Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Metaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solids

ABSTRACT: Metaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solids

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Panicum Virgatum (ncbitaxon:38727) Microbiome

SUBMITTER: Richard J. Giannone Robert L. Hettich

PROVIDER: MSV000088319 | MassIVE | Thu Nov 04 21:21:00 GMT 2021

SECONDARY ACCESSION(S): PXD029582

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Similar Datasets

Metaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solids.

Project description:Economically viable production of cellulosic biofuels requires operation at high solids loadings-on the order of 15 wt%. To this end we characterize Nature's ability to deconstruct and utilize mid-season switchgrass at increasing solid loadings using an anaerobic methanogenic microbiome. This community exhibits undiminished fractional carbohydrate solubilization at loadings ranging from 30 g/L to 150 g/L. Metaproteomic interrogation reveals marked increases in the abundance of specific carbohydrate-active enzyme classes. Significant enrichment of auxiliary activity family 6 enzymes at higher solids suggests a role for Fenton chemistry. Stress-response proteins accompanying these reactions are similarly upregulated at higher solids, as are β-glucosidases, xylosidases, carbohydrate-debranching, and pectin-acting enzymes-all of which indicate that removal of deconstruction inhibitors is important for observed undiminished solubilization. Our work provides insights into the mechanisms by which natural microbiomes effectively deconstruct and utilize lignocellulose at high solids loadings, informing the future development of defined cultures for efficient bioconversion.

| S-EPMC9256739 | biostudies-literature

Lignocellulose fermentation to ethanol or lactate by giant panda gut microbiomes depends ultimately on pH rather than portion of bamboo

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

Meninges from mice with different microbiomes

Project description:RNA was extracted from the meninges of mice from either Specific pathogen free or Germ free facilities or from the offspring of mice reconstituted with different human microbiomes.

2020-11-13 | GSE135620 | GEO

Lignocellulose associated salt marsh microbiome time series metasecretome

Project description:Time series metasecretomes (weeks 1, 3, 5 and ten) of lignocellulose responsive microbiomes enriching on Spartina anglica biomass for 16 weeks in a natural UK salt marsh (Welwick, Humber estuary).

2019-05-29 | MSV000083872 | MassIVE

Lignocellulose fractionation

Project description:Lignocellulose fractionation by microbial consortia

| PRJEB26853 | ENA

Anaerobic rice paddy soil-derived microbiomes

Project description:Arsenic-methylating anaerobic rice paddy soil-derived microbiomes (Raw DNA sequence reads)

| PRJNA714492 | ENA

Transcriptomic analysis of strains evolved for anaerobic xylose utilization [Y223_Y127_Y128]

Project description:Engineering microbes with novel metabolic properties is a critical step for production of biofuels and biochemicals. Synthetic biology enables identification and engineering of metabolic pathways into microbes; however, knowledge of how to reroute cellular regulatory signals and metabolic flux remains lacking. Here we used network analysis of multi-omic data to dissect the mechanism of anaerobic xylose fermentation, a trait important for biochemical production from plant lignocellulose. We compared transcriptomic, proteomic, and phosphoproteomic differences across a series of strains evolved to ferment xylose under various conditions.

2019-03-12 | GSE92907 | GEO

Transcriptomic analysis of strains evolved for anaerobic xylose utilization [Azf1]

2019-03-12 | GSE92906 | GEO

HuMiChip2 for Strain Level Identification and Functional Profiling of Human Microbiomes

Project description:HuMiChip2 was applied to analyze perform both strain-level identification and the functional profiling of human gut microbiomes from alcoholic cirrhosis patients and healthy individuals with alcohol abuse.

2016-08-30 | GSE86162 | GEO

C. saccharolyticus transcriptomes reveal consequences of chemical pre-treatment and genetic modification of lignocellulose

Project description:The genome of the lignocellulose-degrading, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus encodes genes comprising clusters of glycoside hydrolases, ABC transporters and metabolic enzymes that are transcriptionally responsive to carbohydrates. Transcriptomic and biosolubilization analyses were used to determine if C. saccharolyticus could be deployed as a probe to assess the characteristics of plant biomass feedstocks and efficacy of pre-treatment methods, as these both relate to deconstruction strategies for biofuels production. Based on the response of C. saccharolyticus to plant cell wall polysaccharides, genomic loci were identified that reflected the availability of cellulose, glucomannan, pectin and xylan in biomass to microbial degradation. Furthermore, these loci were useful in assessing how various plant biomass feedstocks (genetically and chemically modified Populus sp., unpretreated Populus sp., and chemically modified switchgrass) were amenable C. saccharolyticus solubilization.

2016-11-23 | GSE90445 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data