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Hideji Yoshida, Tomohiro Shimada, Akira Ishihama
In the process of Escherichia coli K-12 growth from exponential phase to stationary, marked alteration takes place in the pattern of overall genome expression through modulation of both parts of the transcriptional and translational apparatus. In transcription, the sigma subunit with promoter recognition properties is replaced from the growth-related factor RpoD by the stationary-phase-specific factor RpoS. The unused RpoD is stored by binding with the anti-sigma factor Rsd. In translation, the functional 70S ribosome is converted to inactive 100S dimers through binding with the ribosome modulation factor (RMF)...
September 2018: MSystems
Jennifer L Dale, Kenneth B Beckman, Julia L E Willett, Jennifer L Nilson, Nagendra P Palani, Joshua A Baller, Adam Hauge, Daryl M Gohl, Raymond Erickson, Dawn A Manias, Michael J Sadowsky, Gary M Dunny
Enterococcus faecalis is a common commensal bacterium in animal gastrointestinal (GI) tracts and a leading cause of opportunistic infections of humans in the modern health care setting. E. faecalis OG1RF is a plasmid-free strain that contains few mobile elements yet retains the robust survival characteristics, intrinsic antibiotic resistance, and virulence traits characteristic of most E. faecalis genotypes. To facilitate interrogation of the core enterococcal genetic determinants for competitive fitness in the GI tract, biofilm formation, intrinsic antimicrobial resistance, and survival in the environment, we generated an arrayed, sequence-defined set of chromosomal transposon insertions in OG1RF...
September 2018: MSystems
Ashley R Coenen, Joshua S Weitz
Microbes are present in high abundances in the environment and in human-associated microbiomes, often exceeding 1 million per ml. Viruses of microbes are present in even higher abundances and are important in shaping microbial populations, communities, and ecosystems. Given the relative specificity of viral infection, it is essential to identify the functional linkages between viruses and their microbial hosts, particularly given dynamic changes in virus and host abundances. Multiple approaches have been proposed to infer infection networks from time series of in situ communities, among which correlation-based approaches have emerged as the de facto standard...
July 2018: MSystems
Jessica L Cleary, Shilpa Kolachina, Benjamin E Wolfe, Laura M Sanchez
Microbial communities of fermented food microbiomes typically exhibit predictable patterns of microbial succession. However, the biochemical mechanisms that control the diversity and dynamics of these communities are not well described. Interactions between bacteria and fungi may be one mechanism controlling the development of cheese rind microbiomes. This study characterizes a specific bacterium-fungus interaction previously discovered on cheese rinds between the bacterium Glutamicibacter arilaitensis (formerly Arthrobacter arilaitensis) and fungi of the genus Penicillium and identifies the specialized metabolites produced during cocultures...
July 2018: MSystems
Angela Pena-Gonzalez, Luis M Rodriguez-R, Chung K Marston, Jay E Gee, Christopher A Gulvik, Cari B Kolton, Elke Saile, Michael Frace, Alex R Hoffmaster, Konstantinos T Konstantinidis
Bacillus anthracis plasmids pXO1 and pXO2 carry the main virulence factors responsible for anthrax. However, the extent of copy number variation within the species and how the plasmids are related to pXO1/pXO2-like plasmids in other species of the Bacillus cereus sensu lato group remain unclear. To gain new insights into these issues, we sequenced 412 B. anthracis strains representing the total phylogenetic and ecological diversity of the species. Our results revealed that B. anthracis genomes carried, on average, 3...
July 2018: MSystems
Andrea Söllinger, Alexander Tøsdal Tveit, Morten Poulsen, Samantha Joan Noel, Mia Bengtsson, Jörg Bernhardt, Anne Louise Frydendahl Hellwing, Peter Lund, Katharina Riedel, Christa Schleper, Ole Højberg, Tim Urich
Ruminant livestock is a major source of the potent greenhouse gas methane. The complex rumen microbiome, consisting of bacteria, archaea, and microbial eukaryotes, facilitates anaerobic plant biomass degradation in the cow rumen, leading to methane emissions. Using an integrated approach combining multidomain quantitative metatranscriptomics with gas and volatile fatty acid (VFA) profiling, we aimed at obtaining the most comprehensive picture of the active rumen microbiome during feed degradation to date. Bacterial, archaeal, and eukaryotic biomass, but also methane emissions and VFA concentrations, increased drastically within an hour after feed intake...
July 2018: MSystems
Matthew L Paff, Benjamin R Jack, Bartram L Smith, James J Bull, Claus O Wilke
Attenuated viruses have numerous applications, in particular in the context of live viral vaccines. However, purposefully designing attenuated viruses remains challenging, in particular if the attenuation is meant to be resistant to rapid evolutionary recovery. Here we develop and analyze a new attenuation method, promoter ablation, using an established viral model, bacteriophage T7. Ablation of promoters of the two most highly expressed T7 proteins (scaffold and capsid) led to major reductions in transcript abundance of the affected genes, with the effect of the double knockout approximately additive of the effects of single knockouts...
July 2018: MSystems
David Bergenholm, Guodong Liu, Petter Holland, Jens Nielsen
To build transcription regulatory networks, transcription factor binding must be analyzed in cells grown under different conditions because their responses and targets differ depending on environmental conditions. We performed whole-genome analysis of the DNA binding of five Saccharomyces cerevisiae transcription factors involved in lipid metabolism, Ino2, Ino4, Hap1, Oaf1, and Pip2, in response to four different environmental conditions in chemostat cultures, which allowed us to keep the specific growth rate constant...
July 2018: MSystems
Taylor K S Richter, Jane M Michalski, Luke Zanetti, Sharon M Tennant, Wilbur H Chen, David A Rasko
Studies of Escherichia coli in the human gastrointestinal tract have focused on pathogens, such as diarrhea-causing enterotoxigenic E. coli (ETEC), while overlooking the resident, nonpathogenic E. coli community. Relatively few genomes of nonpathogenic E. coli strains are available for comparative genomic analysis, and the ecology of these strains is poorly understood. This study examined the diversity and dynamics of resident human gastrointestinal E. coli communities in the face of the ecological challenges presented by pathogen (ETEC) challenge, as well as of antibiotic treatment...
July 2018: MSystems
Emily P Balskus, Peter J Turnbaugh, Dennis W Wolan
The Keystone Symposia will be hosting a conference organized by Emily Balskus, Peter Turnbaugh, and Dennis Wolan entitled "Microbiome: Chemical Mechanisms and Biological Consequences" 10 to 14 March 2019 in Montreal, Québec, Canada. Our goal for this meeting is to focus attention on the intersection of chemistry and biology by bringing together scientists in these two disciplines, while also including talks about other hosts, environmental microbiomes, and multidisciplinary research platforms. The focus of this conference is to emphasize our community's need to continue adopting other scientific disciplines to ultimately generate a broad understanding of microbiomes and the cross talk microbes have with their environment...
July 2018: MSystems
Irina M Velsko, Laurent A F Frantz, Alexander Herbig, Greger Larson, Christina Warinner
Metagenomics enables the study of complex microbial communities from myriad sources, including the remains of oral and gut microbiota preserved in archaeological dental calculus and paleofeces, respectively. While accurate taxonomic assignment is essential to this process, DNA damage characteristic of ancient samples (e.g., reduction in fragment size and cytosine deamination) may reduce the accuracy of read taxonomic assignment. Using a set of in silico -generated metagenomic data sets, we investigated how the addition of ancient DNA (aDNA) damage patterns influences microbial taxonomic assignment by five widely used profilers: QIIME/UCLUST, MetaPhlAn2, MIDAS, CLARK-S, and MALT...
July 2018: MSystems
J Rivera-Pinto, J J Egozcue, V Pawlowsky-Glahn, R Paredes, M Noguera-Julian, M L Calle
High-throughput sequencing technologies have revolutionized microbiome research by allowing the relative quantification of microbiome composition and function in different environments. In this work we focus on the identification of microbial signatures, groups of microbial taxa that are predictive of a phenotype of interest. We do this by acknowledging the compositional nature of the microbiome and the fact that it carries relative information. Thus, instead of defining a microbial signature as a linear combination in real space corresponding to the abundances of a group of taxa, we consider microbial signatures given by the geometric means of data from two groups of taxa whose relative abundances, or balance, are associated with the response variable of interest...
July 2018: MSystems
Sarah Glaven, Kenneth Racicot, Dagmar H Leary, J Philip Karl, Steven Arcidiacono, Blair C R Dancy, Linda A Chrisey, Jason W Soares
The Tri-Service Microbiome Consortium (TSMC) was recently established to enhance collaboration, coordination, and communication of microbiome research among Department of Defense (DoD) organizations. The TSMC aims to serve as a forum for sharing information related to DoD microbiome research, policy, and applications, to monitor global advances relevant to human health and performance, to identify priority objectives, and to facilitate Tri-Service (Army, Navy, and Air Force) collaborative research. The inaugural TSMC workshop held on 10 to 11 May 2017 brought together almost 100 attendees from across the DoD and several key DoD partners...
July 2018: MSystems
Andreas Bremges, Alice C McHardy
No abstract text is available yet for this article.
July 2018: MSystems
Laura E Grieneisen, Ran Blekhman
[This corrects the article DOI: 10.1128/mSystems.00060-18.].
July 2018: MSystems
Robert E Danczak, Michael D Johnston, Chris Kenah, Michael Slattery, Michael J Wilkins
Microbial ecological processes are frequently studied in the presence of perturbations rather than in undisturbed environments, despite the relatively stable conditions dominating many microbial habitats. To examine processes influencing microbial community structuring in the absence of strong external perturbations, three unperturbed aquifers in Ohio (Greene, Licking, and Athens) were sampled over 2 years and analyzed using geochemical measurements, 16S rRNA gene sequencing, and ecological modeling. Redox conditions ranging from highly reducing to more oxidizing distinguished aquifer geochemistry across the three locations...
July 2018: MSystems
Pablo Tsukayama, Manish Boolchandani, Sanket Patel, Erica C Pehrsson, Molly K Gibson, Kenneth L Chiou, Clifford J Jolly, Jeffrey Rogers, Jane E Phillips-Conroy, Gautam Dantas
Environmental microbes have harbored the capacity for antibiotic production for millions of years, spanning the evolution of humans and other vertebrates. However, the industrial-scale use of antibiotics in clinical and agricultural practice over the past century has led to a substantial increase in exposure of these agents to human and environmental microbiota. This perturbation is predicted to alter the ecology of microbial communities and to promote the evolution and transfer of antibiotic resistance (AR) genes...
May 2018: MSystems
Rebekah M Martin, Jie Cao, Weisheng Wu, Lili Zhao, David M Manthei, Ali Pirani, Evan Snitkin, Preeti N Malani, Krishna Rao, Michael A Bachman
Despite insights gained through experimental models, the set of bacterial genes important for human infection is unclear for many of our most threatening pathogens. Klebsiella pneumoniae is a leading cause of health care-associated infections (HAIs) and commonly colonizes hospitalized patients, but the factors that determine whether a particular isolate causes disease or remains a colonizer are poorly understood. To identify bacterial genes associated with K. pneumoniae infection, a case-control study was performed comparing infected and asymptomatic colonized patients...
May 2018: MSystems
M E Nieves-Ramírez, O Partida-Rodríguez, I Laforest-Lapointe, L A Reynolds, E M Brown, A Valdez-Salazar, P Morán-Silva, L Rojas-Velázquez, E Morien, L W Parfrey, M Jin, J Walter, J Torres, M C Arrieta, C Ximénez-García, B B Finlay
Blastocystis is the most prevalent protist of the human intestine, colonizing approximately 20% of the North American population and up to 100% in some nonindustrialized settings. Blastocystis is associated with gastrointestinal and systemic disease but can also be an asymptomatic colonizer in large populations. While recent findings in humans have shown bacterial microbiota changes associated with this protist, it is unknown whether these occur due to the presence of Blastocystis or as a result of inflammation...
May 2018: MSystems
Peter E Larsen, Sarah Zerbs, Philip D Laible, Frank R Collart, Peter Korajczyk, Yang Dai, Philippe Noirot
Bacteria are not simply passive consumers of nutrients or merely steady-state systems. Rather, bacteria are active participants in their environments, collecting information from their surroundings and processing and using that information to adapt their behavior and optimize survival. The bacterial regulome is the set of physical interactions that link environmental information to the expression of genes by way of networks of sensors, transporters, signal cascades, and transcription factors. As bacteria cannot have one dedicated sensor and regulatory response system for every possible condition that they may encounter, the sensor systems must respond to a variety of overlapping stimuli and collate multiple forms of information to make "decisions" about the most appropriate response to a specific set of environmental conditions...
May 2018: MSystems
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