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Research Support, Non-U.S. Gov'ts
Pyrosequencing-based Analysis of Fecal Microbial Communities in Three Purebred Pig Lines
Edward Alain B. Pajarillo , Jong Pyo Chae , Marilen P. Balolong , Hyeun Bum Kim , Kang-Seok Seo , Dae-Kyung Kang
J. Microbiol. 2014;52(8):646-651.   Published online July 18, 2014
DOI: https://doi.org/10.1007/s12275-014-4270-2
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AbstractAbstract
This study examined the fecal bacterial diversity of 15-week-old pigs from three purebred lines: Duroc, Landrace, and Yorkshire. Taxon-dependent and -independent analyses were performed to evaluate differences in the fecal bacterial communities and to identify bacterial genera that can be used to discriminate breeds, following high-throughput pyrosequencing of 16S rRNA genes. Among the breeds evaluated, Landrace had the most diverse bacterial community composition. Prevotella, Blautia, Oscillibacter, and Clostridium were detected in all samples regardless of breed. On the other hand, Catenibacterium, Blautia, Dialister, and Sphaerochaeta were differentially detected among breeds, as demonstrated by the canonical loading plot. The discriminant analysis of principal components plot also showed clear separation of the three purebred pig lines, with a certain degree of similarity between Landrace and Yorkshire pigs and a distinct separation between Duroc pigs and the other two breeds. Other factors not related to breed, such as season or time of sampling and pen effects, may contribute to shaping the gut microbiota of pigs.

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Variations in 16S rRNA-based Microbiome Profiling between Pyrosequencing Runs and between Pyrosequencing Facilities
Minseok Kim , Zhongtang Yu
J. Microbiol. 2014;52(5):355-365.   Published online April 11, 2014
DOI: https://doi.org/10.1007/s12275-014-3443-3
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AbstractAbstract
Pyrosequencing of 16S rRNA gene amplicons on the 454 FLX Titanium platform has been widely used to analyze microbiomes in various environments. However, different results may stem from variations among sequencing runs or among sequencing facilities. This study aimed to evaluate these variations between different pyrosequencing runs by sequencing 16S rRNA gene amplicon libraries generated from three sets of rumen samples twice each on the 454 FLX Titanium system at two independent sequencing facilities. Similar relative abundances were found for predominant taxa represented by large numbers of sequence reads but not for minor taxa represented by small numbers of sequence reads. The two sequencing facilities revealed different bac-terial profiles with respect to both predominant taxa and minor taxa, including the most predominant genus Prevo-tella, the family Lachnospiraceae, and the phylum Proteo-bacteria. Differences in primers used to generate amplicon libraries may be a major source of variations in microbiome profiling. Because different primers and regions of 16S rRNA genes are often used by different researchers, significant variations likely exist among studies. Quantitative interpre-tation for relative abundance of taxa, especially minor taxa, from prevalence of sequence reads and comparisons of re-sults from different studies should be done with caution.

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