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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:<p>Inoculation with homofermentative lactic acid bacteria (LAB) effectively enhances the silage quality of forages. Moreover, feeding such LAB-inoculated silage modulates rumen microbiota composition and metabolites, thereby improving ruminant production performance. Nevertheless, the specific mechanism through which LAB inoculants regulate the silage–rumen–mammary gland axis remains unclear.</p><p>Inoculation with homofermentative Lactiplantibacillus plantarum BX62 improved the alfalfa silage quality. Dairy goats fed the BX62 group silage showed significantly higher milk fat content compared to the control group (no inoculation) (P < 0.05). Integrated analysis of silage microbial metabolomics and experimental validation revealed a significant increase in flavonoid content in the BX62 silage. This was attributed to microbial community restructuring and secretion of carbohydrate-active enzymes (CAZymes), which facilitated plant cell wall degradation and flavonoid release. Rumen metagenomic assembly and binning indicated that feeding flavonoid-rich BX62 silage induced the proliferation of flavonoid-degrading microbes and reshaped the rumen microbiota, which resulted in the upregulation of CAZymes and energy metabolic pathways (e.g., ko00620 Pyruvate metabolism), and enhanced fiber degradation and volatile fatty acid (VFA) production in the rumen. Consequently, acetate-dependent milk fat synthesis was promoted in BX62 group goats as showed by the elevated expressions of acetyl-CoA carboxylase 1 (ACC1), fatty acid synthase (FASN) and acyl-CoA synthetase short-chain family member 2 (ACSS2) in mammary gland. Moreover, four milk fat-positively correlated bacteria species (Eggerthellaceae bacterium, Clostridioides difficile, Candidatus Limivicinus sp., and Collinsella aerofaciens) harboring flavonoid-degrading genes proliferated with elevated flavonoid concentrations in the rumen. In vitro trial further confirmed flavonoid degradation capability in both C. difficile and A. equolifaciens (family Eggerthellaceae), and dose-dependent growth promotion in A. equolifaciens. These results demonstrate that silage-derived flavonoids drive rumen microbiome remodeling and promote mammary lipogenesis through a silage-rumen microbiota-mammary gland triad mechanism.</p>
2026-01-11 | MTBLS13651 | MetaboLights
Project description:<p>Inoculation with homofermentative lactic acid bacteria (LAB) effectively enhances the silage quality of forages. Moreover, feeding such LAB-inoculated silage modulates rumen microbiota composition and metabolites, thereby improving ruminant production performance. Nevertheless, the specific mechanism through which LAB inoculants regulate the silage–rumen–mammary gland axis remains unclear.</p><p>Inoculation with homofermentative <em>Lactiplantibacillus plantarum</em> BX62 improved the alfalfa silage quality. Dairy goats fed the BX62 group silage showed significantly higher milk fat content compared to the control group (no inoculation) (<em>P</em> < 0.05). Integrated analysis of silage microbial metabolomics and experimental validation revealed a significant increase in flavonoid content in the BX62 silage. This was attributed to microbial community restructuring and secretion of carbohydrate-active enzymes (CAZymes), which facilitated plant cell wall degradation and flavonoid release. Rumen metagenomic assembly and binning indicated that feeding flavonoid-rich BX62 silage induced the proliferation of flavonoid-degrading microbes and reshaped the rumen microbiota, which resulted in the upregulation of CAZymes and energy metabolic pathways (e.g., ko00620 Pyruvate metabolism), and enhanced fiber degradation and volatile fatty acid (VFA) production in the rumen. Consequently, acetate-dependent milk fat synthesis was promoted in BX62 group goats as showed by the elevated expressions of acetyl-CoA carboxylase 1 (ACC1), fatty acid synthase (FASN) and acyl-CoA synthetase short-chain family member 2 (ACSS2) in mammary gland. Moreover, four milk fat-positively correlated bacteria species (<em>Eggerthellaceae</em> bacterium, <em>Clostridioides difficile</em>, <em>Candidatus Limivicinus</em> sp., and <em>Collinsella aerofaciens</em>) harboring flavonoid-degrading genes proliferated with elevated flavonoid concentrations in the rumen. <em>In vitro</em> trial further confirmed flavonoid degradation capability in both <em>C. difficile</em> and <em>A. equolifaciens</em> (family <em>Eggerthellaceae</em>), and dose-dependent growth promotion in <em>A. equolifaciens</em>. These results demonstrate that silage-derived flavonoids drive rumen microbiome remodeling and promote mammary lipogenesis through a silage-rumen microbiota-mammary gland triad mechanism.</p>
2026-01-10 | MTBLS13648 | MetaboLights
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:Anthropogenic activities such as urbanization and agriculture can potentially pose a threat to neighboring freshwaters through nitrate and phosphorous contamination, which over time may lead to lake eutrophication. In such nitrogen-polluted environments, oxygen is depleted, and plants die and decompose. This enhances denitrifying microbes that respire under hypoxic/anoxic conditions by reducing nitrate instead of molecular oxygen and using plant remnants (lignocellulose) as carbon source. Microbial lignocellulose degradation has been well-studied for both aerobic- and anaerobic conditions; however, its degradation during denitrification remains largely unknown. Here we have applied a combination of gas kinetics and meta-omics techniques to enrich and analyze microbial communities from 10 eutrophic lakes to identify a set of core microbial metagenome-assembled genomes (MAGs) present in all the eutrophic lakes. We have further investigated their strategies and enzyme profiles for degrading lignocellulose under denitrifying conditions. We identified Pseudomonadota, Bacteroidota, Verrucomicrobiota, and Actinomycetota as the most abundant phyla and they were present in enrichments from all eutrophic lakes having a key role in denitrification and fermentation. Lignocellulose degradation was, however, dominated by species outside the core microbiome, i.e., there were differing key degraders between lakes, suggesting some level of lake-specialization. Among these we observed potential respiratory DNRA pathways, and they expressed a broad range of CAZymes targeting the various lignocellulose subfractions. Interestingly, many of the detected MAGs contained NO dismutases, enzymes postulated to convert NO to molecular oxygen and dinitrogen gas.
2026-04-30 | PXD069160 | Pride