Articles

A comprehensive approach to stool donor screening for faecal microbiota transplantation in China

Faecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridium difficile infections and chronic gastrointestional infections. However, the risks of FMT and the selection process of suit...

Authors: Jianquan He, Xingxiang He, Yonghui Ma, Luxi Yang, Haiming Fang, Shu Shang, Huping Xia, Guanghui Lian, Hailing Tang, Qizhi Wang, Junping Wang, Zhihui Lin, Jianbo Wen, Yuedong Liu, Chunbao Zhai, Wen Wang…

Parsed synthesis of pyocyanin via co-culture enables context-dependent intercellular redox communication

Microbial co-cultures and consortia are of interest in cell-based molecular production and even as “smart” therapeutics in that one can take advantage of division of labor and specialization to expand both the...

Authors: Kayla Chun, Kristina Stephens, Sally Wang, Chen-Yu Tsao, Gregory F. Payne and William E. Bentley

Genetic optimisation of bacteria-induced calcite precipitation in Bacillus subtilis

Microbially induced calcite precipitation (MICP) is an ancient property of bacteria, which has recently gained considerable attention for biotechnological applications. It occurs as a by-product of bacterial m...

Authors: Timothy D. Hoffmann, Kevin Paine and Susanne Gebhard

Proliferation of Bifidobacterium L80 under different proportions of milk protein hydrolysate

The intestinal microecological environment is critical to an infant's growth. For those infants consuming milk power, it is very important to improve the intestinal microecological environment to promote the h...

Authors: Bing Wang, Yang Yang, Xin Bian, Hua-nan Guan, Lin-lin Liu, Xue-xia Li, Qing-qi Guo, Wojciech Piekoszewski, Feng-lian Chen, Na Wu, Zhan-qian Ma, Yan-guo Shi and Na Zhang

The first report on the sortase-mediated display of bioactive protein A from Staphylococcus aureus (SpA) on the surface of the vegetative form of Bacillus subtilis

Protein A (SpA) is one of the most important Staphylococcus aureus cell wall proteins. It includes five immunoglobulin (Ig)-binding domains which can bind to immune complexes through the Fc region of immunoglobul...

Authors: Samira Ghaedmohammadi and Gholamreza Ahmadian

Engineered microbial consortia: strategies and applications

Many applications of microbial synthetic biology, such as metabolic engineering and biocomputing, are increasing in design complexity. Implementing complex tasks in single populations can be a challenge becaus...

Authors: Katherine E. Duncker, Zachary A. Holmes and Lingchong You

Correction to: Genetic and process engineering strategies for enhanced recombinant N-glycoprotein production in bacteria

Authors: Fenryco Pratama, Dennis Linton and Neil Dixon

Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris

Codon optimization is a common method to improve protein expression levels in Pichia pastoris and the current strategy is to replace rare codons with preferred codons to match the codon usage bias. However, codon...

Authors: Yide Huang, Ting Lin, Lingfang Lu, Fan Cai, Jie Lin, Yu′e Jiang and Yao Lin

Recombinant expression of insoluble enzymes in Escherichia coli: a systematic review of experimental design and its manufacturing implications

Recombinant enzyme expression in Escherichia coli is one of the most popular methods to produce bulk concentrations of protein product. However, this method is often limited by the inadvertent formation of inclus...

Authors: Suraj Mital, Graham Christie and Duygu Dikicioglu

Improving CoQ₁₀ productivity by strengthening glucose transmembrane of Rhodobacter sphaeroides

Several Rhodobacter sphaeroides have been widely applied in commercial CoQ₁₀ production, but they have poor glucose use. Strategies for enhancing glucose use have been widely exploited in R. sphaeroides. Neverthe...

Authors: Yuying Yang, Lu Li, Haoyu Sun, Zhen Li, Zhengliang Qi and Xinli Liu

Whole-cell catalysis by surface display of fluorinase on Escherichia coli using N-terminal domain of ice nucleation protein

Fluorinases play a unique role in the production of fluorine-containing organic molecules by biological methods. Whole-cell catalysis is a better choice in the large-scale fermentation processes, and over 60% ...

Authors: Xinming Feng, Miaomiao Jin, Wei Huang, Wei Liu and Mo Xian

Identifying carbohydrate-active enzymes of Cutaneotrichosporon oleaginosus using systems biology

The oleaginous yeast Cutaneotrichosporon oleaginosus represents one of the most promising microbial platforms for resource-efficient and scalable lipid production, with the capacity to accept a wide range of carb...

Authors: Tobias Fuchs, Felix Melcher, Zora Selina Rerop, Jan Lorenzen, Pariya Shaigani, Dania Awad, Martina Haack, Sophia Alice Prem, Mahmoud Masri, Norbert Mehlmer and Thomas B. Brueck

Metabolic flux sampling predicts strain-dependent differences related to aroma production among commercial wine yeasts

Metabolomics coupled with genome-scale metabolic modeling approaches have been employed recently to quantitatively analyze the physiological states of various organisms, including Saccharomyces cerevisiae. Althou...

Authors: William T. Scott Jr., Eddy J. Smid, David E. Block and Richard A. Notebaart

OsnR is an autoregulatory negative transcription factor controlling redox-dependent stress responses in Corynebacterium glutamicum

Corynebacterium glutamicum is used in the industrial production of amino acids and nucleotides. During the course of fermentation, C. glutamicum cells face various stresses and employ multiple regulatory genes to...

Authors: Haeri Jeong, Younhee Kim and Heung-Shick Lee

A synthetic promoter system for well-controlled protein expression with different carbon sources in Saccharomyces cerevisiae

Saccharomyces cerevisiae is an important synthetic biology chassis for microbial production of valuable molecules. Promoter engineering has been frequently applied to generate more synthetic promoters with a vari...

Authors: Jiliang Deng, Yanling Wu, Zhaohui Zheng, Nanzhu Chen, Xiaozhou Luo, Hongting Tang and Jay D. Keasling

Production of soluble regulatory hydrogenase from Ralstonia eutropha in Escherichia coli using a fed-batch-based autoinduction system

Autoinduction systems can regulate protein production in Escherichia coli without the need to monitor cell growth or add inducer at the proper time following culture growth. Compared to classical IPTG induction, ...

Authors: Qin Fan, Peter Neubauer and Matthias Gimpel

Establishment of a co-culture system using Escherichia coli and Pichia pastoris (Komagataella phaffii) for valuable alkaloid production

Plants produce a variety of specialized metabolites, many of which are used in pharmaceutical industries as raw materials. However, certain metabolites may be produced at markedly low concentrations in plants....

Authors: Miya Urui, Yasuyuki Yamada, Yoshito Ikeda, Akira Nakagawa, Fumihiko Sato, Hiromichi Minami and Nobukazu Shitan

Non-destructive quantification of anaerobic gut fungi and methanogens in co-culture reveals increased fungal growth rate and changes in metabolic flux relative to mono-culture

Quantification of individual species in microbial co-cultures and consortia is critical to understanding and designing communities with prescribed functions. However, it is difficult to physically separate spe...

Authors: Patrick A. Leggieri, Corey Kerdman-Andrade, Thomas S. Lankiewicz, Megan T. Valentine and Michelle A. O’Malley

Genetic and process engineering strategies for enhanced recombinant N-glycoprotein production in bacteria

The production of N-linked glycoproteins in genetically amenable bacterial hosts offers great potential for reduced cost, faster/simpler bioprocesses, greater customisation, and utility for distributed manufac...

Authors: Fenryco Pratama, Dennis Linton and Neil Dixon

Degradation of epigallocatechin and epicatechin gallates by a novel tannase Tan_Hcw from Herbaspirillum camelliae

Herbaspirillum camelliae is a gram-negative endophyte isolated from the tea plant. Both strains WT00C and WT00F were found to hydrolyze epigallocatechin-3-gallate (EGCG) and epicatechin-3-gallate (ECG) to release...

Authors: Jia Lei, Yong Zhang, Xuechen Ni, Xuejing Yu and Xingguo Wang

Metabolic engineering design to enhance (R,R)-2,3-butanediol production from glycerol in Bacillus subtilis based on flux balance analysis

Glycerol is a desirable alternative substrate for 2,3-butanediol (2,3-BD) production for sustainable development in biotechnological industries and non-food competitive feedstock. B. subtilis, a “generally recogn...

Authors: Nunthaphan Vikromvarasiri, Tomokazu Shirai and Akihiko Kondo

High value-added products derived from crude glycerol via microbial fermentation using Yarrowia clade yeast

Contemporary biotechnology focuses on many problems related to the functioning of developed societies. Many of these problems are related to health, especially with the rapidly rising numbers of people sufferi...

Authors: Magdalena Rakicka-Pustułka, Joanna Miedzianka, Dominika Jama, Sylwia Kawalec, Kamila Liman, Tomasz Janek, Grzegorz Skaradziński, Waldemar Rymowicz and Zbigniew Lazar

Heterologous production of novel and rare C₃₀-carotenoids using Planococcus carotenoid biosynthesis genes

Members of the genus Planococcus have been revealed to utilize and degrade solvents such as aromatic hydrocarbons and alkanes, and likely to acquire tolerance to solvents. A yellow marine bacterium Planococcus ma...

Authors: Miho Takemura, Chiharu Takagi, Mayuri Aikawa, Kanaho Araki, Seon-Kang Choi, Mitsuhiro Itaya, Kazutoshi Shindo and Norihiko Misawa

Multivalent poultry vaccine development using Protein Glycan Coupling Technology

Poultry is the world's most popular animal-based food and global production has tripled in the past 20 years alone. Low-cost vaccines that can be combined to protect poultry against multiple infections are a c...

Authors: Marta Mauri, Thippeswamy H. Sannasiddappa, Prerna Vohra, Ricardo Corona-Torres, Alexander A. Smith, Cosmin Chintoan-Uta, Abi Bremner, Vanessa S. Terra, Sherif Abouelhadid, Mark P. Stevens, Andrew J. Grant, Jon Cuccui and Brendan W. Wren

Genome mining of novel rubiginones from Streptomyces sp. CB02414 and characterization of the post-PKS modification steps in rubiginone biosynthesis

Rubiginones belong to the angucycline family of aromatic polyketides, and they have been shown to potentiate the vincristine (VCR)-induced cytotoxicity against VCR-resistant cancer cell lines. However, the bio...

Authors: Jingyan Zhang, Ying Sun, Yeji Wang, Xin Chen, Lu Xue, Jingjing Zhang, Xiangcheng Zhu, Yanwen Duan and Xiaohui Yan

Scaling production of GFP1-10 detector protein in E. coli for secretion screening by split GFP assay

The split GFP assay is a well-known technology for activity-independent screening of target proteins. A superfolder GFP is split into two non-fluorescent parts, GFP11 which is fused to the target protein and G...

Authors: Carolin Müller, Chika L. Igwe, Wolfgang Wiechert and Marco Oldiges

Correction to: Recombinant expression of Barnase in Escherichia coli and its application in plasmid purifcation

Authors: Ram Shankar, Nina Schäfer, Marco Schmeer, Joe Max Risse, Karl Friehs and Martin Schleef

Regulating the T7 RNA polymerase expression in E. coli BL21 (DE3) to provide more host options for recombinant protein production

Escherichia coli is the most widely used bacterium in prokaryotic expression system for the production of recombinant proteins. In BL21 (DE3), the gene encoding the T7 RNA polymerase (T7 RNAP) is under control of...

Authors: Fei Du, Yun-Qi Liu, Ying-Shuang Xu, Zi-Jia Li, Yu-Zhou Wang, Zi-Xu Zhang and Xiao-Man Sun

Influence of B. subtilis 3NA mutations in spo0A and abrB on surfactin production in B. subtilis 168

Bacillus subtilis is a well-established host for a variety of bioproduction processes, with much interest focused on the production of biosurfactants such as the cyclic lipopeptide surfactin. Surfactin production...

Authors: Peter Klausmann, Lars Lilge, Moritz Aschern, Katja Hennemann, Marius Henkel, Rudolf Hausmann and Kambiz Morabbi Heravi

Metabolic engineering of Deinococcus radiodurans for pinene production from glycerol

The objective of this work was to engineer Deinococcus radiodurans R1 as a microbial cell factory for the production of pinene, a monoterpene molecule prominently used for the production of fragrances, pharmaceut...

Authors: Seyed Hossein Helalat, Carsten Jers, Mandana Bebahani, Hassan Mohabatkar and Ivan Mijakovic

Immunization with Leishmania tarentolae-derived norovirus virus-like particles elicits high humoral response and stimulates the production of neutralizing antibodies

Noroviruses are a major cause of epidemic and sporadic acute non-bacterial gastroenteritis worldwide. Unfortunately, the development of an effective norovirus vaccine has proven difficult and no prophylactic v...

Authors: Mirosława Panasiuk, Karolina Zimmer, Anna Czarnota, Katarzyna Grzyb, Magdalena Narajczyk, Grażyna Peszyńska-Sularz, Sabina Żołędowska, Dawid Nidzworski, Lilit Hovhannisyan and Beata Gromadzka

Glycerol or crude glycerol as substrates make Pseudomonas aeruginosa achieve anaerobic production of rhamnolipids

The anaerobic production of rhamnolipids is significant in research and application, such as foamless fermentation and in situ production of rhamnolipids in the anoxic environments. Although a few studies reporte...

Authors: Feng Zhao, Yuting Wu, Qingzhi Wang, Mengyao Zheng and Qingfeng Cui

Automation assisted anaerobic phenotyping for metabolic engineering

Microorganisms can be metabolically engineered to produce a wide range of commercially important chemicals. Advancements in computational strategies for strain design and synthetic biological techniques to con...

Authors: Kaushik Raj, Naveen Venayak, Patrick Diep, Sai Akhil Golla, Alexander F. Yakunin and Radhakrishnan Mahadevan

Synthesis of (−)−deoxypodophyllotoxin and (−)−epipodophyllotoxin via a multi-enzyme cascade in E. coli

The aryltetralin lignan (−)−podophyllotoxin is a potent antiviral and anti-neoplastic compound that is mainly found in Podophyllum plant species. Over the years, the commercial demand for this compound rose notab...

Authors: Davide Decembrino, Alessandra Raffaele, Ronja Knöfel, Marco Girhard and Vlada B. Urlacher

Expression, biochemical and structural characterization of high-specific-activity β-amylase from Bacillus aryabhattai GEL-09 for application in starch hydrolysis

β-amylase (EC 3.2.1.2) is an exo-enzyme that shows high specificity for cleaving the α-1,4-glucosidic linkage of starch from the non-reducing end, thereby liberating maltose. In this study, we heterologously e...

Authors: Xuguo Duan, Qiuyu Zhu, Xinyi Zhang, Zhenyan Shen and Yue Huang

Evaluation of bacterial hosts for conversion of lignin-derived p-coumaric acid to 4-vinylphenol

Hydroxycinnamic acids such as p-coumaric acid (CA) are chemically linked to lignin in grassy biomass with fairly labile ester bonds and therefore represent a straightforward opportunity to extract and valorize li...

Authors: Alberto Rodriguez, Jamie A. Meadows, Ning Sun, Blake A. Simmons and John M. Gladden

Optimizing operational parameters for the enzymatic production of furandicarboxylic acid building block

2,5-Furandicarboxylic acid (FDCA) is a precursor for green plastics due to its structural similarity to terephthalic acid, a common precursor of oil-derived polymers, and its potential production from sugars o...

Authors: María Isabel Sánchez-Ruiz, Angel T. Martínez and Ana Serrano

Aspergillus caespitosus ASEF14, an oleaginous fungus as a potential candidate for biodiesel production using sago processing wastewater (SWW)

Oleaginous microorganisms are sustainable alternatives for the production of biodiesel. Among them, oleaginous fungi are known for their rapid growth, short life cycles, no light requirement, easy scalability,...

Authors: Naganandhini Srinivasan, Kiruthika Thangavelu, Ashika Sekar, B. Sanjeev and Sivakumar Uthandi

Recent progress in the application of omics technologies in the study of bio-mining microorganisms from extreme environments

Bio-mining microorganisms are a key factor affecting the metal recovery rate of bio-leaching, which inevitably produces an extremely acidic environment. As a powerful tool for exploring the adaptive mechanisms...

Authors: Min Li and Jianping Wen

Functional characterization of a highly specific l-arabinose transporter from Trichoderma reesei

Lignocellulose biomass has been investigated as a feedstock for second generation biofuels and other value-added products. Some of the processes for biofuel production utilize cellulases and hemicellulases to ...

Authors: Sami Havukainen, Jonai Pujol-Giménez, Mari Valkonen, Matthias A. Hediger and Christopher P. Landowski

Overproducing the BAM complex improves secretion of difficult-to-secrete recombinant autotransporter chimeras

Monomeric autotransporters have been used extensively to transport recombinant proteins or protein domains to the cell surface of Gram-negative bacteria amongst others for antigen display. Genetic fusion of su...

Authors: Trang H. Phan, Coen Kuijl, Dung T. Huynh, Wouter S. P. Jong, Joen Luirink and Peter van Ulsen

Metabolic engineering for high yield synthesis of astaxanthin in Xanthophyllomyces dendrorhous

Astaxanthin is a carotenoid with a number of assets useful for the food, cosmetic and pharmaceutical industries. Nowadays, it is mainly produced by chemical synthesis. However, the process leads to an enantiom...

Authors: Alejandro Torres-Haro, Jorge Verdín, Manuel R. Kirchmayr and Melchor Arellano-Plaza

The iSplit GFP assay detects intracellular recombinant proteins in Bacillus subtilis

Bacillus subtilis is one of the most important microorganisms for recombinant protein production. It possesses the GRAS (generally recognized as safe) status and a potent protein secretion capacity. Secretory pro...

Authors: Patrick Lenz, Fabienne Hilgers, Alina Burmeister, Leonie Zimmermann, Kristina Volkenborn, Alexander Grünberger, Dietrich Kohlheyer, Thomas Drepper, Karl-Erich Jaeger and Andreas Knapp

Transcriptomics reveal different metabolic strategies for acid resistance and gamma-aminobutyric acid (GABA) production in select Levilactobacillus brevis strains

Of the many neurotransmitters in humans, gamma-aminobutyric acid (GABA) shows potential for improving several mental health indications such as stress and anxiety. The microbiota-gut-brain axis is an important...

Authors: Sagarika Banerjee, Matthew Poore, Svetlana Gerdes, Derek Nedveck, Lene Lauridsen, Heidi Thomsen Kristensen, Henrik Max Jensen, Phillip M. Byrd, Arthur C. Ouwehand, Elaine Patterson and Wesley Morovic

Engineering of microbial cells for L-valine production: challenges and opportunities

L-valine is an essential amino acid that has wide and expanding applications with a suspected growing market demand. Its applicability ranges from animal feed additive, ingredient in cosmetic and special nutri...

Authors: Hui Gao, Philibert Tuyishime, Xian Zhang, Taowei Yang, Meijuan Xu and Zhiming Rao

Recombinant expression of Barnase in Escherichia coli and its application in plasmid purification

The use of bovine-origin ribonucleases has been part of the standard protocol for plasmid DNA purification. As the field of gene therapy now enters the clinical stage, such enzymes need to be phased out or alt...

Authors: Ram Shankar, Nina Schäffer, Marco Schmeer, Joe Max Risse, Karl Friehs and Martin Schleef

Combining protein and metabolic engineering strategies for biosynthesis of melatonin in Escherichia coli

Melatonin has attracted substantial attention because of its excellent prospects for both medical applications and crop improvement. The microbial production of melatonin is a safer and more promising alternat...

Authors: Yanfeng Zhang, Yongzhi He, Nan Zhang, JiaJia Gan, Shan Zhang and Zhiyang Dong

Recombinant protein production provoked accumulation of ATP, fructose-1,6-bisphosphate and pyruvate in E. coli K12 strain TG1

Recently it was shown that production of recombinant proteins in E. coli BL21(DE3) using pET based expression vectors leads to metabolic stress comparable to a carbon overfeeding response. Opposite to original ex...

Authors: Jan Weber, Zhaopeng Li and Ursula Rinas

Improving citric acid production of an industrial Aspergillus niger CGMCC 10142: identification and overexpression of a high-affinity glucose transporter with different promoters

Glucose transporters play an important role in the fermentation of citric acid. In this study, a high-affinity glucose transporter (HGT1) was identified and overexpressed in the industrial strain A. niger CGMCC 1...

Authors: Xianli Xue, Futi Bi, Boya Liu, Jie Li, Lan Zhang, Jian Zhang, Qiang Gao and Depei Wang

Bioconversion of sago processing wastewater into biodiesel: Optimization of lipid production by an oleaginous yeast, Candida tropicalis ASY2 and its transesterification process using response surface methodology

Biodiesel is an eco-friendly and renewable energy source and a valuable substitute for petro-diesel. Sago processing wastewater (SWW), a by-product of the cassava processing industry, has starch content rangin...

Authors: Kiruthika Thangavelu, Pugalendhi Sundararaju, Naganandhini Srinivasan and Sivakumar Uthandi