Animal Microbiome

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Effect of the macroalgae Asparagopsis taxiformis on methane production and rumen microbiome assemblage

  • Breanna Michell Roque
  • Charles Garrett Brooke
  • Joshua Ladau
  • Tamsen Polley
  • Lyndsey Jean Marsh
  • Negeen Najafi
  • Pramod Pandey
  • Latika Singh
  • Joan King Salwen
  • Emiley Eloe-Fadrosh
  • Ermias Kebreab
  • Matthias HessEmail author
Research article



Recent studies using batch-fermentation suggest that the red macroalgae Asparagopsis taxiformis has the potential to reduce methane (CH4) production from beef cattle by up to ~ 99% when added to Rhodes grass hay; a common feed in the Australian beef industry. These experiments have shown significant reductions in CH4 without compromising other fermentation parameters (i.e. volatile fatty acid production) with A. taxiformis organic matter (OM) inclusion rates of up to 5%. In the study presented here, A. taxiformis was evaluated for its ability to reduce methane production from dairy cattle fed a mixed ration widely utilized in California, the largest milk producing state in the US.


Fermentation in a semi-continuous in-vitro rumen system suggests that A. taxiformis can reduce methane production from enteric fermentation in dairy cattle by 95% when added at a 5% OM inclusion rate without any obvious negative impacts on volatile fatty acid production. High-throughput 16S ribosomal RNA (rRNA) gene amplicon sequencing showed that seaweed amendment effects rumen microbiome consistent with the Anna Karenina hypothesis, with increased β-diversity, over time scales of approximately 3 days. The relative abundance of methanogens in the fermentation vessels amended with A. taxiformis decreased significantly compared to control vessels, but this reduction in methanogen abundance was only significant when averaged over the course of the experiment. Alternatively, significant reductions of CH4 in the A. taxiformis amended vessels was measured in the early stages of the experiment. This suggests that A. taxiformis has an immediate effect on the metabolic functionality of rumen methanogens whereas its impact on microbiome assemblage, specifically methanogen abundance, is delayed.


The methane reducing effect of A. taxiformis during rumen fermentation makes this macroalgae a promising candidate as a biotic methane mitigation strategy for dairy cattle. But its effect in-vivo (i.e. in dairy cattle) remains to be investigated in animal trials. Furthermore, to obtain a holistic understanding of the biochemistry responsible for the significant reduction of methane, gene expression profiles of the rumen microbiome and the host animal are warranted.


16S rRNA community profiling Asparagopsis taxiformis Feed supplementation Greenhouse gas mitigation In-vitro rumen fermentation Macroalgae Rumen microbiome 


16S rRNA

16 Svedberg ribosomal ribonucleic acid


Analysis of molecular variance


Base pair








Carbon dioxide


Dry matter


Deoxyribonucleic acid


Flame ionization detector




Gas chromatography




Institution of Animal Care and Use Committee




Organic matter


Operational taxonomic unit


Principal coordinate analysis


Polymerase chain reaction


Poly vinyl chloride


Super basic ration


Standard deviation


Total digestible nutrients


Total gas production


Volatile fatty acid



The authors would like to thank Kyra Smart, Susan Parkyn and Ania Kossakowski for their assistance in maintaining the artificial rumen system. Authors also express their appreciation to Dr. DePeters and Doug Gisi for providing access to fistulated animals.


This work was supported by the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory under U.S. Department of Energy Contract No. DE-AC02-05CH11231, by ELM Innovations, by the Hellman Foundation, U.S. Department of Agriculture Contract Number: 2017–67007-25944, and the College of Agricultural and Environmental Sciences at UC Davis.

This work was funded by the College of Agricultural and Environmental Sciences at the University of California, Davis, the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory under U.S. Department of Energy Contract No. DE-AC02-05CH11231, the U.S. Department of Agriculture Contract No. 2017–67007-25944, the Hellman Foundation and by ELM Innovations.

Availability of data and materials

Sequence data generated during this study are available through NCBI’s Sequence Read Archive under the SRA ID SRP152555. Custom-written Java, SQL, and Bash code is available at All other data is included in this published article and its supplementary information files.

Authors’ contributions

Designed the experiment: BR, CB, EK, JS and MH; Performed the experiments: BR, CB, MH and NN; Generated and analyzed the microbiome data: BR, CB, EE-F, JL, MH and NN. Generated and analyzed GC data: BR, CB, LM, LS, MH, NN, PP; Wrote the paper: BR, CB, EE-F, EK JL, JS, LM, MH and TP. All authors read and approved the final manuscript.

Ethics approval

All animal procedures were performed in accordance with the Institution of Animal Care and Use Committee (IACUC) at University of California, Davis under protocol number 19263.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary material

42523_2019_4_MOESM1_ESM.xlsx (3.7 mb)
Additional file 1: Table S1. Quality filtering and OTU distribution at each incubation time. Table S2. Diversity indices at each incubation time. Figures S1A., S1B, S1C Rarefaction curves of equilibration, control and A. taxiformis amended vessels respectively. Figure S2. Principle Coordinate Analysis plot. Table S3. OTU table. Table S4. Raw sequence barcodes for archived 16S rRNA gene amplicon data. Table S5. Results of AMOVA and HOMOVA statistical tests. (XLSX 3751 kb)


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Copyright information

© The Author(s) 2019

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.

Authors and Affiliations

  • Breanna Michell Roque
    • 1
  • Charles Garrett Brooke
    • 1
  • Joshua Ladau
    • 2
  • Tamsen Polley
    • 1
  • Lyndsey Jean Marsh
    • 1
  • Negeen Najafi
    • 1
  • Pramod Pandey
    • 3
  • Latika Singh
    • 3
  • Joan King Salwen
    • 4
  • Emiley Eloe-Fadrosh
    • 2
  • Ermias Kebreab
    • 1
  • Matthias Hess
    • 1
    Email author
  1. 1.Department of Animal ScienceUniversity of CaliforniaDavisUSA
  2. 2.Department of Energy Joint Genome InstituteWalnut CreekUSA
  3. 3.Department of Population Health and ReproductionSchool of Veterinary MedicineDavisUSA
  4. 4.Department of Earth System ScienceStanford UniversityStanfordUSA

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