[HTML][HTML] Automating the design-build-test-learn cycle towards next-generation bacterial cell factories

N Gurdo, DC Volke, D McCloskey, PI Nikel - New Biotechnology, 2023 - Elsevier
Automation is playing an increasingly significant role in synthetic biology. Groundbreaking
technologies, developed over the past 20 years, have enormously accelerated the …

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats

M Simon, C Scheuner, JP Meier-Kolthoff… - The ISME …, 2017 - academic.oup.com
Abstract Marine Rhodobacteraceae (Alphaproteobacteria) are key players of
biogeochemical cycling, comprise up to 30% of bacterial communities in pelagic …

Recent advances in high-throughput 13C-fluxomics

S Heux, C Bergès, P Millard, JC Portais… - Current opinion in …, 2017 - Elsevier
Highlights•13 C-fluxomics provides quantification of metabolic activity in microorganisms.•
Increasing flux analysis capacity has the potential to accelerate strain design.•HT 13 C …

Pseudomonas putida KT2440 strain metabolizes glucose through a cycle formed by enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and pentose …

PI Nikel, M Chavarría, T Fuhrer, U Sauer… - Journal of Biological …, 2015 - ASBMB
The soil bacterium Pseudomonas putida KT2440 lacks a functional Embden-Meyerhof-
Parnas (EMP) pathway, and glycolysis is known to proceed almost exclusively through the …

[HTML][HTML] GC-MS-based 13C metabolic flux analysis resolves the parallel and cyclic glucose metabolism of Pseudomonas putida KT2440 and Pseudomonas …

M Kohlstedt, C Wittmann - Metabolic engineering, 2019 - Elsevier
The genus Pseudomonas comprises approximately 200 species with numerous isolates that
are common inhabitants of soil, water, and vegetation and has been of particular interest for …

Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster

Y Liu, T Brinkhoff, M Berger, A Poehlein, S Voget… - Microbiome, 2023 - Springer
Abstract Background The RCA (Roseobacter clade affiliated) cluster belongs to the family
Roseobacteracea and represents a major Roseobacter lineage in temperate to polar …

Microbiota drive insoluble polysaccharides utilization via microbiome-metabolome interplay during Pu-erh tea fermentation

X Bian, W Miao, M Zhao, Y Zhao, Y Xiao, N Li, JL Wu - Food Chemistry, 2022 - Elsevier
Polysaccharides are abundant components in Pu-erh tea, yet the utilization of insoluble
polysaccharides under the actions of microbiota has rarely been studied. The aim of this …

Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using Δpfk mutants

WD Hollinshead, S Rodriguez, HG Martin… - Biotechnology for …, 2016 - Springer
Background Glycolysis breakdowns glucose into essential building blocks and ATP/NAD (P)
H for the cell, occupying a central role in its growth and bio-production. Among glycolytic …

Metabolism of the fast-growing bacterium Vibrio natriegens elucidated by 13C metabolic flux analysis

CP Long, JE Gonzalez, RM Cipolla… - Metabolic …, 2017 - Elsevier
Vibrio natriegens is a fast-growing, non-pathogenic bacterium that is being considered as
the next-generation workhorse for the biotechnology industry. However, little is known about …

Functional implementation of a linear glycolysis for sugar catabolism in Pseudomonas putida

A Sánchez-Pascuala, L Fernández-Cabezón… - Metabolic …, 2019 - Elsevier
The core metabolism for glucose assimilation of the soil bacterium and platform strain
Pseudomonas putida KT2440 has been reshaped from the native, cyclically-operating …