ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria

Morgan Anne Feeney; Jake Terry Newitt; Emily Addington; Lis Algora-Gallardo; Craig Allan; Lucas Balis; Anna S. Birke; Laia Castaño-Espriu; Louise K. Charkoudian; Rebecca Devine; Damien Gayrard; Jacob Hamilton; Oliver Hennrich; Paul A. Hoskisson; Molly Keith-Baker; Joshua G. Klein; Worarat Kruasuwan; David R. Mark; Yvonne Mast; Rebecca E. McHugh; Thomas C. McLean; Elmira Mohit; John T. Munnoch; Jordan Murray; Katie Noble; Hiroshi Otani; Jonathan Parra; Camila F. Pereira; Louisa Perry; Linamaria Pintor-Escobar; Leighton Pritchard; Samuel M. M. Prudence; Alicia H. Russell; Jana K. Schniete; Ryan F. Seipke; Nelly Sélem-Mojica; Agustina Undabarrena; Kristiina Vind; Gilles P. van Wezel; Barrie Wilkinson; Sarah F. Worsley; Katherine R. Duncan; Lorena T. Fernández-Martínez; Matthew I. Hutchings

doi:10.1099/mgen.0.000824

ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria

Morgan Anne Feeney, Jake Terry Newitt, Emily Addington, Lis Algora-Gallardo, Craig Allan, Lucas Balis, Anna S. Birke, Laia Castaño-Espriu, Louise K. Charkoudian, Rebecca Devine, Damien Gayrard, Jacob Hamilton, Oliver Hennrich, Paul A. Hoskisson, Molly Keith-Baker, Joshua G. Klein, Worarat Kruasuwan, David R. Mark, Yvonne Mast, Rebecca E. McHughThomas C. McLean, Elmira Mohit, John T. Munnoch, Jordan Murray, Katie Noble, Hiroshi Otani, Jonathan Parra, Camila F. Pereira, Louisa Perry, Linamaria Pintor-Escobar, Leighton Pritchard, Samuel M. M. Prudence, Alicia H. Russell, Jana K. Schniete, Ryan F. Seipke, Nelly Sélem-Mojica, Agustina Undabarrena, Kristiina Vind, Gilles P. van Wezel, Barrie Wilkinson, Sarah F. Worsley, Katherine R. Duncan, Lorena T. Fernández-Martínez, Matthew I. Hutchings

Research output: Contribution to journal › Article › peer-review

7 Citations (Scopus)

45 Downloads (Pure)

Abstract

Actinobacteria is an ancient phylum of Gram-positive bacteria with a characteristic high GC content to their DNA. The ActinoBase Wiki is focused on the filamentous actinobacteria, such as Streptomyces species, and the techniques and growth conditions used to study them. These organisms are studied because of their complex developmental life cycles and diverse specialised metabolism which produces many of the antibiotics currently used in the clinic. ActinoBase is a community effort that provides valuable and freely accessible resources, including protocols and practical information about filamentous actinobacteria. It is aimed at enabling knowledge exchange between members of the international research community working with these fascinating bacteria. Actin-oBase is an anchor platform that underpins worldwide efforts to understand the ecology, biology and metabolic potential of these organisms. There are two key differences that set ActinoBase apart from other Wiki-based platforms: [1] ActinoBase is specifically aimed at researchers working on filamentous actinobacteria and is tailored to help users overcome challenges working with these bacteria and [2] it provides a freely accessible resource with global networking opportunities for researchers with a broad range of experience in this field.

Original language	English
Article number	000824
Number of pages	11
Journal	Microbial Genomics
Volume	8
Issue number	7
DOIs	https://doi.org/10.1099/mgen.0.000824
Publication status	Published - 1 Jul 2022

Keywords

actinobacteria
antibiotics
BGCs
CRISPR
specialised metabolites
Streptomyces

Access to Document

10.1099/mgen.0.000824Licence: CC BY 4.0

Feeney-etal-MG-2022-ActinoBase-tools-and-protocols-for-researchers-working-on-StreptomycesFinal published version, 2.81 MBLicence: CC BY 4.0

7 Finished

Fluorous-based diagnostic platform for multiplexed diagnosis and differentiation of viral infections
Burley, G. (Principal Investigator), Corrigan, D. (Co-investigator) & Hoskisson, P. (Co-investigator)
BBSRC (Biotech & Biological Sciences Research Council)
1/08/21 → 31/07/22
Project: Research
Chance and Necessity: Evolution guided antibiotic improvement and discovery
Hoskisson, P. (Principal Investigator)
BBSRC (Biotech & Biological Sciences Research Council)
1/10/19 → 30/09/22
Project: Research
Re-engineering robustness in to industrial antibiotic producing Streptomyces strains (Super Follow on Fund)
Hoskisson, P. (Principal Investigator) & Hunter, I. (Co-investigator)
BBSRC (Biotech & Biological Sciences Research Council)
1/10/19 → 31/08/22
Project: Research

7 Citations
1 Working Paper/Preprint

16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces
Kiepas, A. B., Hoskisson, P. A. & Pritchard, L., 15 Aug 2023, Ithaca, NY, p. 1-31, 31 p.
Research output: Working paper › Working Paper/Preprint

Open Access
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82 Downloads (Pure)

Cite this

Feeney, M. A., Newitt, J. T., Addington, E., Algora-Gallardo, L., Allan, C., Balis, L., Birke, A. S., Castaño-Espriu, L., Charkoudian, L. K., Devine, R., Gayrard, D., Hamilton, J., Hennrich, O., Hoskisson, P. A., Keith-Baker, M., Klein, J. G., Kruasuwan, W., Mark, D. R., Mast, Y., ... Hutchings, M. I. (2022). ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria. Microbial Genomics, 8(7), Article 000824. https://doi.org/10.1099/mgen.0.000824

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title = "ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria",

abstract = "Actinobacteria is an ancient phylum of Gram-positive bacteria with a characteristic high GC content to their DNA. The ActinoBase Wiki is focused on the filamentous actinobacteria, such as Streptomyces species, and the techniques and growth conditions used to study them. These organisms are studied because of their complex developmental life cycles and diverse specialised metabolism which produces many of the antibiotics currently used in the clinic. ActinoBase is a community effort that provides valuable and freely accessible resources, including protocols and practical information about filamentous actinobacteria. It is aimed at enabling knowledge exchange between members of the international research community working with these fascinating bacteria. Actin-oBase is an anchor platform that underpins worldwide efforts to understand the ecology, biology and metabolic potential of these organisms. There are two key differences that set ActinoBase apart from other Wiki-based platforms: [1] ActinoBase is specifically aimed at researchers working on filamentous actinobacteria and is tailored to help users overcome challenges working with these bacteria and [2] it provides a freely accessible resource with global networking opportunities for researchers with a broad range of experience in this field.",

keywords = "actinobacteria, antibiotics, BGCs, CRISPR, specialised metabolites, Streptomyces",

author = "Feeney, {Morgan Anne} and Newitt, {Jake Terry} and Emily Addington and Lis Algora-Gallardo and Craig Allan and Lucas Balis and Birke, {Anna S.} and Laia Casta{\~n}o-Espriu and Charkoudian, {Louise K.} and Rebecca Devine and Damien Gayrard and Jacob Hamilton and Oliver Hennrich and Hoskisson, {Paul A.} and Molly Keith-Baker and Klein, {Joshua G.} and Worarat Kruasuwan and Mark, {David R.} and Yvonne Mast and McHugh, {Rebecca E.} and McLean, {Thomas C.} and Elmira Mohit and Munnoch, {John T.} and Jordan Murray and Katie Noble and Hiroshi Otani and Jonathan Parra and Pereira, {Camila F.} and Louisa Perry and Linamaria Pintor-Escobar and Leighton Pritchard and Prudence, {Samuel M. M.} and Russell, {Alicia H.} and Schniete, {Jana K.} and Seipke, {Ryan F.} and Nelly S{\'e}lem-Mojica and Agustina Undabarrena and Kristiina Vind and {van Wezel}, {Gilles P.} and Barrie Wilkinson and Worsley, {Sarah F.} and Duncan, {Katherine R.} and Fern{\'a}ndez-Mart{\'i}nez, {Lorena T.} and Hutchings, {Matthew I.}",

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Feeney, MA, Newitt, JT, Addington, E, Algora-Gallardo, L, Allan, C, Balis, L, Birke, AS, Castaño-Espriu, L, Charkoudian, LK, Devine, R, Gayrard, D, Hamilton, J, Hennrich, O, Hoskisson, PA , Keith-Baker, M, Klein, JG, Kruasuwan, W, Mark, DR, Mast, Y, McHugh, RE, McLean, TC, Mohit, E, Munnoch, JT, Murray, J, Noble, K, Otani, H, Parra, J, Pereira, CF, Perry, L, Pintor-Escobar, L, Pritchard, L, Prudence, SMM, Russell, AH, Schniete, JK, Seipke, RF, Sélem-Mojica, N, Undabarrena, A, Vind, K, van Wezel, GP, Wilkinson, B, Worsley, SF, Duncan, KR, Fernández-Martínez, LT & Hutchings, MI 2022, 'ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria', Microbial Genomics, vol. 8, no. 7, 000824. https://doi.org/10.1099/mgen.0.000824

TY - JOUR

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T2 - tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria

AU - Feeney, Morgan Anne

AU - Newitt, Jake Terry

AU - Addington, Emily

AU - Algora-Gallardo, Lis

AU - Allan, Craig

AU - Balis, Lucas

AU - Birke, Anna S.

AU - Castaño-Espriu, Laia

AU - Charkoudian, Louise K.

AU - Devine, Rebecca

AU - Gayrard, Damien

AU - Hamilton, Jacob

AU - Hennrich, Oliver

AU - Hoskisson, Paul A.

AU - Keith-Baker, Molly

AU - Klein, Joshua G.

AU - Kruasuwan, Worarat

AU - Mark, David R.

AU - Mast, Yvonne

AU - McHugh, Rebecca E.

AU - McLean, Thomas C.

AU - Mohit, Elmira

AU - Munnoch, John T.

AU - Murray, Jordan

AU - Noble, Katie

AU - Otani, Hiroshi

AU - Parra, Jonathan

AU - Pereira, Camila F.

AU - Perry, Louisa

AU - Pintor-Escobar, Linamaria

AU - Pritchard, Leighton

AU - Prudence, Samuel M. M.

AU - Russell, Alicia H.

AU - Schniete, Jana K.

AU - Seipke, Ryan F.

AU - Sélem-Mojica, Nelly

AU - Undabarrena, Agustina

AU - Vind, Kristiina

AU - van Wezel, Gilles P.

AU - Wilkinson, Barrie

AU - Worsley, Sarah F.

AU - Duncan, Katherine R.

AU - Fernández-Martínez, Lorena T.

AU - Hutchings, Matthew I.

PY - 2022/7/1

Y1 - 2022/7/1

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AB - Actinobacteria is an ancient phylum of Gram-positive bacteria with a characteristic high GC content to their DNA. The ActinoBase Wiki is focused on the filamentous actinobacteria, such as Streptomyces species, and the techniques and growth conditions used to study them. These organisms are studied because of their complex developmental life cycles and diverse specialised metabolism which produces many of the antibiotics currently used in the clinic. ActinoBase is a community effort that provides valuable and freely accessible resources, including protocols and practical information about filamentous actinobacteria. It is aimed at enabling knowledge exchange between members of the international research community working with these fascinating bacteria. Actin-oBase is an anchor platform that underpins worldwide efforts to understand the ecology, biology and metabolic potential of these organisms. There are two key differences that set ActinoBase apart from other Wiki-based platforms: [1] ActinoBase is specifically aimed at researchers working on filamentous actinobacteria and is tailored to help users overcome challenges working with these bacteria and [2] it provides a freely accessible resource with global networking opportunities for researchers with a broad range of experience in this field.

KW - actinobacteria

KW - antibiotics

KW - BGCs

KW - CRISPR

KW - specialised metabolites

KW - Streptomyces

U2 - 10.1099/mgen.0.000824

DO - 10.1099/mgen.0.000824

M3 - Article

SN - 2057-5858

VL - 8

JO - Microbial Genomics

JF - Microbial Genomics

IS - 7

M1 - 000824

ER -

ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria

Abstract

Keywords

Access to Document

Fingerprint

Projects

Fluorous-based diagnostic platform for multiplexed diagnosis and differentiation of viral infections

Chance and Necessity: Evolution guided antibiotic improvement and discovery

Re-engineering robustness in to industrial antibiotic producing Streptomyces strains (Super Follow on Fund)

Research output

16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces

Cite this