Dietary polysaccharides: fermentation potentials of a primitive gut ecosystem.
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ABSTRACT:
PROVIDER: PRJEB29312 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2855680_1.fastq.gz | Fastqsanger.gz | |||
| ERR2855680_2.fastq.gz | Fastqsanger.gz | |||
| ERR2855690_1.fastq.gz | Fastqsanger.gz | |||
| ERR2855690_2.fastq.gz | Fastqsanger.gz | |||
| ERR2855700_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Dietary polysaccharides: fermentation potentials of a primitive gut ecosystem.
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Project description:Dietary polysaccharides: fermentation potentials of a primitive gut ecosystem.
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Project description:This SuperSeries is composed of the following subset Series: GSE15686: Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous laboratory fermentation (I) GSE15691: Meta-transcriptome analysis of a natural spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation (I) GSE15692: Meta-transcriptome analysis of a natural spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation (II) GSE15693: Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous laboratory fermentation (II) Refer to individual Series
2010-07-07 | E-GEOD-15803 | biostudies-arrayexpress
Project description:Glaciers are populated by a large number of microorganisms including bacteria, archaea and microeukaryotes. From an ecological point of view, three ecosystems can be differentiated in glaciers: the supraglacial ecosystem, the subglacial ecosystem and the englacial ecosystem. Several factors such as solar radiation, nutrient availability and water content greatly determine the diversity and abundance of microbial populations, the type of metabolism and the biogeochemical cycles. Firstly, the supraglacial ecosystem, sunlit and oxygenated, is predominantly populated by autotrophic microorganisms. Secondly, the subglacial ecosystem contains a majority of chemoautrotophs that are fed on the mineral salts of the rocks and basal soil. Lastly, the englacial ecosystem is the less studied and the one that contains the smallest number of microorganisms. However, these unknown englacial microorganisms establish a true trophic chain and appear to have an active metabolism. In order to study their metabolic potentials, samples of englacial ice were taken from an Antarctic glacier. The cells were harvested and their proteins were extracted and analyzed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI/TOF/TOF). Several proteins and enzymes were found that demonstrate the existence of cellular activity at subzero temperatures. In this way it is shown that the englacial microorganisms are not quiescent, but that they maintain an active metabolism and play an important role in the glacial microbial community.
2019-08-29 | PXD010060 | Pride
Project description:Glaciers are populated by a large number of microorganisms including bacteria, archaea and microeukaryotes. From an ecological point of view, three ecosystems can be differentiated in glaciers: the supraglacial ecosystem, the subglacial ecosystem and the englacial ecosystem. Several factors such as solar radiation, nutrient availability and water content greatly determine the diversity and abundance of microbial populations, the type of metabolism and the biogeochemical cycles. Firstly, the supraglacial ecosystem, sunlit and oxygenated, is predominantly populated by autotrophic microorganisms. Secondly, the subglacial ecosystem contains a majority of chemoautrotophs that are fed on the mineral salts of the rocks and basal soil. Lastly, the englacial ecosystem is the less studied and the one that contains the smallest number of microorganisms. However, these unknown englacial microorganisms establish a true trophic chain and appear to have an active metabolism. In order to study their metabolic potentials, samples of englacial ice were taken from an Antarctic glacier. The cells were harvested and their proteins were extracted and analyzed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI/TOF/TOF). Several proteins and enzymes were found that demonstrate the existence of cellular activity at subzero temperatures. In this way it is shown that the englacial microorganisms are not quiescent, but that they maintain an active metabolism and play an important role in the glacial microbial community.
2019-08-29 | PXD010185 | Pride
Project description:Temporal shotgun metagenomic dissection of the lambic beer fermentation ecosystem
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Project description:Earthworms are among the most primitive animals and are of fundamental importance to the turnover of organic matter in the terrestrial biosphere. These invertebrates ingest materials that are colonized by microbes, some of which are subject to disruption by the crop/gizzard or other lytic events during gut passage. Protein and RNA are dominant polymers of disrupted microbial cells, and these biopolymers facilitate robust fermentations by surviving ingested bacteria. To further resolve these fermentations, amino acids and ribose (as fermentable constituents of protein and RNA, respectively) were evaluated as potential drivers of fermentation in gut content of the model earthworm Lumbricus terrestris (taxa were examined with 16S rRNA-based analyses). Of eight amino acids tested, glutamate, aspartate, and threonine were most stimulatory and yielded dissimilar fermentations facilitated by contrasting taxa (e.g., glutamate stimulated the Fusobacteriaceae and yielded H2 and formate, whereas aspartate stimulated the Aeromonadaceae and yielded succinate and propionate). A marginal Stickland fermentation was associated with the Peptostreptococcaceae and Lachnospiraceae Ribose fermentation yielded a complex product profile facilitated primarily by the Aeromonadaceae The transient nature of succinate was linked to its decarboxylation to propionate and the Fusobacteriaceae, whereas the transient nature of formate was linked to formate-hydrogen lyase activity and the Peptostreptococcaceae These findings reinforce the likelihood that (i) the animal host and hosted fermentative bacteria compete for the constituents of protein and RNA in the alimentary canal and (ii) diverse gut fermenters engaged in the fermentation of these constituents produce products that can be utilized by earthworms.IMPORTANCE Animal health is linked to gut ecosystems whose primary function is normally the digestion of dietary matter. Earthworms are representative of one of the oldest known animal lineages and, despite their primitive nature, have unique environmental impact by virtue of their dietary consumption of their habitat, i.e., soil-associated matter. A resident gut community is a hallmark of many gut ecosystems of evolutionarily more advanced animals, but the alimentary canal of earthworms is dominated by ingested transient soil microbes. Protein and RNA are (i) the primary organic components of microbial cells that are subject to lysis during gut passage and (ii) fermentable dietary substrates in the alimentary canal. This study examined the gut-associated fermentation of constituents of these biopolymers to determine how their fermentation is integrated to the microbiological dynamics of the gut and might contribute to earthworm-linked transformations of organic matter in the terrestrial biosphere.
| S-EPMC6752017 | biostudies-literature
Project description:Hyperthermophilic bacteria of the genus Thermotoga are known to utilize a wide range of simple and complex polysaccharides. T. maritima's transcriptional response to a variety of mono- and poly-saccharides was previously studied to assign functions to genes involved in carbohydrate uptake and utilization. To compare and contrast closely-related members of the Thermotoga genus, a four-species microarray was developed by expanding a whole genome T. maritima array to include unique genes from three other species (T. neapolitana, T. petrophila, and T. sp. RQ2). This multi-species array was used to investigate the diversity of the genus, specifically the response of each of the four species to a mixture of polysaccharides (galactomannan, glucomannan, xylan, pectin, lichenan, and carboxymethyl cellulose). RNA derived from glucose-grown cultures (glu) was compared to RNA derived from polysaccharide-grown cultures (poly) using a dye swap setup.
2012-01-05 | E-GEOD-29557 | biostudies-arrayexpress
Project description:Lactic acid bacteria (LAB) are of industrial importance in the production of fermented foods, among which sourdough-derived products. Despite their limited metabolic capacity LAB contribute considerably to important characteristics of fermented foods, among which extended shelf-life, microbial safety, improved texture, and enhanced organoleptic properties. Thanks to the considerable amount of LAB genomic information that became available during the last years, transcriptome, and by extension meta-transcriptome studies, are the exquisite research approaches to study whole ecosystem gene expression into more detail. In this study, microarray analyses were performed using RNA sampled during four 10-day spontaneous sourdough fermentations carried out in the laboratory, namely two wheat and two spelt fermentations with daily back-slopping. Hereto, the in-house developed functional gene LAB microarray was used, representing 406 genes that play a key role in sugar and nitrogen metabolism, functional metabolite production, stress responses and health and safety characteristics. The results reveal the activation of different key metabolic pathways, the ability to use different energy sources, and successful acid and oxidative stress responses. Also, a new algorithm was developed to compute a net expression profile for each of the represented genes, thereby exceeding the species level. The labeled aRNA of the sourdough fermentation samples was hybridized using a loop design, i.e. subsequent samples (e.g. 27 h and 51 h, 51 h and 75 h etc.) were hybridized together on the microarray and the loop was closed by hybridizing the last sample with the first.
2010-07-07 | E-GEOD-15693 | biostudies-arrayexpress
Project description:Lactic acid bacteria (LAB) are of industrial importance in the production of fermented foods, among which sourdough-derived products. Despite their limited metabolic capacity LAB contribute considerably to important characteristics of fermented foods, among which extended shelf-life, microbial safety, improved texture, and enhanced organoleptic properties. Thanks to the considerable amount of LAB genomic information that became available during the last years, transcriptome, and by extension meta-transcriptome studies, are the exquisite research approaches to study whole ecosystem gene expression into more detail. In this study, microarray analyses were performed using RNA sampled during four 10-day spontaneous sourdough fermentations carried out in the laboratory, namely two wheat and two spelt fermentations with daily back-slopping. Hereto, the in-house developed functional gene LAB microarray was used, representing 406 genes that play a key role in sugar and nitrogen metabolism, functional metabolite production, stress responses and health and safety characteristics. The results reveal the activation of different key metabolic pathways, the ability to use different energy sources, and successful acid and oxidative stress responses. Also, a new algorithm was developed to compute a net expression profile for each of the represented genes, thereby exceeding the species level. The labeled aRNA of the sourdough fermentation samples was hybridized using a loop design, i.e. subsequent samples (e.g. 27 h and 51 h, 51 h and 75 h etc.) were hybridized together on the microarray and the loop was closed by hybridizing the last sample with the first.
2010-07-07 | E-GEOD-15686 | biostudies-arrayexpress