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Open microbiome dominated by Clostridium and Eubacterium converts methanol into i-butyrate and n-butyrate


Isobutyrate (i-butyrate) is a versatile platform chemical, whose acid form is used as a precursor of plastic and emulsifier. It can be produced microbially either using genetically engineered organisms or via microbiomes, in the latter case starting from methanol and short-chain carboxylates. This opens the opportunity to produce i-butyrate from non-sterile feedstocks. Little is known on the ecology and process conditions leading to i-butyrate production. In this study, we steered i-butyrate production in a bioreactor fed with methanol and acetate under various conditions, achieving maximum i-butyrate productivity of 5.0 mM day−1, with a concurrent production of n-butyrate of 7.9 mM day−1. The production of i-butyrate was reversibly inhibited by methanogenic inhibitor 2-bromoethanesulfonate. The microbial community data revealed the co-dominance of two major OTUs during co-production of i-butyrate and n-butyrate in two distinctive phases throughout a period of 54 days and 28 days, respectively. The cross-comparison of product profile with microbial community composition suggests that the relative abundance of Clostridium sp. over Eubacterium sp. is correlated with i-butyrate productivity over n-butyrate productivity.

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Data availability

All relevant raw fastq files that were used for the microbial community analysis in this study have been deposited in the National Center for Biotechnology Information (NCBI) database (BioProject accession number PRJNA572585).


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The authors would like to thank Jose Maria Carvajal Arroyo and Pieter Candry for their insightful discussion, and Tim Lacoere, Ruben Props, Jan Arends, and Frederiek-Maarten Kerckhof for their suggestions on data analysis.


S.H. is supported by European Union’s Horizon 2020 research and innovation program SuPER-W under the Marie Skłodowska-Curie grant agreement no 676070. R.G. gratefully acknowledges support from the Ghent University BOF fellowship (BOF15/PDO/068). K.R. is supported by European Union’s Horizon 2020 research and innovation program PERCAL under grant agreement no 745828.

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All authors contributed to the study conception and design. Material preparation and data collection and analysis were performed by Shengle Huang. The first draft of the manuscript was written by Shengle Huang and all authors commented on subsequent versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Ramon Ganigué.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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Huang, S., Kleerebezem, R., Rabaey, K. et al. Open microbiome dominated by Clostridium and Eubacterium converts methanol into i-butyrate and n-butyrate. Appl Microbiol Biotechnol 104, 5119–5131 (2020).

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  • Chain elongation
  • Methanol
  • Mixed culture fermentation
  • Isobutyrate production
  • Carboxylate platform