journal
MENU ▼
Read by QxMD icon Read
search

Microbiome

journal
https://www.readbyqxmd.com/read/28511691/tomato-root-microbiota-and-phytophthora-parasitica-associated-disease
#1
Marie Larousse, Corinne Rancurel, Camille Syska, Ferran Palero, Catherine Etienne, Benoît Industri, Xavier Nesme, Marc Bardin, Eric Galiana
BACKGROUND: Interactions between pathogenic oomycetes and microbiota residing on the surface of the host plant root are unknown, despite being critical to inoculum constitution. The nature of these interactions was explored for the polyphagous and telluric species Phytophthora parasitica. RESULTS: Composition of the rhizospheric microbiota of Solanum lycopersicum was characterized using deep re-sequencing of 16S rRNA gene to analyze tomato roots either free of or partly covered with P...
May 16, 2017: Microbiome
https://www.readbyqxmd.com/read/28506317/changes-in-microbial-ecology-after-fecal-microbiota-transplantation-for-recurrent-c-difficile-infection-affected-by-underlying-inflammatory-bowel-disease
#2
Sahil Khanna, Yoshiki Vazquez-Baeza, Antonio González, Sophie Weiss, Bradley Schmidt, David A Muñiz-Pedrogo, John F Rainey, Patricia Kammer, Heidi Nelson, Michael Sadowsky, Alexander Khoruts, Stefan L Farrugia, Rob Knight, Darrell S Pardi, Purna C Kashyap
BACKGROUND: Gut microbiota play a key role in maintaining homeostasis in the human gut. Alterations in the gut microbial ecosystem predispose to Clostridium difficile infection (CDI) and gut inflammatory disorders such as inflammatory bowel disease (IBD). Fecal microbiota transplantation (FMT) from a healthy donor can restore gut microbial diversity and pathogen colonization resistance; consequently, it is now being investigated for its ability to improve inflammatory gut conditions such as IBD...
May 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28506279/uncovering-the-trimethylamine-producing-bacteria-of-the-human-gut-microbiota
#3
Silke Rath, Benjamin Heidrich, Dietmar H Pieper, Marius Vital
BACKGROUND: Trimethylamine (TMA), produced by the gut microbiota from dietary quaternary amines (mainly choline and carnitine), is associated with atherosclerosis and severe cardiovascular disease. Currently, little information on the composition of TMA producers in the gut is available due to their low abundance and the requirement of specific functional-based detection methods as many taxa show disparate abilities to produce that compound. RESULTS: In order to examine the TMA-forming potential of microbial communities, we established databases for the key genes of the main TMA-synthesis pathways, encoding choline TMA-lyase (cutC) and carnitine oxygenase (cntA), using a multi-level screening approach on 67,134 genomes revealing 1107 and 6738 candidates to exhibit cutC and cntA, respectively...
May 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28494786/compositionally-and-functionally-distinct-sinus-microbiota-in-chronic-rhinosinusitis-patients-have-immunological-and-clinically-divergent-consequences
#4
Emily K Cope, Andrew N Goldberg, Steven D Pletcher, Susan V Lynch
BACKGROUND: Chronic rhinosinusitis (CRS) is a heterogeneous disease characterized by persistent sinonasal inflammation and sinus microbiome dysbiosis. The basis of this heterogeneity is poorly understood. We sought to address the hypothesis that a limited number of compositionally distinct pathogenic bacterial microbiota exist in CRS patients and invoke discrete immune responses and clinical phenotypes in CRS patients. RESULTS: Sinus brushings from patients with CRS (n = 59) and healthy individuals (n = 10) collected during endoscopic sinus surgery were analyzed using 16S rRNA gene sequencing, predicted metagenomics, and RNA profiling of the mucosal immune response...
May 12, 2017: Microbiome
https://www.readbyqxmd.com/read/28476139/optimizing-methods-and-dodging-pitfalls-in-microbiome-research
#5
REVIEW
Dorothy Kim, Casey E Hofstaedter, Chunyu Zhao, Lisa Mattei, Ceylan Tanes, Erik Clarke, Abigail Lauder, Scott Sherrill-Mix, Christel Chehoud, Judith Kelsen, Máire Conrad, Ronald G Collman, Robert Baldassano, Frederic D Bushman, Kyle Bittinger
Research on the human microbiome has yielded numerous insights into health and disease, but also has resulted in a wealth of experimental artifacts. Here, we present suggestions for optimizing experimental design and avoiding known pitfalls, organized in the typical order in which studies are carried out. We first review best practices in experimental design and introduce common confounders such as age, diet, antibiotic use, pet ownership, longitudinal instability, and microbial sharing during cohousing in animal studies...
May 5, 2017: Microbiome
https://www.readbyqxmd.com/read/28476135/the-effects-of-inhaled-aztreonam-on-the-cystic-fibrosis-lung-microbiome
#6
Alya A Heirali, Matthew L Workentine, Nicole Acosta, Ali Poonja, Douglas G Storey, Ranjani Somayaji, Harvey R Rabin, Fiona J Whelan, Michael G Surette, Michael D Parkins
BACKGROUND: Aztreonam lysine for inhalation (AZLI) is an inhaled antibiotic used to treat chronic Pseudomonas aeruginosa infection in CF. AZLI improves lung function and quality of life, and reduces exacerbations-improvements attributed to its antipseudomonal activity. Given the extremely high aztreonam concentrations achieved in the lower airways by nebulization, we speculate this may extend its spectrum of activity to other organisms. As such, we sought to determine if AZLI affects the CF lung microbiome and whether community constituents can be used to predict treatment responsiveness...
May 5, 2017: Microbiome
https://www.readbyqxmd.com/read/28473000/tracking-microbial-colonization-in-fecal-microbiota-transplantation-experiments-via-genome-resolved-metagenomics
#7
Sonny T M Lee, Stacy A Kahn, Tom O Delmont, Alon Shaiber, Özcan C Esen, Nathaniel A Hubert, Hilary G Morrison, Dionysios A Antonopoulos, David T Rubin, A Murat Eren
BACKGROUND: Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the recipient gut, and the widely used approaches to study the microbial ecology of FMT experiments fail to provide enough resolution to identify populations that are likely responsible for FMT-derived benefits...
May 4, 2017: Microbiome
https://www.readbyqxmd.com/read/28457228/differences-in-gut-microbial-composition-correlate-with-regional-brain-volumes-in-irritable-bowel-syndrome
#8
Jennifer S Labus, Emily B Hollister, Jonathan Jacobs, Kyleigh Kirbach, Numan Oezguen, Arpana Gupta, Jonathan Acosta, Ruth Ann Luna, Kjersti Aagaard, James Versalovic, Tor Savidge, Elaine Hsiao, Kirsten Tillisch, Emeran A Mayer
BACKGROUND: Preclinical and clinical evidence supports the concept of bidirectional brain-gut microbiome interactions. We aimed to determine if subgroups of irritable bowel syndrome (IBS) subjects can be identified based on differences in gut microbial composition, and if there are correlations between gut microbial measures and structural brain signatures in IBS. METHODS: Behavioral measures, stool samples, and structural brain images were collected from 29 adult IBS and 23 healthy control subjects (HCs)...
May 1, 2017: Microbiome
https://www.readbyqxmd.com/read/28454555/a-critical-assessment-of-the-sterile-womb-and-in-utero-colonization-hypotheses-implications-for-research-on-the-pioneer-infant-microbiome
#9
REVIEW
Maria Elisa Perez-Muñoz, Marie-Claire Arrieta, Amanda E Ramer-Tait, Jens Walter
After more than a century of active research, the notion that the human fetal environment is sterile and that the neonate's microbiome is acquired during and after birth was an accepted dogma. However, recent studies using molecular techniques suggest bacterial communities in the placenta, amniotic fluid, and meconium from healthy pregnancies. These findings have led many scientists to challenge the "sterile womb paradigm" and propose that microbiome acquisition instead begins in utero, an idea that would fundamentally change our understanding of gut microbiota acquisition and its role in human development...
April 28, 2017: Microbiome
https://www.readbyqxmd.com/read/28449706/chemical-and-pathogen-induced-inflammation-disrupt-the-murine-intestinal-microbiome
#10
Mikayla A Borton, Anice Sabag-Daigle, Jikang Wu, Lindsey M Solden, Bridget S O'Banion, Rebecca A Daly, Richard A Wolfe, Juan F Gonzalez, Vicki H Wysocki, Brian M M Ahmer, Kelly C Wrighton
BACKGROUND: Salmonella is one of the most significant food-borne pathogens to affect humans and agriculture. While it is well documented that Salmonella infection triggers host inflammation, the impacts on the gut environment are largely unknown. A CBA/J mouse model was used to evaluate intestinal responses to Salmonella-induced inflammation. In parallel, we evaluated chemically induced inflammation by dextran sodium sulfate (DSS) and a non-inflammation control. We profiled gut microbial diversity by sequencing 16S ribosomal ribonucleic acid (rRNA) genes from fecal and cecal samples...
April 27, 2017: Microbiome
https://www.readbyqxmd.com/read/28441964/fecal-metagenomic-profiles-in-subgroups-of-patients-with-myalgic-encephalomyelitis-chronic-fatigue-syndrome
#11
Dorottya Nagy-Szakal, Brent L Williams, Nischay Mishra, Xiaoyu Che, Bohyun Lee, Lucinda Bateman, Nancy G Klimas, Anthony L Komaroff, Susan Levine, Jose G Montoya, Daniel L Peterson, Devi Ramanan, Komal Jain, Meredith L Eddy, Mady Hornig, W Ian Lipkin
BACKGROUND: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is characterized by unexplained persistent fatigue, commonly accompanied by cognitive dysfunction, sleeping disturbances, orthostatic intolerance, fever, lymphadenopathy, and irritable bowel syndrome (IBS). The extent to which the gastrointestinal microbiome and peripheral inflammation are associated with ME/CFS remains unclear. We pursued rigorous clinical characterization, fecal bacterial metagenomics, and plasma immune molecule analyses in 50 ME/CFS patients and 50 healthy controls frequency-matched for age, sex, race/ethnicity, geographic site, and season of sampling...
April 26, 2017: Microbiome
https://www.readbyqxmd.com/read/28438217/a-powerful-microbiome-based-association-test-and-a-microbial-taxa-discovery-framework-for-comprehensive-association-mapping
#12
Hyunwook Koh, Martin J Blaser, Huilin Li
BACKGROUND: The role of the microbiota in human health and disease has been increasingly studied, gathering momentum through the use of high-throughput technologies. Further identification of the roles of specific microbes is necessary to better understand the mechanisms involved in diseases related to microbiome perturbations. METHODS: Here, we introduce a new microbiome-based group association testing method, optimal microbiome-based association test (OMiAT). OMiAT is a data-driven testing method which takes an optimal test throughout different tests from the sum of powered score tests (SPU) and microbiome regression-based kernel association test (MiRKAT)...
April 24, 2017: Microbiome
https://www.readbyqxmd.com/read/28438184/microbiota-activated-cd103-dcs-stemming-from-microbiota-adaptation-specifically-drive-%C3%AE-%C3%AE-t17-proliferation-and-activation
#13
Chris Fleming, Yihua Cai, Xuan Sun, Venkatakrishna R Jala, Feng Xue, Samantha Morrissey, Yu-Ling Wei, Yueh-Hsiu Chien, Huang-Ge Zhang, Bodduluri Haribabu, Jian Huang, Jun Yan
BACKGROUND: IL-17-producing γδT cells (γδT17) promote autoinflammatory diseases and cancers. Yet, γδT17 peripheral regulation has not been thoroughly explored especially in the context of microbiota-host interaction. The potent antigen-presenting CD103(+) dendritic cell (DC) is a key immune player in close contact with both γδT17 cells and microbiota. This study presents a novel cellular network among microbiota, CD103(+) DCs, and γδT17 cells. METHODS: Immunophenotyping of IL-17r(-/-) mice and IL-17r(-/-) IRF8(-/-) mice were performed by ex vivo immunostaining and flow cytometric analysis...
April 24, 2017: Microbiome
https://www.readbyqxmd.com/read/28390422/high-fat-feeding-rather-than-obesity-drives-taxonomical-and-functional-changes-in-the-gut-microbiota-in-mice
#14
Liang Xiao, Si Brask Sonne, Qiang Feng, Ning Chen, Zhongkui Xia, Xiaoping Li, Zhiwei Fang, Dongya Zhang, Even Fjære, Lisa Kolden Midtbø, Muriel Derrien, Floor Hugenholtz, Longqing Tang, Junhua Li, Jianfeng Zhang, Chuan Liu, Qin Hao, Ulla Birgitte Vogel, Alicja Mortensen, Michiel Kleerebezem, Tine Rask Licht, Huanming Yang, Jian Wang, Yingrui Li, Manimozhiyan Arumugam, Jun Wang, Lise Madsen, Karsten Kristiansen
BACKGROUND: It is well known that the microbiota of high-fat (HF) diet-induced obese mice differs from that of lean mice, but to what extent, this difference reflects the obese state or the diet is unclear. To dissociate changes in the gut microbiota associated with high HF feeding from those associated with obesity, we took advantage of the different susceptibility of C57BL/6JBomTac (BL6) and 129S6/SvEvTac (Sv129) mice to diet-induced obesity and of their different responses to inhibition of cyclooxygenase (COX) activity, where inhibition of COX activity in BL6 mice prevents HF diet-induced obesity, but in Sv129 mice accentuates obesity...
April 8, 2017: Microbiome
https://www.readbyqxmd.com/read/28388930/shifts-among-eukaryota-bacteria-and-archaea-define-the-vertical-organization-of-a-lake-sediment
#15
Christian Wurzbacher, Andrea Fuchs, Katrin Attermeyer, Katharina Frindte, Hans-Peter Grossart, Michael Hupfer, Peter Casper, Michael T Monaghan
BACKGROUND: Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments...
April 8, 2017: Microbiome
https://www.readbyqxmd.com/read/28388929/novel-soil-inhabiting-clades-fill-gaps-in-the-fungal-tree-of-life
#16
Leho Tedersoo, Mohammad Bahram, Rasmus Puusepp, R Henrik Nilsson, Timothy Y James
BACKGROUND: Fungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water. RESULTS: We provide rough phylogenetic placement and principal niche analysis for >40 previously unrecognized fungal groups at the order and class level from global soil samples based on combined 18S (nSSU) and 28S (nLSU) rRNA gene sequences. Especially, Rozellomycota (Cryptomycota), Zygomycota s...
April 8, 2017: Microbiome
https://www.readbyqxmd.com/read/28381231/exposure-to-household-furry-pets-influences-the-gut-microbiota-of-infant-at-3-4%C3%A2-months-following-various-birth-scenarios
#17
Hein M Tun, Theodore Konya, Tim K Takaro, Jeffrey R Brook, Radha Chari, Catherine J Field, David S Guttman, Allan B Becker, Piush J Mandhane, Stuart E Turvey, Padmaja Subbarao, Malcolm R Sears, James A Scott, Anita L Kozyrskyj
BACKGROUND: Early-life exposure to household pets has the capacity to reduce risk for overweight and allergic disease, especially following caesarean delivery. Since there is some evidence that pets also alter the gut microbial composition of infants, changes to the gut microbiome are putative pathways by which pet exposure can reduce these risks to health. To investigate the impact of pre- and postnatal pet exposure on infant gut microbiota following various birth scenarios, this study employed a large subsample of 746 infants from the Canadian Healthy Infant Longitudinal Development Study (CHILD) cohort, whose mothers were enrolled during pregnancy between 2009 and 2012...
April 6, 2017: Microbiome
https://www.readbyqxmd.com/read/28340597/temporal-dynamics-of-the-gut-microbiota-in-people-sharing-a-confined-environment-a-520-day-ground-based-space-simulation-mars500
#18
Silvia Turroni, Simone Rampelli, Elena Biagi, Clarissa Consolandi, Marco Severgnini, Clelia Peano, Sara Quercia, Matteo Soverini, Franck G Carbonero, Giovanna Bianconi, Petra Rettberg, Francesco Canganella, Patrizia Brigidi, Marco Candela
BACKGROUND: The intestinal microbial communities and their temporal dynamics are gaining increasing interest due to the significant implications for human health. Recent studies have shown the dynamic behavior of the gut microbiota in free-living, healthy persons. To date, it is not known whether these dynamics are applicable during prolonged life sharing in a confined and controlled environment. RESULTS: The MARS500 project, the longest ground-based space simulation ever, provided us with a unique opportunity to trace the crew microbiota over 520 days of isolated confinement, such as that faced by astronauts in real long-term interplanetary space flights, and after returning to regular life, for a total of 2 years...
March 24, 2017: Microbiome
https://www.readbyqxmd.com/read/28335814/symbiosis-and-microbiome-flexibility-in-calcifying-benthic-foraminifera-of-the-great-barrier-reef
#19
Martina Prazeres, Tracy Ainsworth, T Edward Roberts, John M Pandolfi, William Leggat
BACKGROUND: Symbiosis is a phenomenon that allows organisms to colonise a wide range of environments and occupy a variety of ecological niches in marine environments. Large benthic foraminifera (LBF) are crucial marine calcifiers that rely on photo-endosymbionts for growth and calcification, yet the influence of environmental conditions in shaping their interactions with prokaryotic and eukaryotic associates is poorly known. RESULTS: Here, we used next-generation sequencing to identify eukaryotic photosynthesizing and prokaryotic microbes associated with the common LBF Amphistegina lobifera across a physio-chemical gradient on the Great Barrier Reef (GBR)...
March 23, 2017: Microbiome
https://www.readbyqxmd.com/read/28335808/potential-for-hydrogen-oxidizing-chemolithoautotrophic-and-diazotrophic-populations-to-initiate-biofilm-formation-in-oligotrophic-deep-terrestrial-subsurface-waters
#20
Xiaofen Wu, Karsten Pedersen, Johanna Edlund, Lena Eriksson, Mats Åström, Anders F Andersson, Stefan Bertilsson, Mark Dopson
BACKGROUND: Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural environments, they have received little attention in the oligotrophic and anaerobic waters found in deep bedrock fractures. This study is the first to use community DNA sequencing to describe biofilm formation under in situ conditions in the deep terrestrial biosphere. RESULTS: In this study, flow cells were attached to boreholes containing either "modern marine" or "old saline" waters of different origin and degree of isolation from the light-driven surface of the earth...
March 23, 2017: Microbiome
journal
journal
48234
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"