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Microbiome programming

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https://www.readbyqxmd.com/read/28640599/a-high-throughput-dna-sequencing-approach-to-determine-sources-of-fecal-bacteria-in-a-lake-superior-estuary
#1
Clairessa M Brown, Christopher Staley, Ping Wang, Brent Dalzell, Chan Lan Chun, Michael J Sadowsky
Current microbial source tracking (MST) methods, employed to determine sources of fecal contamination in waterways, use molecular markers targeting host-associated bacteria in animal or human feces. However, there is a lack of knowledge about fecal microbiome composition in several animals and imperfect marker specificity and sensitivity. To overcome these issues, a community-based MST method has been developed. Here, we describe a study done in the Lake Superior-St. Louis River estuary using SourceTracker, a program that calculates the source contribution to an environment...
June 22, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28636759/rosacea-and-its-association-with-enteral-microbiota-in-korean-females
#2
Jae-Hui Nam, Yeojun Yun, Han-Saem Kim, Han-Na Kim, Ho Joo Jung, Yoosoo Chang, Seungho Ryu, Hocheol Shin, Hyung-Lae Kim, Won-Serk Kim
BACKGROUND: Rosacea is a chronic inflammatory dermatosis affecting the face and eyes. An association between systemic comorbidities and rosacea has been reported, but the link to enteral microbiota is uncertain. OBJECTIVES: We aimed to investigate the link between rosacea and enteral microbiota. METHODS: A cross-sectional study was performed in a sample of Korean women who participated in a health checkup program at the Kangbuk Samsung Hospital Health Screening Center between 23 June 2014 and 5 September 2014...
June 21, 2017: Experimental Dermatology
https://www.readbyqxmd.com/read/28628622/urinary-catheter-associated-microbiota-change-in-accordance-with-treatment-and-infection-status
#3
Laetitia Bossa, Kimberly Kline, Diane McDougald, Bonsan Bonne Lee, Scott A Rice
The use of long-term catheterisation to manage insensate bladders, often associated with spinal cord injury (SCI), increases the risk of microbial colonisation and infection of the urinary tract. Urinary tract infection (UTI) is typically diagnosed and treated based on the culturing of organisms from the urine, although this approach overlooks low titer, slow growing and non-traditional pathogens. Here, we present an investigation of the urinary tract microbiome in catheterised SCI individuals, using T-RFLP and metagenomic sequencing of the microbial community...
2017: PloS One
https://www.readbyqxmd.com/read/28604703/cold-induced-conversion-of-cholesterol-to-bile-acids-in-mice-shapes-the-gut-microbiome-and-promotes-adaptive-thermogenesis
#4
Anna Worthmann, Clara John, Malte C Rühlemann, Miriam Baguhl, Femke-Anouska Heinsen, Nicola Schaltenberg, Markus Heine, Christian Schlein, Ioannis Evangelakos, Chieko Mineo, Markus Fischer, Maura Dandri, Claus Kremoser, Ludger Scheja, Andre Franke, Philip W Shaul, Joerg Heeren
Adaptive thermogenesis is an energy-demanding process that is mediated by cold-activated beige and brown adipocytes, and it entails increased uptake of carbohydrates, as well as lipoprotein-derived triglycerides and cholesterol, into these thermogenic cells. Here we report that cold exposure in mice triggers a metabolic program that orchestrates lipoprotein processing in brown adipose tissue (BAT) and hepatic conversion of cholesterol to bile acids via the alternative synthesis pathway. This process is dependent on hepatic induction of cytochrome P450, family 7, subfamily b, polypeptide 1 (CYP7B1) and results in increased plasma levels, as well as fecal excretion, of bile acids that is accompanied by distinct changes in gut microbiota and increased heat production...
June 12, 2017: Nature Medicine
https://www.readbyqxmd.com/read/28579427/infections-of-wolbachia-may-destabilize-mosquito-population-dynamics
#5
Arndt Telschow, Florian Grziwotz, Philip Crain, Takeshi Miki, James W Mains, George Sugihara, Stephen L Dobson, Chih-Hao Hsieh
Recent efforts in controlling mosquito-borne diseases focus on biocontrol strategies that incapacitate pathogens inside mosquitoes by altering the mosquito's microbiome. A case in point is the introduction of Wolbachia into natural mosquito populations in order to eliminate Dengue virus. However, whether this strategy can successfully control vector-borne diseases is debated; particularly, how artificial infection affects population dynamics of hosts remains unclear. Here, we show that natural Wolbachia infections are associated with unstable mosquito population dynamics by contrasting Wolbachia-infected versus uninfected cage populations of the Asian tiger mosquito (Aedes albopictus)...
June 1, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28536537/-gestaltomics-systems-biology-schemes-for-the-study-of-neuropsychiatric-diseases
#6
REVIEW
Nora A Gutierrez Najera, Osbaldo Resendis-Antonio, Humberto Nicolini
The integration of different sources of biological information about what defines a behavioral phenotype is difficult to unify in an entity that reflects the arithmetic sum of its individual parts. In this sense, the challenge of Systems Biology for understanding the "psychiatric phenotype" is to provide an improved vision of the shape of the phenotype as it is visualized by "Gestalt" psychology, whose fundamental axiom is that the observed phenotype (behavior or mental disorder) will be the result of the integrative composition of every part...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28408909/the-maternal-diet-gut-bacteria-and-bacterial-metabolites-during-pregnancy-influence-offspring-asthma
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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