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Microbiome programming

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https://www.readbyqxmd.com/read/28408909/the-maternal-diet-gut-bacteria-and-bacterial-metabolites-during-pregnancy-influence-offspring-asthma
#1
REVIEW
Lawrence E K Gray, Martin O'Hely, Sarath Ranganathan, Peter David Sly, Peter Vuillermin
This review focuses on the current evidence that maternal dietary and gut bacterial exposures during pregnancy influence the developing fetal immune system and subsequent offspring asthma. Part 1 addresses exposure to a farm environment, antibiotics, and prebiotic and probiotic supplementation that together indicate the importance of bacterial experience in immune programming and offspring asthma. Part 2 outlines proposed mechanisms to explain these associations including bacterial exposure of the fetoplacental unit; immunoglobulin-related transplacental transport of gut bacterial components; cytokine signaling producing fetomaternal immune alignment; and immune programming via metabolites produced by gut bacteria...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28375407/hot-topics-in-primary-care-role-of-the-microbiome-in-disease-implications-for-treatment-of-irritable-bowel-syndrome
#2
REVIEW
Brian E Lacy
Dietary and some other treatments for IBS are supported by a growing body of evidence, much of which comes from programs such as the Human Microbiome Project and Human Gut Microbiome Initiative, which were intended to identify and characterize microorganisms found in association with both healthy and diseased humans. These programs used state-of-the-art technology to characterize the human microbiome from multiple body sites. This evidence indicates that the gut microbiome plays an important role in IBS and some other gastrointestinal (GI) disorders...
April 2017: Journal of Family Practice
https://www.readbyqxmd.com/read/28326156/porphyromonas-gingivalis-is-the-most-abundant-species-detected-in-coronary-and-femoral-arteries
#3
J-L C Mougeot, C B Stevens, B J Paster, M T Brennan, P B Lockhart, F K B Mougeot
An association between oral bacteria and atherosclerosis has been postulated. A limited number of studies have used 16S RNA gene sequencing-based metagenomics approaches to identify bacteria at the species level from atherosclerotic plaques in arterial walls. The objective of this study was to establish detailed oral microbiome profiles, at both genus and species level, of clinically healthy coronary and femoral artery tissues from patients with atherosclerosis. Tissue specimens were taken from clinically non-atherosclerotic areas of coronary or femoral arteries used for attachment of bypass grafts in 42 patients with atherosclerotic cardiovascular disease...
2017: Journal of Oral Microbiology
https://www.readbyqxmd.com/read/28320307/perturbation-of-microbiota-in-one-day-old-broiler-chickens-with-antibiotic-for-24-hours-negatively-affects-intestinal-immune-development
#4
Dirkjan Schokker, Alfons J M Jansman, Gosse Veninga, Naomi de Bruin, Stephanie A Vastenhouw, Freddy M de Bree, Alex Bossers, Johanna M J Rebel, Mari A Smits
BACKGROUND: Gut microbial colonization and development of immune competence are intertwined and are influenced by early-life nutritional, environmental, and management factors. Perturbation of the gut microbiome at young age affects the crosstalk between intestinal bacteria and host cells of the intestinal mucosa. RESULTS: We investigated the effect of a perturbation of the normal early life microbial colonization of the jejunum in 1-day old chickens. Perturbation was induced by administering 0...
March 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28275685/the-clinical-evidence-linking-helicobacter-pylori-to-gastric-cancer
#5
REVIEW
Steven F Moss
Gastric cancer has long been recognized to be accompanied and preceded by chronic gastritis, lasting decades. Arguably, the most important development in our understanding of gastric cancer pathogenesis over the past 50 years has been the realization that, for most cases of gastric cancer, Helicobacter pylori is the cause of the underlying gastritis. Gastritis can promote gastric carcinogenesis, typically via the Correa cascade of atrophic gastritis, intestinal metaplasia, and dysplasia. Nested case-control studies have shown that H pylori infection increases the risk of gastric cancer significantly, both of the intestinal and diffuse subtypes, and that H pylori is responsible for approximately 90% of the world's burden of noncardia gastric cancer...
March 2017: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28270584/viruses-in-the-oceanic-basement
#6
Olivia D Nigro, Sean P Jungbluth, Huei-Ting Lin, Chih-Chiang Hsieh, Jaclyn A Miranda, Christopher R Schvarcz, Michael S Rappé, Grieg F Steward
Microbial life has been detected well into the igneous crust of the seafloor (i.e., the oceanic basement), but there have been no reports confirming the presence of viruses in this habitat. To detect and characterize an ocean basement virome, geothermally heated fluid samples (ca. 60 to 65°C) were collected from 117 to 292 m deep into the ocean basement using seafloor observatories installed in two boreholes (Integrated Ocean Drilling Program [IODP] U1362A and U1362B) drilled in the eastern sediment-covered flank of the Juan de Fuca Ridge...
March 7, 2017: MBio
https://www.readbyqxmd.com/read/28247459/shifting-paradigms-in-restoration-of-the-world-s-coral-reefs
#7
Madeleine J H van Oppen, Ruth D Gates, Linda L Blackall, Neal Cantin, Leela J Chakravarti, Wing Y Chan, Craig Cormick, Angela Crean, Katarina Damjanovic, Hannah Epstein, Peter L Harrison, Thomas A Jones, Margaret Miller, Rachel J Pears, Lesa M Peplow, David A Raftos, Britta Schaffelke, Kristen Stewart, Gergely Torda, David Wachenfeld, Andrew R Weeks, Hollie M Putnam
Many ecosystems around the world are rapidly deteriorating due to both local and global pressures, and perhaps none so precipitously as coral reefs. Management of coral reefs through maintenance (e.g., marine-protected areas, catchment management to improve water quality), restoration, as well as global and national governmental agreements to reduce greenhouse gas emissions (e.g., the 2015 Paris Agreement) is critical for the persistence of coral reefs. Despite these initiatives, the health and abundance of corals reefs are rapidly declining and other solutions will soon be required...
March 1, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28177413/selenium-biofortification-and-phytoremediation-phytotechnologies-a-review
#8
Michela Schiavon, Elizabeth A H Pilon-Smits
The element selenium (Se) is both essential and toxic for most life forms, with a narrow margin between deficiency and toxicity. Phytotechnologies using plants and their associated microbes can address both of these problems. To prevent Se toxicity due to excess environmental Se, plants may be used to phytoremediate Se from soil or water. To alleviate Se deficiency in humans or livestock, crops may be biofortified with Se. These two technologies may also be combined: Se-enriched plant material from phytoremediation could be used as green fertilizer or as fortified food...
January 2017: Journal of Environmental Quality
https://www.readbyqxmd.com/read/28135002/ischemia-reperfusion
#9
Theodore Kalogeris, Christopher P Baines, Maike Krenz, Ronald J Korthuis
Ischemic disorders, such as myocardial infarction, stroke, and peripheral vascular disease, are the most common causes of debilitating disease and death in westernized cultures. The extent of tissue injury relates directly to the extent of blood flow reduction and to the length of the ischemic period, which influence the levels to which cellular ATP and intracellular pH are reduced. By impairing ATPase-dependent ion transport, ischemia causes intracellular and mitochondrial calcium levels to increase (calcium overload)...
December 6, 2016: Comprehensive Physiology
https://www.readbyqxmd.com/read/28025202/calypso-a-user-friendly-web-server-for-mining-and-visualizing-microbiome-environment-interactions
#10
Martha Zakrzewski, Carla Proietti, Jonathan J Ellis, Shihab Hasan, Marie-Jo Brion, Bernard Berger, Lutz Krause
Calypso is an easy-to-use online software suite that allows non-expert users to mine, interpret and compare taxonomic information from metagenomic or 16S rDNA datasets. Calypso has a focus on multivariate statistical approaches that can identify complex environment-microbiome associations. The software enables quantitative visualizations, statistical testing, multivariate analysis, supervised learning, factor analysis, multivariable regression, network analysis and diversity estimates. Comprehensive help pages, tutorials and videos are provided via a wiki page...
March 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28025198/dace-a-scalable-dp-means-algorithm-for-clustering-extremely-large-sequence-data
#11
Linhao Jiang, Yichao Dong, Ning Chen, Ting Chen
Motivation: Advancements in next-generation sequencing technology have produced large amounts of reads at low cost in a short time. In metagenomics, 16S and 18S rRNA gene have been widely used as marker genes to profile diversity of microorganisms in environmental samples. Through clustering of sequencing reads we can determine both number of OTUs and their relative abundance. In many applications, clustering of very large sequencing data with high efficiency and accuracy is essential for downstream analysis...
March 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/27984120/a-simple-statistical-test-of-taxonomic-or-functional-homogeneity-using-replicated-microbiome-sequencing-samples
#12
Daniel H Huson, Mike Steel, Mohamed El-Hadidi, Suparna Mitra, Silke Peter, Matthias Willmann
One important question in microbiome analysis is how to assess the homogeneity of the microbial composition in a given environment, with respect to a given analysis method. Do different microbial samples taken from the same environment follow the same taxonomic distribution of organisms, or the same distribution of functions? Here we provide a non-parametric statistical "triangulation test" to address this type of question. The test requires that multiple replicates are available for each of the biological samples, and it is based on three-way computational comparisons of samples...
October 27, 2016: Journal of Biotechnology
https://www.readbyqxmd.com/read/27983723/viruses-and-the-origin-of-microbiome-selection-and-immunity
#13
Steven D Quistad, Juris A Grasis, Jeremy J Barr, Forest L Rohwer
The last common metazoan ancestor (LCMA) emerged over half a billion years ago. These complex metazoans provided newly available niche space for viruses and microbes. Modern day contemporaries, such as cnidarians, suggest that the LCMA consisted of two cell layers: a basal endoderm and a mucus-secreting ectoderm, which formed a surface mucus layer (SML). Here we propose a model for the origin of metazoan immunity based on external and internal microbial selection mechanisms. In this model, the SML concentrated bacteria and their associated viruses (phage) through physical dynamics (that is, the slower flow fields near a diffusive boundary layer), which selected for mucin-binding capabilities...
April 2017: ISME Journal
https://www.readbyqxmd.com/read/27935992/intense-exercise-and-aerobic-conditioning-associated-with-chromium-or-l-carnitine-supplementation-modified-the-fecal-microbiota-of-fillies
#14
Maria Luiza Mendes de Almeida, Walter Heinz Feringer, Júlia Ribeiro Garcia Carvalho, Isadora Mestriner Rodrigues, Lilian Rezende Jordão, Mayara Gonçalves Fonseca, Adalgiza Souza Carneiro de Rezende, Antonio de Queiroz Neto, J Scott Weese, Márcio Carvalho da Costa, Eliana Gertrudes de Macedo Lemos, Guilherme de Camargo Ferraz
Recent studies performed in humans and rats have reported that exercise can alter the intestinal microbiota. Athletic horses perform intense exercise regularly, but studies characterizing horse microbiome during aerobic conditioning programs are still limited. Evidence has indicated that this microbial community is involved in the metabolic homeostasis of the host. Research on ergogenic substances using new sequencing technologies have been limited to the intestinal microbiota and there is a considerable demand for scientific studies that verify the effectiveness of these supplements in horses...
2016: PloS One
https://www.readbyqxmd.com/read/27912059/microbiota-diurnal-rhythmicity-programs-host-transcriptome-oscillations
#15
Christoph A Thaiss, Maayan Levy, Tal Korem, Lenka Dohnalová, Hagit Shapiro, Diego A Jaitin, Eyal David, Deborah R Winter, Meital Gury-BenAri, Evgeny Tatirovsky, Timur Tuganbaev, Sara Federici, Niv Zmora, David Zeevi, Mally Dori-Bachash, Meirav Pevsner-Fischer, Elena Kartvelishvily, Alexander Brandis, Alon Harmelin, Oren Shibolet, Zamir Halpern, Kenya Honda, Ido Amit, Eran Segal, Eran Elinav
The intestinal microbiota undergoes diurnal compositional and functional oscillations that affect metabolic homeostasis, but the mechanisms by which the rhythmic microbiota influences host circadian activity remain elusive. Using integrated multi-omics and imaging approaches, we demonstrate that the gut microbiota features oscillating biogeographical localization and metabolome patterns that determine the rhythmic exposure of the intestinal epithelium to different bacterial species and their metabolites over the course of a day...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27898428/beneficial-effects-of-a-dietary-weight-loss-intervention-on-human-gut-microbiome-diversity-and-metabolism-are-not-sustained-during-weight-maintenance
#16
Femke-Anouska Heinsen, Daniela Fangmann, Nike Müller, Dominik M Schulte, Malte C Rühlemann, Kathrin Türk, Ute Settgast, Wolfgang Lieb, John F Baines, Stefan Schreiber, Andre Franke, Matthias Laudes
OBJECTIVE: In the present study, we examined the effect of a very low-calorie diet(VLCD)-based obesity program on human gut microbiome diversity and metabolism during weight loss and weight maintenance. METHODS: Obese subjects underwent 3 months of VLCD followed by 3 months of weight maintenance. A lean and an obese control group were included. The microbiome was characterized by performing high-throughput dual-indexed 16S rDNA amplicon sequencing. RESULTS: At baseline, a significant difference in the Firmicutes/Bacteroidetes ratio between the lean and obese individuals was observed (p = 0...
2016: Obesity Facts
https://www.readbyqxmd.com/read/27793228/microbes-and-oxytocin-benefits-for-host-physiology-and-behavior
#17
S E Erdman, T Poutahidis
It is now understood that gut bacteria exert effects beyond the local boundaries of the gastrointestinal tract to include distant tissues and overall health. Prototype probiotic bacterium Lactobacillus reuteri has been found to upregulate hormone oxytocin and systemic immune responses to achieve a wide array of health benefits involving wound healing, mental health, metabolism, and myoskeletal maintenance. Together these display that the gut microbiome and host animal interact via immune-endocrine-brain signaling networks...
2016: International Review of Neurobiology
https://www.readbyqxmd.com/read/27702710/fructans-in-the-first-1000-days-of-life-and-beyond-and-for-pregnancy
#18
REVIEW
Agus Firmansyah, Nalinee Chongviriyaphan, Drupadi Hs Dillon, Nguyen Cong Khan, Tatsuya Morita, Kraisid Tontisirin, Le Danh Tuyen, Weiping Wang, Jacques Bindels, Paul Deurenberg, Sherlin Ong, Jo Hautvast, Diederick Meyer, Elaine E Vaughan
Inulin-based prebiotics are non-digestible polysaccharides that influence the composition of the gut microbiota in infants and children, notably eliciting a bifidogenic effect with high short chain fatty acid levels. Inulin, a generic term that comprises β-(2,1)-linked linear fructans, is typically isolated from the chicory plant root, and derivatives such as oligofructose and long chain inulin appear to have different physiological properties. The first 1000 days of a child's life are increasingly recognized as a critical timeframe for health also into adulthood, whereby nutrition plays a key role...
December 2016: Asia Pacific Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/27531910/disease-severity-and-immune-activity-relate-to-distinct-interkingdom-gut-microbiome-states-in-ethnically-distinct-ulcerative-colitis-patients
#19
Jordan S Mar, Brandon J LaMere, Din L Lin, Sophia Levan, Michelle Nazareth, Uma Mahadevan, Susan V Lynch
UNLABELLED: Significant gut microbiota heterogeneity exists among ulcerative colitis (UC) patients, though the clinical implications of this variance are unknown. We hypothesized that ethnically distinct UC patients exhibit discrete gut microbiotas with unique metabolic programming that differentially influence immune activity and clinical status. Using parallel 16S rRNA and internal transcribed spacer 2 sequencing of fecal samples (UC, 30; healthy, 13), we corroborated previous observations of UC-associated bacterial diversity depletion and demonstrated significant Saccharomycetales expansion as characteristic of UC gut dysbiosis...
August 16, 2016: MBio
https://www.readbyqxmd.com/read/27491050/genomics-and-transcriptomics-based-patient-selection-for-cancer-treatment-with-immune-checkpoint-inhibitors-a-review
#20
REVIEW
Krijn K Dijkstra, Paula Voabil, Ton N Schumacher, Emile E Voest
Importance: Checkpoint blockade therapy targeting cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and the programmed cell death protein 1 pathways (PD-1/PD-L1) have achieved success in treating a number of malignancies. However, only a subset of patients responds to these therapies, and optimization of patient selection for treatment is imperative to avoid adverse effects without clinical benefit and keep costs manageable. Observations: The past few years have witnessed checkpoint inhibition becoming a first-line treatment option with US Food and Drug Administration approvals for various tumor types...
November 1, 2016: JAMA Oncology
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