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Nature Microbiology

Jason Pinger, Dragana Nešić, Liaqat Ali, Francisco Aresta-Branco, Mirjana Lilic, Shanin Chowdhury, Hee-Sook Kim, Joseph Verdi, Jayne Raper, Michael A J Ferguson, F Nina Papavasiliou, C Erec Stebbins
The African trypanosome Trypanosoma brucei spp. is a paradigm for antigenic variation, the orchestrated alteration of cell surface molecules to evade host immunity. The parasite elicits robust antibody-mediated immune responses to its variant surface glycoprotein (VSG) coat, but evades immune clearance by repeatedly accessing a large genetic VSG repertoire and 'switching' to antigenically distinct VSGs. This persistent immune evasion has been ascribed exclusively to amino-acid variance on the VSG surface presented by a conserved underlying protein architecture...
July 9, 2018: Nature Microbiology
Jillian M Petersen, Anna Kemper, Harald Gruber-Vodicka, Ulisse Cardini, Matthijs van der Geest, Manuel Kleiner, Silvia Bulgheresi, Marc Mußmann, Craig Herbold, Brandon K B Seah, Chakkiath Paul Antony, Dan Liu, Alexandra Belitz, Miriam Weber
In this Article, the completeness and number of contigs for draft genomes from two individuals of Laxus oneistus are incorrect in the main text, although the correct information is included in Table 1. The original and corrected versions of the relevant sentence are shown in the correction notice.
June 27, 2018: Nature Microbiology
Waldan K Kwong, Hao Zheng, Nancy A Moran
In this Brief Communication, the authors omitted references to several previous studies that have demonstrated that the TCA variant shown has also been found in several other bacterial species, specifically among some anaerobic Deltaproteobacteria. The Brief Communication focused on showing that this variant is more widespread than previously known, particularly in animal-associated bacteria. Using genetic approaches, Kwong et al. demonstrated this alternative cycle in additional, distantly related organisms...
June 27, 2018: Nature Microbiology
Francis Impens, Nathalie Rolhion, Lilliana Radoshevich, Christophe Bécavin, Mélodie Duval, Jeffrey Mellin, Francisco García Del Portillo, M Graciela Pucciarelli, Allison H Williams, Pascale Cossart
This Article contains a URL for a publically available whole-genome browser ( ). However, due to technical constraint, this website has been replaced with an alternative ( ).
June 25, 2018: Nature Microbiology
Fei He, Yuvaraj Bhoobalan-Chitty, Lan B Van, Anders L Kjeldsen, Matteo Dedola, Kira S Makarova, Eugene V Koonin, Ditlev E Brodersen, Xu Peng
In the original version of this Article, molecular weight markers in Figs 1c, 2c,d and 4d were displaced during the production process, so that they were not correctly aligned with the corresponding bands. In addition, in Fig. 4c, molecular masses given for three different elution volumes were displaced so that they appeared to the left of the correct positions. These errors have now been corrected.
June 21, 2018: Nature Microbiology
Jeffrey I Cohen
In the version of this News and Views originally published, the author made an incorrect reference to 'mice deficient in Mx1'. This has now been corrected so that the text instead refers to 'mice congenic for Mx1'. The full corrected sentence reads as "Pretreatment of mice congenic for Mx1, an ISG that is critical for protection of animals from influenza, with intranasal neomycin significantly improved survival; however, about 50% of the mice died."
June 19, 2018: Nature Microbiology
Damian W Rivett, Thomas Bell
Bacterial communities are essential for the functioning of the Earth's ecosystems 1 . A key challenge is to quantify the functional roles of bacterial taxa in nature to understand how the properties of ecosystems change over time or under different environmental conditions 2 . Such knowledge could be used, for example, to understand how bacteria modulate biogeochemical cycles 3 , and to engineer bacterial communities to optimize desirable functional processes 4 . Communities of bacteria are, however, extraordinarily complex with hundreds of interacting taxa in every gram of soil and every millilitre of pond water 5 ...
June 18, 2018: Nature Microbiology
Marc Swidergall, Norma V Solis, Michail S Lionakis, Scott G Filler
In the version of this Article originally published, the authors described the ANT compound used in their study as 4-(2,5-dimethyl-1H-pyrrol-1-yl)-2-hydroxybenzoic acid (ANT). The authors now wish to clarify that the ANT compound used was actually a 2,5-dimethylpyrrolyl benzoic acid derivative1 that has been shown to inhibit not only the enzymatic activity of EphA2, but also several unrelated enzymes2 . The description of the compound in the Article has now been changed to 4-(2,5-dimethyl-1H-pyrrol-1-yl)-2-hydroxybenzoic acid derivative (ANT) to reflect this...
June 12, 2018: Nature Microbiology
Tom O Delmont, Christopher Quince, Alon Shaiber, Özcan C Esen, Sonny Tm Lee, Michael S Rappé, Sandra L MacLellan, Sebastian Lücker, A Murat Eren
Nitrogen fixation in the surface ocean impacts global marine nitrogen bioavailability and thus microbial primary productivity. Until now, cyanobacterial populations have been viewed as the main suppliers of bioavailable nitrogen in this habitat. Although PCR amplicon surveys targeting the nitrogenase reductase gene have revealed the existence of diverse non-cyanobacterial diazotrophic populations, subsequent quantitative PCR surveys suggest that they generally occur in low abundance. Here, we use state-of-the-art metagenomic assembly and binning strategies to recover nearly one thousand non-redundant microbial population genomes from the TARA Oceans metagenomes...
June 11, 2018: Nature Microbiology
Ghina Chougui, Soundasse Munir-Matloob, Roy Matkovic, Michaël M Martin, Marina Morel, Hichem Lahouassa, Marjorie Leduc, Bertha Cecilia Ramirez, Lucie Etienne, Florence Margottin-Goguet
To evade host immune defences, human immunodeficiency viruses 1 and 2 (HIV-1 and HIV-2) have evolved auxiliary proteins that target cell restriction factors. Viral protein X (Vpx) from the HIV-2/SIVsmm lineage enhances viral infection by antagonizing SAMHD1 (refs 1,2 ), but this antagonism is not sufficient to explain all Vpx phenotypes. Here, through a proteomic screen, we identified another Vpx target-HUSH (TASOR, MPP8 and periphilin)-a complex involved in position-effect variegation 3 . HUSH downregulation by Vpx is observed in primary cells and HIV-2-infected cells...
June 11, 2018: Nature Microbiology
Courtney K Ellison, Triana N Dalia, Alfredo Vidal Ceballos, Joseph Che-Yen Wang, Nicolas Biais, Yves V Brun, Ankur B Dalia
Natural transformation is a broadly conserved mechanism of horizontal gene transfer in bacterial species that can shape evolution and foster the spread of antibiotic resistance determinants, promote antigenic variation and lead to the acquisition of novel virulence factors. Surface appendages called competence pili promote DNA uptake during the first step of natural transformation 1 ; however, their mechanism of action has remained unclear owing to an absence of methods to visualize these structures in live cells...
June 11, 2018: Nature Microbiology
Christopher J Schofield
No abstract text is available yet for this article.
June 11, 2018: Nature Microbiology
Matthew B Reeves
In the version of this News & Views originally published, ref. 6 was incorrectly cited instead of ref. 5 at the end of the sentence shown below. This has now been corrected."Indeed, a proof of concept study has shown that latently expressed US28 can be targeted using an immunotoxin-based approach to eliminate infected cells in vitro5 ."
June 8, 2018: Nature Microbiology
Zackary J Jay, Jacob P Beam, Mensur Dlakić, Douglas B Rusch, Mark A Kozubal, William P Inskeep
The discovery of archaeal lineages is critical to our understanding of the universal tree of life and evolutionary history of the Earth. Geochemically diverse thermal environments in Yellowstone National Park provide unprecedented opportunities for studying archaea in habitats that may represent analogues of early Earth. Here, we report the discovery and characterization of a phylum-level archaeal lineage proposed and herein referred to as the 'Marsarchaeota', after the red planet. The Marsarchaeota contains at least two major subgroups prevalent in acidic, microaerobic geothermal Fe(III) oxide microbial mats across a temperature range from ~50-80 °C...
May 14, 2018: Nature Microbiology
Sukanya Iyer, Dai Le, Bo Ryoung Park, Minsu Kim
Bacteria adapt to environmental stress by producing proteins that provide stress protection. However, stress can severely perturb the kinetics of gene expression, disrupting protein production. Here, we characterized how Escherichia coli mitigates such perturbations under nutrient stress through the kinetic coordination of transcription and translation. We observed that, when translation became limiting under nitrogen starvation, transcription elongation slowed accordingly. This slowdown was mediated by (p)ppGpp, the alarmone whose primary role is thought to be promoter regulation...
May 14, 2018: Nature Microbiology
Angelino T Tromp, Michiel Van Gent, Pauline Abrial, Amandine Martin, Joris P Jansen, Carla J C De Haas, Kok P M Van Kessel, Bart W Bardoel, Elisabeth Kruse, Emilie Bourdonnay, Michael Boettcher, Michael T McManus, Christopher J Day, Michael P Jennings, Gérard Lina, François Vandenesch, Jos A G Van Strijp, Robert Jan Lebbink, Pieter-Jan A Haas, Thomas Henry, András N Spaan
The staphylococcal bi-component leukocidins Panton-Valentine leukocidin (PVL) and γ-haemolysin CB (HlgCB) target human phagocytes. Binding of the toxins' S-components to human complement C5a receptor 1 (C5aR1) contributes to cellular tropism and human specificity of PVL and HlgCB. To investigate the role of both leukocidins during infection, we developed a human C5aR1 knock-in (hC5aR1KI ) mouse model. HlgCB, but unexpectedly not PVL, contributed to increased bacterial loads in tissues of hC5aR1KI mice. Compared to humans, murine hC5aR1KI neutrophils showed a reduced sensitivity to PVL, which was mediated by the toxin's F-component LukF-PV...
May 7, 2018: Nature Microbiology
Andrew I Flyak, Natalia Kuzmina, Charles D Murin, Christopher Bryan, Edgar Davidson, Pavlo Gilchuk, Christopher P Gulka, Philipp A Ilinykh, Xiaoli Shen, Kai Huang, Palaniappan Ramanathan, Hannah Turner, Marnie L Fusco, Rebecca Lampley, Nurgun Kose, Hannah King, Gopal Sapparapu, Benjamin J Doranz, Thomas G Ksiazek, David W Wright, Erica Ollmann Saphire, Andrew B Ward, Alexander Bukreyev, James E Crowe
Ebola virus (EBOV) in humans causes a severe illness with high mortality rates. Several strategies have been developed in the past to treat EBOV infection, including the antibody cocktail ZMapp, which has been shown to be effective in nonhuman primate models of infection 1 and has been used under compassionate-treatment protocols in humans 2 . ZMapp is a mixture of three chimerized murine monoclonal antibodies (mAbs)3-6 that target EBOV-specific epitopes on the surface glycoprotein7,8 . However, ZMapp mAbs do not neutralize other species from the genus Ebolavirus, such as Bundibugyo virus (BDBV), Reston virus (RESTV) or Sudan virus (SUDV)...
May 7, 2018: Nature Microbiology
Hua Zhang, Yan Li, Hong-Bo Wang, Ao Zhang, Mei-Ling Chen, Zhi-Xin Fang, Xiao-Dong Dong, Shi-Bing Li, Yong Du, Dan Xiong, Jiang-Yi He, Man-Zhi Li, Yan-Min Liu, Ai-Jun Zhou, Qian Zhong, Yi-Xin Zeng, Elliott Kieff, Zhiqiang Zhang, Benjamin E Gewurz, Bo Zhao, Mu-Sheng Zeng
In the version of this Letter originally published, the authors reported on the use of 2,5-dimethylpyrrolyl benzoic acid to block Ephrin receptors. In 2011, it was reported that newly synthesized 2,5-dimethylpyrrolyl benzoic acid lacked the previously reported EphA2 antagonizing activity1. However, the purchased compound did in fact have the activity initially reported, suggesting that an uncharacterized alteration occurred during storage. The authors therefore wish to clarify that the compound used in their study should be more accurately referred to as a 2,5-dimethylpyrrolyl benzoic acid derivative...
April 20, 2018: Nature Microbiology
Jian Guo, Susanne Wilken, Valeria Jimenez, Chang Jae Choi, Charles Ansong, Richard Dannebaum, Lisa Sudek, David S Milner, Charles Bachy, Emily Nahas Reistetter, Virginia A Elrod, Denis Klimov, Samuel O Purvine, Chia-Lin Wei, Govindarajan Kunde-Ramamoorthy, Thomas A Richards, Ursula Goodenough, Richard D Smith, Stephen J Callister, Alexandra Z Worden
Marine algae perform approximately half of global carbon fixation, but their growth is often limited by the availability of phosphate or other nutrients1,2 . As oceans warm, the area of phosphate-limited surface waters is predicted to increase, resulting in ocean desertification3,4 . Understanding the responses of key eukaryotic phytoplankton to nutrient limitation is therefore critical5,6 . We used advanced photo-bioreactors to investigate how the widespread marine green alga Micromonas commoda grows under transitions from replete nutrients to chronic phosphate limitation and subsequent relief, analysing photosystem changes and broad cellular responses using proteomics, transcriptomics and biophysical measurements...
July 2018: Nature Microbiology
Karthika Rajeeve, Sudip Das, Bhupesh K Prusty, Thomas Rudel
Chlamydia trachomatis, an obligate intracellular human pathogen, is a major cause of sexually transmitted diseases. Infections often occur without symptoms, a feature that has been attributed to the ability of the pathogen to evade the host immune response. We show here that C. trachomatis paralyses the host immune system by preventing the activation of polymorphic nuclear leukocytes (PMNs). PMNs infected with Chlamydia fail to produce neutrophil extracellular traps and the bacteria are able to survive in PMNs for extended periods of time...
July 2018: Nature Microbiology
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