Phylum-wide propionate degradation and its potential connection to poly-γ-glutamate biosynthesis in Candidatus Cloacimonadota phylum [* Cross-Reference *]

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Magdalena Całusińska; Malte Herold; Dominika Klimek; Marie Bertucci; Sébastien Lemaigre; Sébastien Cambier; Simone Zorzan; Céline C. Leclercq; Jan Dolfing; Maria Westerholm; Bettina Müller; Leila Nasirzadeh; Anna Schnürer; Paul Wilmes; Philippe Delfosse; Xavier Goux, 2026, "Phylum-wide propionate degradation and its potential connection to poly-γ-glutamate biosynthesis in Candidatus Cloacimonadota phylum [* Cross-Reference *]", https://lore.list.lu/citation?persistentId=perma:LIST.J2KAC1, LIST Open Repository, V1

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Description	Abstract The candidate phylum Cloacimonadota is frequently detected in anaerobic environments such as anaerobic digestion (AD) reactors, hydrothermal vents, and deep-sea sediments, yet its metabolism remains poorly understood due to the lack of cultured representatives. Metagenomic evidence suggests capacities for amino acid fermentation, cellulose degradation, and production of carbohydrate-active enzymes, with particular interest in their presumed role in syntrophic propionate oxidation (SPO), a key bottleneck in AD. However, a complete methylmalonyl-CoA (mmc) pathway, central to SPO, has not been previously identified in Cloacimonadota genomes. Here, we report results from a lab-scale anaerobic baffled reactor fed with sugar beet pulp, where a sharp increase in an uncultured Cloacimonadota OTU coincided with recovery of methanogenesis and enhanced methane production. Metagenomic and metatranscriptomic analyses enabled metabolic reconstruction of this OTU, complemented by a curated database of 47 genome-resolved Cloacimonadota species. Comparative genomics revealed conserved protein clusters indicative of an alternative mmc pathway, suggesting that this variant of the SPO pathway is a widespread, phylum-specific trait potentially linked to protein degradation and poly-γ-glutamate biosynthesis. Network analysis identified the methanogenic archaeon Methanothrix as a primary syntrophic partner, an interaction further supported by propionate-fed enrichment cultures showing co-occurrence of Cloacimonadota and Methanothrix species. Our study sheds light on the Cloacimonadota metabolism, advancing our understanding of their ecological roles and potential for biotechnological applications. (2025-11-11) *This entry has been automatically imported via OpenAlex by LIST harvest scripts. Please refer to https://doi.org/10.1101/2025.11.11.687785 for the original and latest version of the publication* (2026-07-01)
Subject	Earth and Environmental Sciences; Engineering; Physics
Keyword	Methanogenesis, Metagenomics, Phylum, Propionate, Metabolic pathway, KEGG, Bacteria, Enrichment culture
License/Data Use Agreement	CC BY 4.0


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Persistent Identifier	perma:LIST.J2KAC1
Publication Date	2026-07-06
Title	Phylum-wide propionate degradation and its potential connection to poly-γ-glutamate biosynthesis in Candidatus Cloacimonadota phylum [* Cross-Reference *]
Other Identifier	https://doi.org/10.1101/2025.11.11.687785 OpenAlex ID: https://openalex.org/W4416232042
Author	Magdalena Całusińska (Luxembourg Institute of Science and Technology) - ORCID: https://orcid.org/0000-0003-2270-2217 Malte Herold (Luxembourg Institute of Science and Technology) - ORCID: https://orcid.org/0000-0003-2627-0159 Dominika Klimek (Luxembourg Institute of Science and Technology) - ORCID: https://orcid.org/0000-0002-6713-8333 Marie Bertucci (Luxembourg Institute of Science and Technology) - ORCID: https://orcid.org/0009-0003-5131-0746 Sébastien Lemaigre (Luxembourg Institute of Science and Technology) - ORCID: https://orcid.org/0000-0002-3204-293X Sébastien Cambier (Luxembourg Institute of Science and Technology) - ORCID: https://orcid.org/0000-0001-7761-5212 Simone Zorzan (Luxembourg Institute of Science and Technology) - ORCID: https://orcid.org/0000-0003-0550-3224 Céline C. Leclercq (Luxembourg Institute of Science and Technology) - ORCID: https://orcid.org/0000-0003-0565-4591 Jan Dolfing (Northumbria University) - ORCID: https://orcid.org/0000-0002-7220-530X Maria Westerholm (Swedish University of Agricultural Sciences) - ORCID: https://orcid.org/0000-0003-2150-8762 Bettina Müller (Swedish University of Agricultural Sciences) Leila Nasirzadeh (Swedish University of Agricultural Sciences) Anna Schnürer (Swedish University of Agricultural Sciences) - ORCID: https://orcid.org/0000-0003-0038-553X Paul Wilmes (University of Luxembourg) - ORCID: https://orcid.org/0000-0002-6478-2924 Philippe Delfosse (University of Luxembourg) - ORCID: https://orcid.org/0009-0003-9371-209X Xavier Goux (Luxembourg Institute of Science and Technology) - ORCID: https://orcid.org/0000-0002-0815-2194
Point of Contact	Use email button above to contact. LIST QDKM (LIST)
Description	Abstract The candidate phylum Cloacimonadota is frequently detected in anaerobic environments such as anaerobic digestion (AD) reactors, hydrothermal vents, and deep-sea sediments, yet its metabolism remains poorly understood due to the lack of cultured representatives. Metagenomic evidence suggests capacities for amino acid fermentation, cellulose degradation, and production of carbohydrate-active enzymes, with particular interest in their presumed role in syntrophic propionate oxidation (SPO), a key bottleneck in AD. However, a complete methylmalonyl-CoA (mmc) pathway, central to SPO, has not been previously identified in Cloacimonadota genomes. Here, we report results from a lab-scale anaerobic baffled reactor fed with sugar beet pulp, where a sharp increase in an uncultured Cloacimonadota OTU coincided with recovery of methanogenesis and enhanced methane production. Metagenomic and metatranscriptomic analyses enabled metabolic reconstruction of this OTU, complemented by a curated database of 47 genome-resolved Cloacimonadota species. Comparative genomics revealed conserved protein clusters indicative of an alternative mmc pathway, suggesting that this variant of the SPO pathway is a widespread, phylum-specific trait potentially linked to protein degradation and poly-γ-glutamate biosynthesis. Network analysis identified the methanogenic archaeon Methanothrix as a primary syntrophic partner, an interaction further supported by propionate-fed enrichment cultures showing co-occurrence of Cloacimonadota and Methanothrix species. Our study sheds light on the Cloacimonadota metabolism, advancing our understanding of their ecological roles and potential for biotechnological applications. (2025-11-11) *This entry has been automatically imported via OpenAlex by LIST harvest scripts. Please refer to https://doi.org/10.1101/2025.11.11.687785 for the original and latest version of the publication* (2026-07-01)
Subject	Earth and Environmental Sciences; Engineering; Physics
Keyword	Methanogenesis Metagenomics Phylum Propionate Metabolic pathway KEGG Bacteria Enrichment culture
Topic Classification	Anaerobic Digestion and Biogas Production Microbial Fuel Cells and Bioremediation Wastewater Treatment and Nitrogen Removal
Deposit Date	2025-11-11
Data Type	Preprint
Data Source	bioRxiv (Cold Spring Harbor Laboratory)

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