Article
Biotechnology & Applied Microbiology
Sisi Liu, Yuanyuan Xia, Haiquan Yang, Wei Shen, Xianzhong Chen
Summary: In this study, a high-yield recombinant strain of Salidroside was successfully constructed using a multi-copy integration strategy in the non-coding region of the genome, laying the foundation for efficient green biosynthesis of Salidroside.
BIOCHEMICAL ENGINEERING JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Lina Qi, Chunxiao Liu, Lukasz Peplowski, Wei Shen, Haiquan Yang, Yuanyuan Xia, Xianzhong Chen
Summary: In this study, a random mutant library of EcHpaB was established using error-prone PCR to improve its ability to convert tyrosol to hydroxytyrosol. A highly efficient synthetic enzyme mutant strain YMG5*R-HpaBTLEHC was screened, which could efficiently convert 50 mM tyrosol with a yield of hydroxytyrosol reaching 48.2 mM (7.43 g/L). This study demonstrates the successful development of a highly efficient synthetic enzyme mutant for the production of hydroxytyrosol, which has the potential to significantly improve its commercial viability.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Daoyi Guo, Xiao Fu, Yue Sun, Xun Li, Hong Pan
Summary: A new biosynthetic pathway was constructed in Escherichia coli for the production of tyrosol acetate and hydroxytyrosol acetate, starting with the production of tyrosol and extending the pathway with the overexpression of alcohol acetyltransferase and hydroxylase enzymes. This study provides a novel approach for biosynthesis of these bioactive compounds with potentially increased bioavailability for various applications in food and cosmetics industries.
ENZYME AND MICROBIAL TECHNOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Huijing Wang, Lian Wang, Jianbin Chen, Minglong Hu, Fang Fang, Jingwen Zhou
Summary: By preparing an edible oil-based lipid nanoparticle (LNP) system, the oral bioaccessibility of flavonoids, including quercetin, naringenin, and hesperetin, was enhanced. In simulated digestion assays, LNPs were hydrolyzed under small intestine conditions, successfully protecting the encapsulated flavonoids, and the relative bioaccessibility of flavonoids was increased to more than 71%.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Yi Yan, Yajun Bai, Xiaohui Zheng, Yujie Cai
Summary: Due to its strong antioxidant capacity, hydroxytyrosol (HT) has a long history of use in cosmetics and food industries. However, current methods of isolating HT are not optimal, which leads to the need for more efficient synthesis methods. This study aimed to create an Escherichia coli (E. coli) whole cell system capable of synthesizing HT from dopamine by constructing a custom biosynthetic pathway. Through overexpression of enzymes and identifying rate-limiting enzymes, the synthesis of HT was significantly boosted. This study establishes a biocatalytic pathway for the synthesis of new building blocks for industrially high-performance HT.
BIOCHEMICAL ENGINEERING JOURNAL
(2023)
Article
Multidisciplinary Sciences
Vidhyavathi Raman, Clemencia M. Rojas, Balaji Vasudevan, Kevin Dunning, Jaydeep Kolape, Sunhee Oh, Jianfei Yun, Lishan Yang, Guangming Li, Bikram D. Pant, Qingzhen Jiang, Kirankumar S. Mysore
Summary: This study developed a strategy to increase the efficiency of plant transformation by engineering Agrobacterium and suppressing host defense responses. The results showed that the transformation efficiency of wheat, alfalfa and switchgrass increased by 250%-400% using the engineered Agrobacterium.
NATURE COMMUNICATIONS
(2022)
Review
Microbiology
Lindsey Dzierozynski, Jessica Queen, Cynthia L. Sears
Summary: This commentary discusses the influence of host genetics on the microbiome and highlights the need for mechanistic experimental studies to understand the interplay between host genes and the microbiome.
CELL HOST & MICROBE
(2023)
Article
Biotechnology & Applied Microbiology
Yi Yan, Yajun Bai, Xiaohui Zheng, Yujie Cai
Summary: Hydroxytyrosol (HT), a polyphenolic molecule, is highly valued and used in various industries. Researchers have modified Escherichia coli to enhance the expression of key enzymes and compared different DODC enzymes for efficient HT production. The results showed that the DODC enzyme from Homo sapiens is superior.
ENZYME AND MICROBIAL TECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Sierra M. Brooks, Celeste Marsan, Kevin B. Reed, Shuo-Fu Yuan, Dustin-Dat Nguyen, Adit Trivedi, Gokce Altin-Yavuzarslan, Nathan Ballinger, Alshakim Nelson, Hal S. Alper
Summary: Researchers have developed a tripartite microbial coculture system for the de novo production of plant-derived phenylpropanoids. The system has shown improved stability and flexibility, and has the potential to be used for the production of various industrial products.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
An-Ni Zhang, Jeffry M. Gaston, Chengzhen L. Dai, Shijie Zhao, Mathilde Poyet, Mathieu Groussin, Xiaole Yin, Li-Guan Li, Mark C. M. van Loosdrecht, Edward Topp, Michael R. Gillings, William P. Hanage, James M. Tiedje, Katya Moniz, Eric J. Alm, Tong Zhang
Summary: Antibiotic resistance genes are common among bacteria, but not all pose high risks to human health. Researchers have developed an omics-based framework to rank these genes by risk, taking into account their enrichment in human associated environments, gene mobility, and host pathogenicity.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Guilhem Royer, Jose-Manuel Ortiz de La Rosa, Xavier Vuillemin, Beatrice Lacombe, Francoise Chau, Olivier Clermont, Melanie Mercier-Darty, Jean-Winoc Decousser, Jean-Damien Ricard, Patrice Nordmann, Erick Denamur, Laurent Poirel
Summary: Chlorhexidine is a widely used antiseptic, but there is a growing concern about decreased susceptibility to this compound in bacteria. This study investigated the resistance mechanisms of Escherichia coli to chlorhexidine through whole-genome sequence analysis. The results showed that two different evolutionary paths lead to chlorhexidine decreased susceptibility, one involving a retrograde phospholipid transport system and the other associated with efflux pump TetA.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2022)
Article
Multidisciplinary Sciences
Gi Bae Kim, Ji Yeon Kim, Jong An Lee, Charles J. Norsigian, Bernhard O. Palsson, Sang Yup Lee
Summary: The functional annotation of open reading frames in microbial genomes is still incomplete. In this study, a deep learning model called DeepECtransformer was developed to predict specific catalytic functions for un-annotated genes. Experimental validation confirmed the accuracy of the predicted enzymatic activities for three proteins and revealed that the neural network relies on functional motifs of enzymes to predict EC numbers.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Jason Youn, Navneet Rai, Ilias Tagkopoulos
Summary: This study presents a machine learning framework for automating knowledge discovery through knowledge graph construction, inconsistency resolution, and iterative link prediction. Applied to antibiotic data, the framework identifies novel antibiotic resistant genes in E. coli and validates them through wet-lab experiments.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Lajos Kalmar, Srishti Gupta, Iain R. L. Kean, Xiaoliang Ba, Nazreen Hadjirin, Elizabeth M. Lay, Stefan P. W. de Vries, Michael Bateman, Harriet Bartlet, Juan Hernandez-Garcia, Alexander W. Tucker, Olivier Restif, Mark P. Stevens, James L. N. Wood, Duncan J. Maskell, Andrew J. Grant, Mark A. Holmes
Summary: Shotgun metagenomics is a powerful tool for identifying AMR genes in microbiomes but lacks the ability to link extrachromosomal DNA to bacterial chromosomes. We present HAM-ART, a comprehensive pipeline for generating metagenome-assembled genomes that includes both chromosomal and extrachromosomal AMR genes. The pipeline's performance was demonstrated in a study comparing pig faecal microbiomes from low- and high-antimicrobial use farms, revealing significant differences in AMR gene distribution.
Article
Microbiology
Lorina Badger-Emeka, Naheed Kausar, Edric Estrella, Glenda Belgira Angeles
Summary: Uropathogenic Escherichia coli is the most common cause of urinary tract infections, and it has multidrug resistance and extended-spectrum beta-lactamase (ESBL) characteristics. This study investigated the antimicrobial susceptibility patterns and associated virulence determinants of UPEC isolates and found that phylogroups B2 and D carried the most virulence genes.