Phylogenomics and genetic analysis of solvent-producing Clostridium species

Rasmus O. Jensen; Frederik Schulz; Simon Roux; Dawn M. Klingeman; Wayne P. Mitchell; Daniel Udwary; Sarah Moraïs; Vinicio Reynoso; James Winkler; Shilpa Nagaraju; Sashini De Tissera; Nicole Shapiro; Natalia Ivanova; T. B.K. Reddy; Itzhak Mizrahi; Sagar M. Utturkar; Edward A. Bayer; Tanja Woyke; Nigel J. Mouncey; Michael C. Jewett; Séan D. Simpson; Michael Köpke; David T. Jones; Steven D. Brown

doi:10.1038/s41597-024-03210-6

Phylogenomics and genetic analysis of solvent-producing Clostridium species

Rasmus O. Jensen
, Frederik Schulz
, Simon Roux
, Dawn M. Klingeman
, Wayne P. Mitchell
, Daniel Udwary
, Sarah Moraïs
, Vinicio Reynoso
, James Winkler
, Shilpa Nagaraju
, Sashini De Tissera
, Nicole Shapiro
, Natalia Ivanova
, T. B.K. Reddy
, Itzhak Mizrahi
, Sagar M. Utturkar
, Edward A. Bayer
, Tanja Woyke
, Nigel J. Mouncey
, Michael C. Jewett

Séan D. Simpson, Michael Köpke, David T. Jones, Steven D. Brown

Biological Systems Design Group

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

17 Scopus citations

Abstract

The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii, 57 C. saccharobutylicum, 4 C. saccharoperbutylacetonicum, 5 C. butyricum, 7 C. acetobutylicum, and 3 C. tetanomorphum genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or Escherichia coli for enhanced chemical production. Recently, gene sequences from this collection were used to engineer Clostridium autoethanogenum, a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production, as well as butanol, butanoic acid, hexanol and hexanoic acid production.

Original language	English
Article number	432
Journal	Scientific Data
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41597-024-03210-6
State	Published - Dec 2024

Funding

We thank Zamin Yang, Jason Whitham, and Jace Natzke (ORNL) for assistance in extracting genomic DNA. This material is based upon work supported by the Biosystems Design program of the U.S. Department of Energy (DOE), Office of Science (SC), Office of Biological and Environmental Research (BER) under Award Number DE-SC0018249, the BER Bioenergy Research Centers’ (BRCs) BioEnergy Science Center (BESC) and the Center for Bioenergy Innovation (CBI). The work (proposal: 10.46936/10.25585/60000855) conducted by the U.S. Department of Energy Joint Genome Institute ( https://ror.org/04xm1d337 ), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. Illumina data generated at Hudson Alpha is based upon work supported by the Department of Energy, Office of Energy Efficiency and Renewable Energy (EERE), under Award Number DE-EE0007566. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05- 00OR22725.

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Jensen, R. O., Schulz, F., Roux, S., Klingeman, D. M., Mitchell, W. P., Udwary, D., Moraïs, S., Reynoso, V., Winkler, J., Nagaraju, S., De Tissera, S., Shapiro, N., Ivanova, N., Reddy, T. B. K., Mizrahi, I., Utturkar, S. M., Bayer, E. A., Woyke, T., Mouncey, N. J., ... Brown, S. D. (2024). Phylogenomics and genetic analysis of solvent-producing Clostridium species. Scientific Data , 11(1), Article 432. https://doi.org/10.1038/s41597-024-03210-6

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title = "Phylogenomics and genetic analysis of solvent-producing Clostridium species",

abstract = "The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii, 57 C. saccharobutylicum, 4 C. saccharoperbutylacetonicum, 5 C. butyricum, 7 C. acetobutylicum, and 3 C. tetanomorphum genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or Escherichia coli for enhanced chemical production. Recently, gene sequences from this collection were used to engineer Clostridium autoethanogenum, a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production, as well as butanol, butanoic acid, hexanol and hexanoic acid production.",

author = "Jensen, \{Rasmus O.\} and Frederik Schulz and Simon Roux and Klingeman, \{Dawn M.\} and Mitchell, \{Wayne P.\} and Daniel Udwary and Sarah Mora{\"i}s and Vinicio Reynoso and James Winkler and Shilpa Nagaraju and \{De Tissera\}, Sashini and Nicole Shapiro and Natalia Ivanova and Reddy, \{T. B.K.\} and Itzhak Mizrahi and Utturkar, \{Sagar M.\} and Bayer, \{Edward A.\} and Tanja Woyke and Mouncey, \{Nigel J.\} and Jewett, \{Michael C.\} and Simpson, \{S{\'e}an D.\} and Michael K{\"o}pke and Jones, \{David T.\} and Brown, \{Steven D.\}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2024.",

year = "2024",

month = dec,

doi = "10.1038/s41597-024-03210-6",

language = "English",

volume = "11",

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Jensen, RO, Schulz, F, Roux, S, Klingeman, DM, Mitchell, WP, Udwary, D, Moraïs, S, Reynoso, V, Winkler, J, Nagaraju, S, De Tissera, S, Shapiro, N, Ivanova, N, Reddy, TBK, Mizrahi, I, Utturkar, SM, Bayer, EA, Woyke, T, Mouncey, NJ, Jewett, MC, Simpson, SD, Köpke, M, Jones, DT & Brown, SD 2024, 'Phylogenomics and genetic analysis of solvent-producing Clostridium species', Scientific Data , vol. 11, no. 1, 432. https://doi.org/10.1038/s41597-024-03210-6

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T1 - Phylogenomics and genetic analysis of solvent-producing Clostridium species

AU - Jensen, Rasmus O.

AU - Schulz, Frederik

AU - Roux, Simon

AU - Klingeman, Dawn M.

AU - Mitchell, Wayne P.

AU - Udwary, Daniel

AU - Moraïs, Sarah

AU - Reynoso, Vinicio

AU - Winkler, James

AU - Nagaraju, Shilpa

AU - De Tissera, Sashini

AU - Shapiro, Nicole

AU - Ivanova, Natalia

AU - Reddy, T. B.K.

AU - Mizrahi, Itzhak

AU - Utturkar, Sagar M.

AU - Bayer, Edward A.

AU - Woyke, Tanja

AU - Mouncey, Nigel J.

AU - Jewett, Michael C.

AU - Simpson, Séan D.

AU - Köpke, Michael

AU - Jones, David T.

AU - Brown, Steven D.

PY - 2024/12

Y1 - 2024/12

N2 - The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii, 57 C. saccharobutylicum, 4 C. saccharoperbutylacetonicum, 5 C. butyricum, 7 C. acetobutylicum, and 3 C. tetanomorphum genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or Escherichia coli for enhanced chemical production. Recently, gene sequences from this collection were used to engineer Clostridium autoethanogenum, a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production, as well as butanol, butanoic acid, hexanol and hexanoic acid production.

AB - The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii, 57 C. saccharobutylicum, 4 C. saccharoperbutylacetonicum, 5 C. butyricum, 7 C. acetobutylicum, and 3 C. tetanomorphum genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or Escherichia coli for enhanced chemical production. Recently, gene sequences from this collection were used to engineer Clostridium autoethanogenum, a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production, as well as butanol, butanoic acid, hexanol and hexanoic acid production.

UR - https://www.scopus.com/pages/publications/85172803956

U2 - 10.1038/s41597-024-03210-6

DO - 10.1038/s41597-024-03210-6

M3 - Article

C2 - 38693191

AN - SCOPUS:85172803956

SN - 2052-4463

VL - 11

JO - Scientific Data

JF - Scientific Data

IS - 1

M1 - 432

ER -

Phylogenomics and genetic analysis of solvent-producing Clostridium species

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