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01 11, 2018;8 (1): 525.

Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential.

Lorena Carro, Imen Nouioui, Vartul Sangal, Jan P Meier-Kolthoff, Martha E Trujillo, Maria Del Carmen Montero-Calasanz, Nevzat Sahin, Darren Lee Smith, Kristi E Kim, Paul Peluso, Shweta Deshpande, Tanja Woyke, Nicole Shapiro, Nikos C Kyrpides, Hans-Peter Klenk, Markus Göker, Michael Goodfellow
Author Information
  1. Lorena Carro: School of Biology, Newcastle University, Newcastle upon Tyne, UK. lcg@usal.es. ORCID
  2. Imen Nouioui: School of Biology, Newcastle University, Newcastle upon Tyne, UK.
  3. Vartul Sangal: Department of Biomedical Sciences, Northumbria University, Newcastle upon Tyne, UK.
  4. Jan P Meier-Kolthoff: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany. ORCID
  5. Martha E Trujillo: Departamento de Microbiologia y Genetica, Lab 214, Universidad de Salamanca, Salamanca, Spain.
  6. Maria Del Carmen Montero-Calasanz: School of Biology, Newcastle University, Newcastle upon Tyne, UK. ORCID
  7. Nevzat Sahin: Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, Kurupelit-Samsun, Turkey. ORCID
  8. Darren Lee Smith: Department of Biomedical Sciences, Northumbria University, Newcastle upon Tyne, UK.
  9. Kristi E Kim: Pacific Biosciences, 1380 Willow Rd, Menlo Park, California, USA.
  10. Paul Peluso: Pacific Biosciences, 1380 Willow Rd, Menlo Park, California, USA.
  11. Shweta Deshpande: DOE Joint Genome Institute, Walnut Creek, California, USA.
  12. Tanja Woyke: DOE Joint Genome Institute, Walnut Creek, California, USA. ORCID
  13. Nicole Shapiro: DOE Joint Genome Institute, Walnut Creek, California, USA.
  14. Nikos C Kyrpides: DOE Joint Genome Institute, Walnut Creek, California, USA.
  15. Hans-Peter Klenk: School of Biology, Newcastle University, Newcastle upon Tyne, UK. hans-peter.klenk@newcastle.ac.uk.
  16. Markus Göker: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany. ORCID
  17. Michael Goodfellow: School of Biology, Newcastle University, Newcastle upon Tyne, UK.
PMID: 29323202 DOI: 10.1038/s41598-017-17392-0

Abstract

There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.

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MeSH Term

Base Composition
Genome, Bacterial
Industrial Microbiology
Micromonospora
Phylogeny
Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.
Article has an altmetric score of 4

Word Cloud

Created with Highcharts 10.0.0strainsmicromonosporaetypepotentialgenusMicromonosporabiotechnologicalecologicaldraftgenomesshowedcorrespondingsequencesgenesgenomedatadescriptionsclusterskeyneedclarifyrelationshipswithinactinobacterialfamilyMicromonosporaceaegivenimportance40twonon-typemadeavailableGenomicEncyclopediaBacteriaArchaeaprojectusedgeneratephylogenomictreeassignedwellsupportedphyleticlinesevidenttreesbasedsingleconcatenatedconservedDNAG+CratiosderivedspeciesimpreciseEmendedincludeprecisebasecompositionapproximatesizesantiSMASHanalysesshowpreviouslyunrealisedsynthesizenovelspecializedmetabolitesCloseonethousandbiosyntheticgenedetectedincludingNRPSPKSterpenessiderophoresdiscontinuouslydistributedtherebyopeningprospectprioritisinggiftednaturalproductdiscoverydistributionstressrelatedprovideinsightadaptenvironmentalvariablesGenesassociatedplantinteractionshighlightuseagriculturebiotechnologyGenome-basedclassificationfocus

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