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MSystems

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https://www.readbyqxmd.com/read/28083564/direct-heme-uptake-by-phytoplankton-associated-roseobacter-bacteria
#1
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
#2
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
https://www.readbyqxmd.com/read/28066818/microbiome-helper-a-custom-and-streamlined-workflow-for-microbiome-research
#3
André M Comeau, Gavin M Douglas, Morgan G I Langille
Sequence-based approaches to study microbiomes, such as 16S rRNA gene sequencing and metagenomics, are uncovering associations between microbial taxa and a myriad of factors. A drawback of these approaches is that the necessary sequencing library preparation and bioinformatic analyses are complicated and continuously changing, which can be a barrier for researchers new to the field. We present three essential components to conducting a microbiome experiment from start to finish: first, a simplified and step-by-step custom gene sequencing protocol that requires limited lab equipment, is cost-effective, and has been thoroughly tested and utilized on various sample types; second, a series of scripts to integrate various commonly used bioinformatic tools that is available as a standalone installation or as a single downloadable virtual image; and third, a set of bioinformatic workflows and tutorials to provide step-by-step guidance and education for those new to the microbiome field...
January 2017: MSystems
https://www.readbyqxmd.com/read/28066817/transcriptional-profiling-of-the-oral-pathogen-streptococcus-mutans-in-response-to-competence-signaling-peptide-xip
#4
Iwona B Wenderska, Andrew Latos, Benjamin Pruitt, Sara Palmer, Grace Spatafora, Dilani B Senadheera, Dennis G Cvitkovitch
In the cariogenic Streptococcus mutans, competence development is regulated by the ComRS signaling system comprised of the ComR regulator and the ComS prepeptide to the competence signaling peptide XIP (ComX-inducing peptide). Aside from competence development, XIP signaling has been demonstrated to regulate cell lysis, and recently, the expression of bacteriocins, small antimicrobial peptides used by bacteria to inhibit closely related species. Our study further explores the effect of XIP signaling on the S...
January 2017: MSystems
https://www.readbyqxmd.com/read/28066816/from-genomes-to-phenotypes-traitar-the-microbial-trait-analyzer
#5
Aaron Weimann, Kyra Mooren, Jeremy Frank, Phillip B Pope, Andreas Bremges, Alice C McHardy
The number of sequenced genomes is growing exponentially, profoundly shifting the bottleneck from data generation to genome interpretation. Traits are often used to characterize and distinguish bacteria and are likely a driving factor in microbial community composition, yet little is known about the traits of most microbes. We describe Traitar, the microbial trait analyzer, which is a fully automated software package for deriving phenotypes from a genome sequence. Traitar provides phenotype classifiers to predict 67 traits related to the use of various substrates as carbon and energy sources, oxygen requirement, morphology, antibiotic susceptibility, proteolysis, and enzymatic activities...
November 2016: MSystems
https://www.readbyqxmd.com/read/28028549/ssunique-detecting-sequence-novelty-in-microbiome-surveys
#6
Michael D J Lynch, Josh D Neufeld
High-throughput sequencing of small-subunit (SSU) rRNA genes has revolutionized understanding of microbial communities and facilitated investigations into ecological dynamics at unprecedented scales. Such extensive SSU rRNA gene sequence libraries, constructed from DNA extracts of environmental or host-associated samples, often contain a substantial proportion of unclassified sequences, many representing organisms with novel taxonomy (taxonomic "blind spots") and potentially unique ecology. Indeed, these novel taxonomic lineages are associated with so-called microbial "dark matter," which is the genomic potential of these lineages...
November 2016: MSystems
https://www.readbyqxmd.com/read/28028548/spatial-molecular-architecture-of-the-microbial-community-of-a-peltigera-lichen
#7
Neha Garg, Yi Zeng, Anna Edlund, Alexey V Melnik, Laura M Sanchez, Hosein Mohimani, Alexey Gurevich, Vivian Miao, Stefan Schiffler, Yan Wei Lim, Tal Luzzatto-Knaan, Shengxin Cai, Forest Rohwer, Pavel A Pevzner, Robert H Cichewicz, Theodore Alexandrov, Pieter C Dorrestein
Microbes are commonly studied as individual species, but they exist as mixed assemblages in nature. At present, we know very little about the spatial organization of the molecules, including natural products that are produced within these microbial networks. Lichens represent a particularly specialized type of symbiotic microbial assemblage in which the component microorganisms exist together. These composite microbial assemblages are typically comprised of several types of microorganisms representing phylogenetically diverse life forms, including fungi, photosymbionts, bacteria, and other microbes...
November 2016: MSystems
https://www.readbyqxmd.com/read/27981240/genomewide-dam-methylation-in-escherichia-coli-during-long-term-stationary-phase
#8
Lacey L Westphal, Peter Sauvey, Matthew M Champion, Ian M Ehrenreich, Steven E Finkel
DNA methylation in prokaryotes is widespread. The most common modification of the genome is the methylation of adenine at the N-6 position. In Escherichia coli K-12 and many gammaproteobacteria, this modification is catalyzed by DNA adenine methyltransferase (Dam) at the GATC consensus sequence and is known to modulate cellular processes including transcriptional regulation of gene expression, initiation of chromosomal replication, and DNA mismatch repair. While studies thus far have focused on the motifs associated with methylated adenine (meA), the frequency of meA across the genome, and temporal dynamics during early periods of incubation, here we conduct the first study on the temporal dynamics of adenine methylation in E...
November 2016: MSystems
https://www.readbyqxmd.com/read/27981239/ionic-liquids-impact-the-bioenergy-feedstock-degrading-microbiome-and-transcription-of-enzymes-relevant-to-polysaccharide-hydrolysis
#9
Yu-Wei Wu, Brendan Higgins, Chaowei Yu, Amitha P Reddy, Shannon Ceballos, Lawrence D Joh, Blake A Simmons, Steven W Singer, Jean S VanderGheynst
Ionic liquid (IL) pretreatment is a promising approach for the conversion of lignocellulose to biofuels. The toxicity of residual IL, however, negatively impacts the performance of industrial enzymes and microorganisms in hydrolysis and fermentation. In this study, a thermophilic microbial community was cultured on switchgrass amended with various levels of the ionic liquid 1-ethyl-3-methylimidazolium acetate. Changes in the microbial community composition and transcription of genes relevant to IL tolerance and lignocellulose hydrolysis were quantified...
November 2016: MSystems
https://www.readbyqxmd.com/read/27933319/a-metabolic-widget-adjusts-the-phosphoenolpyruvate-dependent-fructose-influx-in-pseudomonas-putida
#10
Max Chavarría, Ángel Goñi-Moreno, Víctor de Lorenzo, Pablo I Nikel
Fructose uptake in the soil bacterium Pseudomonas putida occurs through a canonical phosphoenolpyruvate (PEP)-dependent sugar transport system (PTS(Fru)). The logic of the genetic circuit that rules its functioning is puzzling: the transcription of the fruBKA operon, encoding all the components of PTS(Fru), can escape the repression exerted by the catabolite repressor/activator protein Cra solely in the presence of intracellular fructose-1-P, an agonist formed only when fructose has been already transported...
November 2016: MSystems
https://www.readbyqxmd.com/read/27933318/global-analysis-and-comparison-of-the-transcriptomes-and-proteomes-of-group-a-streptococcus-biofilms
#11
Jeffrey A Freiberg, Yoann Le Breton, Bao Q Tran, Alison J Scott, Janette M Harro, Robert K Ernst, Young Ah Goo, Emmanuel F Mongodin, David R Goodlett, Kevin S McIver, Mark E Shirtliff
To gain a better understanding of the genes and proteins involved in group A Streptococcus (GAS; Streptococcus pyogenes) biofilm growth, we analyzed the transcriptome, cellular proteome, and cell wall proteome from biofilms at different stages and compared them to those of plankton-stage GAS. Using high-throughput RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) shotgun proteomics, we found distinct expression profiles in the transcriptome and proteome. A total of 46 genes and 41 proteins showed expression across the majority of biofilm time points that was consistently higher or consistently lower than that seen across the majority of planktonic time points...
November 2016: MSystems
https://www.readbyqxmd.com/read/27921083/integrated-role-of-bifidobacterium-animalis-subsp-lactis-supplementation-in-gut-microbiota-immunity-and-metabolism-of-infant-rhesus-monkeys
#12
Xuan He, Carolyn M Slupsky, James W Dekker, Neill W Haggarty, Bo Lönnerdal
To investigate the impact of probiotic supplementation of infant formula on immune parameters, intestinal microbiota, and metabolism, five individually housed infant rhesus monkeys exclusively fed standard infant formula supplemented with probiotics (Bifidobacterium animalis subsp. lactis HN019) from birth until 3 months of age were compared with five standard formula-fed and five breast-fed monkeys. Anthropometric measurements, serum insulin, immune parameters, fecal microbiota, and metabolic profiles of serum, urine, and feces were evaluated...
November 2016: MSystems
https://www.readbyqxmd.com/read/27868089/adaptive-evolution-of-phosphorus-metabolism-in-prochlorococcus
#13
John R Casey, Adil Mardinoglu, Jens Nielsen, David M Karl
Inorganic phosphorus is scarce in the eastern Mediterranean Sea, where the high-light-adapted ecotype HLI of the marine picocyanobacterium Prochlorococcus marinus thrives. Physiological and regulatory control of phosphorus acquisition and partitioning has been observed in HLI both in culture and in the field; however, the optimization of phosphorus metabolism and associated gains for its phosphorus-limited-growth (PLG) phenotype have not been studied. Here, we reconstructed a genome-scale metabolic network of the HLI axenic strain MED4 (iJC568), consisting of 568 metabolic genes in relation to 794 reactions involving 680 metabolites distributed in 6 subcellular locations...
November 2016: MSystems
https://www.readbyqxmd.com/read/27822559/distinguishing-between-microbial-habitats-unravels-ecological-complexity-in-coral-microbiomes
#14
Amy Apprill, Laura G Weber, Alyson E Santoro
The diverse prokaryotic communities associated with reef-building corals may provide important ecological advantages to their threatened hosts. The consistency of relationships between corals and specific prokaryotes, however, is debated, and the locations where microbially mediated processes occur in the host are not resolved. Here, we examined how the prokaryotic associates of five common Caribbean corals with different evolutionary and ecological traits differ across mucus and tissue habitats. We used physical and chemical separation of coral mucus and tissue and sequencing of partial small-subunit rRNA genes of bacteria and archaea from these samples to demonstrate that coral tissue and mucus harbor unique reservoirs of prokaryotes, with 23 to 49% and 31 to 56% of sequences exclusive to the tissue and mucus habitats, respectively...
September 2016: MSystems
https://www.readbyqxmd.com/read/27822558/microbial-communities-are-well-adapted-to-disturbances-in-energy-input
#15
Nuria Fernandez-Gonzalez, Julie A Huber, Joseph J Vallino
Although microbial systems are well suited for studying concepts in ecological theory, little is known about how microbial communities respond to long-term periodic perturbations beyond diel oscillations. Taking advantage of an ongoing microcosm experiment, we studied how methanotrophic microbial communities adapted to disturbances in energy input over a 20-day cycle period. Sequencing of bacterial 16S rRNA genes together with quantification of microbial abundance and ecosystem function were used to explore the long-term dynamics (510 days) of methanotrophic communities under continuous versus cyclic chemical energy supply...
September 2016: MSystems
https://www.readbyqxmd.com/read/27822557/migraines-are-correlated-with-higher-levels-of-nitrate-nitrite-and-nitric-oxide-reducing-oral-microbes-in-the-american-gut-project-cohort
#16
Antonio Gonzalez, Embriette Hyde, Naseer Sangwan, Jack A Gilbert, Erik Viirre, Rob Knight
Nitrates, such as cardiac therapeutics and food additives, are common headache triggers, with nitric oxide playing an important role. Facultative anaerobic bacteria in the oral cavity may contribute migraine-triggering levels of nitric oxide through the salivary nitrate-nitrite-nitric oxide pathway. Using high-throughput sequencing technologies, we detected observable and significantly higher abundances of nitrate, nitrite, and nitric oxide reductase genes in migraineurs versus nonmigraineurs in samples collected from the oral cavity and a slight but significant difference in fecal samples...
September 2016: MSystems
https://www.readbyqxmd.com/read/27822556/impact-of-sample-type-and-dna-isolation-procedure-on-genomic-inference-of-microbiome-composition
#17
Berith E Knudsen, Lasse Bergmark, Patrick Munk, Oksana Lukjancenko, Anders Priemé, Frank M Aarestrup, Sünje J Pamp
Explorations of complex microbiomes using genomics greatly enhance our understanding about their diversity, biogeography, and function. The isolation of DNA from microbiome specimens is a key prerequisite for such examinations, but challenges remain in obtaining sufficient DNA quantities required for certain sequencing approaches, achieving accurate genomic inference of microbiome composition, and facilitating comparability of findings across specimen types and sequencing projects. These aspects are particularly relevant for the genomics-based global surveillance of infectious agents and antimicrobial resistance from different reservoirs...
September 2016: MSystems
https://www.readbyqxmd.com/read/27822555/novel-syntrophic-populations-dominate-an-ammonia-tolerant-methanogenic-microbiome
#18
J A Frank, M Ø Arntzen, L Sun, L H Hagen, A C McHardy, S J Horn, V G H Eijsink, A Schnürer, P B Pope
Biogas reactors operating with protein-rich substrates have high methane potential and industrial value; however, they are highly susceptible to process failure because of the accumulation of ammonia. High ammonia levels cause a decline in acetate-utilizing methanogens and instead promote the conversion of acetate via a two-step mechanism involving syntrophic acetate oxidation (SAO) to H2 and CO2, followed by hydrogenotrophic methanogenesis. Despite the key role of syntrophic acetate-oxidizing bacteria (SAOB), only a few culturable representatives have been characterized...
September 2016: MSystems
https://www.readbyqxmd.com/read/27822554/farnesoid-x-receptor-signaling-shapes-the-gut-microbiota-and-controls-hepatic-lipid-metabolism
#19
Limin Zhang, Cen Xie, Robert G Nichols, Siu H J Chan, Changtao Jiang, Ruixin Hao, Philip B Smith, Jingwei Cai, Margaret N Simons, Emmanuel Hatzakis, Costas D Maranas, Frank J Gonzalez, Andrew D Patterson
The gut microbiota modulates obesity and associated metabolic phenotypes in part through intestinal farnesoid X receptor (FXR) signaling. Glycine-β-muricholic acid (Gly-MCA), an intestinal FXR antagonist, has been reported to prevent or reverse high-fat diet (HFD)-induced and genetic obesity, insulin resistance, and fatty liver; however, the mechanism by which these phenotypes are improved is not fully understood. The current study investigated the influence of FXR activity on the gut microbiota community structure and function and its impact on hepatic lipid metabolism...
September 2016: MSystems
https://www.readbyqxmd.com/read/27822553/mockrobiota-a-public-resource-for-microbiome-bioinformatics-benchmarking
#20
Nicholas A Bokulich, Jai Ram Rideout, William G Mercurio, Arron Shiffer, Benjamin Wolfe, Corinne F Maurice, Rachel J Dutton, Peter J Turnbaugh, Rob Knight, J Gregory Caporaso
Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data resources, available at http://caporaso-lab.github.io/mockrobiota/. The materials contained in mockrobiota include data set and sample metadata, expected composition data (taxonomy or gene annotations or reference sequences for mock community members), and links to raw data (e...
September 2016: MSystems
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