KBase: the United States department of energy systems biology knowledgebase
Although similar integrative tools exist (Supplementary Note 2), no other open platform
shares all KBase's features, which include the following:(i) comprehensive support for data …
shares all KBase's features, which include the following:(i) comprehensive support for data …
Bioconversion of glycerol into biofuels—opportunities and challenges
Rising pollutants and greenhouse gas emissions from fossil fuels are serious environmental
concerns that led to a tremendous focus of scientific research. The use of renewable …
concerns that led to a tremendous focus of scientific research. The use of renewable …
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants …
For over 10 years, ModelSEED has been a primary resource for the construction of draft
genome-scale metabolic models based on annotated microbial or plant genomes. Now …
genome-scale metabolic models based on annotated microbial or plant genomes. Now …
Methods for automated genome-scale metabolic model reconstruction
In the era of next-generation sequencing and ubiquitous assembly and binning of
metagenomes, new putative genome sequences are being produced from isolate and …
metagenomes, new putative genome sequences are being produced from isolate and …
Unraveling core functional microbiota in traditional solid-state fermentation by high-throughput amplicons and metatranscriptomics sequencing
Z Song, H Du, Y Zhang, Y Xu - Frontiers in microbiology, 2017 - frontiersin.org
Fermentation microbiota is specific microorganisms that generate different types of
metabolites in many productions. In traditional solid-state fermentation, the structural …
metabolites in many productions. In traditional solid-state fermentation, the structural …
Designing metabolic division of labor in microbial communities
Microbes face a trade-off between being metabolically independent and relying on
neighboring organisms for the supply of some essential metabolites. This balance of …
neighboring organisms for the supply of some essential metabolites. This balance of …
Nitrate removal characteristics and 13C metabolic pathways of aerobic denitrifying bacterium Paracoccus denitrificans Z195
H Zhang, S Li, B Ma, T Huang, H Qiu, Z Zhao… - Bioresource …, 2020 - Elsevier
Strain Z195 was isolated and identified as Paracoccus denitrificans. Z195 exhibited efficient
aerobic denitrification and carbon removal abilities, and removed 93.74% of total nitrogen …
aerobic denitrification and carbon removal abilities, and removed 93.74% of total nitrogen …
Profiling the composition and metabolic activities of microbial community in fermented grain for the Chinese strong-flavor Baijiu production by using the …
X Hu, K Wang, M Chen, J Fan, S Han, J Hou… - Food Research …, 2020 - Elsevier
The composition and function of microbial community analyzed by sequencing 16S
rRNA/ITS gene amplicons (DNA level) were compared with those derived by using …
rRNA/ITS gene amplicons (DNA level) were compared with those derived by using …
The DOE systems biology knowledgebase (KBase)
Abstract The US Department of Energy Systems Biology Knowledgebase (KBase) is an
open-source software and data platform designed to meet the grand challenge of systems …
open-source software and data platform designed to meet the grand challenge of systems …
The inhibitory effect of cadmium and/or mercury on soil enzyme activity, basal respiration, and microbial community structure in coal mine–affected agricultural soil
L Zheng, Y Li, W Shang, X Dong, Q Tang… - Annals of Microbiology, 2019 - Springer
Abstract Purpose The Cd and Hg contents in soils can be elevated due to coal mining. To
estimate the effects of these two heavy metals on soil enzymes and the key microbial …
estimate the effects of these two heavy metals on soil enzymes and the key microbial …