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ABSTRACT:
PROVIDER: PRJNA867541 | ENA |
REPOSITORIES: ENA
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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:Purpose:Bamboo shoots rapidly lose water and accumulate lignin when stored under room temperature, while low temperature conditioning (LTC, 4℃) can alleviate lignification and reduce weightlessness rate. However, few transcriptional response and profiling datasets are available to explore the LTC mechanism of bamboo shoots.The goal of this study is to provides insights into the regulation of Lei bamboo (Phyllostachys violascens) shoots during postharvest cold storage by transcriptome analysis. Methods:Total RNA was extracted using RNAiso Plus (Takara, Japan) according to the protocol, and after quality testing, was used for library construction and transcriptome sequencing by Illumina Novaseq™ 6000. The quality-controlled reads were aligned to the Phyllostachys edulis reference genome (http://gigadb.org/dataset/100498). The edgeR program25 was used for differential expression analyses. Results: After raw data filtering, a high clean data rate from each sample was achieved, and the assessment result for the clean data by FastQC all demonstrated that our sequencing data was of high quality, full representativeness and validity. Compared with CK, a total of 7,452 DEGs were identified during LT storage. The Pearson’s correlation coefficient (r) and principle component analysis (PCA) results all suggested a high correlation among all samples. The above results suggest an effective LT treatment of postharvest bamboo shoots and a high-quality bioinformatics analysis of our RNA-seq results. Conclusions: Our study represents the first detailed analysis of Lei bamboo (Phyllostachys violascens) shoots during postharvest cold storage transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would reveal the essence of ripening and senescence of fruits and vegetables.
2020-10-01 | GSE149182 | 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: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: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