Gut metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA701542 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15012300_1.fastq.gz | Fastqsanger.gz | |||
| SRR15012300_2.fastq.gz | Fastqsanger.gz | |||
| SRR15012301_1.fastq.gz | Fastqsanger.gz | |||
| SRR15012301_2.fastq.gz | Fastqsanger.gz | |||
| SRR15012302_1.fastq.gz | Fastqsanger.gz |
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Project description:The iconic giant panda is an endangered species known worldwide for its peculiar dietary habits. While retaining the digestive system of a carnivore, the giant panda successfully moved into a diet almost exclusively based on bamboo. Digestion of lignocellulose is believed to be conducted solely by its gut microbiome, provided that no lignocellulose-degrading enzyme was found in the giant panda’s genome. Many reports focused on which lignocellulose component feeds the giant panda, while little effort was made to link the products of bamboo fermentation to the panda’s dietary choices. In the present study, fermentation of either green leaves or yellow pith was conducted in the laboratory using gut microbiomes derived from either green or yellow stools, respectively. Green leaves were fermented to ethanol, lactate and acetate, while yellow pith to lactate resembling, respectively, hetero/homo-fermentation patterns. Several microbial pathways (assessed by metaproteomics) related to hemicellulose rather than cellulose degradation. However, alpha-amylases (E.C. 3.2.1.1) from the giant panda itself were the most predominant enzyme (up to 60% of all metaproteins), indicating that they have a primary role in bamboo digestion. The distinct fermentation profiles resulting from digestion of selected portions of bamboo may be part of the feeding strategy of giant pandas.
2020-03-02 | PXD010872 | Pride
Project description:Giant panda are carnivorous bears which feed almost exclusively on plant biomass (i.e. bamboo). The potential contribution of its gut microbiome to lignocellulose degradation has been mostly investigated with cultivation-independent approaches. Recently, we reported on the first lab-scale cultivation of giant panda gut microbiomes and described their actual fermentation capacity. Fermentation of bamboo leaf using green dung resulted in a neutral pH, the main products being ethanol, lactate and H2. Fermentation of bamboo pith using yellow dung resulted in an acidic pH, the main product being lactate. Here, we cultivated giant panda gut microbiomes to test 1) the impact of mixed dung as inoculum; 2) the fermentation capacity of solid lignocellulose as opposed to organics-rich biofluids in the dung; 3) the artificial shift of pH from neutral to acidic on bamboo leaf fermentation. Our results indicate that i) gut microbiomes fermentation of solid lignocellulose contributes up to a maximum of 1/3 even in the presence of organics-rich biofluids; ii) alcohols are an important product of bamboo leaf fermentation at neutral pH; iii) aside hemicellulose, gut microbiomes may degrade plant cell membranes to produce glycerol; iv) pH, rather than portion of bamboo, ultimately determines fermentation profiles and gut microbiome assemblage.
2021-06-11 | PXD018503 | Pride
Project description:Pieris brassicae gut 16S metabarcoding reads
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Project description:The prevention or delay of brain senescence would enhance the quality of life for older persons. We investigated the effects of soybean extracts in senescence-accelerated (SAMP10) mice. This mouse is a model of brain senescence with a short life span, cerebral atrophy and cognitive dysfunction. Mice were fed a diet containing soybean extracts from 1 to 12 months of age. The effects of green and yellow soybean extracts were compared with a control diet without soybean extracts. Cognitive functions were higher in aged mice fed green soybean than age-matched control mice and mice fed yellow soybean. We further investigated transcriptome of the SAMP10 hippocampus indicated that expression levels of 36 genes were significantly higher and 19 genes were lower in mice that ingested green soybean than in mice that ingested yellow soybean. Some of the evidences were reconfirmed by real time PCR analysis; the levels of Cdh1 and Ptgds mRNA were significantly higher and that the level of Aplp1 was significantly lower in aged SAMP10 mice fed green soybean than mice ingested yellow soybean and control mice. Additionally, the amount of amyloid beta 40 and 42 was lower in the insoluble fraction of aged SAMP10 mice fed green soybean than control mice and mice fed yellow soybean, although the levels of amyloid beta 40 and 42 in the soluble fraction were not different. Lipocalin-type prostaglandin D2 synthase (L-PGDS) has been proposed as the endogenous amyloid beta - chaperone, suggesting that amyloid aggregation was lower in mice fed green soybean than control mice and mice fed yellow soybean. These results indicate that the intake of green soybean improved cognitive function in aged mice, and suppressed amyloid beta accumulation. Green soybean might help healthy aging of the brain in older persons. The effect of green and yellow soybean extracts on cognitive function in aged SAMP10 mice. Mice were fed a CE-2 diet containing 3.0% soybean extracts taken from both yellow and green soybean species, from 1 to 12 months of age. Total RNA was extracted from the stored hippocampus for DNA microarray analysis.
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Project description:Monitor changes in the proteome of senescing leaves, using protein MS data obtained from the same leaf groups used for imaging. Arabidopsis thaliana mature leaves were grouped according to their chlorophyll content: Dark Green (DG), Green (G), Light Green (LG) and Yellow (Y), containing 100, 45, 25 and 6.5% chlorophyll relative to DG, respectivelyArabidopsis thaliana mature leaves were grouped according to their chlorophyll content: Dark Green (DG), Green (G), Light Green (LG) and Yellow (Y), containing 100, 45, 25 and 6.5% chlorophyll relative to DG, respectively
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Project description:Erythromycin (ERY) is a commonly used antibiotic that can be found in wastewater effluents globally. Due to the mechanisms by which they kill and prevent bacterial growth, antibiotics can have significant unwanted impacts on the fish gut microbiome. The overall objective of this project was to assess the effects of erythromycin and an antibiotic mixture on fish gut microbiomes. The project was split into two experiments to assess gut microbiome in response to exposure with ERY alone or in mixture with other common antibiotics. The objectives of experiment 1 were to understand uptake and depuration of ERY in juvenile rainbow trout (RBT) over a 7 d uptake followed by a 7 d depuration period using three concentrations of ERY. Furthermore, throughout the study changes in gut microbiome response were assessed. In experiment 2, a follow-up study was conducted using an identical experimental design to assess the impacts of an antibiotic-mixture (ERY, ampicillin, metronidazole, and ciprofloxacin at 100 µg/g each). Here, three matrices were analyzed, with gut collected for 16s metabarcoding, plasma for untargeted metabolomics, and brain for mRNA-seq analysis. ERY was depurated from the fish relatively quickly and gut microbiome dysbiosis was observed at 7 d after exposure, with a slight recovery after the 7 d depuration period. A greater number of plasma metabolites was dysregulated at 14 d compared to 7 d revealing temporality compared to gut microbiome dysbiosis. Furthermore, several transformation products of antibiotics and biomarker metabolites were observed in plasma due to antibiotic exposure. Brain transcriptome revealed only slight alterations due to antibiotic exposure. The results of these studies will help inform aquaculture practitioners and risk assessors when assessing the potential impacts of antibiotics in fish feed and the environment, with implications for host health.
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Project description:The prevention or delay of brain senescence would enhance the quality of life for older persons. We investigated the effects of soybean extracts in senescence-accelerated (SAMP10) mice. This mouse is a model of brain senescence with a short life span, cerebral atrophy and cognitive dysfunction. Mice were fed a diet containing soybean extracts from 1 to 12 months of age. The effects of green and yellow soybean extracts were compared with a control diet without soybean extracts. Cognitive functions were higher in aged mice fed green soybean than age-matched control mice and mice fed yellow soybean. We further investigated transcriptome of the SAMP10 hippocampus indicated that expression levels of 36 genes were significantly higher and 19 genes were lower in mice that ingested green soybean than in mice that ingested yellow soybean. Some of the evidences were reconfirmed by real time PCR analysis; the levels of Cdh1 and Ptgds mRNA were significantly higher and that the level of Aplp1 was significantly lower in aged SAMP10 mice fed green soybean than mice ingested yellow soybean and control mice. Additionally, the amount of amyloid beta 40 and 42 was lower in the insoluble fraction of aged SAMP10 mice fed green soybean than control mice and mice fed yellow soybean, although the levels of amyloid beta 40 and 42 in the soluble fraction were not different. Lipocalin-type prostaglandin D2 synthase (L-PGDS) has been proposed as the endogenous amyloid beta - chaperone, suggesting that amyloid aggregation was lower in mice fed green soybean than control mice and mice fed yellow soybean. These results indicate that the intake of green soybean improved cognitive function in aged mice, and suppressed amyloid beta accumulation. Green soybean might help healthy aging of the brain in older persons.
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