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https://www.readbyqxmd.com/read/27921083/integrated-role-of-bifidobacterium-animalis-subsp-lactis-supplementation-in-gut-microbiota-immunity-and-metabolism-of-infant-rhesus-monkeys
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
https://www.readbyqxmd.com/read/27822552/microbial-succession-and-flavor-production-in-the-fermented-dairy-beverage-kefir
#10
Aaron M Walsh, Fiona Crispie, Kieran Kilcawley, Orla O'Sullivan, Maurice G O'Sullivan, Marcus J Claesson, Paul D Cotter
Kefir is a putatively health-promoting dairy beverage that is produced when a kefir grain, consisting of a consortium of microorganisms, is added to milk to initiate a natural fermentation. Here, a detailed analysis was carried out to determine how the microbial population, gene content, and flavor of three kefirs from distinct geographic locations change over the course of 24-h fermentations. Metagenomic sequencing revealed that Lactobacillus kefiranofaciens was the dominant bacterial species in kefir during early stages of fermentations but that Leuconostoc mesenteroides became more prevalent in later stages...
September 2016: MSystems
https://www.readbyqxmd.com/read/27822551/individualized-responses-of-gut-microbiota-to-dietary-intervention-modeled-in-humanized-mice
#11
Samuel A Smits, Angela Marcobal, Steven Higginbottom, Justin L Sonnenburg, Purna C Kashyap
Diet plays an important role in shaping the structure and function of the gut microbiota. The microbes and microbial products in turn can influence various aspects of host physiology. One promising route to affect host function and restore health is by altering the gut microbiome using dietary intervention. The individuality of the microbiome may pose a significant challenge, so we sought to determine how different microbiotas respond to the same dietary intervention in a controlled setting. We modeled gut microbiotas from three healthy donors in germfree mice and defined compositional and functional alteration following a change in dietary microbiota-accessible carbohydrates (MACs)...
September 2016: MSystems
https://www.readbyqxmd.com/read/27822550/differential-gene-expression-of-three-mastitis-causing-escherichia-coli-strains-grown-under-planktonic-swimming-and-swarming-culture-conditions
#12
John D Lippolis, Brian W Brunelle, Timothy A Reinhardt, Randy E Sacco, Tyler C Thacker, Torey P Looft, Thomas A Casey
Bacterial motility is thought to play an important role in virulence. We have previously shown that proficient bacterial swimming and swarming in vitro is correlated with the persistent intramammary infection phenotype observed in cattle. However, little is known about the gene regulation differences important for different motility phenotypes in Escherichia coli. In this work, three E. coli strains that cause persistent bovine mastitis infections were grown in three media that promote different types of motility (planktonic, swimming, and swarming)...
July 2016: MSystems
https://www.readbyqxmd.com/read/27822549/evolution-of-ubiquinone-biosynthesis-multiple-proteobacterial-enzymes-with-various-regioselectivities-to-catalyze-three-contiguous-aromatic-hydroxylation-reactions
#13
Ludovic Pelosi, Anne-Lise Ducluzeau, Laurent Loiseau, Frédéric Barras, Dominique Schneider, Ivan Junier, Fabien Pierrel
The ubiquitous ATP synthase uses an electrochemical gradient to synthesize cellular energy in the form of ATP. The production of this electrochemical gradient relies on liposoluble proton carriers like ubiquinone (UQ), which is used in the respiratory chains of eukaryotes and proteobacteria. The biosynthesis of UQ requires three hydroxylation reactions on contiguous positions of an aromatic ring. In Escherichia coli, each of three UQ flavin monooxygenases (FMOs), called UbiF, UbiH, and UbiI, modifies a single position of the aromatic ring...
July 2016: MSystems
https://www.readbyqxmd.com/read/27822548/asm-journals-eliminate-impact-factor-information-from-journal-websites
#14
EDITORIAL
Arturo Casadevall, Stefano Bertuzzi, Michael J Buchmeier, Roger J Davis, Harold Drake, Ferric C Fang, Jack Gilbert, Barbara M Goldman, Michael J Imperiale, Philip Matsumura, Alexander J McAdam, Marcela F Pasetti, Rozanne M Sandri-Goldin, Thomas Silhavy, Louis Rice, Jo-Anne H Young, Thomas Shenk
Many scientists attempt to publish their work in a journal with the highest possible journal impact factor (IF). Despite widespread condemnation of the use of journal IFs to assess the significance of published work, these numbers continue to be widely misused in publication, hiring, funding, and promotion decisions (1, 2).
July 2016: MSystems
https://www.readbyqxmd.com/read/27822547/what-have-we-learned-about-the-microbiomes-of-indoor-environments
#15
REVIEW
Brent Stephens
The advent and application of high-throughput molecular techniques for analyzing microbial communities in the indoor environment have led to illuminating findings and are beginning to change the way we think about human health in relation to the built environment. Here I review recent studies on the microbiology of the built environment, organize their findings into 12 major thematic categories, and comment on how these studies have or have not advanced knowledge in each area beyond what we already knew from over 100 years of applying culture-based methods to building samples...
July 2016: MSystems
https://www.readbyqxmd.com/read/27822546/zonal-soil-type-determines-soil-microbial-responses-to-maize-cropping-and-fertilization
#16
Mengxin Zhao, Bo Sun, Linwei Wu, Qun Gao, Feng Wang, Chongqing Wen, Mengmeng Wang, Yuting Liang, Lauren Hale, Jizhong Zhou, Yunfeng Yang
Soil types heavily influence ecological dynamics. It remains controversial to what extent soil types shape microbial responses to land management changes, largely due to lack of in-depth comparison across various soil types. Here, we collected samples from three major zonal soil types spanning from cold temperate to subtropical climate zones. We examined bacterial and fungal community structures, as well as microbial functional genes. Different soil types had distinct microbial biomass levels and community compositions...
July 2016: MSystems
https://www.readbyqxmd.com/read/27822545/proteome-remodeling-in-response-to-sulfur-limitation-in-candidatus-pelagibacter-ubique
#17
Daniel P Smith, Carrie D Nicora, Paul Carini, Mary S Lipton, Angela D Norbeck, Richard D Smith, Stephen J Giovannoni
The alphaproteobacterium "Candidatus Pelagibacter ubique" strain HTCC1062 and most other members of the SAR11 clade lack genes for assimilatory sulfate reduction, making them dependent on organosulfur compounds that occur naturally in seawater. To investigate how these cells adapt to sulfur limitation, batch cultures were grown in defined medium containing either limiting or nonlimiting amounts of dimethylsulfoniopropionate (DMSP) as the sole sulfur source. Protein and mRNA expression were measured before, during, and after the transition from exponential growth to stationary phase...
July 2016: MSystems
https://www.readbyqxmd.com/read/27822544/multiplexed-metagenomic-deep-sequencing-to-analyze-the-composition-of-high-priority-pathogen-reagents
#18
Michael R Wilson, Greg Fedewa, Mark D Stenglein, Judith Olejnik, Linda J Rennick, Sham Nambulli, Friederike Feldmann, W Paul Duprex, John H Connor, Elke Mühlberger, Joseph L DeRisi
Laboratories studying high-priority pathogens need comprehensive methods to confirm microbial species and strains while also detecting contamination. Metagenomic deep sequencing (MDS) inventories nucleic acids present in laboratory stocks, providing an unbiased assessment of pathogen identity, the extent of genomic variation, and the presence of contaminants. Double-stranded cDNA MDS libraries were constructed from RNA extracted from in vitro-passaged stocks of six viruses (La Crosse virus, Ebola virus, canine distemper virus, measles virus, human respiratory syncytial virus, and vesicular stomatitis virus)...
July 2016: MSystems
https://www.readbyqxmd.com/read/27822543/the-oral-and-skin-microbiomes-of-captive-komodo-dragons-are-significantly-shared-with-their-habitat
#19
Embriette R Hyde, Jose A Navas-Molina, Se Jin Song, Jordan G Kueneman, Gail Ackermann, Cesar Cardona, Gregory Humphrey, Don Boyer, Tom Weaver, Joseph R Mendelson, Valerie J McKenzie, Jack A Gilbert, Rob Knight
Examining the way in which animals, including those in captivity, interact with their environment is extremely important for studying ecological processes and developing sophisticated animal husbandry. Here we use the Komodo dragon (Varanus komodoensis) to quantify the degree of sharing of salivary, skin, and fecal microbiota with their environment in captivity. Both species richness and microbial community composition of most surfaces in the Komodo dragon's environment are similar to the Komodo dragon's salivary and skin microbiota but less similar to the stool-associated microbiota...
July 2016: MSystems
https://www.readbyqxmd.com/read/27822542/rna-sequencing-based-genome-reannotation-of-the-dermatophyte-arthroderma-benhamiae-and-characterization-of-its-secretome-and-whole-gene-expression-profile-during-infection
#20
Van Du T Tran, Niccolò De Coi, Marc Feuermann, Emanuel Schmid-Siegert, Elena-Tatiana Băguţ, Bernard Mignon, Patrice Waridel, Corinne Peter, Sylvain Pradervand, Marco Pagni, Michel Monod
Dermatophytes are the most common agents of superficial mycoses in humans and animals. The aim of the present investigation was to systematically identify the extracellular, possibly secreted, proteins that are putative virulence factors and antigenic molecules of dermatophytes. A complete gene expression profile of Arthroderma benhamiae was obtained during infection of its natural host (guinea pig) using RNA sequencing (RNA-seq) technology. This profile was completed with those of the fungus cultivated in vitro in two media containing either keratin or soy meal protein as the sole source of nitrogen and in Sabouraud medium...
July 2016: MSystems
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