Distribution of microbial carrageenan foraging pathways reveals a widespread latent trait within the ruminant intestinal microbiome

Seaweeds represent a promising source of sustainable, alternative feeds for livestock. Despite their increasing popularity in agriculture, the dietary fate of seaweed polysaccharides, such as carrageenan, is unknown. Here, we apply functional microbiome analyses of ruminant gastrointestinal tract microbiomes to discover catabolic enzymes specific for carrageenan digestion from the red seaweed Mazzaella japonica. M. japonica preferentially increased Bacteroides abundance within the feces over the rumen, and bacterial isolates have the capacity to use carrageenans as a sole carbon source. We identify carrageenan-active polysaccharide utilization loci (CarPULs) and characterize recombinant GH16 subfamily 17 carrageenases, informing previously uncharacterized substrate specificities for the subfamily, and providing insights into pathway specialization of divergent CarPULs. Selective enrichment and metagenomic mining reveals that carrageenan catabolism is widespread among geographically and taxonomically distinct ruminants, suggesting it is a latent trait widely distributed in the Order Artiodactyla and carried within their microbiomes as part of the microbial "dark matter". These pathways are structurally distinct from those found in marine bacteria, highlighting a complex and ancient evolutionary history of CarPULs in ruminant microbiomes.

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Publication Details

Journal
Nature Communications
Published
2026-05-12
DOI
https://doi.org/10.1038/s41467-026-70776-7
Primary Topic
Seaweed-derived Bioactive Compounds
Type
article
Field-Weighted Citation Impact
0.00

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article

Distribution of microbial carrageenan foraging pathways reveals a widespread latent trait within the ruminant intestinal microbiome

Phillip Byron Pope, Ianina Altshuler, Jeffrey P. Tingley, Douglas P. Whiteside et al.
Nature Communications
Seaweed-derived Bioactive Compounds
article

Distribution of microbial carrageenan foraging pathways reveals a widespread latent trait within the ruminant intestinal microbiome

Phillip Byron Pope, Ianina Altshuler, Jeffrey P. Tingley, Douglas P. Whiteside, Greta Reintjes, Leeann Klassen, Kristin E. Low, Trushar R. Patel, Anna Y. Shearer, Liam Mihalynuk, Nic Jujihara, Live H. Hagen, Edgar Smith, Thea O. Andersen, D. Wade Abbott, Xiaohui Xing, Alisdair B. Boraston, Spencer Serin
article en

Abstract

Seaweeds represent a promising source of sustainable, alternative feeds for livestock. Despite their increasing popularity in agriculture, the dietary fate of seaweed polysaccharides, such as carrageenan, is unknown. Here, we apply functional microbiome analyses of ruminant gastrointestinal tract microbiomes to discover catabolic enzymes specific for carrageenan digestion from the red seaweed Mazzaella japonica. M. japonica preferentially increased Bacteroides abundance within the feces over the rumen, and bacterial isolates have the capacity to use carrageenans as a sole carbon source. We identify carrageenan-active polysaccharide utilization loci (CarPULs) and characterize recombinant GH16 subfamily 17 carrageenases, informing previously uncharacterized substrate specificities for the subfamily, and providing insights into pathway specialization of divergent CarPULs. Selective enrichment and metagenomic mining reveals that carrageenan catabolism is widespread among geographically and taxonomically distinct ruminants, suggesting it is a latent trait widely distributed in the Order Artiodactyla and carried within their microbiomes as part of the microbial "dark matter". These pathways are structurally distinct from those found in marine bacteria, highlighting a complex and ancient evolutionary history of CarPULs in ruminant microbiomes.

Nature CommunicationsVol. 17(1)
University of Lethbridge (CA), BC Hydro (Canada) (CA), Translational Research Institute (AU), Agriculture and Agri-Food Canada (CA), Queensland University of Technology (AU), University of Calgary (CA), University of Bremen (DE), University of Victoria (CA), Toronto Zoo (CA), North Island College (CA), École Polytechnique Fédérale de Lausanne (CH), Norwegian University of Life Sciences (NO), Lethbridge College (CA)
University of Lethbridge, Thompson Rivers University, Deutsche Forschungsgemeinschaft, Novo Nordisk, Norges Forskningsråd, Norges Miljø- og Biovitenskapelige Universitet, Natural Sciences and Engineering Research Council of Canada, Agriculture and Agri-Food Canada
Zero hunger
Openalex Percentile: Top 4%
Seaweed-derived Bioactive Compounds
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