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Christian Lieven, Markus J Herrgård, Nikolaus Sonnenschein
Developing methylotrophic bacteria into cell factories that meet the chemical demand of the future could be both economical and environmentally friendly. Methane is not only an abundant, low-cost resource but also a potent greenhouse gas, the capture of which could help to reduce greenhouse gas emissions. Rational strain design workflows rely on the availability of carefully combined knowledge often in the form of genome-scale metabolic models to construct high-producer organisms. In this review, we present the most recent genome-scale metabolic models in aerobic methylotrophy and their applications...
June 19, 2018: Biotechnology Journal
Radhe Shyam, Nicolas Charbonnel, Aurélie Job, Christelle Blavignac, Christiane Forestier, Claude Taillefumier, Sophie Faure
Amphipathic cationic peptoids (N-substituted glycine oligomers) represent a promising class of antimicrobial peptide mimics. The aim of this study is to explore the potential of the triazolium group as a cationic moiety and helix inducer to develop potent antimicrobial helical peptoids. We report here the first solid-phase synthesis of peptoid oligomers incorporating 1,2,3-triazolium-type side chains, and their evaluation against Escherichia coli, Enterococcus faecalis and Staphylococcus aureus. Several triazolium-based oligomers, even of short length, selectively kill bacteria over mammalian cells...
June 19, 2018: ChemMedChem
Jing Hou, Heping Zheng, Wen-Shyong Tzou, David R Cooper, Maksymilian Chruszcz, Mahendra D Chordia, Keehwan Kwon, Marek Grabowski, Wladek Minor
Vibrio cholerae, the causative pathogen of the life-threatening infection cholera, encodes two copies of β-ketoacyl-ACP synthase III (vcFabH1 and vcFabH2). vcFabH1 and vcFabH2 are pathogenic proteins associated with fatty acid synthesis, lipid metabolism, and potential applications in biofuel production. Our biochemical assays characterize vcFabH1 as exhibiting specificity for acetyl-CoA and CoA thioesters with short acyl chains, similar to that observed for FabH homologs found in most Gram-negative bacteria...
June 19, 2018: FEBS Journal
Tingting Zhang, Jiaojiao Miao, Na Han, Yujun Qiang, Wen Zhang
Advances in high-throughput sequencing have led to unprecedented growth in the amount of available genome sequencing data, especially for bacterial genomes, which has been accompanied by a challenge for the storage and management of such huge datasets. To facilitate bacterial research and related studies, we have developed the Mypathogen database (MPD), which provides access to users for searching, downloading, storing and sharing bacterial genomics data. The MPD represents the first pathogenic database for microbial genomes and metagenomes, and currently covers pathogenic microbial genomes (6604 genera, 11 071 species, 41 906 strains) and metagenomic data from host, air, water and other sources (28 816 samples)...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Laís Sara Egas, Erik Neiva Ribeiro de Carvalho Reis, Leonardo Freitas da Silva, João Paulo Bonardi, Valthierre Nunes de Lima, Pedro Henrique Silva Gomes Ferreira, Ciro Borges Duailibe de Deus, Idelmo Rangel Garcia Júnior
Necrotizing fasciitis (NF) is a devastating disease that typically affects immunocompromised patients, chronically debilitated patients or drug users, but can also affect healthy patients. Necrotizing fasciitis can rapidly produce septic shock and requires immediate surgical management of the necrotic tissue. It is a bacterial infection that progresses rapidly and has a high mortality generally caused by aerobic and anaerobic bacteria. The patient was immunocompromised and drug user. During treatment, a combination of broad-spectrum antibiotic therapy with Ciprofloxacin and Metronidazole, besides the use of activated charcoal dressing composed of carbonized fabric and impregnated with 0...
June 18, 2018: Journal of Craniofacial Surgery
Hongyue Li, Xiang Zhang, Hao Long, Chaoqun Hu, Yongcan Zhou, Shifeng Wang, Shaowen Ke, Zhenyu Xie
Porites andrewsi white syndrome (PAWS), caused by Vibrio alginolyticus strains XSBZ03 and XSBZ14, poses a serious threat to corals in the South China Sea. To obtain a specific target against which to develop a rapid PCR detection method for the coral pathogenic strain XSBZ03, the 16S-23S rRNA gene intergenic spacer (IGS) region of 4 strains of V. alginolyticus, including the XSBZ03 and XSBZ14 strains, was amplified, sequenced and analyzed. Six types of IGS were found: IGS0, IGSG, IGSIA, IGSAG, IGSGLV, and IGSGLAV...
June 19, 2018: Diseases of Aquatic Organisms
Anaïs Brosse, Maude Guillier
Small regulatory RNAs are now recognized as key regulators of gene expression in bacteria. They accumulate under specific conditions, most often because their synthesis is directly controlled by transcriptional regulators, including but not limited to alternative sigma factors and response regulators of two-component systems. In turn, small RNAs regulate, mostly at the posttranscriptional level, expression of multiple genes, among which are genes encoding transcriptional regulators. Small RNAs are thus embedded in mixed regulatory circuits combining transcriptional and posttranscriptional controls, and whose properties are discussed here...
May 2018: Microbiology Spectrum
Katharina Höfer, Andres Jäschke
The increasingly complex functionality of RNA is contrasted by its simple chemical composition. RNA is generally built from only four different nucleotides (adenine, guanine, cytosine, and uracil). To date, >160 chemical modifications are known to decorate RNA molecules and thereby alter their function or stability. Many RNA modifications are conserved throughout bacteria, archaea, and eukaryotes, while some are unique to each branch of life. Most known modifications occur at internal positions, while there is limited diversity at the termini...
May 2018: Microbiology Spectrum
Karen M Wassarman
6S RNA is a small RNA regulator of RNA polymerase (RNAP) that is present broadly throughout the bacterial kingdom. Initial functional studies in Escherichia coli revealed that 6S RNA forms a complex with RNAP resulting in regulation of transcription, and cells lacking 6S RNA have altered survival phenotypes. The last decade has focused on deepening the understanding of several aspects of 6S RNA activity, including (i) addressing questions of how broadly conserved 6S RNAs are in diverse organisms through continued identification and initial characterization of divergent 6S RNAs; (ii) the nature of the 6S RNA-RNAP interaction through examination of variant proteins and mutant RNAs, cross-linking approaches, and ultimately a cryo-electron microscopic structure; (iii) the physiological consequences of 6S RNA function through identification of the 6S RNA regulon and promoter features that determine 6S RNA sensitivity; and (iv) the mechanism and cellular impact of 6S RNA-directed synthesis of product RNAs (i...
May 2018: Microbiology Spectrum
Geovana B Michael, Janine T Bossé, Stefan Schwarz
Members of the highly heterogeneous family Pasteurellaceae cause a wide variety of diseases in humans and animals. Antimicrobial agents are the most powerful tools to control such infections. However, the acquisition of resistance genes, as well as the development of resistance-mediating mutations, significantly reduces the efficacy of the antimicrobial agents. This article gives a brief description of the role of selected members of the family Pasteurellaceae in animal infections and of the most recent data on the susceptibility status of such members...
May 2018: Microbiology Spectrum
Sara M Pires, Ana Sofia Duarte, Tine Hald
Source attribution and microbial risk assessment methods have been widely applied for the control of several foodborne pathogens worldwide by identifying (i) the most important pathogen sources and (ii) the risk represented by specific foods and the critical points in these foods' production chains for microbial control. Such evidence has proved crucial for risk managers to identify and prioritize effective food safety and public health strategies. In the context of antimicrobial resistance (AMR) from livestock and pets, the utility of these methods is recognized, but a number of challenges have largely prevented their application and routine use...
May 2018: Microbiology Spectrum
Carolyn E Adler, Alejandro Sánchez Alvarado
RNA interference (RNAi) is currently the only method available in planaria for assessing the function of particular genes. We describe here a method for performing body-wide gene knockdown, relying on dsRNA production in bacteria and subsequent delivery to planaria by feeding a liver-bacteria mixture. This method is ideal for screening many genes in parallel, in a cost-effective and reliable manner. We also describe a ligation-independent cloning strategy, which is used to rapidly transfer single genes into an RNAi vector that is also appropriate for downstream applications such as in situ hybridizations...
2018: Methods in Molecular Biology
Kristina M Mahan, Rosemary K Le, Tyrone Wells, Seth Anderson, Joshua S Yuan, Ryan J Stoklosa, Aditya Bhalla, David B Hodge, Arthur J Ragauskas
Livestock and fish farming are rapidly growing industries facing the simultaneous pressure of increasing production demands and limited protein required to produce feed. Bacteria that can convert low-value non-food waste streams into singe cell protein (SCP) present an intriguing route for rapid protein production. The oleaginous bacterium Rhodococcus opacus serves as a model organism for understanding microbial lipid production. SCP production has not been explored using an organism from this genus. In the present research, R...
June 18, 2018: Journal of Industrial Microbiology & Biotechnology
W W Y Voon, B J Muhialdin, N L Yusof, Y Rukayadi, A S Meor Hussin
Bio-cellulose is the microbial extracellular cellulose that is produced by growing several microorganisms on agriculture by-products, and it is used in several food applications. This study aims to utilize sago by-product, coconut water, and the standard medium Hestrin-Schramm as the carbon sources in the culture medium for bio-cellulose production. The bacteria Beijerinkia fluminensis WAUPM53 and Gluconacetobacter xylinus 0416 were selected based on their bio-cellulose production activity. The structure was determined by Fourier transform infrared spectroscopy and scanning electron microscopy, while the toxicity safety was evaluated by brine shrimp lethality test...
June 19, 2018: Applied Biochemistry and Biotechnology
Pedro Leão, Frederico J Gueiros-Filho, Dennis A Bazylinski, Ulysses Lins, Fernanda Abreu
Magnetotactic bacteria, for the most part, are free-living, motile, unicellular prokaryotes that inhabit almost all marine and freshwater environments. One notable exception to the unicellular mode, however, are the magnetotactic multicellular prokaryotes. These morphologically unique prokaryotes (e.g., Candidatus Magnetoglobus multicellularis) are motile aggregates of 20-40 genetically identical, Gram-negative cells organised as a sphere (or ovoid in shape) and only motile as a unit. No specific close physical association between magnetotactic bacteria and non-magnetotactic microorganisms has ever been reported...
June 18, 2018: Antonie Van Leeuwenhoek
Kevin Yehl, Timothy Lu
The semiconductor revolution that began in the 20th century has transformed society. Key to this revolution has been the integrated circuit, which enabled exponential scaling of computing devices using silicon-based transistors over many decades. Analogously, decreasing costs in DNA sequencing and synthesis, along with the development of robust genetic circuits, are enabling a "biocomputing revolution". First-generation gene circuits largely relied on assembling various transcriptional regulatory elements to execute digital and analog computing functions in living cells...
December 2017: Current Opinion in Biomedical Engineering
Chin-Hua Chang, Chew-Teng Kor, Chia-Lin Wu, Ping-Fang Chiu, Jhao-Rong Li, Chun-Chieh Tsai, Teng-Hsiang Chang, Chia-Chu Chang
Background: The vermiform appendix serves as a "safe house" for maintaining normal gut bacteria and appendectomy may impair the intestinal microbiota. Appendectomy is expected to profoundly alter the immune system and modulate the pathogenic inflammatory immune responses of the gut. Recent studies have shown that a dysbiotic gut increases the risk of cardiovascular disease and chronic kidney disease (CKD). Therefore, we hypothesized that appendectomy would increase the risk of CKD...
2018: PeerJ
Bo Zhang, Lijuan Yan, Qiang Li, Jie Zou, Hao Tan, Wei Tan, Weihong Peng, Xiaolin Li, Xiaoping Zhang
Background: Ganoderma lucidum , a valuable medicinal fungus, is widely distributed in China. It grows alongside with a complex microbial ecosystem in the substrate. As sequencing technology advances, it is possible to reveal the composition and functions of substrate-associated bacterial communities. Methods: We analyzed the bacterial community dynamics in the substrate during the four typical growth stages of G. lucidum using next-generation sequencing. Results: The physicochemical properties of the substrate (e...
2018: PeerJ
Hailiang Li, Shaoming Mao, Huahai Chen, Liying Zhu, Wei Liu, Xin Wang, Yeshi Yin
( S )-equol is one of the major metabolites of daidzein that is produced by human and animal gut bacteria. Most of the physiological functions of soybean isoflavones, such as anti-oxidative activity, anti-cancer activity, and cardiovascular protection have been ascribed to ( S )-equol. However, only 30-50% people contain this kind of equol-producing bacteria, and therefore are able to convert daidzein to ( S )-equol. Administration of ( S )-equol may be more beneficial than soybean isoflavones. The aim of this study was to construct an engineered ( S )-equol resistant Escherichia coli to enhance ( S )-equol production in vitro ...
2018: Frontiers in Microbiology
Tobias Busche, Konstantinos C Tsolis, Joachim Koepff, Yuriy Rebets, Christian Rückert, Mohamed B Hamed, Arne Bleidt, Wolfgang Wiechert, Mariia Lopatniuk, Ahmed Yousra, Jozef Anné, Spyridoula Karamanou, Marco Oldiges, Jörn Kalinowski, Andriy Luzhetskyy, Anastassios Economou
Gram-positive Streptomyces bacteria are profuse secretors of polypeptides using complex, yet unknown mechanisms. Many of their secretory proteins are proteases that play important roles in the acquisition of amino acids from the environment. Other proteases regulate cellular proteostasis. To begin dissecting the possible role of proteases in Streptomyces secretion, we applied a multi-omics approach. We probed the role of the 190 proteases of Streptomyces lividans strain TK24 in protein secretion in defined media at different stages of growth...
2018: Frontiers in Microbiology
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