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Nature Microbiology

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https://www.readbyqxmd.com/read/29335555/metatranscriptome-of-human-faecal-microbial-communities-in-a-cohort-of-adult-men
#1
Galeb S Abu-Ali, Raaj S Mehta, Jason Lloyd-Price, Himel Mallick, Tobyn Branck, Kerry L Ivey, David A Drew, Casey DuLong, Eric Rimm, Jacques Izard, Andrew T Chan, Curtis Huttenhower
The gut microbiome is intimately related to human health, but it is not yet known which functional activities are driven by specific microorganisms' ecological configurations or transcription. We report a large-scale investigation of 372 human faecal metatranscriptomes and 929 metagenomes from a subset of 308 men in the Health Professionals Follow-Up Study. We identified a metatranscriptomic 'core' universally transcribed over time and across participants, often by different microorganisms. In contrast to the housekeeping functions enriched in this core, a 'variable' metatranscriptome included specialized pathways that were differentially expressed both across participants and among microorganisms...
January 15, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29335554/stability-of-the-human-faecal-microbiome-in-a-cohort-of-adult-men
#2
Raaj S Mehta, Galeb S Abu-Ali, David A Drew, Jason Lloyd-Price, Ayshwarya Subramanian, Paul Lochhead, Amit D Joshi, Kerry L Ivey, Hamed Khalili, Gordon T Brown, Casey DuLong, Mingyang Song, Long H Nguyen, Himel Mallick, Eric B Rimm, Jacques Izard, Curtis Huttenhower, Andrew T Chan
Characterizing the stability of the gut microbiome is important to exploit it as a therapeutic target and diagnostic biomarker. We metagenomically and metatranscriptomically sequenced the faecal microbiomes of 308 participants in the Health Professionals Follow-Up Study. Participants provided four stool samples-one pair collected 24-72 h apart and a second pair ~6 months later. Within-person taxonomic and functional variation was consistently lower than between-person variation over time. In contrast, metatranscriptomic profiles were comparably variable within and between subjects due to higher within-subject longitudinal variation...
January 15, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29335553/mutations-in-ppe38-block-pe_pgrs-secretion-and-increase-virulence-of-mycobacterium-tuberculosis
#3
Louis S Ates, Anzaan Dippenaar, Roy Ummels, Sander R Piersma, Aniek D van der Woude, Kim van der Kuij, Fabien Le Chevalier, Dulce Mata-Espinosa, Jorge Barrios-Payán, Brenda Marquina-Castillo, Carolina Guapillo, Connie R Jiménez, Arnab Pain, Edith N G Houben, Robin M Warren, Roland Brosch, Rogelio Hernández-Pando, Wilbert Bitter
Mycobacterium tuberculosis requires a large number of secreted and exported proteins for its virulence, immune modulation and nutrient uptake. Most of these proteins are transported by the different type VII secretion systems1,2. The most recently evolved type VII secretion system, ESX-5, secretes dozens of substrates belonging to the PE and PPE families, which are named for conserved proline and glutamic acid residues close to the amino terminus3,4. However, the role of these proteins remains largely elusive 1 ...
January 15, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29335552/a-pathway-for-biological-methane-production-using-bacterial-iron-only-nitrogenase
#4
Yanning Zheng, Derek F Harris, Zheng Yu, Yanfen Fu, Saroj Poudel, Rhesa N Ledbetter, Kathryn R Fixen, Zhi-Yong Yang, Eric S Boyd, Mary E Lidstrom, Lance C Seefeldt, Caroline S Harwood
Methane (CH4) is a potent greenhouse gas that is released from fossil fuels and is also produced by microbial activity, with at least one billion tonnes of CH4 being formed and consumed by microorganisms in a single year 1 . Complex methanogenesis pathways used by archaea are the main route for bioconversion of carbon dioxide (CO2) to CH4 in nature2-4. Here, we report that wild-type iron-iron (Fe-only) nitrogenase from the bacterium Rhodopseudomonas palustris reduces CO2 simultaneously with nitrogen gas (N2) and protons to yield CH4, ammonia (NH3) and hydrogen gas (H2) in a single enzymatic step...
January 15, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29311645/author-correction-fluorescent-d-amino-acids-reveal-bi-cellular-cell-wall-modifications-important-for-bdellovibrio-bacteriovorus-predation
#5
Erkin Kuru, Carey Lambert, Jonathan Rittichier, Rob Till, Adrien Ducret, Adeline Derouaux, Joe Gray, Jacob Biboy, Waldemar Vollmer, Michael VanNieuwenhze, Yves V Brun, R Elizabeth Sockett
In the original version of this Article, a grant number and acknowledgement were omitted. The Acknowledgements section should have stated that one of the 3D SIM microscopes used for this research was supported by Medical Research Council UK grant (MR/K015753/1) to S. Foster, University of Sheffield, UK, and that the authors thank C. Walther and S. Foster for the access and their kind help with this. This has now been corrected in all versions of the Article.
January 8, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29311644/dynamics-of-metatranscription-in-the-inflammatory-bowel-disease-gut-microbiome
#6
Melanie Schirmer, Eric A Franzosa, Jason Lloyd-Price, Lauren J McIver, Randall Schwager, Tiffany W Poon, Ashwin N Ananthakrishnan, Elizabeth Andrews, Gildardo Barron, Kathleen Lake, Mahadev Prasad, Jenny Sauk, Betsy Stevens, Robin G Wilson, Jonathan Braun, Lee A Denson, Subra Kugathasan, Dermot P B McGovern, Hera Vlamakis, Ramnik J Xavier, Curtis Huttenhower
Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Genetic, environmental and microbial factors have been implicated in the onset and exacerbation of IBD. However, the mechanisms associating gut microbial dysbioses and aberrant immune responses remain largely unknown. The integrative Human Microbiome Project seeks to close these gaps by examining the dynamics of microbiome functionality in disease by profiling the gut microbiomes of >100 individuals sampled over a 1-year period...
January 8, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29292384/ephrin-receptor-a2-is-a-functional-entry-receptor-for-epstein-barr-virus
#7
Jia Chen, Karthik Sathiyamoorthy, Xianming Zhang, Samantha Schaller, Bethany E Perez White, Theodore S Jardetzky, Richard Longnecker
Epstein-Barr virus (EBV) is an oncogenic virus that infects more than 90% of the world's population 1 . EBV predominantly infects human B cells and epithelial cells, which is initiated by fusion of the viral envelope with a host cellular membrane 2 . The mechanism of EBV entry into B cells has been well characterized 3 . However, the mechanism for epithelial cell entry remains elusive. Here, we show that the integrins αvβ5, αvβ6 and αvβ8 do not function as entry and fusion receptors for epithelial cells, whereas Ephrin receptor tyrosine kinase A2 (EphA2) functions well for both...
January 1, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29292383/ephrin-receptor-a2-is-an-epithelial-cell-receptor-for-epstein-barr-virus-entry
#8
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
Epstein-Barr virus (EBV) is causally associated with nasopharyngeal carcinoma, 10% of gastric carcinoma and various B cell lymphomas 1 . EBV infects both B cells and epithelial cells 2 . Recently, we reported that epidermal growth factor and Neuropilin 1 markedly enhanced EBV entry into nasopharyngeal epithelial cells 3 . However, knowledge of how EBV infects epithelial cells remains incomplete. To understand the mechanisms through which EBV infects epithelial cells, we integrated microarray and RNA interference screen analyses and found that Ephrin receptor A2 (EphA2) is important for EBV entry into the epithelial cells...
January 1, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29255255/archaeal-cells-share-common-size-control-with-bacteria-despite-noisier-growth-and-division
#9
Ye-Jin Eun, Po-Yi Ho, Minjeong Kim, Salvatore LaRussa, Lydia Robert, Lars D Renner, Amy Schmid, Ethan Garner, Ariel Amir
In nature, microorganisms exhibit different volumes spanning six orders of magnitude 1 . Despite their capability to create different sizes, a clonal population in a given environment maintains a uniform size across individual cells. Recent studies in eukaryotic and bacterial organisms showed that this homogeneity in cell size can be accomplished by growing a constant size between two cell cycle events (that is, the adder model 2-6 ). Demonstration of the adder model led to the hypothesis that this phenomenon is a consequence of convergent evolution...
December 18, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29255254/dietary-pectic-glycans-are-degraded-by-coordinated-enzyme-pathways-in-human-colonic-bacteroides
#10
Ana S Luis, Jonathon Briggs, Xiaoyang Zhang, Benjamin Farnell, Didier Ndeh, Aurore Labourel, Arnaud Baslé, Alan Cartmell, Nicolas Terrapon, Katherine Stott, Elisabeth C Lowe, Richard McLean, Kaitlyn Shearer, Julia Schückel, Immacolata Venditto, Marie-Christine Ralet, Bernard Henrissat, Eric C Martens, Steven C Mosimann, D Wade Abbott, Harry J Gilbert
The major nutrients available to human colonic Bacteroides species are glycans, exemplified by pectins, a network of covalently linked plant cell wall polysaccharides containing galacturonic acid (GalA). Metabolism of complex carbohydrates by the Bacteroides genus is orchestrated by polysaccharide utilization loci (PULs). In Bacteroides thetaiotaomicron, a human colonic bacterium, the PULs activated by different pectin domains have been identified; however, the mechanism by which these loci contribute to the degradation of these GalA-containing polysaccharides is poorly understood...
December 18, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29234139/author-correction-recovery-of-nearly-8-000-metagenome-assembled-genomes-substantially-expands-the-tree-of-life
#11
Donovan H Parks, Christian Rinke, Maria Chuvochina, Pierre-Alain Chaumeil, Ben J Woodcroft, Paul N Evans, Philip Hugenholtz, Gene W Tyson
In the original version of this Article, the authors stated that the archaeal phylum Parvarchaeota was previously represented by only two single-cell genomes (ARMAN-4_'5-way FS' and ARMAN-5_'5-way FS'). However, these are in fact unpublished, low-quality metagenome-assembled genomes (MAGs) obtained from Richmond Mine, California. In addition, the authors overlooked two higher-quality published Parvarchaeota MAGs from the same habitat, ARMAN-4 (ADCE00000000) and ARMAN-5 (ADHF00000000) (B. J. Baker et al., Proc...
December 12, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29203882/pasta-repeats-of-the-protein-kinase-stkp-interconnect-cell-constriction-and-separation-of-streptococcus-pneumoniae
#12
Laure Zucchini, Chryslène Mercy, Pierre Simon Garcia, Caroline Cluzel, Virginie Gueguen-Chaignon, Frédéric Galisson, Céline Freton, Sébastien Guiral, Céline Brochier-Armanet, Patrice Gouet, Christophe Grangeasse
Eukaryotic-like serine/threonine kinases (eSTKs) with extracellular PASTA repeats are key membrane regulators of bacterial cell division. How PASTA repeats govern eSTK activation and function remains elusive. Using evolution- and structural-guided approaches combined with cell imaging, we disentangle the role of each PASTA repeat of the eSTK StkP from Streptococcus pneumoniae. While the three membrane-proximal PASTA repeats behave as interchangeable modules required for the activation of StkP independently of cell wall binding, they also control the septal cell wall thickness...
December 4, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29203881/in-vivo-tropism-of-salmonella-typhi-toxin-to-cells-expressing-a-multiantennal-glycan-receptor
#13
Yi-An Yang, Sohyoung Lee, Jun Zhao, Andrew J Thompson, Ryan McBride, Buyankhishig Tsogtbaatar, James C Paulson, Ruth Nussinov, Lingquan Deng, Jeongmin Song
Typhoid fever is a life-threatening disease, but little is known about the molecular bases for its unique clinical presentation. Typhoid toxin, a unique virulence factor of Salmonella Typhi (the cause of typhoid fever), recapitulates in an animal model many symptoms of typhoid fever. Typhoid toxin binding to its glycan receptor Neu5Ac is central, but, due to the ubiquity of Neu5Ac, how typhoid toxin causes specific symptoms remains elusive. Here we show that typhoid toxin displays in vivo tropism to cells expressing multiantennal glycoprotein receptors, particularly on endothelial cells of arterioles in the brain and immune cells, which is in line with typhoid symptoms...
December 4, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29180726/intergenerational-transfer-of-antibiotic-perturbed-microbiota-enhances-colitis-in-susceptible-mice
#14
Anjelique F Schulfer, Thomas Battaglia, Yelina Alvarez, Luc Bijnens, Victoria E Ruiz, Melody Ho, Serina Robinson, Tonya Ward, Laura M Cox, Arlin B Rogers, Dan Knights, R Balfour Sartor, Martin J Blaser
Antibiotic exposure in children has been associated with the risk of inflammatory bowel disease (IBD). Antibiotic use in children or in their pregnant mother can affect how the intestinal microbiome develops, so we asked whether the transfer of an antibiotic-perturbed microbiota from mothers to their children could affect their risk of developing IBD. Here we demonstrate that germ-free adult pregnant mice inoculated with a gut microbial community shaped by antibiotic exposure transmitted their perturbed microbiota to their offspring with high fidelity...
November 27, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29180725/activation-of-vibrio-cholerae-quorum-sensing-promotes-survival-of-an-arthropod-host
#15
Layla Kamareddine, Adam C N Wong, Audrey S Vanhove, Saiyu Hang, Alexandra E Purdy, Katharine Kierek-Pearson, John M Asara, Afsar Ali, J Glenn Morris, Paula I Watnick
Vibrio cholerae colonizes the human terminal ileum to cause cholera, and the arthropod intestine and exoskeleton to persist in the aquatic environment. Attachment to these surfaces is regulated by the bacterial quorum-sensing signal transduction cascade, which allows bacteria to assess the density of microbial neighbours. Intestinal colonization with V. cholerae results in expenditure of host lipid stores in the model arthropod Drosophila melanogaster. Here we report that activation of quorum sensing in the Drosophila intestine retards this process by repressing V...
November 27, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29158606/detecting-macroecological-patterns-in-bacterial-communities-across-independent-studies-of-global-soils
#16
Kelly S Ramirez, Christopher G Knight, Mattias de Hollander, Francis Q Brearley, Bede Constantinides, Anne Cotton, Si Creer, Thomas W Crowther, John Davison, Manuel Delgado-Baquerizo, Ellen Dorrepaal, David R Elliott, Graeme Fox, Robert I Griffiths, Chris Hale, Kyle Hartman, Ashley Houlden, David L Jones, Eveline J Krab, Fernando T Maestre, Krista L McGuire, Sylvain Monteux, Caroline H Orr, Wim H van der Putten, Ian S Roberts, David A Robinson, Jennifer D Rocca, Jennifer Rowntree, Klaus Schlaeppi, Matthew Shepherd, Brajesh K Singh, Angela L Straathof, Jennifer M Bhatnagar, Cécile Thion, Marcel G A van der Heijden, Franciska T de Vries
The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries...
November 20, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29158605/deep-sequencing-of-hiv-1-reverse-transcripts-reveals-the-multifaceted-antiviral-functions-of-apobec3g
#17
Darja Pollpeter, Maddy Parsons, Andrew E Sobala, Sashika Coxhead, Rupert D Lang, Annie M Bruns, Stelios Papaioannou, James M McDonnell, Luis Apolonia, Jamil A Chowdhury, Curt M Horvath, Michael H Malim
Following cell entry, the RNA genome of HIV-1 is reverse transcribed into double-stranded DNA that ultimately integrates into the host-cell genome to establish the provirus. These early phases of infection are notably vulnerable to suppression by a collection of cellular antiviral effectors, called restriction or resistance factors. The host antiviral protein APOBEC3G (A3G) antagonizes the early steps of HIV-1 infection through the combined effects of inhibiting viral cDNA production and cytidine-to-uridine-driven hypermutation of this cDNA...
November 20, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29158604/antiviral-cd8-t-cells-induce-zika-virus-associated-paralysis-in-mice
#18
Kellie A Jurado, Laura J Yockey, Patrick W Wong, Sarah Lee, Anita J Huttner, Akiko Iwasaki
Zika virus (ZIKV) is an emerging, mosquito-borne RNA virus. The rapid spread of ZIKV within the Americas has unveiled microcephaly 1 and Guillain-Barré syndrome 2,3 as ZIKV-associated neurological complications. Recent reports have also indicated other neurological manifestations to be associated with ZIKV, including myelitis 4 , meningoencephalitis 5 and fatal encephalitis 6 . Here, we investigate the neuropathogenesis of ZIKV infection in type I interferon receptor IFNAR knockout (Ifnar1 -/- ) mice, an infection model that exhibits high viral burden within the central nervous system...
November 20, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29133884/epha2-is-an-epithelial-cell-pattern-recognition-receptor-for-fungal-%C3%AE-glucans
#19
Marc Swidergall, Norma V Solis, Michail S Lionakis, Scott G Filler
Oral epithelial cells discriminate between pathogenic and non-pathogenic stimuli, and only induce an inflammatory response when they are exposed to high levels of a potentially harmful microorganism. The pattern recognition receptors (PRRs) in epithelial cells that mediate this differential response are poorly understood. Here, we demonstrate that the ephrin type-A receptor 2 (EphA2) is an oral epithelial cell PRR that binds to exposed β-glucans on the surface of the fungal pathogen Candida albicans. Binding of C...
November 13, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29133882/discovery-of-an-expansive-bacteriophage-family-that-includes-the-most-abundant-viruses-from-the-human-gut
#20
Natalya Yutin, Kira S Makarova, Ayal B Gussow, Mart Krupovic, Anca Segall, Robert A Edwards, Eugene V Koonin
Metagenomic sequence analysis is rapidly becoming the primary source of virus discovery (1-3) . A substantial majority of the currently available virus genomes come from metagenomics, and some of these represent extremely abundant viruses, even if never grown in the laboratory. A particularly striking case of a virus discovered via metagenomics is crAssphage, which is by far the most abundant human-associated virus known, comprising up to 90% of sequences in the gut virome (4) . Over 80% of the predicted proteins encoded in the approximately 100 kilobase crAssphage genome showed no significant similarity to available protein sequences, precluding classification of this virus and hampering further study...
November 13, 2017: Nature Microbiology
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