Pros and Cons of Ion-Torrent Next Generation Sequencing versus Terminal Restriction Fragment Length Polymorphism T-RFLP for Studying the Rumen Bacterial Community

The development of next generation sequencing has challenged the use of other molecular fingerprinting methods used to study microbial diversity. We analysed the bacterial diversity in the rumen of defaunated sheep following the introduction of different protozoal populations, using both next genera...

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Vydané v:	PloS one Ročník 9; číslo 7; s. e101435
Hlavní autori:	de la Fuente, Gabriel, Belanche, Alejandro, Girwood, Susan E., Pinloche, Eric, Wilkinson, Toby, Newbold, C. Jamie
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	United States Public Library of Science 22.07.2014 Public Library of Science (PLoS)
Predmet:	Ammonia Animals Base Sequence Biology and Life Sciences Cattle Chemical fingerprinting Ciliophora - physiology Diet DNA fingerprinting DNA, Bacterial - genetics Ecosystems Fermentation Gene polymorphism High-Throughput Nucleotide Sequencing Microbiota - genetics Microorganisms Nutrition research Polymorphism Polymorphism, Restriction Fragment Length Protozoa Relative abundance Restriction fragment length polymorphism Rumen Rumen - microbiology Sequence Analysis, DNA Sheep Sheep, Domestic - microbiology United Kingdom > UK
ISSN:	1932-6203, 1932-6203
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Shrnutí:	The development of next generation sequencing has challenged the use of other molecular fingerprinting methods used to study microbial diversity. We analysed the bacterial diversity in the rumen of defaunated sheep following the introduction of different protozoal populations, using both next generation sequencing (NGS: Ion Torrent PGM) and terminal restriction fragment length polymorphism (T-RFLP). Although absolute number differed, there was a high correlation between NGS and T-RFLP in terms of richness and diversity with R values of 0.836 and 0.781 for richness and Shannon-Wiener index, respectively. Dendrograms for both datasets were also highly correlated (Mantel test = 0.742). Eighteen OTUs and ten genera were significantly impacted by the addition of rumen protozoa, with an increase in the relative abundance of Prevotella, Bacteroides and Ruminobacter, related to an increase in free ammonia levels in the rumen. Our findings suggest that classic fingerprinting methods are still valuable tools to study microbial diversity and structure in complex environments but that NGS techniques now provide cost effect alternatives that provide a far greater level of information on the individual members of the microbial population.
Bibliografia:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 ObjectType-Article-2 ObjectType-Feature-1 content type line 23 Competing Interests: The authors have declared that no competing interests exist. Conceived and designed the experiments: GF AB CJN. Performed the experiments: GF AB. Analyzed the data: GF AB SEG TW EP. Wrote the paper: GF AB EP SEG CJN.
ISSN:	1932-6203 1932-6203
DOI:	10.1371/journal.pone.0101435