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MSystems

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https://www.readbyqxmd.com/read/28593198/biphasic-metabolism-and-host-interaction-of-a-chlamydial-symbiont
#1
Lena König, Alexander Siegl, Thomas Penz, Susanne Haider, Cecilia Wentrup, Julia Polzin, Evelyne Mann, Stephan Schmitz-Esser, Daryl Domman, Matthias Horn
Chlamydiae are obligate intracellular bacteria comprising well-known human pathogens and ubiquitous symbionts of protists, which are characterized by a unique developmental cycle. Here we comprehensively analyzed gene expression dynamics of Protochlamydia amoebophila during infection of its Acanthamoeba host by RNA sequencing. This revealed a highly dynamic transcriptional landscape, where major transcriptional shifts are conserved among chlamydial symbionts and pathogens. Our data served to propose a time-resolved model for type III protein secretion during the developmental cycle, and we provide evidence for a biphasic metabolism of P...
May 2017: MSystems
https://www.readbyqxmd.com/read/28593197/significant-impacts-of-increasing-aridity-on-the-arid-soil-microbiome
#2
Julia W Neilson, Katy Califf, Cesar Cardona, Audrey Copeland, Will van Treuren, Karen L Josephson, Rob Knight, Jack A Gilbert, Jay Quade, J Gregory Caporaso, Raina M Maier
Global deserts occupy one-third of the Earth's surface and contribute significantly to organic carbon storage, a process at risk in dryland ecosystems that are highly vulnerable to climate-driven ecosystem degradation. The forces controlling desert ecosystem degradation rates are poorly understood, particularly with respect to the relevance of the arid-soil microbiome. Here we document correlations between increasing aridity and soil bacterial and archaeal microbiome composition along arid to hyperarid transects traversing the Atacama Desert, Chile...
May 2017: MSystems
https://www.readbyqxmd.com/read/28593196/quantitative-proteomics-shows-extensive-remodeling-induced-by-nitrogen-limitation-in-prochlorococcusmarinus-ss120
#3
Maria Agustina Domínguez-Martín, Guadalupe Gómez-Baena, Jesús Díez, Maria José López-Grueso, Robert J Beynon, José Manuel García-Fernández
Prochlorococcus requires the capability to accommodate to environmental changes in order to proliferate in oligotrophic oceans, in particular regarding nitrogen availability. A precise knowledge of the composition and changes in the proteome can yield fundamental insights into such a response. Here we report a detailed proteome analysis of the important model cyanobacterium Prochlorococcus marinus SS120 after treatment with azaserine, an inhibitor of ferredoxin-dependent glutamate synthase (GOGAT), to simulate extreme nitrogen starvation...
May 2017: MSystems
https://www.readbyqxmd.com/read/28567447/comparative-genomic-analysis-reveals-habitat-specific-genes-and-regulatory-hubs-within-the-genus-novosphingobium
#4
Roshan Kumar, Helianthous Verma, Shazia Haider, Abhay Bajaj, Utkarsh Sood, Kalaiarasan Ponnusamy, Shekhar Nagar, Mallikarjun N Shakarad, Ram Krishan Negi, Yogendra Singh, J P Khurana, Jack A Gilbert, Rup Lal
Species belonging to the genus Novosphingobium are found in many different habitats and have been identified as metabolically versatile. Through comparative genomic analysis, we identified habitat-specific genes and regulatory hubs that could determine habitat selection for Novosphingobium spp. Genomes from 27 Novosphingobium strains isolated from diverse habitats such as rhizosphere soil, plant surfaces, heavily contaminated soils, and marine and freshwater environments were analyzed. Genome size and coding potential were widely variable, differing significantly between habitats...
May 2017: MSystems
https://www.readbyqxmd.com/read/28567446/meta-analysis-to-define-a-core-microbiota-in-the-swine-gut
#5
Devin B Holman, Brian W Brunelle, Julian Trachsel, Heather K Allen
The swine gut microbiota encompasses a large and diverse population of bacteria that play a significant role in pig health. As such, a number of recent studies have utilized high-throughput sequencing of the 16S rRNA gene to characterize the composition and structure of the swine gut microbiota, often in response to dietary feed additives. It is important to determine which factors shape the composition of the gut microbiota among multiple studies and if certain bacteria are always present in the gut microbiota of swine, independently of study variables such as country of origin and experimental design...
May 2017: MSystems
https://www.readbyqxmd.com/read/28497122/the-microbiome-mitochondrion-connection-common-ancestries-common-mechanisms-common-goals
#6
Alfredo Franco-Obregón, Jack A Gilbert
Lynn Margulis in the 1960s elegantly proposed a shared phylogenetic history between bacteria and mitochondria; this relationship has since become a cornerstone of modern cellular biology. Yet, an interesting facet of the interaction between the microbiome and mitochondria has been mostly ignored, that of the systems biology relationship that underpins host health and longevity. The mitochondria are descendants of primordial aerobic pleomorphic bacteria (likely genus Rickettsia) that entered (literally and functionally) into a mutualistic partnership with ancient anaerobic microbes (likely Archaea)...
May 2017: MSystems
https://www.readbyqxmd.com/read/28428981/correction-for-gonzalez-et-al-migraines-are-correlated-with-higher-levels-of-nitrate-nitrite-and-nitric-oxide-reducing-oral-microbes-in-the-american-gut-project-cohort
#7
Antonio Gonzalez, Embriette Hyde, Naseer Sangwan, Jack A Gilbert, Erik Viirre, Rob Knight
[This corrects the article DOI: 10.1128/mSystems.00105-16.].
March 2017: MSystems
https://www.readbyqxmd.com/read/28382331/a-genome-scale-model-of-shewanella-piezotolerans-simulates-mechanisms-of-metabolic-diversity-and-energy-conservation
#8
Keith Dufault-Thompson, Huahua Jian, Ruixue Cheng, Jiefu Li, Fengping Wang, Ying Zhang
Shewanella piezotolerans strain WP3 belongs to the group 1 branch of the Shewanella genus and is a piezotolerant and psychrotolerant species isolated from the deep sea. In this study, a genome-scale model was constructed for WP3 using a combination of genome annotation, ortholog mapping, and physiological verification. The metabolic reconstruction contained 806 genes, 653 metabolites, and 922 reactions, including central metabolic functions that represented nonhomologous replacements between the group 1 and group 2 Shewanella species...
March 2017: MSystems
https://www.readbyqxmd.com/read/28382330/metatranscriptomics-supports-the-mechanism-for-biocathode-electroautotrophy-by-candidatus-tenderia-electrophaga
#9
Brian J Eddie, Zheng Wang, W Judson Hervey, Dagmar H Leary, Anthony P Malanoski, Leonard M Tender, Baochuan Lin, Sarah M Strycharz-Glaven
Biocathodes provide a stable electron source to drive reduction reactions in electrotrophic microbial electrochemical systems. Electroautotrophic biocathode communities may be more robust than monocultures in environmentally relevant settings, but some members are not easily cultivated outside the electrode environment. We previously used metagenomics and metaproteomics to propose a pathway for coupling extracellular electron transfer (EET) to carbon fixation in "Candidatus Tenderia electrophaga," an uncultivated but dominant member of an electroautotrophic biocathode community...
March 2017: MSystems
https://www.readbyqxmd.com/read/28345060/genome-reduction-and-microbe-host-interactions-drive-adaptation-of-a-sulfur-oxidizing-bacterium-associated-with-a-cold-seep-sponge
#10
Ren-Mao Tian, Weipeng Zhang, Lin Cai, Yue-Him Wong, Wei Ding, Pei-Yuan Qian
As the most ancient metazoan, sponges have established close relationships with particular microbial symbionts. However, the characteristics and physiology of thioautotrophic symbionts in deep-sea sponges are largely unknown. Using a tailored "differential coverage binning" method on 22-Gb metagenomic sequences, we recovered the nearly complete genome of a sulfur-oxidizing bacterium (SOB) that dominates the microbiota of the cold seep sponge Suberites sp. Phylogenetic analyses suggested that this bacterium (an unclassified gammaproteobacterium termed "Gsub") may represent a new deep-sea SOB group...
March 2017: MSystems
https://www.readbyqxmd.com/read/28345059/health-and-disease-imprinted-in-the-time-variability-of-the-human-microbiome
#11
Jose Manuel Martí, Daniel Martínez-Martínez, Teresa Rubio, César Gracia, Manuel Peña, Amparo Latorre, Andrés Moya, Carlos P Garay
The animal microbiota (including the human microbiota) plays an important role in keeping the physiological status of the host healthy. Research seeks greater insight into whether changes in the composition and function of the microbiota are associated with disease. We analyzed published 16S rRNA and shotgun metagenomic sequencing (SMS) data pertaining to the gut microbiotas of 99 subjects monitored over time. Temporal fluctuations in the microbial composition revealed significant differences due to factors such as dietary changes, antibiotic intake, age, and disease...
March 2017: MSystems
https://www.readbyqxmd.com/read/28317029/listeriomics-an-interactive-web-platform-for-systems-biology-of-listeria
#12
Christophe Bécavin, Mikael Koutero, Nicolas Tchitchek, Franck Cerutti, Pierre Lechat, Nicolas Maillet, Claire Hoede, Hélène Chiapello, Christine Gaspin, Pascale Cossart
As for many model organisms, the amount of Listeria omics data produced has recently increased exponentially. There are now >80 published complete Listeria genomes, around 350 different transcriptomic data sets, and 25 proteomic data sets available. The analysis of these data sets through a systems biology approach and the generation of tools for biologists to browse these various data are a challenge for bioinformaticians. We have developed a web-based platform, named Listeriomics, that integrates different tools for omics data analyses, i...
March 2017: MSystems
https://www.readbyqxmd.com/read/28289733/correcting-for-microbial-blooms-in-fecal-samples-during-room-temperature-shipping
#13
Amnon Amir, Daniel McDonald, Jose A Navas-Molina, Justine Debelius, James T Morton, Embriette Hyde, Adam Robbins-Pianka, Rob Knight
The use of sterile swabs is a convenient and common way to collect microbiome samples, and many studies have shown that the effects of room-temperature storage are smaller than physiologically relevant differences between subjects. However, several bacterial taxa, notably members of the class Gammaproteobacteria, grow at room temperature, sometimes confusing microbiome results, particularly when stability is assumed. Although comparative benchmarking has shown that several preservation methods, including the use of 95% ethanol, fecal occult blood test (FOBT) and FTA cards, and Omnigene-GUT kits, reduce changes in taxon abundance during room-temperature storage, these techniques all have drawbacks and cannot be applied retrospectively to samples that have already been collected...
March 2017: MSystems
https://www.readbyqxmd.com/read/28289732/adaptation-of-escherichia-coli-to-long-term-serial-passage-in-complex-medium-evidence-of-parallel-evolution
#14
Karin E Kram, Christopher Geiger, Wazim Mohammed Ismail, Heewook Lee, Haixu Tang, Patricia L Foster, Steven E Finkel
Experimental evolution of bacterial populations in the laboratory has led to identification of several themes, including parallel evolution of populations adapting to carbon starvation, heat stress, and pH stress. However, most of these experiments study growth in defined and/or constant environments. We hypothesized that while there would likely continue to be parallelism in more complex and changing environments, there would also be more variation in what types of mutations would benefit the cells. In order to test our hypothesis, we serially passaged Escherichia coli in a complex medium (Luria-Bertani broth) throughout the five phases of bacterial growth...
March 2017: MSystems
https://www.readbyqxmd.com/read/28289731/deblur-rapidly-resolves-single-nucleotide-community-sequence-patterns
#15
Amnon Amir, Daniel McDonald, Jose A Navas-Molina, Evguenia Kopylova, James T Morton, Zhenjiang Zech Xu, Eric P Kightley, Luke R Thompson, Embriette R Hyde, Antonio Gonzalez, Rob Knight
High-throughput sequencing of 16S ribosomal RNA gene amplicons has facilitated understanding of complex microbial communities, but the inherent noise in PCR and DNA sequencing limits differentiation of closely related bacteria. Although many scientific questions can be addressed with broad taxonomic profiles, clinical, food safety, and some ecological applications require higher specificity. Here we introduce a novel sub-operational-taxonomic-unit (sOTU) approach, Deblur, that uses error profiles to obtain putative error-free sequences from Illumina MiSeq and HiSeq sequencing platforms...
March 2017: MSystems
https://www.readbyqxmd.com/read/28289730/indirect-interspecies-regulation-transcriptional-and-physiological-responses-of-a-cyanobacterium-to-heterotrophic-partnership
#16
Hans C Bernstein, Ryan S McClure, Vera Thiel, Natalie C Sadler, Young-Mo Kim, William B Chrisler, Eric A Hill, Donald A Bryant, Margaret F Romine, Janet K Jansson, Jim K Fredrickson, Alexander S Beliaev
The mechanisms by which microbes interact in communities remain poorly understood. Here, we interrogated specific interactions between photoautotrophic and heterotrophic members of a model consortium to infer mechanisms that mediate metabolic coupling and acclimation to partnership. This binary consortium was composed of a cyanobacterium, Thermosynechococcus elongatus BP-1, which supported growth of an obligate aerobic heterotroph, Meiothermus ruber strain A, by providing organic carbon, O2, and reduced nitrogen...
March 2017: MSystems
https://www.readbyqxmd.com/read/28289729/invasive-plants-rapidly-reshape-soil-properties-in-a-grassland-ecosystem
#17
Sean M Gibbons, Ylva Lekberg, Daniel L Mummey, Naseer Sangwan, Philip W Ramsey, Jack A Gilbert
Plant invasions often reduce native plant diversity and increase net primary productivity. Invaded soils appear to differ from surrounding soils in ways that impede restoration of diverse native plant communities. We hypothesize that invader-mediated shifts in edaphic properties reproducibly alter soil microbial community structure and function. Here, we take a holistic approach, characterizing plant, prokaryotic, and fungal communities and soil physicochemical properties in field sites, invasion gradients, and experimental plots for three invasive plant species that cooccur in the Rocky Mountain West...
March 2017: MSystems
https://www.readbyqxmd.com/read/28293682/genome-sequence-of-the-thermotolerant-foodborne-pathogen-salmonella-enterica-serovar-senftenberg-atcc-43845-and-phylogenetic-analysis-of-loci-encoding-increased-protein-quality-control-mechanisms
#18
Scott V Nguyen, Gregory P Harhay, James L Bono, Timothy P L Smith, Dayna M Harhay
Salmonella enterica subsp. enterica bacteria are important foodborne pathogens with major economic impact. Some isolates exhibit increased heat tolerance, a concern for food safety. Analysis of a finished-quality genome sequence of an isolate commonly used in heat resistance studies, S. enterica subsp. enterica serovar Senftenberg 775W (ATCC 43845), demonstrated an interesting observation that this strain contains not just one, but two horizontally acquired thermotolerance locus homologs. These two loci reside on a large 341...
January 2017: MSystems
https://www.readbyqxmd.com/read/28293681/community-level-differences-in-the-microbiome-of-healthy-wild-mallards-and-those-infected-by-influenza-a-viruses
#19
Holly H Ganz, Ladan Doroud, Alana J Firl, Sarah M Hird, Jonathan A Eisen, Walter M Boyce
Waterfowl, especially ducks and geese, are primary reservoirs for influenza A viruses (IAVs) that evolve and emerge as important pathogens in domestic animals and humans. In contrast to humans, where IAVs infect the respiratory tract and cause significant morbidity and mortality, IAVs infect the gastrointestinal tract of waterfowl and cause little or no pathology and are spread by fecal-oral transmission. For this reason, we examined whether IAV infection is associated with differences in the cloacal microbiome of mallards (Anas platyrhyncos), an important host of IAVs in North America and Eurasia...
January 2017: MSystems
https://www.readbyqxmd.com/read/28293680/comparative-genome-analyses-of-vibrio-anguillarum-strains-reveal-a-link-with-pathogenicity-traits
#20
Daniel Castillo, Paul D Alvise, Ruiqi Xu, Faxing Zhang, Mathias Middelboe, Lone Gram
Vibrio anguillarum is a marine bacterium that can cause vibriosis in many fish and shellfish species, leading to high mortalities and economic losses in aquaculture. Although putative virulence factors have been identified, the mechanism of pathogenesis of V. anguillarum is not fully understood. Here, we analyzed whole-genome sequences of a collection of V. anguillarum strains and compared them to virulence of the strains as determined in larval challenge assays. Previously identified virulence factors were globally distributed among the strains, with some genetic diversity...
January 2017: MSystems
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