Metagenome-scale community metabolic modelling for understanding the role of gut microbiota in human health

S Beura, P Kundu, AK Das, A Ghosh - Computers in biology and medicine, 2022 - Elsevier
Metabolic activities of the microbial population are important to maintain the balance of
almost all the ecosystems on earth. In the human gut environment, these microbial …

Plant growth-promoting bacteria of soil: designing of consortia beneficial for crop production

AM Timofeeva, MR Galyamova, SE Sedykh - Microorganisms, 2023 - mdpi.com
Plant growth-promoting bacteria are commonly used in agriculture, particularly for seed
inoculation. Multispecies consortia are believed to be the most promising form of these …

Microbial community metabolic modeling: a community data‐driven network reconstruction

CS Henry, HC Bernstein, P Weisenhorn… - Journal of cellular …, 2016 - Wiley Online Library
Metabolic network modeling of microbial communities provides an in‐depth understanding
of community‐wide metabolic and regulatory processes. Compared to single organism …

Mechanistic models of microbial community metabolism

LR Dillard, DD Payne, JA Papin - Molecular Omics, 2021 - pubs.rsc.org
Microbial communities affect many facets of human health and well-being. Naturally
occurring bacteria, whether in nature or the human body, rarely exist in isolation. A deeper …

Flux sampling in genome-scale metabolic modeling of microbial communities

PE Gelbach, H Cetin, SD Finley - BMC bioinformatics, 2024 - Springer
Background Microbial communities play a crucial role in ecosystem function through
metabolic interactions. Genome-scale modeling is a promising method to understand these …

Emerging methods for genome-scale metabolic modeling of microbial communities

C Tarzi, G Zampieri, N Sullivan, C Angione - Trends in Endocrinology & …, 2024 - cell.com
Genome-scale metabolic models (GEMs) are consolidating as platforms for studying mixed
microbial populations, by combining biological data and knowledge with mathematical rigor …

Constraint-based modeling in microbial food biotechnology

MH Rau, AA Zeidan - Biochemical Society Transactions, 2018 - portlandpress.com
Genome-scale metabolic network reconstruction offers a means to leverage the value of the
exponentially growing genomics data and integrate it with other biological knowledge in a …

[HTML][HTML] Characterization of oil extracted from wild apricot seeds kernel using submerged alcoholic fermentation and its quality characteristics

M Nausad, H Kumar, G Sharma, K Dulta, A Dviwedi… - Process …, 2024 - Elsevier
The current study investigated the impact of Saccharomyces cerevisiae fermentation on
apricot kernel oil extraction and the resulting quality characteristics of the oil. The seed …

Metabolic network modeling for computer‐aided design of microbial interactions

HS Song, WC Nelson, JY Lee… - Emerging areas in …, 2018 - Wiley Online Library
Interest in applying microbial communities to biotechnology continues to increase.
Successful engineering of microbial communities requires a fundamental shift in focus from …

Application of the metabolic modeling pipeline in KBase to categorize reactions, predict essential genes, and predict pathways in an isolate genome

BH Allen, N Gupta, JN Edirisinghe, JP Faria… - … Biology: Methods and …, 2022 - Springer
Abstract The DOE Systems Biology Knowledgebase (KBase) platform offers a range of
powerful tools for the reconstruction, refinement, and analysis of genome-scale metabolic …