High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing

Ross, Elizabeth M., Moate, Peter J., Bath, Carolyn R., Davidson, Sophie E., Sawbridge, Tim I., Guthridge, Kathryn M., Cocks, Ben G. and Hayes, Ben J. (2012) High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing. BMC Genetics, 13 . doi:10.1186/1471-2156-13-53

Author Ross, Elizabeth M.
Moate, Peter J.
Bath, Carolyn R.
Davidson, Sophie E.
Sawbridge, Tim I.
Guthridge, Kathryn M.
Cocks, Ben G.
Hayes, Ben J.
Title High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing
Journal name BMC Genetics   Check publisher's open access policy
ISSN 1471-2156
Publication date 2012-07-02
Sub-type Article (original research)
DOI 10.1186/1471-2156-13-53
Open Access Status DOI
Volume 13
Total pages 14
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Formatted abstract
Background: Variation of microorganism communities in the rumen of cattle (Bos taurus) is of great interest because of possible links to economically or environmentally important traits, such as feed conversion efficiency or methane emission levels. The resolution of studies investigating this variation may be improved by utilizing untargeted massively parallel sequencing (MPS), that is, sequencing without targeted amplification of genes. The objective of this study was to develop a method which used MPS to generate " rumen metagenome profiles" , and to investigate if these profiles were repeatable among samples taken from the same cow. Given faecal samples are much easier to obtain than rumen fluid samples; we also investigated whether rumen metagenome profiles were predictive of faecal metagenome profiles.
Results: Rather than focusing on individual organisms within the rumen, our method used MPS data to generate quantitative rumen micro-biome profiles, regardless of taxonomic classifications. The method requires a previously assembled reference metagenome. A number of such reference metagenomes were considered, including two rumen derived metagenomes, a human faecal microflora metagenome and a reference metagenome made up of publically available prokaryote sequences. Sequence reads from each test sample were aligned to these references. The " rumen metagenome profile" was generated from the number of the reads that aligned to each contig in the database. We used this method to test the hypothesis that rumen fluid microbial community profiles vary more between cows than within multiple samples from the same cow. Rumen fluid samples were taken from three cows, at three locations within the rumen. DNA from the samples was sequenced on the Illumina GAIIx. When the reads were aligned to a rumen metagenome reference, the rumen metagenome profiles were repeatable (P < 0.00001) by cow regardless of location of sampling rumen fluid. The repeatability was estimated at 9%, albeit with a high standard error, reflecting the small number of animals in the study. Finally, we compared rumen microbial profiles to faecal microbial profiles. Our hypothesis, that there would be a stronger correlation between faeces and rumen fluid from the same cow than between faeces and rumen fluid from different cows, was not supported by our data (with much greater significance of rumen versus faeces effect than animal effect in mixed linear model).
Conclusions: We have presented a simple and high throughput method of metagenome profiling to assess the similarity of whole metagenomes, and illustrated its use on two novel datasets. This method utilises widely used freeware. The method should be useful in the exploration and comparison of metagenomes.
Keyword Metagenome profiling
Microbial population comparison
Rumen microbiome
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ
Additional Notes Article number 53

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
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Citation counts: TR Web of Science Citation Count  Cited 25 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 30 times in Scopus Article | Citations
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