Technical note: Comparison of biomarker and molecular biological methods for estimating methanogen abundance

C. A. McCartney, I. D. Bull, S. M. Waters, R. J. Dewhurst

Research output: Contribution to journalArticle

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Abstract

Quantitative real-time PCR (qPCR) has become a popular method for estimation of methanogen abundance in the ruminant digestive tract. However, there is no established method in terms of primer choice and quantification, which means that results are variable and not directly comparable between studies. Archaeol has been proposed as an alternative marker for methanogen abundance, as it is ubiquitous in methanogenic Archaea and can be quantified by gas chromatography-mass spectrometry (GC-MS). The aim of this experiment was to compare total methanogen populations estimated using the new archaeol approach with estimates based on qPCR. Specific primer sets and probes were used to detect dominant ruminal methanogen species Methanobrevibacter ruminantium, Methanobrevibacter smithii, Methanospheara stadtmanae, and total methanogen populations. There was variation in the relationships between total methanogen abundance estimates based on archaeol and qPCR. In addition the universal methanogen primers appeared to preferentially amplify genes from M. smithii. Archaeol had the strongest relationship with the dominant rumen methanogen M. ruminantium, whereas the total methanogen primers had a comparatively weak relationship with archaeol. Archaeol analysis was a useful adjunct to molecular biology methods but it seems that a valid specific primer for M. ruminantium would be more useful than a biased primer for total methanogens.
Original languageEnglish
Pages (from-to)5724-5728
Number of pages5
JournalJournal of Animal Science
Volume91
Issue number12
Early online date21 Oct 2013
DOIs
Publication statusPublished - Dec 2013

Fingerprint

methanogens
Ruminants
biomarkers
Methanobrevibacter
Biomarkers
ruminants
Methanobrevibacter smithii
Archaea
Rumen
methodology
Gas Chromatography-Mass Spectrometry
Population
Gastrointestinal Tract
Real-Time Polymerase Chain Reaction
Molecular Biology
Genes
digestive tract
molecular biology
rumen
quantitative polymerase chain reaction

Keywords

  • Archaea
  • Archaeol
  • Methanogens
  • qPCR
  • Ruminant Digestive Tract

Cite this

Technical note : Comparison of biomarker and molecular biological methods for estimating methanogen abundance. / McCartney, C. A. ; Bull, I. D. ; Waters, S. M.; Dewhurst, R. J.

In: Journal of Animal Science, Vol. 91, No. 12, 12.2013, p. 5724-5728.

Research output: Contribution to journalArticle

McCartney, C. A. ; Bull, I. D. ; Waters, S. M. ; Dewhurst, R. J. / Technical note : Comparison of biomarker and molecular biological methods for estimating methanogen abundance. In: Journal of Animal Science. 2013 ; Vol. 91, No. 12. pp. 5724-5728.
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