Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22364071_1.fastq.gz | Fastqsanger.gz | |||
| SRR22364071_2.fastq.gz | Fastqsanger.gz | |||
| SRR22364072_1.fastq.gz | Fastqsanger.gz | |||
| SRR22364072_2.fastq.gz | Fastqsanger.gz | |||
| SRR22364073_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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:Bamboo represents the only major lineage of grasses that is native to forests and is one of the most important non-timber forest products in the world. Moso bamboo is a large woody bamboo that has ecological, economic and cultural value in Asia and accounts for ~70% of the total bamboo growth area (Peng et al., 2013). In the aspect of epigenetics of Moso bamboo,the total genomic DNA methylation rates in Moso bamboo at different chronological ages were significantly different (Yuan et al., 2014). Those show that the flowering of Moso bamboo are closely related to epigenetic modification. However, DNA methylation in single base resolution has never been reported in moso bamboo. In this study, leaves from three-week bamboo, one-year bamboo, flower in next year bamboo, flowering bamboo and Flower florets was used for bisulfite sequencing (BS-seq), and RNA-Seq. Genome-wide methylation profile and gene expression analysis were constructed to reveal the factors to regualte the phase transition from vegetative to reproductive growth in moso bamboo.
2021-04-30 | GSE121216 | GEO
Project description:Bamboo represents the only major lineage of grasses that is native to forests and is one of the most important non-timber forest products in the world. Moso bamboo is a large woody bamboo that has ecological, economic and cultural value in Asia and accounts for ~70% of the total bamboo growth area (Peng et al., 2013). In the aspect of epigenetics of Moso bamboo,the total genomic DNA methylation rates in Moso bamboo at different chronological ages were significantly different (Yuan et al., 2014). Those show that the flowering of Moso bamboo are closely related to epigenetic modification. However, DNA methylation in single base resolution has never been reported in moso bamboo. In this study, leaves from three-week bamboo, one-year bamboo, flower in next year bamboo, flowering bamboo and Flower florets was used for bisulfite sequencing (BS-seq), and RNA-Seq. Genome-wide methylation profile and gene expression analysis were constructed to reveal the factors to regualte the phase transition from vegetative to reproductive growth in moso bamboo.
2021-04-30 | GSE122135 | GEO
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:<p>Bamboo rats (<em>Rhizomys pruinosus</em>) are among the few mammals that lives on a bamboo-based diet which is mainly composed of lignocellulose. However, the mechanisms of adaptation of their gut microbiome and metabolic systems in the degradation of lignocellulose are largely unknown. Here, we conducted a multi-omics analysis on bamboo rats to investigate the interaction between their gut microbiomes and metabolic systems in the pre- and post-weaning periods, and observed significant relationships between dietary types, gut microbiome, serum metabolome and host gene expression. For comparison, published gut microbial data from the famous bamboo-eating giant panda (<em>Ailuropoda melanoleuca</em>) were also used for analysis. We found that the adaptation of the gut microbiome of the bamboo rat to a lignocellulose diet is related to a member switch in the order Bacteroidales from family <em>Bacteroidaceae</em> to family <em>Muribaculaceae</em>, while for the famous bamboo-eating giant panda, several aerobes and facultative anaerobes increase after weaning. The conversion of bacteria with an increased relative abundance in bamboo rats after weaning enriched diverse carbohydrate-active enzymes (CAZymes) associated with lignocellulose degradation and functionally enhanced the biosynthesis of amino acids and B vitamins. Meanwhile, the circulating concentration of short chain fatty acids (SCFAs) derived metabolites and the metabolic capacity of linoleic acid in the host were significantly elevated. Our findings suggest that fatty acid metabolism, including linoleic acid and SCFAs, are the main energy sources for bamboo rats in response to the low-nutrient</p>
2022-04-22 | MTBLS4161 | MetaboLights
Project description:The small RNA libraries from Moso bamboo (Phyllostachy heterocycla) roots and leaves were constructed by using high definition adapters . The small RNA profiles were analyzed. A collection of micro RNAs with similarity to the micro RNA entries in mirbase were discovered. The putative genomic loci of the micro RNAs were identified. Analysis of small RNA profiles from the root and leaf tissues of young Moso Bamboo seedlings
2014-08-01 | E-GEOD-55305 | biostudies-arrayexpress
Project description:We adopted the high-throughput sequencing technology and compared the transcriptomes of Moso bamboo rhizome buds in germination stage and late development stage. We found that the development of Moso bamboo rhizome lateral buds was coordinated by multiple pathways, including meristem development, sugar metabolism and phytohormone signaling. Phytohormones have fundamental impacts on the plant development. We found the evidence of several major hormones participating in the development of Moso bamboo rhizome lateral bud. Furthermore, we showed direct evidence that Gibberellic Acids (GA) signaling participated in the Moso bamboo stem elongation.
2019-12-14 | GSE142030 | GEO
Project description:Moso bamboo (Phyllostachys edulis (Carrière) J. Houz.), ) is one of the most importantessential economic bamboo species in China. However, the woods quality and yield of bamboo shoots were significantly threatened by diverse environmental conditions. significantly threaten the quality of wood and yield of bamboo shoots. In this study, to explore the molecular mechanism of abiotic stress response, we report the RNA-seq analyses of mosoMoso bamboo treated with drought, salt, SA and ABA at three -time courses. A total of 224.4 Gb clean data were generate in to explore the molecular mechanism of the abiotic stress response. The full-length transcriptome sequencing of these four treatments generated a total of 224.4 Gb data after quality trimming, and approximately 5.83Gban average of 6.615 Gb clean data were per sample was generated in per sample. The comparative analyses of the generated transcriptome data in this study will provide a valuable resource for identifying regulatory genes and potential pathways involved in various abiotic stresses in mosoMoso bamboo.
2021-10-01 | GSE169067 | GEO
Project description:Bamboo is a large Poaceae perennial with 1,642 species worldwide. We reported single-cell transcriptomes of 14,279 filtered single cells derived from the basal root tips of Moso bamboo.
2023-08-21 | GSE229126 | GEO