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Research in Microbiology

Andrew M Kropinski
Research on bacteriophages has significantly enhanced our understanding of molecular biology, the genomes of prokaryotic cells, and viral ecology. Phages and lysins offer a viable alternative to the declining utility of antibiotics in this post-antibiotic era. They also provide ideal teaching tools for genomics and bioinformatics. This article touches on the first 100 years of phage research with the author commenting on what he thinks are the highlights, and what needs to be addressed.
May 16, 2018: Research in Microbiology
N Hoyle, P Zhvaniya, N Balarjishvili, D Bolkvadze, L Nadareishvili, D Nizharadze, J Wittmann, C Rohde, M Kutateladze
Respiratory infections can lead to serious complications in CF patients, especially when infected with antibiotic resistant bacteria. Alternative treatments for these infections are being sought out to help address this problem. We present a clinical case of a cystic fibrosis (CF) patient, with multi-drug resistant (MDR) Achromobacter xylosoxidans chronic lung infection who was successfully managed with bacteriophage therapy.
May 16, 2018: Research in Microbiology
Daniel Gelman, Shaul Beyth, Vanda Lerrer, Karen Adler, Ronit Poradosu-Cohen, Shunit Coppenhagen-Glazer, Ronen Hazan
Clinical applications of bacteriophage therapy have been recently gathering significant attention worldwide, used mostly as rescue therapy in cases of near-fatal antibiotic failure. Thus, clinically relevant in-vivo models presenting both short- and long-term implications of phage therapy given as rescue treatment for fulminant infections are of highest importance. In this study, a cocktail consisting of two lytic bacteriophages was used to evaluate the therapeutic efficacy of phage therapy as a rescue treatment for severe septic peritonitis in a mouse model...
May 16, 2018: Research in Microbiology
Colin Buttimer, Yannick Born, Alan Lucid, Martin J Loessner, Lars Fieseler, Aidan Coffey
To date, a small number of jumbo myoviruses have been reported to possess atypical whisker-like structures along the surface of their contractile tails. Erwinia amylovora phage vB_EamM_Y3 is another example. It possesses a genome of 261,365 kbp with 333 predicted ORFs. Using a combination of BLASTP, Interproscan and HHpred, about 21% of its putative proteins could be assigned functions involved in nucleotide metabolism, DNA replication, virion structure and cell wall degradation. The phage was found to have a signal-arrest-release (SAR) endolysin (Y3_301) possessing a soluble lytic transglycosylase domain...
May 16, 2018: Research in Microbiology
Nina S Atanasova, Tatiana A Demina, Sudar N V Krishnam Rajan Shanthi, Hanna M Oksanen, Dennis H Bamford
Certain pleomorphic archaeal viruses are highly infectious even at saturated salt. These viruses belong to the genus Betapleolipovirus of the recently described archaeal virus family Pleolipoviridae. Pleolipoviruses comprise single-stranded or double-stranded, circular or linear DNA genomes that share countless homologs among various archaeal genetic elements. Here we describe a new extremely halophilic betapleolipovirus, Halorubrum pleomorphic virus 9 (HRPV9), which has an integrase gene. We also identified new genes encoding minor pleolipoviral structural proteins...
May 14, 2018: Research in Microbiology
Lea Wittorf, Christopher M Jones, Germán Bonilla-Rosso, Sara Hallin
Reduction of nitrite to nitric oxide in denitrification is catalysed by two different nitrite reductases, encoded by nirS or nirK. Long considered mutually exclusive and functionally redundant in denitrifying bacteria, we show expression of both genes co-occurring in Pseudomonas stutzeri. The differential expression patterns between strain AN10 and JM300 in relation to oxygen and nitrate and their different denitrification phenotypes, with AN10 reducing nitrate more rapidly and accumulating nitrite, suggest that nirS and nirK can have different roles...
May 9, 2018: Research in Microbiology
Shilpi Gupta, Alexander Lemenze, Robert J Donnelly, Nancy D Connell, Daniel E Kadouri
The use of predatory bacteria as a potential live therapeutic to control human infection is gaining increased attention. Earlier work with Micavibrio spp. and Bdellovibrio spp. has demonstrated the ability of these predators to control drug-resistant Gram-negative pathogens, Tier-1 select agents and biofilms. Additional studies also confirmed that introducing high doses of the predators into animals does not negatively impact animal well-being and might assist in reducing bacterial burden in vivo. The survival of predators requires extreme proximity to the prey cell, which might bring about horizontal transfer of genetic material, such as genes encoding for pathogenic genetic islands that would indirectly facilitate the spread of genetic material to other organisms...
May 8, 2018: Research in Microbiology
Xin Zhao, Rui Liu, Hao Tang, George Osei-Adjei, Shungao Xu, Ying Zhang, Xinxiang Huang
Bacterial non-coding RNAs (ncRNAs) are widely studied and found to play important roles in regulating various cellular processes. Recently, many ncRNAs have been discovered to be transcribed or processed from 3' untranslated regions (3' UTRs). Here we reported a novel 3' UTR-derived ncRNA, RibS, which could influence biofilm formation of Salmonella enterica serovar Typhi (S. Typhi). RibS was confirmed to be a ∼700 nt processed product produced by RNase III-catalyzed cleavage from the 3' UTR of riboflavin synthase subunit alpha mRNA, RibE...
May 8, 2018: Research in Microbiology
Marcus G Eales, Enrico Ferrari, Alan D Goddard, Lorna Lancaster, Peter Sanderson, Clare Miller
Acinetobacter baumannii has been identified by the WHO as a high priority pathogen. It can be resistant to multiple antibiotics and colistin sulphate is often used as a last-resort treatment. However, the potentially severe side-effects of colistin are well documented and this study compared the bactericidal and anti-biofilm activity of two synthetic nature-inspired antimicrobial peptides, bicarinalin and BP100, with colistin. The minimum bactericidal concentration (MBC) against planktonic A. baumannii was approximately 0...
May 8, 2018: Research in Microbiology
Elena Perrin, Giovanni Bacci, Laurent Garrelly, Francesco Canganella, Giovanna Bianconi, Renato Fani, Alessio Mengoni
Performed inside International Space Station (ISS) from 2011 to 2016, VIABLE (eValuatIon And monitoring of microBiofiLms insidE International Space Station) ISS was a long-lasting experiment aimed at evaluating the bacterial contamination on different surface space materials subjected to different pre-treatment, to provide useful information for future space missions. In this work, surfaces samples of the VIABLE ISS experiment were analyzed to determine both the total bacterial load (ATP-metry, qPCR) and the composition of the microbial communities (16S rRNA genes amplicon sequencing)...
May 8, 2018: Research in Microbiology
Daniela Torres, Iliana Benavidez, Florencia Donadio, Elias Mongiardini, Susana Rosas, Stijn Spaepen, Jozef Vanderleyden, Aleš Pěnčík, Ondřej Novák, Miroslav Strnad, Jitka Frébortová, Fabricio Cassán
Bacterial metabolism of phytohormones includes several processes such as biosynthesis, catabolism, conjugation, hydrolysis and homeostatic regulation. However, only biosynthesis and occasionally catabolism are studied in depth in microorganisms. In this work, we evaluated and reconsidered IAA metabolism in B. japonicum E109, one of the most widely used strains for soybean inoculation around the world. The genomic analysis of the strain showed the presence of several genes responsible for IAA biosynthesis, mainly via indole-3-acetonitrile (IAN), indole-3-acetamide (IAM) and tryptamine (TAM) pathways...
May 8, 2018: Research in Microbiology
Xiaohan Jiang, Xiaomin Li, Shuangyong Sun, Lingyan Jiang
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a major intracellular pathogen of humans and animals and its survival and growth in macrophages is essential for its pathogenicity. The S. Typhimurium genome encodes more than 50 putative regulatory proteins, but their involvement in pathogenicity and their regulatory roles are largely unknown. In this study, we investigated the biological function of the S. Typhimurium STM4320 gene (named varN), which encodes a putative MerR family transcriptional regulator...
May 8, 2018: Research in Microbiology
Jisun Kim, Sunhee Ha, Woojun Park
Six genes encoding cold-shock-like proteins, including cspE, are contained within the genome of Acinetobacter oleivorans DR1. All six genes are similar in size as well as amino acid identity, but appear to be differentially regulated under stressful conditions. Four of these genes (cspA, cspB, cspC and cspE) were functionally important during cold shock because of their gradual upregulation during a temperature decrease under our assay conditions. cspE also showed higher expression during alkane degradation and antibiotic exposure...
May 8, 2018: Research in Microbiology
Kristen E Howery, Emrah Şimşek, Minsu Kim, Philip N Rather
Using a variety of techniques, we demonstrate the Class I regulator of the flagellar cascade, FlhD4 C2 , can activate its own expression in Proteus mirabilis. This activation was direct, as the FlhD4 C2 protein specifically bound to its promoter region. The expression of bacterial genes under a positive feedback control can exhibit varying levels between cells due to stochastic fluctuations that activate the feedback loop and result in some cells in an "ON" state. Cells containing a chromosomal flhDC::gfp transcriptional fusion exhibited a heterogeneous pattern of expression within the population during growth on agar surfaces and the percentage of cells expressing GFP increased as cells approached swarmer cell differentiation...
March 23, 2018: Research in Microbiology
Hiroshi Nikaido
Transporters of the RND superfamily are well-known as the major drug efflux pumps of Gram-negative bacteria. However, they are widespread in organisms ranging from Archaea to Eukaryotes, and perform diverse functions. This review gives a brief overview of these diverse members of the superfamily with emphasis on their structure and functions.
March 22, 2018: Research in Microbiology
Shimon Schuldiner
Multidrug transporters function in a coordinated mode to provide an essential first-line defense mechanism that prevents antibiotics fromreaching lethal concentrations, until a number of stable efficient adaptations occur that allow survival. Single-component efflux transporters remove the toxic compounds from the cytoplasm to the periplasmic space where TolC-dependent transporters expel them from the cell. The close interaction between the two types of transporters ensures handling of a wide range of xenobiotics and prevents rapid leak of the hydrophobic substrates back into the cell...
March 21, 2018: Research in Microbiology
Galina V Smirnova, Aleksey V Tyulenev, Nadezda G Muzyka, Oleg N Oktyabrsky
Amino acid starvation causes an RelA-dependent increase in the regulatory nucleotide (p)ppGpp that leads to pleiotropic changes in Escherichia coli metabolism, but the role of (p)ppGpp in regulation of respiration remains unclear. Here we demonstrate that amino acid starvation is accompanied by sharp RelA-dependent inhibition of respiration. The sharp phase of inhibition is absent in relA mutants, and can be prevented by translation inhibitors chloramphenicol and tetracycline, which abolish accumulation of (p)ppGpp...
April 2018: Research in Microbiology
Luz A López-Ramírez, Nahúm V Hernández, Nancy E Lozoya-Pérez, Leila M Lopes-Bezerra, Héctor M Mora-Montes
Sporothrix schenckii is one of the causative agents of the deep-seated mycosis sporotrichosis, a fungal infection with worldwide distribution. Fungus-specific molecules and biosynthetic pathways are potential targets for the development of new antifungal drugs. The MNT1/KRE2 gene family is a group of genes that encode fungus-specific Golgi-resident mannosyltransferases that participate in the synthesis of O-linked and N-linked glycans. While this family is composed of five and nine members in Candida albicans and Saccharomyces cerevisiae, respectively, the S...
April 2018: Research in Microbiology
Lacey L Westphal, Jasmine Lau, Zuly Negro, Ivan J Moreno, Wazim Ismail Mohammed, Heewook Lee, Haixu Tang, Steven E Finkel, Karin E Kram
Experimental evolution studies have characterized the genetic strategies microbes utilize to adapt to their environments, mainly focusing on how microbes adapt to constant and/or defined environments. Using a system that incubates Escherichia coli in different complex media in long-term batch culture, we have focused on how heterogeneity and environment affects adaptive landscapes. In this system, there is no passaging of cells, and therefore genetic diversity is lost only through negative selection, without the experimentally-imposed bottlenecking common in other platforms...
April 2018: Research in Microbiology
Yi-Ling Lo, Chyi-Liang Chen, Lunda Shen, Ying-Ching Chen, Yi-Hsin Wang, Chung-Chan Lee, Lian-Chen Wang, Chih-Hsien Chuang, Rajendra Prasad Janapatla, Cheng-Hsun Chiu, Hwan-You Chang
FliA is known to be a sigma factor that regulates bacterial flagella gene expression. Accumulating evidence suggests that FliA is involved in bacterial behavior other than motility. To elucidate the contribution of FliA to Pseudomonas aeruginosa pathophysiology, we analyzed the biological properties and gene expression profiles of a ΔfliA mutant. Transcriptome analysis results demonstrated that the expression levels of flagella biogenesis genes decreased dramatically in the mutant; consequently, the ΔfliA mutant failed to synthesize flagella and exhibited reduced motility...
April 2018: Research in Microbiology
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