MicrobiologyOpen

Cover image for Vol. 4 Issue 6

Early View (Online Version of Record published before inclusion in an issue)

Edited by Pierre Cornelis, Microbial Interactions, VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium

Impact Factor: 2.213

ISI Journal Citation Reports © Ranking: 2014: 75/119 (Microbiology)

Online ISSN: 2045-8827

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  1. Original Research

    1. You have full text access to this OnlineOpen article
      Toxin MqsR cleaves single-stranded mRNA with various 5' ends

      Nityananda Chowdhury, Brian W. Kwan, Louise C. McGibbon, Paul Babitzke and Thomas K. Wood

      Article first published online: 5 FEB 2016 | DOI: 10.1002/mbo3.335

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      Using RNA that is single-stranded, double-stranded, or folds into a stem loop or pseudoknot, we found that toxin MqsR of the MqsR/MqsA TA system cleaves primarily single-stranded RNA. Furthermore, we found that 5′ processing is not required for the RNA to be a substrate since MqsR has activity on RNA with 5′-ppp, 5′-p and 5′-OH ends. Hence, MqsR cleavage of mRNA does not depend on preprocessing by RNA pyrophosphohydrolase (RppH) to remove pyrophosphate like RNase E, the primary enzyme for mRNA turnover, which implies that once activated by stress, toxin MqsR can rapidly degrade nearly all the mRNA (all but 14 Escherichia coli transcripts have 5′-GCU sites) as well as possibly tRNA and rRNA.

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      High-throughput sequencing reveals the core gut microbiome of Bar-headed goose (Anser indicus) in different wintering areas in Tibet

      Wen Wang, Jian Cao, Fang Yang, Xuelian Wang, Sisi Zheng, Kirill Sharshov and Laixing Li

      Article first published online: 4 FEB 2016 | DOI: 10.1002/mbo3.327

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      We show that the gut microbial communities of bar-headed geese have representatives of 14 phyla and are dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The additive abundance of these four most dominant phyla was above 96% across all the samples. At the genus level, the sequences represented 150 genera. A set of 19 genera were present in all samples and considered as core gut microbiome.

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      New insights into FtsZ rearrangements during the cell division of Escherichia coli from single-molecule localization microscopy of fixed cells

      Alexey D. Vedyaykin, Innokentii E. Vishnyakov, Vasilisa S. Polinovskaya, Mikhail A. Khodorkovskii and Anton V. Sabantsev

      Article first published online: 3 FEB 2016 | DOI: 10.1002/mbo3.336

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      Single-molecule localization microscopy (SMLM) combined with IF was used to visualize FtsZ in fixed Esherichia coli cells. This approach allowed us to obtain images of FtsZ structures at different stages of cell division and measure dimensions of Z-ring.

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      Effects of norspermidine on Pseudomonas aeruginosa biofilm formation and eradication

      Lin Qu, Pengfei She, Yangxia Wang, Fengxia Liu, Di Zhang, Lihua Chen, Zhen Luo, Huan Xu, Yong Qi and Yong Wu

      Article first published online: 27 JAN 2016 | DOI: 10.1002/mbo3.338

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      Norspermidine could inhibit biofi lm formation and eradicate 24- h mature biofi lm in Pseudomonas aeruginosa , prevent cell- surface attachment, and downregulate QS- related gene expression.

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      Oscillating behavior of Clostridium difficile Min proteins in Bacillus subtilis

      Jana Makroczyová, Ján Jamroškovič, Eva Krascsenitsová, Nad'a Labajová and Imrich Barák

      Article first published online: 27 JAN 2016 | DOI: 10.1002/mbo3.337

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      The placement of the bacterial division septum at the midcell site is very precise and it is partially controlled by Min system in many rod-shaped bacteria. Escherichia coli Min system oscillates from pole to pole in contrast with less dynamic Bacillus subtilis Min system. Interestingly, many Clostridia species contain homologs proteins from both Min systems. Because of C.difficile anaerobic life style and its confined genetic toolbox, we investigated the mechanism of action of the C.difficile Min proteins in B.subtilis and we showed that this system exhibits oscillatory behavior in the host.

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      Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea

      Qi Ye, Ying Wu, Zhuoyi Zhu, Xiaona Wang, Zhongqiao Li and Jing Zhang

      Article first published online: 27 JAN 2016 | DOI: 10.1002/mbo3.330

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      In this study, we detected newly hypoxic areas near the Changjiang Estuary during August 2013. We found that decomposition of complex organic matter by specific groups of aerobic Planctomycetes and Bacteroidetes might contribute to O2 depletion in the strongly stratified areas. Hydrogen sulfide produced by sulfate-reducing bacteria might be detoxified by putative Gammaproteobacteria-affiliated sulfur-oxidizing bacteria, which may serve as primary producers in the benthic food webs. Our results provided new insights into understanding further the mechanism of dissolved oxygen depletion contributed by the sedimentary microbial community near the Changjiang Estuary.

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      Comparative genome-wide analysis reveals that Burkholderia contaminans MS14 possesses multiple antimicrobial biosynthesis genes but not major genetic loci required for pathogenesis

      Peng Deng, Xiaoqiang Wang, Sonya M. Baird, Kurt C. Showmaker, Leif Smith, Daniel G. Peterson and Shien Lu

      Article first published online: 14 JAN 2016 | DOI: 10.1002/mbo3.333

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      Burkholderia contaminans MS14 shows significant antimicrobial activities against plant and animal pathogenic fungi and bacteria. The MS14 whole genome was sequenced. The genome analysis revealed MS14 harbored multiple antimicrobial-related gene loci. In addition, MS14 genome lacks key virulence-related genes by comparison to the pathogenic Burkholderia species.

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      Development of new host-specific Bacteroides qPCRs for the identification of fecal contamination sources in water

      Marta Gómez-Doñate, Arnau Casanovas-Massana, Maite Muniesa and Anicet R. Blanch

      Article first published online: 14 JAN 2016 | DOI: 10.1002/mbo3.313

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      New qPCR assays that target host-specific Bacteroidal 16S ribosomal RNA genes, to determine four different source of fecal contamination in water, have been developed and compared with other previously developed Bacteroidetes microbial source tracking targets. The designed Bacteroides assays are a useful target for source tracking, being rapid, straightforward, and accurate.

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      Identification and antimicrobial resistance prevalence of pathogenic Escherichia coli strains from treated wastewater effluents in Eastern Cape, South Africa

      Martins A. Adefisoye and Anthony I. Okoh

      Article first published online: 13 JAN 2016 | DOI: 10.1002/mbo3.319

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      Discharged final effluents of wastewater treatment plants are potential point source of multidrug-resistant pathogen in receiving surface waters. Antibiotic-resistant genes from discharged effluents can be transferred to other pathogens in the receiving water environment, thus, constituting significant public health threat. The combination of deadly duo of drug resistance and emerging virulence in pathogenic bacteria brings about a worrisome situation of possible lack of therapeutic options particularly in immunocompromised individuals.

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      The programming effects of nutrition-induced catch-up growth on gut microbiota and metabolic diseases in adult mice

      Jia Zheng, Xinhua Xiao, Qian Zhang, Miao Yu, Jianping Xu, Cuijuan Qi and Tong Wang

      Article first published online: 8 JAN 2016 | DOI: 10.1002/mbo3.328

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      Our work is novel in showing the “programming” effects of maternal nutrition imbalance on gut microbiota and metabolic diseases in adult mice. It is suggested that therapeutic interventions targeting gut microbiota may be a new theoretical basis for preventing the onset of such metabolic diseases in individuals with previous episodes of growth restriction.

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      Microvirga massiliensis sp. nov., the human commensal with the largest genome

      Aurélia Caputo, Jean-Christophe Lagier, Saïd Azza, Catherine Robert, Donia Mouelhi, Pierre-Edouard Fournier and Didier Raoult

      Article first published online: 8 JAN 2016 | DOI: 10.1002/mbo3.329

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      Microvirga massiliensis JC119T has the largest bacterial genome of an isolate in humans. Here, we describe the features of M. massiliensis JC119T, together with the genome sequence information and its annotation.

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      Fructose-1,6-bisphosphate aldolase of Neisseria meningitidis binds human plasminogen via its C-terminal lysine residue

      Fariza Shams, Neil J. Oldfield, Si Kei Lai, Sarfraz A. Tunio, Karl G. Wooldridge and David P. J. Turner

      Article first published online: 5 JAN 2016 | DOI: 10.1002/mbo3.331

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      Fructose-1,6-bisphosphate aldolase (FBA) was previously shown to be surface-exposed in meningococci and involved in adhesion to host cells. In this study, FBA was shown to be present on the surface of both pathogenic and commensal neisseriae, and surface localization and anchoring was demonstrated to be independent of aldolase activity. Importantly, meningococcal FBA was found to bind to human glu-plasminogen in a dose-dependent manner. Site-directed mutagenesis demonstrated that the C-terminal lysine residue of FBA was required for this interaction, whereas subterminal lysine residues were not involved.

    13. You have full text access to this OnlineOpen article
      White collar 1-induced photolyase expression contributes to UV-tolerance of Ustilago maydis

      Annika Brych, Judita Mascarenhas, Elaine Jaeger, Elzbieta Charkiewicz, Richard Pokorny, Michael Bölker, Gunther Doehlemann and Alfred Batschauer

      Article first published online: 20 DEC 2015 | DOI: 10.1002/mbo3.322

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      We show in this contribution that the phytopathogenic fungus Ustilago maydis responds to blue light under control of white collar 1 (Wco1). Among the blue light-induced genes are the photolyase DNA repair enzymes. The Δwco1 mutant is less tolerant against UV-B consistent with lack of photolyase induction in the mutant.

    14. You have full text access to this OnlineOpen article
      Transcriptomic profiling of Methylococcus capsulatus (Bath) during growth with two different methane monooxygenases

      Øivind Larsen and Odd A. Karlsen

      Article first published online: 20 DEC 2015 | DOI: 10.1002/mbo3.324

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      Copper has a significant impact on the physiology of the obligate methanotroph Methylococcus capsulatus (Bath). Here, we explore the effect of copper on the expression of the large complement of c-type cytochromes present in the M. capsulatus genome combining transcriptomics, proteomics, and bioinformatics.

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      Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach

      Philippe Bordron, Mauricio Latorre, Maria-Paz Cortés, Mauricio González, Sven Thiele, Anne Siegel, Alejandro Maass and Damien Eveillard

      Article first published online: 17 DEC 2015 | DOI: 10.1002/mbo3.315

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      We aims to decipher functional roles within a microbial ecosystem composed of five bacteria involved into the copper bioleaching in Chilean mines. Integrating genomic and metabolic knowledge and under the single-cell hypothesis, we deciphered sets of genes, called SGS, that (1) are almost consecutive on their respective genomes, (2) take an active part in metabolic pathways, and (3) whose associated metabolic reactions are also closely connected within metabolic networks. Our analysis suggested that only few functional metabolic genes are horizontally transferred within the consortium and the use of SGS pinpoints a functional compartmentalization among the investigated species and exhibits putative bacterial interactions necessary for promoting these pathways.

    16. You have full text access to this OnlineOpen article
      Comparison of myxobacterial diversity and evaluation of isolation success in two niches: Kiritimati Island and German compost

      Kathrin I. Mohr, Marc Stechling, Joachim Wink, Elke Wilharm and Marc Stadler

      Article first published online: 15 DEC 2015 | DOI: 10.1002/mbo3.325

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      The diversity of myxobacteria from Kiritimati Island and German compost was evaluated by both cultivation-based and cultivation-independent methods. Phylogenetic analyses of the strains in comparison revealed a great potential of undescribed myxobacteria in both sampling sites. However, high deficits are demonstrated in the cultivation success of the myxobacterial diversity detected by cultivation-independent approaches.

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      Systematic analysis of the kalimantacin assembly line NRPS module using an adapted targeted mutagenesis approach

      Birgit Uytterhoeven, Kenny Appermans, Lijiang Song, Joleen Masschelein, Thomas Lathouwers, Chris W. Michiels and Rob Lavigne

      Article first published online: 15 DEC 2015 | DOI: 10.1002/mbo3.326

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      In this study, the specificity of the glycine-incorporating adenylation domain of the nonribosomal peptide synthetases (NRPS) module in the kalimantacin biosynthetic assembly line is adapted by use of a Pseudomonas-specific specificity-conferring code. A very efficient ligation independent cloning method is presented to replace the active site sequence of the adenylation domain in the parent strain with a chemically synthesized DNA fragment with the intended mutations. This study emphasizes the need for fundamental knowledge in the substrate specificity of the different domains in hybrid PKS/NRPS clusters.

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      Comparison of fecal pooling methods and DNA extraction kits for the detection of Mycobacterium avium subspecies paratuberculosis

      Akiko Mita, Yasuyuki Mori, Tetsuo Nakagawa, Tomoko Tasaki, Katsuo Utiyama and Hitomi Mori

      Article first published online: 15 DEC 2015 | DOI: 10.1002/mbo3.318

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      The aim of the study was to develop a sensitive method using quantitative real-time polymerase chain reaction (qPCR) with pooled fecal samples for the screening of Johne's disease (JD). There was no loss of sensitivity in pools of 10 subjects or less by using the new method. These results suggest that new method is a sensitive, practical, and cost-effective screening test for the detection of MAP-infected cattle and the monitoring of JD-free herds.

    19. You have full text access to this OnlineOpen article
      Temperature stress promotes cell division arrest in Xanthomonas citri subsp. citri

      Júlia A. P. Sumares, Luana Galvão Morão, Paula M. M. Martins, Daniela A. B. Martins, Eleni Gomes, José Belasque Jr and Henrique Ferreira

      Article first published online: 13 DEC 2015 | DOI: 10.1002/mbo3.323

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      Heat stress induces cell synchronization in Xanthomonas citri.

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      Diversity and functional analysis of light-driven pumping rhodopsins in marine Flavobacteria

      Yong Min Kwon, So-Young Kim, Kwang-Hwan Jung and Sang-Jin Kim

      Article first published online: 13 DEC 2015 | DOI: 10.1002/mbo3.321

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      Phylogenetic analysis of microbial rhodopsins in our isolates revealed that one rhodopsin belongs to the PR-clade (DTE motif) and the other rhodopsins were affiliated with NaR (NDQ motif) and ClR-clades (NTQ motif).

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      Altered acetylation and succinylation profiles in Corynebacterium glutamicum in response to conditions inducing glutamate overproduction

      Yuta Mizuno, Megumi Nagano-Shoji, Shosei Kubo, Yumi Kawamura, Ayako Yoshida, Hisashi Kawasaki, Makoto Nishiyama, Minoru Yoshida and Saori Kosono

      Article first published online: 11 DEC 2015 | DOI: 10.1002/mbo3.320

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      The profiles of two major lysine acyl-modifications, acetylation and succinylation, were significantly altered upon glutamate overproduction in C. glutamicum. A label-free semi-quantitative proteomic analysis identified 604 acetylated proteins with 1328 unique acetylation sites and 288 succinylated proteins with 651 unique succinylation sites.

    22. You have full text access to this OnlineOpen article
      Molecular insights into the enzymatic diversity of flavin-trafficking protein (Ftp; formerly ApbE) in flavoprotein biogenesis in the bacterial periplasm

      Ranjit K. Deka, Chad A. Brautigam, Wei Z. Liu, Diana R. Tomchick and Michael V. Norgard

      Article first published online: 2 DEC 2015 | DOI: 10.1002/mbo3.306

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      A flavin-trafficking protein (Ftp) in Treponema pallidum (Ftp_Tp) is the first bacterial periplasmic metal-dependent FAD pyrophosphatase described that hydrolyzes FAD into AMP and FMN. Orthologs of Ftp_Tp in other bacteria (formerly termed ApbE) appear to lack this hydrolytic activity; rather, they bind to and flavinylate the redox subunit, NqrC, via their metal-dependent FMN transferase activity. In the current study, we identified a bimetal center in the crystal structure of Escherichia coli Ftp (Ftp_Ec) and show via mutagenesis that a single amino acid substitution converts it from an FAD-binding protein to an Mg2+-dependent FAD pyrophosphatase.

    23. You have full text access to this OnlineOpen article
      Identification of regions within the Legionella pneumophila VipA effector protein involved in actin binding and polymerization and in interference with eukaryotic organelle trafficking

      Joana N. Bugalhão, Luís Jaime Mota and Irina S. Franco

      Article first published online: 2 DEC 2015 | DOI: 10.1002/mbo3.316

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      In this work, we have identified the regions of the Legionella pneumophila effector VipA involved in its subcellular localization, binding to actin and ability to polymerize microfilaments. Taken together, the results assign a fundamental role to the C-terminal region in the interaction and nucleation of actin filaments, whereas the N-terminal is also necessary to disrupt eukaryotic organelle trafficking.

    24. You have full text access to this OnlineOpen article
      Meta-audit of laboratory ISO accreditation inspections: measuring the old emperor's clothes

      Ian G. Wilson, Michael Smye and Ian J. C. Wallace

      Article first published online: 1 DEC 2015 | DOI: 10.1002/mbo3.314

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      ISO laboratory accreditation is claimed to assure the quality of results and service. We reassessed the significance of compliance audits and found they had negligible impact on quality.

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      The selective expression of carbonic anhydrase genes of Aspergillus nidulans in response to changes in mineral nutrition and CO2 concentration

      Leilei Xiao, Bin Lian, Cuiling Dong and Fanghua Liu

      Article first published online: 9 NOV 2015 | DOI: 10.1002/mbo3.311

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      One of the two CA genes is a preference gene when A. nidulans grows in special living environments. CA1 is involved mainly with the acquisition of mineral elements, while CA2 mainly adapts to changes in CO2 concentration. The directional selection of A. nidulans CA isozyme can ease some of the adverse effects on life processes brought about by external changes in the environment. It can also help A. nidulans avoid the waste of materials and energy caused by the gene's overexpression. Inversely, their adaption may impact mineral weathering and/or CO2 concentration, and even global change.

    26. You have full text access to this OnlineOpen article
      Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions

      Katharina Burbach, Jana Seifert, Dietmar H. Pieper and Amélia Camarinha-Silva

      Article first published online: 5 NOV 2015 | DOI: 10.1002/mbo3.312

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      A general DNA extraction procedure is crucial to make porcine studies more comparable and a standardization of methods is important to gain reliable knowledge on bacterial community profiles. This study compared the efficiency of extracting DNA, of porcine ileum digesta and feces samples, with 15 manual and four automated kits and identifies the most suitable one for a comprehensive investigation of the porcine gastrointestinal microbiota. The phylogenetic profiles of two regions of the 16S rRNA gene (V1–2 and V5–6) were analyzed and a high correlation between community structures was observed at genus and family level for ileum digesta and feces.

    27. You have full text access to this OnlineOpen article
      Breathing air to save energy – new insights into the ecophysiological role of high-affinity [NiFe]-hydrogenase in Streptomyces avermitilis

      Quentin Liot and Philippe Constant

      Article first published online: 5 NOV 2015 | DOI: 10.1002/mbo3.310

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      A combination of transcriptomic and mutagenesis approaches was used to shed light on the potential ecophysiological role of the high-affinity [NiFe]-hydrogenase in Streptomyces avermitilis. We propose that H2 is restricted to support the seed bank of Streptomyces under a unique survival–mixotrophic energy mode and discuss important ecological implications of this finding.

    28. You have full text access to this OnlineOpen article
      Poor survival of Methicillin-resistant Staphylococcus aureus on inanimate objects in the public spaces

      Hisanori Domon, Yoshio Uehara, Masataka Oda, Hiromi Seo, Noriko Kubota and Yutaka Terao

      Article first published online: 26 OCT 2015 | DOI: 10.1002/mbo3.308

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      Genomic profiling of Staphylococcus aureus isolates on shopping baskets.

    29. You have full text access to this OnlineOpen article
      Bypasses in intracellular glucose metabolism in iron-limited Pseudomonas putida

      Samantha S. Sasnow, Hua Wei and Ludmilla Aristilde

      Article first published online: 16 SEP 2015 | DOI: 10.1002/mbo3.287

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      We applied a stable isotope-assisted metabolomics approach to explore the underlying carbon metabolism in iron (Fe)-limited Pseudomonas putida KT2440 grown on glucose. Metabolic 13C flux analysis under Fe limitation indicated a decrease in carbon fluxes through the Entner–Doudoroff pathway and through Fe-containing metabolic enzymes. In addition to siderophore production for promoting Fe acquisition, imbalance between glucose uptake and biomass growth could be explained largely by enhanced gluconate secretion that rerouted glucose in excess of Fe-limited intracellular metabolism.

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