Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1305713 | ENA |
REPOSITORIES: ENA
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Project description:Furans (furfural and 5-hydroxymethylfurfural (HMF)), phenolic aldehydes (4-hydroxybenzaldehyde, syringaldehyde, and vanillin), and weak acids (acetic acid and formic acid) are the main degradation products of lignocellulose pretreatment process and seriously inhibit the cellullas enzyme activity and the fermentation process.
2022-07-21 | GSE208427 | 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:The Lactobacillus buchneri CD034 strain, known to improve the ensiling process of green fodder and the quality of the silage itself was transcriptionally analyzed by sequencing of transcriptomes isolated under anaerobic vs. aerobic conditions. L. buchneri CD034 was first cultivated under anaerobic conditions and then shifted to aerobic conditions by aeration with 21% oxygen. Cultivations already showed that oxygen was consumed by L. buchneri CD034 after aeration of the culture while growth of L. buchneri CD034 was still observed. RNA sequencing data revealed that irrespective of the oxygen status of the culture, the most abundantly transcribed genes are required for basic cell functions such as protein biosynthesis, energy metabolism and lactic acid fermentation. Under aerobic conditions, 283 genes were found to be transcriptionally up-regulated while 198 genes were found to be down-regulated (p-value < 0.01). Up-regulated genes i. a. play a role in oxygen consumption via oxidation of pyruvate or lactate (pox, lctO). Additionally, genes encoding proteins required for decomposition of reactive oxygen species (ROS) such as glutathione reductase or NADH peroxidase were also found to be up-regulated. Genes related to pH homeostasis and redox potential balance were found to be down-regulated under aerobic conditions. Overall, genes required for lactic acid fermentation were hardly affected by the growth conditions applied. Genes identified to be differentially transcribed depending on the aeration status of the culture are suggested to specify the favorable performance of the strain in silage formation.
2017-02-10 | GSE67802 | GEO
Project description:Two-stage two-phase biogas reactor systems consisting each of one batch downflow hydrolysis reactor (HR, vol. 10 L), one process fluid storage tank (vol. 10 L), and one downstream upflow anaerobic filter reactor (AF, vol. 10 L), were operated at mesophilic (M, 37 °C) and thermophilic (T, 55 °C) temperatures and over a period of > 750 d (Figure 1, Additional file 1). For each reactor system and for each process temperature, two replicates were conducted in parallel, denominated further as biological replicates. Further process details were as previously published. Start-up of all fermenters were performed using liquid fermenter material from a biogas plant converting cattle manure in co-digestion with grass and maize silage and other biomass at varying concentrations and at mesophilic temperatures. Silage of perennial ryegrass (Lolium perenne L.) was digested as sole substrate in batches of varying amounts with retention times of 28 d (storage of bale silage at -20 °C, cutting length 3 cm, volatile substances (VS) 32 % of fresh mass (FM), total Kjeldahl nitrogen 7.6 g kgFM-1, NH4+-N 0.7 g kgFM-1, acetic acid 2.6 g kgFM-1, propionic acid < 0.04 g kgFM-1, lactic acid 2.6 g kgFM-1, ethanol 2.2 g kgFM-1, C/N ratio 19.3, chemical oxygen demand (COD) 357.7 g kgFM-1, analysis of chemical properties according to [6]. No spoilage was observed in the silage. Biogas yields were calculated as liters normalized to 0 °C and 1013 hPa (LN) per kilogram volatile substances (kgVS). For chemical analysis, samples were taken from the effluents of HR and AF. For sequencing of 16S rRNA gene amplicon libraries, microbial metagenomes, and microbial metatranscriptomes, samples were taken from the silage digestate in the HR digested for 2 d. At this time point, high AD rates were detected as indicated by the fast increase of volatile fatty acids (VFA), e.g., acetic acid. Sampling was performed at two different organic loading rates (OLR), i.e., batch-fermentation of 500 g (denominated as “low OLR”, samples MOLR500 and TOLR500) and 1,500 g silage (denominated as “increased OLR”, samples MOLR1500 and TOLR1500).
2019-04-19 | E-MTAB-7533 | biostudies-arrayexpress
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:Effect of the moisture content on lignocellulose degradation, lactic acid fermentation and the bacterial community of Sudan grass ensiled with bacteria-enzyme inoculants Raw sequence reads
| PRJNA1155273 | ENA
Project description:White rot fungi, such as Irpex lacteus, offer significant potential for lignocellulose degradation and protein synthesis in sustainable biofuel and animal feed production,but optimizing nitrogen sources to balance fungal growth, lignin degradation, and protein synthesis remains a critical challenge.This study investigated the effects of ammonium chloride (NH₄Cl) and sodium nitrate (NaNO₃) on I. lacteus fermentation in wheat straw, with a focus on the regulation of nitrogen source.Transcriptomic analysis revealed that NaNO₃ upregulated genes associated with nitrogen uptake and cellulose/hemicellulose degradation,while exerting less repression on key ligninolytic enzymes, such as manganese peroxidase and cytochrome P450, compared to NH₄Cl.These findings suggest that NaNO₃ enhances I. lacteus metabolism by harmonizing lignin degradation with efficient nitrogen conversion.
2025-05-21 | GSE297384 | GEO
Project description:To explore the mechanism of selective degradation of lignocellulose components by P. incarnate T-7, TMT labeling quantitative proteomic analysis was performed to explore the differential expression of secretory proteins of P. incarnate T-7 by submerged fermentation on poplar wood substrate relative to glucose substrates
2021-09-10 | PXD025248 | Pride