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https://www.readbyqxmd.com/read/28905001/genome-enabled-insights-into-the-ecophysiology-of-the-comammox-bacterium-candidatus-nitrospira-nitrosa
#1
Pamela Y Camejo, Jorge Santo Domingo, Katherine D McMahon, Daniel R Noguera
The recently discovered comammox bacteria have the potential to completely oxidize ammonia to nitrate. These microorganisms are part of the Nitrospira genus and are present in a variety of environments, including biological nutrient removal (BNR) systems. However, the physiological traits within and between comammox and nitrite-oxidizing bacterium (NOB)-like Nitrospira species have not been analyzed in these ecosystems. In this study, we identified Nitrospira strains dominating the nitrifying community of a sequencing batch reactor (SBR) performing BNR under microaerobic conditions...
September 2017: MSystems
https://www.readbyqxmd.com/read/28905000/transcriptome-analysis-of-polyhydroxybutyrate-cycle-mutants-reveals-discrete-loci-connecting-nitrogen-utilization-and-carbon-storage-in-sinorhizobium-meliloti
#2
Maya D'Alessio, Ricardo Nordeste, Andrew C Doxey, Trevor C Charles
Polyhydroxybutyrate (PHB) and glycogen polymers are produced by bacteria as carbon storage compounds under unbalanced growth conditions. To gain insights into the transcriptional mechanisms controlling carbon storage in Sinorhizobium meliloti, we investigated the global transcriptomic response to the genetic disruption of key genes in PHB synthesis and degradation and in glycogen synthesis. Under both nitrogen-limited and balanced growth conditions, transcriptomic analysis was performed with genetic mutants deficient in PHB synthesis (phbA, phbB, phbAB, and phbC), PHB degradation (bdhA, phaZ, and acsA2), and glycogen synthesis (glgA1)...
September 2017: MSystems
https://www.readbyqxmd.com/read/28904999/linking-spatial-structure-and-community-level-biotic-interactions-through-cooccurrence-and-time-series-modeling-of-the-human-intestinal-microbiota
#3
Eric J de Muinck, Knut E A Lundin, Pål Trosvik
The gastrointestinal (GI) microbiome is a densely populated ecosystem where dynamics are determined by interactions between microbial community members, as well as host factors. The spatial organization of this system is thought to be important in human health, yet this aspect of our resident microbiome is still poorly understood. In this study, we report significant spatial structure of the GI microbiota, and we identify general categories of spatial patterning in the distribution of microbial taxa along a healthy human GI tract...
September 2017: MSystems
https://www.readbyqxmd.com/read/28904998/parallel-evolution-of-group-b-streptococcus-hypervirulent-clonal-complex-17-unveils-new-pathoadaptive-mutations
#4
Alexandre Almeida, Isabelle Rosinski-Chupin, Céline Plainvert, Pierre-Emmanuel Douarre, Maria J Borrego, Claire Poyart, Philippe Glaser
Group B Streptococcus (GBS) is a commensal of the gastrointestinal and genitourinary tracts, while a prevailing cause of neonatal disease worldwide. Of the various clonal complexes (CCs), CC17 is overrepresented in GBS-infected newborns for reasons that are still largely unknown. Here, we report a comprehensive genomic analysis of 626 CC17 isolates collected worldwide, identifying the genetic traits behind their successful adaptation to humans and the underlying differences between carriage and clinical strains...
September 2017: MSystems
https://www.readbyqxmd.com/read/28904997/development-of-inflammatory-bowel-disease-is-linked-to-a-longitudinal-restructuring-of-the-gut-metagenome-in-mice
#5
Thomas Sharpton, Svetlana Lyalina, Julie Luong, Joey Pham, Emily M Deal, Courtney Armour, Christopher Gaulke, Shomyseh Sanjabi, Katherine S Pollard
The gut microbiome is linked to inflammatory bowel disease (IBD) severity and altered in late-stage disease. However, it is unclear how gut microbial communities change over the course of IBD development, especially in regard to function. To investigate microbiome-mediated disease mechanisms and discover early biomarkers of IBD, we conducted a longitudinal metagenomic investigation in an established mouse model of IBD, where damped transforming growth factor β (TGF-β) signaling in T cells leads to peripheral immune activation, weight loss, and severe colitis...
September 2017: MSystems
https://www.readbyqxmd.com/read/28861526/metabolic-network-analysis-and-metatranscriptomics-reveal-auxotrophies-and-nutrient-sources-of-the-cosmopolitan-freshwater-microbial-lineage-aci
#6
Joshua J Hamilton, Sarahi L Garcia, Brittany S Brown, Ben O Oyserman, Francisco Moya-Flores, Stefan Bertilsson, Rex R Malmstrom, Katrina T Forest, Katherine D McMahon
An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, while our perception of their ecological niches is based on reconstruction of their metabolic potential. In this work, we demonstrate how the "seed set framework," which computes the set of compounds that an organism must acquire from its environment (E...
July 2017: MSystems
https://www.readbyqxmd.com/read/28861525/impacts-of-penicillin-binding-protein-2-inactivation-on-%C3%AE-lactamase-expression-and-muropeptide-profile-in-stenotrophomonas-maltophilia
#7
Yi-Wei Huang, Yu Wang, Yun Lin, Chin Lin, Yi-Tsung Lin, Cheng-Chih Hsu, Tsuey-Ching Yang
Penicillin binding proteins (PBPs) are involved in peptidoglycan synthesis, and their inactivation is linked to β-lactamase expression in ampR-β-lactamase module-harboring Gram-negative bacteria. There are seven annotated PBP genes, namely, mrcA, mrcB, pbpC, mrdA, ftsI, dacB, and dacC, in the Stenotrophomonas maltophilia genome, and these genes encode PBP1a, PBP1b, PBP1c, PBP2, PBP3, PBP4, and PBP6, respectively. In addition, S. maltophilia harbors two β-lactamase genes, L1 and L2, whose expression is induced via β-lactam challenge...
July 2017: MSystems
https://www.readbyqxmd.com/read/28845461/large-scale-phylogenomics-of-the-lactobacillus-casei-group-highlights-taxonomic-inconsistencies-and-reveals-novel-clade-associated-features
#8
Sander Wuyts, Stijn Wittouck, Ilke De Boeck, Camille N Allonsius, Edoardo Pasolli, Nicola Segata, Sarah Lebeer
Although the genotypic and phenotypic properties of the Lactobacillus casei group have been studied extensively, the taxonomic structure has been the subject of debate for a long time. Here, we performed a large-scale comparative analysis by using 183 publicly available genomes supplemented with a Lactobacillus strain isolated from the human upper respiratory tract. On the basis of this analysis, we identified inconsistencies in the taxonomy and reclassified all of the genomes according to their most closely related type strains...
July 2017: MSystems
https://www.readbyqxmd.com/read/28845460/integration-of-metabolomics-and-transcriptomics-reveals-a-complex-diet-of-mycobacterium-tuberculosis-during-early-macrophage-infection
#9
Michael Zimmermann, Maria Kogadeeva, Martin Gengenbacher, Gayle McEwen, Hans-Joachim Mollenkopf, Nicola Zamboni, Stefan Hugo Ernst Kaufmann, Uwe Sauer
Nutrient acquisition from the host environment is crucial for the survival of intracellular pathogens, but conceptual and technical challenges limit our knowledge of pathogen diets. To overcome some of these technical roadblocks, we exploited an experimentally accessible model for early infection of human macrophages by Mycobacterium tuberculosis, the etiological agent of tuberculosis, to study host-pathogen interactions with a multi-omics approach. We collected metabolomics and complete transcriptome RNA sequencing (dual RNA-seq) data of the infected macrophages, integrated them in a genome-wide reaction pair network, and identified metabolic subnetworks in host cells and M...
July 2017: MSystems
https://www.readbyqxmd.com/read/28845459/moderate-exercise-has-limited-but-distinguishable-effects-on-the-mouse-microbiome
#10
Emily V Lamoureux, Scott A Grandy, Morgan G I Langille
The gut microbiome is known to have a complex yet vital relationship with host health. While both exercise and the gut microbiome have been shown to impact human health independently, the direct effects of moderate exercise on the intestinal microbiota remain unclear. In this study, we compared gut microbial diversity and changes in inflammatory markers associated with exercise over an 8-week period in mice that performed either voluntary exercise (VE) (n = 10) or moderate forced exercise (FE) (n = 11) and mice that did not perform any exercise (n = 21)...
July 2017: MSystems
https://www.readbyqxmd.com/read/28845458/paperblast-text-mining-papers-for-information-about-homologs
#11
Morgan N Price, Adam P Arkin
Large-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources (Swiss-Prot, GeneRIF, and EcoCyc) that link protein sequences to scientific articles...
July 2017: MSystems
https://www.readbyqxmd.com/read/28808691/fluoride-depletes-acidogenic-taxa-in-oral-but-not-gut-microbial-communities-in-mice
#12
Koji Yasuda, Tiffany Hsu, Carey A Gallini, Lauren J Mclver, Emma Schwager, Andy Shi, Casey R DuLong, Randall N Schwager, Galeb S Abu-Ali, Eric A Franzosa, Wendy S Garrett, Curtis Huttenhower, Xochitl C Morgan
Fluoridation of drinking water and dental products prevents dental caries primarily by inhibiting energy harvest in oral cariogenic bacteria (such as Streptococcus mutans and Streptococcus sanguinis), thus leading to their depletion. However, the extent to which oral and gut microbial communities are affected by host fluoride exposure has been underexplored. In this study, we modeled human fluoride exposures to municipal water and dental products by treating mice with low or high levels of fluoride over a 12-week period...
July 2017: MSystems
https://www.readbyqxmd.com/read/28770906/pathovar-transcriptomes
#13
COMMENT
Amy Platenkamp, Jay L Mellies
Archetypal pathogenic bacterial strains are often used to elucidate regulatory networks of an entire pathovar, which encompasses multiple lineages and phylogroups. With enteropathogenic Escherichia coli (EPEC) as a model system, Hazen and colleagues (mSystems 6:e00024-17, 2017, https://doi.org/10.1128/mSystems.00024-17) used 9 isolates representing 8 lineages and 3 phylogroups to find that isolates with similar genomic sequences exhibit similarities in global transcriptomes under conditions of growth in medium that induces virulence gene expression...
July 2017: MSystems
https://www.readbyqxmd.com/read/28766584/transcriptional-variation-of-diverse-enteropathogenic-escherichia-coli-isolates-under-virulence-inducing-conditions
#14
Tracy H Hazen, Sean C Daugherty, Amol C Shetty, James P Nataro, David A Rasko
Enteropathogenic Escherichia coli (EPEC) bacteria are a diverse group of pathogens that cause moderate to severe diarrhea in young children in developing countries. EPEC isolates can be further subclassified as typical EPEC (tEPEC) isolates that contain the bundle-forming pilus (BFP) or as atypical EPEC (aEPEC) isolates that do not contain BFP. Comparative genomics studies have recently highlighted the considerable genomic diversity among EPEC isolates. In the current study, we used RNA sequencing (RNA-Seq) to characterize the global transcriptomes of eight tEPEC isolates representing the identified genomic diversity, as well as one aEPEC isolate...
July 2017: MSystems
https://www.readbyqxmd.com/read/28761936/clostridium-difficile-colonizes-alternative-nutrient-niches-during-infection-across-distinct-murine-gut-microbiomes
#15
Matthew L Jenior, Jhansi L Leslie, Vincent B Young, Patrick D Schloss
Clostridium difficile is the largest single cause of hospital-acquired infection in the United States. A major risk factor for Clostridium difficile infection (CDI) is prior exposure to antibiotics, as they disrupt the gut bacterial community which protects from C. difficile colonization. Multiple antibiotic classes have been associated with CDI susceptibility, many leading to distinct community structures stemming from variation in bacterial targets of action. These community structures present separate metabolic challenges to C...
July 2017: MSystems
https://www.readbyqxmd.com/read/28761935/the-skin-microbiome-of-cohabiting-couples
#16
Ashley A Ross, Andrew C Doxey, Josh D Neufeld
Distinct microbial communities inhabit individuals as part of the human skin microbiome and are continually shed to the surrounding environment. Microbial communities from 17 skin sites of 10 sexually active cohabiting couples (20 individuals) were sampled to test whether cohabitation impacts an individual's skin microbiome, leading to shared skin microbiota among partner pairs. Amplified 16S rRNA genes of bacteria and archaea from a total of 340 skin swabs were analyzed by high-throughput sequencing, and the results demonstrated that cohabitation was significantly associated with microbial community composition, although this association was greatly exceeded by characteristics of body location and individuality...
July 2017: MSystems
https://www.readbyqxmd.com/read/28761934/metabolic-fingerprints-from-the-human-oral-microbiome-reveal-a-vast-knowledge-gap-of-secreted-small-peptidic-molecules
#17
Anna Edlund, Neha Garg, Hosein Mohimani, Alexey Gurevich, Xuesong He, Wenyuan Shi, Pieter C Dorrestein, Jeffrey S McLean
Recent research indicates that the human microbiota play key roles in maintaining health by providing essential nutrients, providing immune education, and preventing pathogen expansion. Processes underlying the transition from a healthy human microbiome to a disease-associated microbiome are poorly understood, partially because of the potential influences from a wide diversity of bacterium-derived compounds that are illy defined. Here, we present the analysis of peptidic small molecules (SMs) secreted from bacteria and viewed from a temporal perspective...
July 2017: MSystems
https://www.readbyqxmd.com/read/28761933/insights-into-butyrate-production-in-a-controlled-fermentation-system-via-gene-predictions
#18
S Esquivel-Elizondo, Z E Ilhan, E I Garcia-Peña, R Krajmalnik-Brown
Butyrate is a common fatty acid produced in important fermentative systems, such as the human/animal gut and other H2 production systems. Despite its importance, there is little information on the partnerships between butyrate producers and other bacteria. The objective of this work was to uncover butyrate-producing microbial communities and possible metabolic routes in a controlled fermentation system aimed at butyrate production. The butyrogenic reactor was operated at 37°C and pH 5.5 with a hydraulic retention time of 31 h and a low hydrogen partial pressure (PH2)...
July 2017: MSystems
https://www.readbyqxmd.com/read/28761932/parasite-microbiome-project-systematic-investigation-of-microbiome-dynamics-within-and-across-parasite-host-interactions
#19
Nolwenn M Dheilly, Daniel Bolnick, Seth Bordenstein, Paul J Brindley, Cédric Figuères, Edward C Holmes, Joaquín Martínez Martínez, Anna J Phillips, Robert Poulin, Karyna Rosario
Understanding how microbiomes affect host resistance, parasite virulence, and parasite-associated diseases requires a collaborative effort between parasitologists, microbial ecologists, virologists, and immunologists. We hereby propose the Parasite Microbiome Project to bring together researchers with complementary expertise and to study the role of microbes in host-parasite interactions. Data from the Parasite Microbiome Project will help identify the mechanisms driving microbiome variation in parasites and infected hosts and how that variation is associated with the ecology and evolution of parasites and their disease outcomes...
July 2017: MSystems
https://www.readbyqxmd.com/read/28744484/the-protein-interactome-of-streptococcus-pneumoniae-and-bacterial-meta-interactomes-improve-function-predictions
#20
S Wuchty, S V Rajagopala, S M Blazie, J R Parrish, S Khuri, R L Finley, P Uetz
The functions of roughly a third of all proteins in Streptococcus pneumoniae, a significant human-pathogenic bacterium, are unknown. Using a yeast two-hybrid approach, we have determined more than 2,000 novel protein interactions in this organism. We augmented this network with meta-interactome data that we defined as the pool of all interactions between evolutionarily conserved proteins in other bacteria. We found that such interactions significantly improved our ability to predict a protein's function, allowing us to provide functional predictions for 299 S...
May 2017: MSystems
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