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MSystems

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https://www.readbyqxmd.com/read/28317029/listeriomics-an-interactive-web-platform-for-systems-biology-of-listeria
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
https://www.readbyqxmd.com/read/28251186/uncovering-the-horseshoe-effect-in-microbial-analyses
#10
James T Morton, Liam Toran, Anna Edlund, Jessica L Metcalf, Christian Lauber, Rob Knight
The horseshoe effect is a phenomenon that has long intrigued ecologists. The effect was commonly thought to be an artifact of dimensionality reduction, and multiple techniques were developed to unravel this phenomenon and simplify interpretation. Here, we provide evidence that horseshoes arise as a consequence of distance metrics that saturate-a familiar concept in other fields but new to microbial ecology. This saturation property loses information about community dissimilarity, simply because it cannot discriminate between samples that do not share any common features...
January 2017: MSystems
https://www.readbyqxmd.com/read/28251185/correction-for-walsh-et-al-microbial-succession-and-flavor-production-in-the-fermented-dairy-beverage-kefir
#11
Aaron M Walsh, Fiona Crispie, Kieran Kilcawley, Orla O'Sullivan, Maurice G O'Sullivan, Marcus J Claesson, Paul D Cotter
[This corrects the article DOI: 10.1128/mSystems.00052-16.].
January 2017: MSystems
https://www.readbyqxmd.com/read/28217746/integrated-regulatory-and-metabolic-networks-of-the-marine-diatom-phaeodactylum-tricornutum-predict-the-response-to-rising-co2-levels
#12
Jennifer Levering, Christopher L Dupont, Andrew E Allen, Bernhard O Palsson, Karsten Zengler
Diatoms are eukaryotic microalgae that are responsible for up to 40% of the ocean's primary productivity. How diatoms respond to environmental perturbations such as elevated carbon concentrations in the atmosphere is currently poorly understood. We developed a transcriptional regulatory network based on various transcriptome sequencing expression libraries for different environmental responses to gain insight into the marine diatom's metabolic and regulatory interactions and provide a comprehensive framework of responses to increasing atmospheric carbon levels...
January 2017: MSystems
https://www.readbyqxmd.com/read/28217745/the-baltic-sea-virome-diversity-and-transcriptional-activity-of-dna-and-rna-viruses
#13
Lisa Zeigler Allen, John P McCrow, Karolina Ininbergs, Christopher L Dupont, Jonathan H Badger, Jeffery M Hoffman, Martin Ekman, Andrew E Allen, Birgitta Bergman, J Craig Venter
Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Torneträsk in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as impacted aspects of Baltic Sea viral communities. Taxonomic signatures representative of phages within the widely distributed order Caudovirales were identified with enrichments in lesser-known families such as Podoviridae and Siphoviridae...
January 2017: MSystems
https://www.readbyqxmd.com/read/28191504/distinct-biogeographic-patterns-for-archaea-bacteria-and-fungi-along-the-vegetation-gradient-at-the-continental-scale-in-eastern-china
#14
Bin Ma, Zhongmin Dai, Haizhen Wang, Melissa Dsouza, Xingmei Liu, Yan He, Jianjun Wu, Jorge L M Rodrigues, Jack A Gilbert, Philip C Brookes, Jianming Xu
The natural forest ecosystem in Eastern China, from tropical forest to boreal forest, has declined due to cropland development during the last 300 years, yet little is known about the historical biogeographic patterns and driving processes for the major domains of microorganisms along this continental-scale natural vegetation gradient. We predicted the biogeographic patterns of soil archaeal, bacterial, and fungal communities across 110 natural forest sites along a transect across four vegetation zones in Eastern China...
January 2017: MSystems
https://www.readbyqxmd.com/read/28191503/differences-in-gut-metabolites-and-microbial-composition-and-functions-between-egyptian-and-u-s-children-are-consistent-with-their-diets
#15
V Shankar, M Gouda, J Moncivaiz, A Gordon, N V Reo, L Hussein, O Paliy
Previous studies indicated that populations consuming a Mediterranean diet rich in fiber, vegetables, and fruits have a significantly lower risk of cardiovascular and metabolic diseases than populations of industrialized societies consuming diets enriched in processed carbohydrates, animal proteins, and fats. To explore the potential contributions of gut microbiota to the observed diet-related metabolic effects, we conducted an integrative analysis of distal gut microbiota composition and functions and intestinal metabolites in Egyptian and U...
January 2017: MSystems
https://www.readbyqxmd.com/read/28168224/lifestyle-and-horizontal-gene-transfer-mediated-evolution-of-mucispirillum-schaedleri-a-core-member-of-the-murine-gut-microbiota
#16
Alexander Loy, Carina Pfann, Michaela Steinberger, Buck Hanson, Simone Herp, Sandrine Brugiroux, João Carlos Gomes Neto, Mark V Boekschoten, Clarissa Schwab, Tim Urich, Amanda E Ramer-Tait, Thomas Rattei, Bärbel Stecher, David Berry
Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, M. schaedleri has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides...
January 2017: MSystems
https://www.readbyqxmd.com/read/28144631/studying-vertical-microbiome-transmission-from-mothers-to-infants-by-strain-level-metagenomic-profiling
#17
Francesco Asnicar, Serena Manara, Moreno Zolfo, Duy Tin Truong, Matthias Scholz, Federica Armanini, Pamela Ferretti, Valentina Gorfer, Anna Pedrotti, Adrian Tett, Nicola Segata
The gut microbiome becomes shaped in the first days of life and continues to increase its diversity during the first months. Links between the configuration of the infant gut microbiome and infant health are being shown, but a comprehensive strain-level assessment of microbes vertically transmitted from mother to infant is still missing. We collected fecal and breast milk samples from multiple mother-infant pairs during the first year of life and applied shotgun metagenomic sequencing followed by computational strain-level profiling...
January 2017: MSystems
https://www.readbyqxmd.com/read/28144630/balance-trees-reveal-microbial-niche-differentiation
#18
James T Morton, Jon Sanders, Robert A Quinn, Daniel McDonald, Antonio Gonzalez, Yoshiki Vázquez-Baeza, Jose A Navas-Molina, Se Jin Song, Jessica L Metcalf, Embriette R Hyde, Manuel Lladser, Pieter C Dorrestein, Rob Knight
Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the microbial taxa that differentiate these samples can be challenging. These issues stem from the compositional nature of 16S rRNA gene data (or, more generally, taxon or functional gene data); the changes in the relative abundance of one taxon influence the apparent abundances of the others...
January 2017: MSystems
https://www.readbyqxmd.com/read/28083564/direct-heme-uptake-by-phytoplankton-associated-roseobacter-bacteria
#19
Shane L Hogle, Bianca Brahamsha, Katherine A Barbeau
Iron is an essential micronutrient and can limit the growth of both marine phytoplankton and heterotrophic bacterioplankton. In this study, we investigated the molecular basis of heme transport, an organic iron acquisition pathway, in phytoplankton-associated Roseobacter bacteria and explored the potential role of bacterial heme uptake in the marine environment. We searched 153 Roseobacter genomes and found that nearly half contained putative complete heme transport systems with nearly the same synteny. We also examined a publicly available coculture transcriptome and found that Roseobacter strain Sulfitobacter sp...
January 2017: MSystems
https://www.readbyqxmd.com/read/28066819/growth-on-chitin-impacts-the-transcriptome-and-metabolite-profiles-of-antibiotic-producing-vibrio-coralliilyticus-s2052-and-photobacterium-galatheae-s2753
#20
Sonia Giubergia, Christopher Phippen, Kristian Fog Nielsen, Lone Gram
Members of the Vibrionaceae family are often associated with chitin-containing organisms, and they are thought to play a major role in chitin degradation. The purpose of the present study was to determine how chitin affects the transcriptome and metabolome of two bioactive Vibrionaceae strains, Vibrio coralliilyticus and Photobacterium galatheae. We focused on chitin degradation genes and secondary metabolites based on the assumption that these molecules in nature confer an advantage to the producer. Growth on chitin caused upregulation of genes related to chitin metabolism and of genes potentially involved in host colonization and/or infection...
January 2017: MSystems
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