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Nature Microbiology

Hervé Nicoloff, Karin Hjort, Bruce R Levin, Dan I Andersson
When choosing antibiotics to treat bacterial infections, it is assumed that the susceptibility of the target bacteria to an antibiotic is reflected by laboratory estimates of the minimum inhibitory concentration (MIC) needed to prevent bacterial growth. A caveat of using MIC data for this purpose is heteroresistance, the presence of a resistant subpopulation in a main population of susceptible cells. We investigated the prevalence and mechanisms of heteroresistance in 41 clinical isolates of the pathogens Escherichia coli, Salmonella enterica, Klebsiella pneumoniae and Acinetobacter baumannii against 28 different antibiotics...
February 11, 2019: Nature Microbiology
Timothy A Blauwkamp, Simone Thair, Michael J Rosen, Lily Blair, Martin S Lindner, Igor D Vilfan, Trupti Kawli, Fred C Christians, Shivkumar Venkatasubrahmanyam, Gregory D Wall, Anita Cheung, Zoë N Rogers, Galit Meshulam-Simon, Liza Huijse, Sanjeev Balakrishnan, James V Quinn, Desiree Hollemon, David K Hong, Marla Lay Vaughn, Mickey Kertesz, Sivan Bercovici, Judith C Wilber, Samuel Yang
Thousands of pathogens are known to infect humans, but only a fraction are readily identifiable using current diagnostic methods. Microbial cell-free DNA sequencing offers the potential to non-invasively identify a wide range of infections throughout the body, but the challenges of clinical-grade metagenomic testing must be addressed. Here we describe the analytical and clinical validation of a next-generation sequencing test that identifies and quantifies microbial cell-free DNA in plasma from 1,250 clinically relevant bacteria, DNA viruses, fungi and eukaryotic parasites...
February 11, 2019: Nature Microbiology
Hugo Bisio, Matteo Lunghi, Mathieu Brochet, Dominique Soldati-Favre
Toxoplasma gondii establishes a lifelong chronic infection in humans and animals1 . Host cell entry and egress are key steps in the lytic cycle of this obligate intracellular parasite, ensuring its survival and dissemination. Egress is temporally orchestrated, underpinned by the exocytosis of secretory organelles called micronemes. At any point during intracellular replication, deleterious environmental changes such as the loss of host cell integrity can trigger egress2 through the activation of the cyclic guanosine monophosphate-dependent protein kinase G3 ...
February 11, 2019: Nature Microbiology
Ran Zhang, Lin Cao, Mengtian Cui, Zixian Sun, Mingxu Hu, Rouxuan Zhang, William Stuart, Xiaochu Zhao, Zirui Yang, Xueming Li, Yuna Sun, Shentao Li, Wei Ding, Zhiyong Lou, Zihe Rao
Adeno-associated virus (AAV) is a leading vector for virus-based gene therapy. The receptor for AAV (AAVR; also named KIAA0319L) was recently identified, and the precise characterization of AAV-AAVR recognition is in immediate demand. Taking advantage of a particle-filtering algorithm, we report here the cryo-electron microscopy structure of the AAV2-AAVR complex at 2.8 Å resolution. This structure reveals that of the five Ig-like polycystic kidney disease (PKD) domains in AAVR, PKD2 binds directly to the spike region of the AAV2 capsid adjacent to the icosahedral three-fold axis...
February 11, 2019: Nature Microbiology
Marco Mariotti, Gustavo Salinas, Toni Gabaldón, Vadim N Gladyshev
Selenoproteins are a diverse group of proteins containing selenocysteine (Sec)-the twenty-first amino acid-incorporated during translation via a unique recoding mechanism1,2 . Selenoproteins fulfil essential roles in many organisms1 , yet are not ubiquitous across the tree of life3-7 . In particular, fungi were deemed devoid of selenoproteins4,5,8 . However, we show here that Sec is utilized by nine species belonging to diverse early-branching fungal phyla, as evidenced by the genomic presence of both Sec machinery and selenoproteins...
February 11, 2019: Nature Microbiology
Xing-Lou Yang, Chee Wah Tan, Danielle E Anderson, Ren-Di Jiang, Bei Li, Wei Zhang, Yan Zhu, Xiao Fang Lim, Peng Zhou, Xiang-Ling Liu, Wuxiang Guan, Libiao Zhang, Shi-Yue Li, Yun-Zhi Zhang, Lin-Fa Wang, Zheng-Li Shi
In the version of this Letter originally published, in the 'Phylogenetic analysis' section of the Methods, the authors mistakenly stated that the GenBank accession number for the Ravn virus genome sequence was FJ750958. The correct accession number is DQ447649 for Ravn virus, Kenya, 1987. Accordingly, the label 'RAVN2007' in Fig. 1b should have been 'RAVV1987'. This mistake does not change any conclusions in this study. This statement and figure have now been amended in all versions of the Letter, and the Supplementary Information file has been updated accordingly...
February 8, 2019: Nature Microbiology
Tommi Vatanen, Damian R Plichta, Juhi Somani, Philipp C Münch, Timothy D Arthur, Andrew Brantley Hall, Sabine Rudolf, Edward J Oakeley, Xiaobo Ke, Rachel A Young, Henry J Haiser, Raivo Kolde, Moran Yassour, Kristiina Luopajärvi, Heli Siljander, Suvi M Virtanen, Jorma Ilonen, Raivo Uibo, Vallo Tillmann, Sergei Mokurov, Natalya Dorshakova, Jeffrey A Porter, Alice C McHardy, Harri Lähdesmäki, Hera Vlamakis, Curtis Huttenhower, Mikael Knip, Ramnik J Xavier
In the version of this Article originally published, in the first sentence of the second paragraph of the Discussion section, the word "operingrationally" should have read "operationally". This has now been amended in all versions of the Article.
February 5, 2019: Nature Microbiology
Mariona Nadal-Ribelles, Saiful Islam, Wu Wei, Pablo Latorre, Michelle Nguyen, Eulàlia de Nadal, Francesc Posas, Lars M Steinmetz
Single-cell RNA sequencing has revealed extensive cellular heterogeneity within many organisms, but few methods have been developed for microbial clonal populations. The yeast genome displays unusually dense transcript spacing, with interleaved and overlapping transcription from both strands, resulting in a minuscule but complex pool of RNA that is protected by a resilient cell wall. Here, we have developed a sensitive, scalable and inexpensive yeast single-cell RNA-seq (yscRNA-seq) method that digitally counts transcript start sites in a strand- and isoform-specific manner...
February 4, 2019: Nature Microbiology
Wooseok Song, Minju Joo, Ji-Hyun Yeom, Eunkyoung Shin, Minho Lee, Hyung-Kyoon Choi, Jihwan Hwang, Yong-In Kim, Ramin Seo, J Eugene Lee, Christopher J Moore, Yong-Hak Kim, Seong-Il Eyun, Yoonsoo Hahn, Jeehyeon Bae, Kangseok Lee
It is generally assumed that each organism has evolved to possess a unique ribosomal RNA (rRNA) species optimal for its physiological needs. However, some organisms express divergent rRNAs, the functional roles of which remain unknown. Here, we show that ribosomes containing the most variable rRNAs, encoded by the rrnI operon (herein designated as I-ribosomes), direct the preferential translation of a subset of mRNAs in Vibrio vulnificus, enabling the rapid adaptation of bacteria to temperature and nutrient shifts...
February 4, 2019: Nature Microbiology
Mireia Valles-Colomer, Gwen Falony, Youssef Darzi, Ettje F Tigchelaar, Jun Wang, Raul Y Tito, Carmen Schiweck, Alexander Kurilshikov, Marie Joossens, Cisca Wijmenga, Stephan Claes, Lukas Van Oudenhove, Alexandra Zhernakova, Sara Vieira-Silva, Jeroen Raes
The relationship between gut microbial metabolism and mental health is one of the most intriguing and controversial topics in microbiome research. Bidirectional microbiota-gut-brain communication has mostly been explored in animal models, with human research lagging behind. Large-scale metagenomics studies could facilitate the translational process, but their interpretation is hampered by a lack of dedicated reference databases and tools to study the microbial neuroactive potential. Surveying a large microbiome population cohort (Flemish Gut Flora Project, n = 1,054) with validation in independent data sets (ntotal  = 1,070), we studied how microbiome features correlate with host quality of life and depression...
February 4, 2019: Nature Microbiology
Guy Schleyer, Nir Shahaf, Carmit Ziv, Yonghui Dong, Roy A Meoded, Eric J N Helfrich, Daniella Schatz, Shilo Rosenwasser, Ilana Rogachev, Asaph Aharoni, Jörn Piel, Assaf Vardi
Tapping into the metabolic crosstalk between a host and its virus can reveal unique strategies employed during infection. Viral infection is a dynamic process that generates an evolving metabolic landscape. Gaining a continuous view into the infection process is highly challenging and is limited by current metabolomics approaches, which typically measure the average of the entire population at various stages of infection. Here, we took an innovative approach to study the metabolic basis of host-virus interactions between the bloom-forming alga Emiliania huxleyi and its specific virus...
February 4, 2019: Nature Microbiology
Yonatan Ganor, Fernando Real, Alexis Sennepin, Charles-Antoine Dutertre, Lisa Prevedel, Lin Xu, Daniela Tudor, Bénédicte Charmeteau, Anne Couedel-Courteille, Sabrina Marion, Ali-Redha Zenak, Jean-Pierre Jourdain, Zhicheng Zhou, Alain Schmitt, Claude Capron, Eliseo A Eugenin, Rémi Cheynier, Marc Revol, Sarra Cristofari, Anne Hosmalin, Morgane Bomsel
Human immunodeficiency virus type 1 (HIV-1) eradication is prevented by the establishment on infection of cellular HIV-1 reservoirs that are not fully characterized, especially in genital mucosal tissues (the main HIV-1 entry portal on sexual transmission). Here, we show, using penile tissues from HIV-1-infected individuals under suppressive combination antiretroviral therapy, that urethral macrophages contain integrated HIV-1 DNA, RNA, proteins and intact virions in virus-containing compartment-like structures, whereas viral components remain undetectable in urethral T cells...
February 4, 2019: Nature Microbiology
Malika Saint, François Bertaux, Wenhao Tang, Xi-Ming Sun, Laurence Game, Anna Köferle, Jürg Bähler, Vahid Shahrezaei, Samuel Marguerat
Phenotypic cell-to-cell variability is a fundamental determinant of microbial fitness that contributes to stress adaptation and drug resistance. Gene expression heterogeneity underpins this variability but is challenging to study genome-wide. Here we examine the transcriptomes of >2,000 single fission yeast cells exposed to various environmental conditions by combining imaging, single-cell RNA sequencing and Bayesian true count recovery. We identify sets of highly variable genes during rapid proliferation in constant culture conditions...
February 4, 2019: Nature Microbiology
Yusuke Okuno, Takayuki Murata, Yoshitaka Sato, Hideki Muramatsu, Yoshinori Ito, Takahiro Watanabe, Tatsuya Okuno, Norihiro Murakami, Kenichi Yoshida, Akihisa Sawada, Masami Inoue, Keisei Kawa, Masao Seto, Koichi Ohshima, Yuichi Shiraishi, Kenichi Chiba, Hiroko Tanaka, Satoru Miyano, Yohei Narita, Masahiro Yoshida, Fumi Goshima, Jun-Ichi Kawada, Tetsuya Nishida, Hitoshi Kiyoi, Seiichi Kato, Shigeo Nakamura, Satoko Morishima, Tetsushi Yoshikawa, Shigeyoshi Fujiwara, Norio Shimizu, Yasushi Isobe, Masaaki Noguchi, Atsushi Kikuta, Keiji Iwatsuki, Yoshiyuki Takahashi, Seiji Kojima, Seishi Ogawa, Hiroshi Kimura
In the version of this Letter originally published, in the sentence beginning "The major driver role of DDX3X mutations...", the citation "Fig. 2a-f" should have been "Fig. 2". In addition, in the sentence beginning "Another finding of interest was the presence of identical driver mutations...", the citation "Fig. 3a,b and Fig. 4" should have been "Fig. 3". This has now been amended in all versions of the Letter.
January 30, 2019: Nature Microbiology
Andrew R J Curson, Beth T Williams, Benjamin J Pinchbeck, Leanne P Sims, Ana Bermejo Martínez, Peter Paolo L Rivera, Deepak Kumaresan, Elena Mercadé, Lewis G Spurgin, Ornella Carrión, Simon Moxon, Rose Ann Cattolico, Unnikrishnan Kuzhiumparambil, Paul Guagliardo, Peta L Clode, Jean-Baptiste Raina, Jonathan D Todd
In the version of this Letter originally published, the Methods incorrectly stated that all phytoplankton cultures were sampled in mid-exponential phase. The low-nitrogen cultures were sampled in early stationary phase and at the point at which Fv/Fm values decreased, to indicate that cultures were experiencing low-nitrogen conditions. All other phytoplankton cultures were sampled in exponential phase. Growth and Fv/Fm data are provided here on high- and low-nitrogen cultures (Figs 1, 2 and 3) to clarify and support this correction...
January 30, 2019: Nature Microbiology
Audra E Devoto, Joanne M Santini, Matthew R Olm, Karthik Anantharaman, Patrick Munk, Jenny Tung, Elizabeth A Archie, Peter J Turnbaugh, Kimberley D Seed, Ran Blekhman, Frank M Aarestrup, Brian C Thomas, Jillian F Banfield
Bacteriophages (phages) dramatically shape microbial community composition, redistribute nutrients via host lysis and drive evolution through horizontal gene transfer. Despite their importance, much remains to be learned about phages in the human microbiome. We investigated the gut microbiomes of humans from Bangladesh and Tanzania, two African baboon social groups and Danish pigs; many of these microbiomes contain phages belonging to a clade with genomes >540 kilobases in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phages...
January 28, 2019: Nature Microbiology
Atsushi Taguchi, Michael A Welsh, Lindsey S Marmont, Wonsik Lee, Megan Sjodt, Andrew C Kruse, Daniel Kahne, Thomas G Bernhardt, Suzanne Walker
The peptidoglycan cell wall is essential for the survival and morphogenesis of bacteria1 . For decades, it was thought that only class A penicillin-binding proteins (PBPs) and related enzymes effected peptidoglycan synthesis. Recently, it was shown that RodA-a member of the unrelated SEDS protein family-also acts as a peptidoglycan polymerase2-4 . Not all bacteria require RodA for growth; however, its homologue, FtsW, is a core member of the divisome complex that appears to be universally essential for septal cell wall assembly5,6 ...
January 28, 2019: Nature Microbiology
Vanessa Diniz Atayde, Alonso da Silva Lira Filho, Visnu Chaparro, Aude Zimmermann, Caroline Martel, Maritza Jaramillo, Martin Olivier
Leishmania are ancient eukaryotes that have retained the exosome pathway through evolution. Leishmania RNA virus 1 (LRV1)-infected Leishmania species are associated with a particularly aggressive mucocutaneous disease triggered in response to the double-stranded RNA (dsRNA) virus. However, it is unclear how LRV1 is exposed to the mammalian host cells. In higher eukaryotes, some viruses are known to utilize the host exosome pathway for their formation and cell-to-cell spread. As a result, exosomes derived from infected cells contain viral material or particles...
January 28, 2019: Nature Microbiology
Jakob T Rostøl, Luciano A Marraffini
Type III-A CRISPR-Cas systems employ the Cas10-Csm complex to destroy bacteriophages and plasmids, using a guide RNA to locate complementary RNA molecules from the invader and trigger an immune response that eliminates the infecting DNA. In addition, these systems possess the non-specific RNase Csm6, which provides further protection for the host. While the role of Csm6 in immunity during phage infection has been determined, how this RNase is used against plasmids is unclear. Here, we show that Staphylococcus epidermidis Csm6 is required for immunity when transcription across the plasmid target is infrequent, leading to impaired target recognition and inefficient DNA degradation by the Cas10-Csm complex...
January 28, 2019: Nature Microbiology
Amitesh Anand, Connor A Olson, Laurence Yang, Anand V Sastry, Edward Catoiu, Kumari Sonal Choudhary, Patrick V Phaneuf, Troy E Sandberg, Sibei Xu, Ying Hefner, Richard Szubin, Adam M Feist, Bernhard O Palsson
Pseudogenes represent open reading frames that have been damaged by mutations, rendering the gene product non-functional. Pseudogenes are found in many genomes and are not always eliminated, even if they are potentially 'wasteful'. This raises a fundamental question about their prevalence. Here we report pseudogene efeU repair that restores the iron uptake system of Escherichia coli under a designed selection pressure during adaptive laboratory evolution.
January 28, 2019: Nature Microbiology
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