Abstract:Little is known about the archaeal diversity of fermented seafood; most of the earlier studies of fermented food have focused on lactic acid bacteria (LAB) in the fermentation process. In this study, the archaeal and bacterial diversity in seven kinds of fermented seafood were culture-independently examined using barcoded pyrosequencing and PCR-denaturing gradient gel electrophoresis (DGGE) methods. The multiplex barcoded pyrosequencing was performed in a single run, with multiple samples tagged uniquely by mu… Show more
“…A rarefaction curve with no plateau indicated the need for additional sampling to reveal the extent of ecosystem diversity Sequences classified as Crenarchaeota, Chlamydiae, Spirochaetes, BRC1, Armatimonadetes, Nitrospira, TM7, Tenericutes, Synergistetes, WS3, Caldiserica, Cyanobacteria, Euryarchaeota, Elusimicrobia, Fusobacteria, Thermodesulfobacteria, Chlorobi, DeinococcusThermus and unclassified phyla were summarized in the group of "other" phyla. (Roh et al, 2010). In this study, all rarefaction curves failed to reach saturation (Fig.…”
Section: Diversity Of Microbial Communitymentioning
“…A rarefaction curve with no plateau indicated the need for additional sampling to reveal the extent of ecosystem diversity Sequences classified as Crenarchaeota, Chlamydiae, Spirochaetes, BRC1, Armatimonadetes, Nitrospira, TM7, Tenericutes, Synergistetes, WS3, Caldiserica, Cyanobacteria, Euryarchaeota, Elusimicrobia, Fusobacteria, Thermodesulfobacteria, Chlorobi, DeinococcusThermus and unclassified phyla were summarized in the group of "other" phyla. (Roh et al, 2010). In this study, all rarefaction curves failed to reach saturation (Fig.…”
Section: Diversity Of Microbial Communitymentioning
“…Neither Sanger nor next-generation sequencing is able to circumvent potential biases introduced by PCR, because they are all based on PCR. In this study, due to the difficulty of extracting DNA from coal and rock samples, we have used nested PCR to amplify the 16S rRNA gene, which is also used to analyze the microbial communities in fermented seafood by pyrosequencing (Roh et al, 2009). Although nested PCR might introduce more potential bias and mask actual microbial diversity, it has been reported that more microbial diversity was found using nested PCR compared to direct PCR (Vissers et al, 2009).…”
a b s t r a c t a r t i c l e i n f oIt is generally believed that biogenic coal bed methane (CBM) is an end product of coal biodegradation by methanogenic archaea and syntrophic bacteria. In this work, the archaeal and bacterial communities of CBM reservoir associated with Ordos Basin in China were investigated using 454 pyrosequencing. Sampling produced water, coal and rock in the reservoir, a total of 46,598 sequence reads were obtained. All archaea were methanogens with the genus Methanolobus predominating. The genus consisted of 81.18% of pyrosequencing reads in water sample and > 99% in coal and rock samples. Although the phylum Proteobacteria was the main component of all samples, bacterial communities in coal and rock samples were similar at the genus level, which were distinctly separated with water sample. The results strongly suggested that methylotrophic methanogenesis governed the biogenic CBM formation. The separation of microbial communities between water and coal, rock samples should be considered when investigating the process of coal biodegradation and the generation of new biogenic CBM.
“…However, recent advances in massively parallel, short-amplicon sequencing technologies have launched a breakthrough in microbial ecology studies of wine-and foodfermentation systems (14,(21)(22)(23)(24)(25)(26)(27), putting hitherto untenable ecological questions within reach.…”
Wine grapes present a unique biogeography model, wherein microbial biodiversity patterns across viticultural zones not only answer questions of dispersal and community maintenance, they are also an inherent component of the quality, consumer acceptance, and economic appreciation of a culturally important food product. On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone. This study used a high-throughput, short-amplicon sequencing approach to demonstrate that regional, site-specific, and grapevariety factors shape the fungal and bacterial consortia inhabiting wine-grape surfaces. Furthermore, these microbial assemblages are correlated to specific climatic features, suggesting a link between vineyard environmental conditions and microbial inhabitation patterns. Taken together, these factors shape the unique microbial inputs to regional wine fermentations, posing the existence of nonrandom "microbial terroir" as a determining factor in regional variation among wine grapes.viticulture | agriculture | metagenomics | next-generation sequencing
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