: 31881843 PMCID: PMC6935241 DOI: 10.1186/s12866-019-1664-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 11/26/2019] [Indexed: 01/14/2023] Open
Abstract
Background Cronobacter sakazakii is an emerging opportunistic bacterial pathogen known to cause neonatal and pediatric infections, including meningitis, necrotizing enterocolitis, and bacteremia. Multiple disease outbreaks of C. sakazakii have been documented in the past few decades, yet little is known of its genomic diversity, adaptation, and evolution. Here, we analyzed the pan-genome characteristics and phylogenetic relationships of 237 genomes of C. sakazakii and 48 genomes of related Cronobacter species isolated from diverse sources. Results The C. sakazakii pan-genome contains 17,158 orthologous gene clusters, and approximately 19.5% of these constitute the core genome. Phylogenetic analyses reveal the presence of at least ten deep branching monophyletic lineages indicative of ancestral diversification. We detected enrichment of functions involved in proton transport and rotational mechanism in accessory genes exclusively found in human-derived strains. In environment-exclusive accessory genes, we detected enrichment for those involved in tryptophan biosynthesis and indole metabolism. However, we did not find significantly enriched gene functions for those genes exclusively found in food strains. The most frequently detected virulence genes are those that encode proteins associated with chemotaxis, enterobactin synthesis, ferrienterobactin transporter, type VI secretion system, galactose metabolism, and mannose metabolism. The genes fos which encodes resistance against fosfomycin, a broad-spectrum cell wall synthesis inhibitor, and mdf(A) which encodes a multidrug efflux transporter were found in nearly all genomes. We found that a total of 2991 genes in the pan-genome have had a history of recombination. Many of the most frequently recombined genes are associated with nutrient acquisition, metabolism and toxin production. Conclusions Overall, our results indicate that the presence of a large accessory gene pool, ability to switch between ecological niches, a diverse suite of antibiotic resistance, virulence and niche-specific genes, and frequent recombination partly explain the remarkable adaptability of C. sakazakii within and outside the human host. These findings provide critical insights that can help define the development of effective disease surveillance and control strategies for Cronobacter-related diseases.
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Affiliation(s)
- Isaiah Paolo A Lee
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
| | - Cheryl P Andam
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA.
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Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. Mar Drugs 2019; 17:md17100576. [PMID: 31614509 PMCID: PMC6835618 DOI: 10.3390/md17100576] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/13/2022] Open
Abstract
The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.
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Abstract
Horizontal gene transfer is a rapid and efficient way to diversify bacterial gene pools. Currently, little is known about this gene flux within natural soil populations. Using comparative genomics of Streptomyces strains belonging to the same species and isolated at microscale, we reveal frequent transfer of a significant fraction of the pangenome. We show that it occurs at a time scale enabling the population to diversify and to cope with its changing environment, notably, through the production of public goods. In this work, by comparing genomes of closely related individuals of Streptomyces isolated at a spatial microscale (millimeters or centimeters), we investigated the extent and impact of horizontal gene transfer in the diversification of a natural Streptomyces population. We show that despite these conspecific strains sharing a recent common ancestor, all harbored significantly different gene contents, implying massive and rapid gene flux. The accessory genome of the strains was distributed across insertion/deletion events (indels) ranging from one to several hundreds of genes. Indels were preferentially located in the arms of the linear chromosomes (ca. 12 Mb) and appeared to form recombination hot spots. Some of them harbored biosynthetic gene clusters (BGCs) whose products confer an inhibitory capacity and may constitute public goods that can favor the cohesiveness of the bacterial population. Moreover, a significant proportion of these variable genes were either plasmid borne or harbored signatures of actinomycete integrative and conjugative elements (AICEs). We propose that conjugation is the main driver for the indel flux and diversity in Streptomyces populations.
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