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Related Articles 16SrRNA bacterial tag-encoded amplicons pyrosequencing for rapid deciphering of the microbiome of fermented foods: the case of fermented pearl-millet slurries.
Appl Environ Microbiol. 2009 May 1;
Authors: Humblot C, Guyot JP
Pearl millet slurries, mixed or not with groundnuts, were chosen as a model to investigate the feasibility of obtaining a rapid overview of community structure and population dynamics of fermented foods using 16SrRNA bacterial tag-encoded amplicon pyrosequencing. From 14 fermented samples collected either in a traditional small-scale processing unit in Burkina Faso or at laboratory scale, 137 469 sequences of bacterial 16SrRNA gene amplicons were characterized. Except for a few Proteobacteria, almost all the bacterial sequences were attributed to cultivable bacteria. This approach enabled 80.7% of the sequences to be attributed to a family and 70% to a genus, but did not enable identification to the species level. The bacterial sequences were assigned to four phyla, with Firmicutes representing the highest diversity, followed by Proteobacteria, Actinobacteria and Bacteroidetes, which were only found in the slurries prepared in traditional production units. Most of the Firmicutes were lactic acid bacteria mainly represented by members of the Lactobacillus, Pediococcus, Leuconostoc and Weissella genera, whose ratio varied from the onset to the end of the fermentation. The other bacteria present at the beginning of fermentation were generally no longer detected at the end, which is consistent with already known patterns in the microbial ecology of fermented foods. In conclusion, this method seems very promising for rapid and preliminary microbial characterization in many samples of an unknown food sample, by determining numerous nucleic sequences simultaneously without the need for cloning and cultivation dependent methods.
PMID: 19411407 [PubMed - as supplied by publisher]
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Related Articles 16SrRNA bacterial tag-encoded amplicons pyrosequencing for rapid deciphering of the microbiome of fermented foods: the case of fermented pearl-millet slurries.
Appl Environ Microbiol. 2009 May 1;
Authors: Humblot C, Guyot JP
Pearl millet slurries, mixed or not with groundnuts, were chosen as a model to investigate the feasibility of obtaining a rapid overview of community structure and population dynamics of fermented foods using 16SrRNA bacterial tag-encoded amplicon pyrosequencing. From 14 fermented samples collected either in a traditional small-scale processing unit in Burkina Faso or at laboratory scale, 137 469 sequences of bacterial 16SrRNA gene amplicons were characterized. Except for a few Proteobacteria, almost all the bacterial sequences were attributed to cultivable bacteria. This approach enabled 80.7% of the sequences to be attributed to a family and 70% to a genus, but did not enable identification to the species level. The bacterial sequences were assigned to four phyla, with Firmicutes representing the highest diversity, followed by Proteobacteria, Actinobacteria and Bacteroidetes, which were only found in the slurries prepared in traditional production units. Most of the Firmicutes were lactic acid bacteria mainly represented by members of the Lactobacillus, Pediococcus, Leuconostoc and Weissella genera, whose ratio varied from the onset to the end of the fermentation. The other bacteria present at the beginning of fermentation were generally no longer detected at the end, which is consistent with already known patterns in the microbial ecology of fermented foods. In conclusion, this method seems very promising for rapid and preliminary microbial characterization in many samples of an unknown food sample, by determining numerous nucleic sequences simultaneously without the need for cloning and cultivation dependent methods.
PMID: 19411407 [PubMed - as supplied by publisher]
More...