Article
Biochemistry & Molecular Biology
Irina S. Panina, Sergey V. Balandin, Andrey V. Tsarev, Anton O. Chugunov, Andrey A. Tagaev, Ekaterina I. Finkina, Daria V. Antoshina, Elvira V. Sheremeteva, Alexander S. Paramonov, Jasmin Rickmeyer, Gabriele Bierbaum, Roman G. Efremov, Zakhar O. Shenkarev, Tatiana V. Ovchinnikova
Summary: To date, several lantibiotics have been found to target lipid II, a peptidoglycan precursor in bacterial cytoplasmic membrane. The alpha-component of lichenicidin, a two-component lantibiotic, contains potential lipid II binding sites. NMR spectroscopy and MD simulations provided evidence that the C-terminal domain of lichenicidin interacts with lipid II. The contact area of lipid II includes pyrophosphate, disaccharide residues, and bactoprenol's first isoprene units.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Oliver Goldbeck, Dominik Weixler, Bernhard J. Eikmanns, Christian U. Riedel
Summary: Post-translationally modified, (methyl-)lanthionine-containing peptides produced by Gram-positive bacteria, known as lantibiotics, show potent activity against various bacterial pathogens, including multidrug-resistant strains. The genus Corynebacterium presents widespread lantibiotic resistance traits, such as cell envelope modifications, ABC-transporters, and peptidases. Identification of conserved lantibiotic resistance operons in Corynebacterium highlights potential targets for further research on lantibiotic resistance mechanisms.
Article
Microbiology
Saswati Biswas
Summary: Through a heterologous biosynthetic system, we successfully produced biologically active nonnative novel lantibiotics. Streptococcus mutans T8 strain was used as the host organism and 10 homologs of mutacin II were expressed. By fusing the core regions of the selected lantibiotic peptides to the leader sequence of mutacin II, we obtained a bioactive novel lantibiotic with high sequence variation compared to mutacin II. This study demonstrates the potential of using mutacin II biosynthesis machinery for the production of novel lantibiotics.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Jeanne Romero-Severson, Thomas E. Moran, Donna G. Shrader, Francisco R. Fields, Susan Pandey-Joshi, Clayton L. Thomas, Emily C. Palmer, Joshua D. Shrout, Michael E. Pfrender, Shaun W. Lee
Summary: Bacteriocins are a diverse group of antimicrobial peptides found in various commensal and probiotic organisms. In this study, a novel strain of Bacillus safensis C3 was isolated from mung bean seeds, which exhibited antibacterial activity against human and plant pathogens. Genome sequencing revealed three biosynthetic systems in C3 that produce bacteriocin-based peptides, offering potential for therapeutic development and food safety applications.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Microbiology
Svetoslav Dimitrov Todorov, Iskra Vitanova Ivanova, Igor Popov, Richard Weeks, Michael Leonidas Chikindas
Summary: Representatives of the genus Bacillus are versatile microorganisms with widespread applications in traditional fermentation and modern biotechnology. They have numerous beneficial properties, serving as starter cultures for fermented foods, producers of enzymes, antibiotics, and bioactive peptides, and as probiotics for humans and animals. Despite their well-documented benefits, questions regarding their safety and spore formation in practical applications have been raised, prompting further exploration in this review.
CRITICAL REVIEWS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Sungmin Jung, Chaerin Woo, Joanna Ivy Irorita Fugaban, Jorge Enrique Vazquez Bucheli, Wilhelm Heinrich Holzapfel, Svetoslav Dimitrov Todorov
Summary: This study aimed to identify a bacteriocin-producing strain for controlling the food-borne pathogen Listeria monocytogenes. Five strains were isolated from kimchi with activity against the target bacterium, and ST05DL was selected for further study due to its specific inhibitory activity.
PROBIOTICS AND ANTIMICROBIAL PROTEINS
(2021)
Review
Biochemistry & Molecular Biology
Shusuke Tomoshige, Minoru Ishikawa
Summary: PROTACs, as bifunctional molecules, have shown poor bioavailability due to their high molecular weight, but recent developments focusing on in vivo synthesis and using PROTACs as chemical tools have significant implications for drug discovery.
BIOORGANIC & MEDICINAL CHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Joanna Ivy Irorita Fugaban, Clarizza May Dioso, Gee Hyeun Choi, Jorge Enrique Vazquez Bucheli, Min-Tze Liong, Wilhelm Heinrich Holzapfel, Svetoslav Dimitrov Todorov
Summary: The aim of this project was to identify bacteriocinogenic Bacillus strains with activity against Staphylococcus spp., which could be used in the formulation of pharmaceutical antimicrobial preparations. The selected strains were evaluated for their safety, beneficial properties, and potential production of antimicrobials. The results suggest that the expressed antimicrobials from these strains could be realistically used in the treatment of Staphylococcus-associated infections. Biotechnological approaches need to be developed for cost-effective production, isolation, and purification of the expressed antimicrobials by these Bacillus strains.
PROBIOTICS AND ANTIMICROBIAL PROTEINS
(2022)
Editorial Material
Biochemistry & Molecular Biology
Ben Vermaercke, Vincent Bonin, Pierre Vanderhaeghen
Summary: Transplantation of human cortical neurons into the rodent brain offers new opportunities for studying human neural function and disease in vivo, from the molecular to circuit levels.
Article
Food Science & Technology
Jing Zhang, Shaobin Gu, Tianrong Zhang, Ying Wu, Jinliang Ma, Lina Zhao, Xin Li, Jie Zhang
Summary: Bacillus coagulans CGMCC 9951, a conventional probiotic, was found to produce two bacteriocins with potential antibacterial activity against various pathogenic bacteria. These bacteriocins primarily inhibit the growth of gram-positive bacteria by damaging the cell membrane and causing leakage of cell contents and inactivation of genomic DNA, ultimately affecting bacterial growth and reproduction.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Joanna Ivy Irorita Fugaban, Jorge Enrique Vazquez Bucheli, Wilhelm Heinrich Holzapfel, Svetoslav Dimitrov Todorov
Summary: Bacillus velezensis, Bacillus amyloliquefaciens, and Bacillus subtilis strains isolated from artisanal-produced kimchi showed antimicrobial activity against Listeria monocytogenes, with some strains possibly having additional non-proteinaceous molecular structure related antimicrobial activity. These strains also expressed surfactin as an additional factor in their complex antimicrobial activity. Additionally, the studied Bacillus strains were resistant to some evaluated antibiotics and were positive producers for biogenic amines production.
FERMENTATION-BASEL
(2021)
Article
Multidisciplinary Sciences
Noriaki Ide, Miki Kawada-Matsuo, Mi Nguyen-Tra Le, Junzo Hisatsune, Hiromi Nishi, Toshinori Hara, Norikazu Kitamura, Seiya Kashiyama, Michiya Yokozaki, Hiroyuki Kawaguchi, Hiroki Ohge, Motoyuki Sugai, Hitoshi Komatsuzawa
Summary: Clinical isolates of Clostridioides difficile can be classified into two groups with high and low susceptibility to nisin A, and the differences in susceptibility may be related to the amino acid sequences of CprABC. Genotypic variations in C. difficile strains confer different susceptibilities to bacteriocins, such as nisin A, epidermin, and mutacin III.
Article
Multidisciplinary Sciences
Kenta Nakazono, Mi Nguyen-Tra Le, Miki Kawada-Matsuo, Noy Kimheang, Junzo Hisatsune, Yuichi Oogai, Masanobu Nakata, Norifumi Nakamura, Motoyuki Sugai, Hitoshi Komatsuzawa
Summary: This study reports the complete sequences of two plasmids coding for bacteriocins from S. epidermidis, which are partially different from previously reported sequences. Additionally, this study provides the first report of the complete sequence of an epidermin-carrying plasmid, pEpi56.
Article
Biology
Bingqiang Wen, Guolun Wang, Enhong Li, Olena A. Kolesnichenko, Zhaowei Tu, Senad Divanovic, Tanya Kalin, Vladimir V. Kalinichenko
Summary: A fully functional bone marrow (BM) was generated from mouse embryonic stem cells (ESCs) using rat embryos as "bioreactors". Mouse ESCs differentiated into multiple hematopoietic and stromal cell types that were indistinguishable from normal mouse BM cells. This method has the potential to accelerate the development of cell therapies for life-threatening disorders.
Article
Biotechnology & Applied Microbiology
Gee Hyeun Choi, Joanna Ivy Irorita Fugaban, Clarizza May Dioso, Jorge Enrique Vazquez Bucheli, Wilhelm Heinrich Holzapfel, Svetoslav Dimitrov Todorov
Summary: Two Bacillus strains isolated from kimchi, Bacillus tequilensis ST816CD and Bacillus subtilis ST830CD, showed antimicrobial properties and were found to produce non-proteinaceous antimicrobial substances. These strains also expressed genes associated with the production of surfactants.
FERMENTATION-BASEL
(2021)
Article
Infectious Diseases
Diana Dias, Andreia Cruz, Carlos Fonseca, Sonia Mendo, Tania S. Caetano
Summary: In recent years, the interaction between wildlife and humans has been increasing due to human activities. It is important to understand the impact of these interactions on the health of wild animals and the potential risks of zoonotic diseases. This study used metabarcoding to analyze the fecal microbiota of red deer and identified several potential human and veterinary pathogens. The study also found the occurrence of antibiotic resistance genes, some of which are considered future threats to human health.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Article
Biochemical Research Methods
Goncalo Figueiredo, Carina Pedrosa Costa, Joana Lourenco, Tania Caetano, Silvia M. Rocha, Sonia Mendo
Summary: Microbial metabolomics is used to analyze and understand the metabolites produced and released by microorganisms in specific conditions. This research aims to investigate the impact of culture media changes on the metabolic profile and production of biotechnologically relevant compounds in Pedobacter lusitanus NL19 and Pedobacter himalayensis MTCC 6384. The study identified 320 metabolites belonging to different chemical families and associated 80 metabolites with various metabolic pathways. The findings provide insights into how slight changes in culture media composition can affect microbial metabolism and have potential applications in metabolomics pipeline construction and biotechnology.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Biology
Thales Costa, Elena Cassin, Catarina Moreirinha, Sonia Mendo, Tania Sousa Caetano
Summary: This study investigates the transcription, antimicrobial activity, and biomolecular profile of halophilic archaea genes involved in the biosynthesis of peptide secondary metabolites. The results suggest that the ycaO and medM genes are transcriptionally active, with medM2 showing the highest transcript level. The deletion of the ycaO gene does not affect the antimicrobial activity of H. mediterranei.
Article
Biotechnology & Applied Microbiology
Joana C. Barbosa, Eva Moesker, Raquel Faria, Roderich D. Sussmuth, Sonia Mendo, Tania Caetano
Summary: This study investigated the activity of lichenicidin A2 (LicA2) trimming proteases (LicP and LicT). The presence of a negatively charged amino acid residue at the cleavage site was found to be important for the efficacy of LicP. Mutations in the lichenicidin hexapeptide and alterations in the GG-motif resulted in higher processing rates. This research is important for understanding the activity of lantibiotic-related transporters and proteases and their potential application in industrial processes.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sylvester Hoffmann, Maik Damm, Leonard Roth, Roderich D. Suessmuth
Summary: This study investigates the activation mechanism of hydroxy acid substrates in non-ribosomal peptide synthetases (NRPSs). By homology modelling and molecular docking, it was found that the selection of hydroxy acid is determined by its interaction with the backbone carbonyls rather than a specific side chain. These findings contribute to the understanding of non-amino acid substrate activation and have implications for the engineering of depsipeptide synthetases.
Article
Food Science & Technology
Ignazio Avella, Maik Damm, Ines Freitas, Wolfgang Wuster, Nahla Lucchini, Oscar Zuazo, Roderich D. Suessmuth, Fernando Martinez-Freiria
Summary: This study analyzed the venom of Vipera seoanei snakes from different locations and found that there is little variation in venom composition, which may be due to recent population expansion or other factors.
Article
Food Science & Technology
Rita Vedor, Daniela Machado, Joana Cristina Barbosa, Diana Almeida, Ana Maria Gomes
Summary: This study evaluated the viability of probiotics in chocolates with different cocoa percentages and found that dark chocolates with higher cocoa content could be a promising carrier for specific probiotic strains.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Mariam Kholany, Nicolas Schaeffer, Ines P. E. Macario, Telma Veloso, Tania Caetano, Joana L. Pereira, Ana C. R. V. Dias, Joao A. P. Coutinho, Soinia P. M. Ventura
Summary: Haloarchaea, a class of marine microbial resources, can be a promising source of valuable compounds such as bacterioruberin. Natural and biocompatible hydrophobic eutectic solvents (HES) based on menthol and carboxylic acids were investigated for the extraction of bacterioruberin. The menthol and levulinic acid mixture showed the best results and proteins could be recovered by adding water to the extract, forming a protein-rich interfacial precipitate. The process intensification was achieved by reusing the eutectic phase over multiple extraction cycles, resulting in a bacterioruberin-rich extract.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Microbiology
Claudia Covas, Goncalo Figueiredo, Margarida Gomes, Tiago Santos, Sonia Mendo, Tania S. Caetano
Summary: Secondary metabolites from environmental bacteria provide solutions for various health and environmental challenges. The study focuses on uncovering the diversity of biosynthetic gene clusters encoded in the genomes of Pedobacter spp. The potential for the production of various secondary metabolites, including RiPPs, terpenes, hybrid SMs, PKs, NRPs, and siderophores, is revealed.
Article
Polymer Science
Daniela Machado, Mariana Fonseca, Rita Vedor, Sergio Sousa, Joana Cristina Barbosa, Ana Maria Gomes
Summary: This study evaluated the viability and stability of Akkermansia muciniphila during encapsulation using a calcium-alginate hydrogelated matrix. The results revealed that encapsulated A. muciniphila exhibited high stability and improved viability compared to free cells, both during refrigerated aerobic storage and under simulated gastrointestinal conditions. These findings suggest that encapsulation using a calcium-alginate hydrogelated matrix is a promising strategy for safeguarding the viability of A. muciniphila in adverse environments.
Review
Multidisciplinary Sciences
Roland Hellinger, Arnar Sigurdsson, Wenxin Wu, Elena V. Romanova, Lingjun Li, Jonathan V. Sweedler, Roderich D. Suessmuth, Christian W. Gruber
Summary: Peptidomics combines genomics, modern proteomics, analytical chemistry, and computational biology techniques for peptide discovery and characterization. Peptides are biopolymers composed of 2-50 amino acids, often produced by cellular machinery or enzymes. They play important physiological roles as signaling molecules and toxins, and have emerging applications in biomarker discovery and therapeutics. Peptidomics involves qualitative and quantitative analysis of peptides in biological samples using a specialized set of tools and workflows.
NATURE REVIEWS METHODS PRIMERS
(2023)
