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Microbiome programming

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https://www.readbyqxmd.com/read/29728381/crown-of-thorns-sea-star-acanthaster-cf-solaris-have-tissue-characteristic-microbiomes-with-potential-roles-in-health-and-reproduction
#1
Lone Høj, Natalie Levy, Brett K Baillie, Peta L Clode, Raphael C Strohmaier, Nachshon Siboni, Nicole S Webster, Sven Uthicke, David G Bourne
Outbreaks of coral-eating crown-of-thorns sea stars (CoTS; Acanthaster spp. complex) cause substantial coral loss, hence there is considerable interest in developing prevention and control strategies. We characterised the microbiome of captive CoTS and assessed whether dysbiosis was evident in sea stars during a disease event. Most tissue types had a distinct microbiome. The exception was female gonads, which were highly variable amongst individuals. Male gonads were dominated (>97% of reads) by a single Mollicutes -related OTU...
May 4, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29686981/self-sampling-for-human-papillomavirus-testing-increased-cervical-cancer-screening-participation-and-incorporation-in-international-screening-programs
#2
REVIEW
Sarah Gupta, Christina Palmer, Elisabeth M Bik, Juan P Cardenas, Harold Nuñez, Laurens Kraal, Sara W Bird, Jennie Bowers, Alison Smith, Nathaniel A Walton, Audrey D Goddard, Daniel E Almonacid, Susan Zneimer, Jessica Richman, Zachary S Apte
In most industrialized countries, screening programs for cervical cancer have shifted from cytology (Pap smear or ThinPrep) alone on clinician-obtained samples to the addition of screening for human papillomavirus (HPV), its main causative agent. For HPV testing, self-sampling instead of clinician-sampling has proven to be equally accurate, in particular for assays that use nucleic acid amplification techniques. In addition, HPV testing of self-collected samples in combination with a follow-up Pap smear in case of a positive result is more effective in detecting precancerous lesions than a Pap smear alone...
2018: Frontiers in Public Health
https://www.readbyqxmd.com/read/29679832/natural-revegetation-of-a-semiarid-habitat-alters-taxonomic-and-functional-diversity-of-soil-microbial-communities
#3
Yanqing Guo, Xiaotian Chen, Yuanyuan Wu, Lu Zhang, Jimin Cheng, Gehong Wei, Yanbing Lin
Revegetation of degraded lands has a profound impact on the maintenance and stability of ecosystem processes. However, the impacts of this land use change on functional diversity of soil microbial communities are poorly understood. Here, using 16S rRNA gene amplicon and shotgun metagenomic sequencing, we compared the taxonomic and functional communities of soil microbiome, and analyzed the effects of plant diversity and soil chemical properties, in a chronosequence of restored ex-farmland that had been naturally revegetated to grassland over periods of 5, 15 and 30years with adjacent farmland, on the Loess Plateau, China...
April 18, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29678199/megan-lr-new-algorithms-allow-accurate-binning-and-easy-interactive-exploration-of-metagenomic-long-reads-and-contigs
#4
Daniel H Huson, Benjamin Albrecht, Caner Bağcı, Irina Bessarab, Anna Górska, Dino Jolic, Rohan B H Williams
BACKGROUND: There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce increasing numbers of longer reads (of varying lengths in the range of 10k-1M bps, say), but of low quality. There is an increasing interest in using long reads in microbiome sequencing, and there is a need to adapt short read tools to long read datasets...
April 20, 2018: Biology Direct
https://www.readbyqxmd.com/read/29662547/pd-l1-expression-testing-in-non-small-cell-lung-cancer
#5
REVIEW
Cristina Teixidó, Noelia Vilariño, Roxana Reyes, Noemí Reguart
In recent years, immunotherapy has revolutionized and changed the standard of care in patients with advanced non-small cell lung cancer (NSCLC). Immune checkpoint inhibitors, fundamentally those that act by blocking the programmed cell death receptor-1 (PD-1) and its ligand the programmed cell death ligand-1 (PD-L1) have emerged as novel treatment strategies in NSCLC, demonstrating undoubted superiority over chemotherapy in terms of efficacy. Several of these immune checkpoint modulators have recently gained regulatory approval for the treatment of advanced NSCLC, such as nivolumab, atezolizumab and pembrolizumab in first-line (only the latter) and second-line settings, and more recently, durvalumab as maintenance after chemoradiotherapy in locally advanced disease...
2018: Therapeutic Advances in Medical Oncology
https://www.readbyqxmd.com/read/29589768/ioc-consensus-statement-dietary-supplements-and-the-high-performance-athlete
#6
Ronald J Maughan, Louise M Burke, Jiri Dvorak, D Enette Larson-Meyer, Peter Peeling, Stuart M Phillips, Eric S Rawson, Neil P Walsh, Ina Garthe, Hans Geyer, Romain Meeusen, Luc van Loon, Susan M Shirreffs, Lawrence L Spriet, Mark Stuart, Alan Vernec, Kevin Currell, Vidya M Ali, Richard G M Budgett, Arne Ljungqvist, Margo Mountjoy, Yannis Pitsiladis, Torbjørn Soligard, Uğur Erdener, Lars Engebretsen
Nutrition usually makes a small but potentially valuable contribution to successful performance in elite athletes, and dietary supplements can make a minor contribution to this nutrition program. Nonetheless, supplement use is widespread at all levels of sport. Products described as supplements target different issues, including the management of micronutrient deficiencies, supply of convenient forms of energy and macronutrients, and provision of direct benefits to performance or indirect benefits such as supporting intense training regimens...
March 28, 2018: International Journal of Sport Nutrition and Exercise Metabolism
https://www.readbyqxmd.com/read/29567829/the-pancreatic-cancer-microbiome-promotes-oncogenesis-by-induction-of-innate-and-adaptive-immune-suppression
#7
Smruti Pushalkar, Mautin Hundeyin, Donnele Daley, Constantinos P Zambirinis, Emma Kurz, Ankita Mishra, Navyatha Mohan, Berk Aykut, Mykhaylo Usyk, Luisana E Torres, Gregor Werba, Kevin Zhang, Yuqi Guo, Qianhao Li, Neha Akkad, Sarah Lall, Benjamin Wadowski, Johana Gutierrez, Juan Andres Kochen Rossi, Jeremy W Herzog, Brian Diskin, Alejandro Torres-Hernandez, Josh Leinwand, Wei Wang, Pardeep S Taunk, Shivraj Savadkar, Malvin Janal, Anjana Saxena, Xin Li, Deirdre Cohen, R Balfour Sartor, Deepak Saxena, George Miller
We found that the cancerous pancreas harbors a markedly more abundant microbiome compared with normal pancreas in both mice and humans, and select bacteria are differentially increased in the tumorous pancreas compared with gut. Ablation of the microbiome protects against preinvasive and invasive pancreatic ductal adenocarcinoma (PDA), whereas transfer of bacteria from PDA-bearing hosts, but not controls, reverses tumor protection. Bacterial ablation was associated with immunogenic reprogramming of the PDA tumor microenvironment, including a reduction in myeloid-derived suppressor cells and an increase in M1 macrophage differentiation, promoting TH1 differentiation of CD4+ T cells and CD8+ T-cell activation...
April 2018: Cancer Discovery
https://www.readbyqxmd.com/read/29556109/dynamic-root-exudate-chemistry-and-microbial-substrate-preferences-drive-patterns-in-rhizosphere-microbial-community-assembly
#8
Kateryna Zhalnina, Katherine B Louie, Zhao Hao, Nasim Mansoori, Ulisses Nunes da Rocha, Shengjing Shi, Heejung Cho, Ulas Karaoz, Dominique Loqué, Benjamin P Bowen, Mary K Firestone, Trent R Northen, Eoin L Brodie
Like all higher organisms, plants have evolved in the context of a microbial world, shaping both their evolution and their contemporary ecology. Interactions between plant roots and soil microorganisms are critical for plant fitness in natural environments. Given this co-evolution and the pivotal importance of plant-microbial interactions, it has been hypothesized, and a growing body of literature suggests, that plants may regulate the composition of their rhizosphere to promote the growth of microorganisms that improve plant fitness in a given ecosystem...
April 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29507905/pyrroloquinoline-quinone-prevents-developmental-programming-of-microbial-dysbiosis-and-macrophage-polarization-to-attenuate-liver-fibrosis-in-offspring-of-obese-mice
#9
Jacob E Friedman, Evgenia Dobrinskikh, Alba Alfonso-Garcia, Alexander Fast, Rachel C Janssen, Taylor K Soderborg, Aimee L Anderson, Julie A Reisz, Angelo D'Alessandro, Daniel N Frank, Charles E Robertson, Becky A de la Houssaye, Linda K Johnson, David J Orlicky, Xiaoxin X Wang, Moshe Levi, Eric O Potma, Karim C El Kasmi, Karen R Jonscher
Increasingly, evidence suggests that exposure to maternal obesity creates an inflammatory environment in utero , exerting long-lasting postnatal signatures on the juvenile innate immune system and microbiome that may predispose offspring to development of fatty liver disease. We found that exposure to a maternal Western-style diet (WD) accelerated fibrogenesis in the liver of offspring and was associated with early recruitment of proinflammatory macrophages at 8-12 weeks and microbial dysbiosis as early as 3 weeks of age...
March 2018: Hepatology Communications
https://www.readbyqxmd.com/read/29499056/nubbin-isoform-antagonism-governs-drosophila-intestinal-immune-homeostasis
#10
Bo G Lindberg, Xiongzhuo Tang, Widad Dantoft, Priya Gohel, Shiva Seyedoleslami Esfahani, Jessica M Lindvall, Ylva Engström
Gut immunity is regulated by intricate and dynamic mechanisms to ensure homeostasis despite a constantly changing microbial environment. Several regulatory factors have been described to participate in feedback responses to prevent aberrant immune activity. Little is, however, known about how transcriptional programs are directly tuned to efficiently adapt host gut tissues to the current microbiome. Here we show that the POU/Oct gene nubbin (nub) encodes two transcription factor isoforms, Nub-PB and Nub-PD, which antagonistically regulate immune gene expression in Drosophila...
March 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29497108/human-milk-oligosaccharides-protect-against-the-development-of-autoimmune-diabetes-in-nod-mice
#11
Ling Xiao, Belinda Van't Land, Phillip A Engen, Ankur Naqib, Stefan J Green, Angie Nato, Thea Leusink-Muis, Johan Garssen, Ali Keshavarzian, Bernd Stahl, Gert Folkerts
Development of Type 1 diabetes (T1D) is influenced by non-genetic factors, such as optimal microbiome development during early life that "programs" the immune system. Exclusive and prolonged breastfeeding is an independent protective factor against the development of T1D, likely via bioactive components. Human Milk Oligosaccharides (HMOS) are microbiota modulators, known to regulate immune responses directly. Here we show that early life provision (only for a period of six weeks) of 1% authentic HMOS (consisting of both long-chain, as well as short-chain structures), delayed and suppressed T1D development in non-obese diabetic mice and reduced development of severe pancreatic insulitis in later life...
March 1, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29460474/specific-synbiotics-in-early-life-protect-against-diet-induced-obesity-in-adult-mice
#12
Mona Mischke, Tulika Arora, Sebastian Tims, Eefje Engels, Nina Sommer, Kees van Limpt, Annemarie Baars, Raish Oozeer, Annemarie Oosting, Fredrik Bäckhed, Jan Knol
AIMS: The metabolic state of human adults is associated with their gut microbiome. The symbiosis between host and microbiome is initiated at birth, and early life microbiome perturbation can disturb health throughout life. Here, we determined how beneficial microbiome interventions in early life affect metabolic health in adulthood. METHODS: Postnatal diets were supplemented with either prebiotics (scGOS/lcFOS) or synbiotics (scGOS/lcFOS with Bifidobacterium breve M-16 V) until post-natal (PN) day 42 in a well-established rodent model for nutritional programming...
February 20, 2018: Diabetes, Obesity & Metabolism
https://www.readbyqxmd.com/read/29414011/simultaneous-determination-of-trimethylamine-n-oxide-choline-betaine-by-uplc-ms-ms-in-human-plasma-an-application-in-acute-stroke-patients
#13
Weibang Yu, Chuncao Xu, Guomin Li, Weipeng Hong, Ziyi Zhou, Canxing Xiao, Yuanqi Zhao, Yefeng Cai, Min Huang, Jing Jin
Trimethylamine-N-oxide (TMAO) is derived from the gut microbiome and tissues metabolism of dietary choline and betaine. These molecules are closely related to the development of cardiovascular and cerebrovascular diseases. A rapid, sensitive and accurate method has been developed and validated for the simultaneous determination of trimethylamine N-oxide (TMAO), choline and betaine in human plasma using d9-trimethylamine N-oxide (TMAO), d9-choline, d9-betaine as the internal standard (IS). After methanol precipitation with 10 μL plasma samples, the analytes were extracted and then separated on Amide column (2...
April 15, 2018: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/29403516/metagenomic-and-metatranscriptomic-analyses-of-diverse-watermelon-cultivars-reveal-the-role-of-fruit-associated-microbiome-in-carbohydrate-metabolism-and-ripening-of-mature-fruits
#14
Thangasamy Saminathan, Marleny García, Bandana Ghimire, Carlos Lopez, Abiodun Bodunrin, Padma Nimmakayala, Venkata L Abburi, Amnon Levi, Nagamani Balagurusamy, Umesh K Reddy
The plant microbiome is a key determinant of plant health and productivity, and changes in the plant microbiome can alter the tolerance to biotic and abiotic stresses and the quality of end produce. Little is known about the microbial diversity and its effect on carbohydrate metabolism in ripe fruits. In this study, we aimed to understand the diversity and function of microorganisms in relation to carbohydrate metabolism of ripe watermelon fruits. We used 16S metagenomics and RNAseq metatranscriptomics for analysis of red (PI459074, Congo, and SDRose) and yellow fruit-flesh cultivars (PI227202, PI435990, and JBush) of geographically and metabolically diverse watermelon cultivars...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29388309/the-influence-of-genetics-defensive-chemistry-and-the-fungal-microbiome-on-disease-outcome-in-whitebark-pine-trees
#15
Lorinda S Bullington, Ylva Lekberg, Richard Sniezko, Beau Larkin
The invasive fungal pathogen Cronartium ribicola infects and kills whitebark pine (Pinus albicaulis) throughout western North America. Whitebark pine has been proposed for listing under the Endangered Species Act in the USA, and the loss of this species is predicted to have severe impacts on ecosystem composition and function in high-elevation forests. Numerous fungal endophytes live inside whitebark pine tissues and may influence the severity of C. ribicola infection, either directly by inhibition of pathogen growth or indirectly by the induction of chemical defensive pathways in the tree...
February 1, 2018: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29378945/adaptation-of-commensal-proliferating-escherichia-coli-to-the-intestinal-tract-of-young-children-with-cystic-fibrosis
#16
Susana Matamouros, Hillary S Hayden, Kyle R Hager, Mitchell J Brittnacher, Kristina Lachance, Eli J Weiss, Christopher E Pope, Anne-Flore Imhaus, Colin P McNally, Elhanan Borenstein, Lucas R Hoffman, Samuel I Miller
The mature human gut microbiota is established during the first years of life, and altered intestinal microbiomes have been associated with several human health disorders. Escherichia coli usually represents less than 1% of the human intestinal microbiome, whereas in cystic fibrosis (CF), greater than 50% relative abundance is common and correlates with intestinal inflammation and fecal fat malabsorption. Despite the proliferation of E. coli and other Proteobacteria in conditions involving chronic gastrointestinal tract inflammation, little is known about adaptation of specific characteristics associated with microbiota clonal expansion...
February 13, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29365082/early-microbial-colonization-affects-dna-methylation-of-genes-related-to-intestinal-immunity-and-metabolism-in-preterm-pigs
#17
Xiaoyu Pan, Desheng Gong, Duc Ninh Nguyen, Xinxin Zhang, Qi Hu, Hanlin Lu, Merete Fredholm, Per T Sangild, Fei Gao
Epigenetic regulation may play an important role in mediating microbe-host interactions and adaptation of intestinal gene expression to bacterial colonization just after birth. This is particularly important after preterm birth because the immature intestine is hypersensitive to invading bacteria. We compared the intestinal DNA methylome and microbiome between conventional (CON) and antibiotics-treated (AB) preterm pigs, used as a model for preterm infants. Oral AB treatment reduced bacterial density (∼100-fold), diversity and fermentation, improved the resistance to necrotizing enterocolitis (NEC) and changed the genome-wide DNA methylation in the distal small intestine...
January 19, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29333363/creating-a-multi-center-rare-disease-consortium-the-consortium-of-eosinophilic-gastrointestinal-disease-researchers-cegir
#18
Katherine Cheng, Sandeep K Gupta, Susanna Kantor, Jonathan T Kuhl, Seema S Aceves, Peter A Bonis, Kelley E Capocelli, Christina Carpenter, Mirna Chehade, Margaret H Collins, Evan S Dellon, Gary W Falk, Rashmi Gopal-Srivastava, Nirmala Gonsalves, Ikuo Hirano, Eileen C King, John Leung, Jeffrey P Krischer, Vincent A Mukkada, Alain Schoepfer, Jonathan M Spergel, Alex Straumann, Guang-Yu Yang, Glenn T Furuta, Marc E Rothenberg
 Eosinophilic gastrointestinal disorders (EGIDs) affect various segments of the gastrointestinal tract. Since these disorders are rare, collaboration is essential to enroll subjects in clinical studies and study the broader population. The Rare Diseases Clinical Research Network (RDCRN), a program of the National Center for Advancing Translational Sciences (NCATS), funded the Consortium of Eosinophilic Gastrointestinal Disease Researchers (CEGIR) in 2014 to advance the field of EGIDs. CEGIR facilitates collaboration among various centers, subspecialties, patients, professional organizations and patient-advocacy groups and includes 14 clinical sites...
December 18, 2017: Translational Science of Rare Diseases
https://www.readbyqxmd.com/read/29313208/perspective-on-immune-oncology-with-liquid-biopsy-peripheral-blood-mononuclear-cells-and-microbiome-with-non-invasive-biomarkers-in-cancer-patients
#19
REVIEW
A Mitsuhashi, Y Okuma
Antibodies against immune checkpoint inhibitors such as anti-programmed cell death protein 1 (PD-1) and anti-programmed death ligand 1 (PD-L1) play a key role in the treatment of advanced lung cancer. To examine the clinical benefits of these agents, preclinical and clinical studies have been conducted to identify definitive biomarkers associated with cancer status. Analysis of the blood and feces of tumor patients has attracted attention in recent studies attempting to identify non-invasive biomarkers such as cytokines, soluble PD-L1, peripheral blood mononuclear cells, and gut microbiota...
January 8, 2018: Clinical & Translational Oncology
https://www.readbyqxmd.com/read/29259388/genital-tract-infections-in-an-isolated-community-100-women-of-the-pr%C3%A3-ncipe-island
#20
Pedro Vieira-Baptista, Svitrigaile Grinceviciene, Gert Bellen, Carlos Sousa, Conceição Saldanha, Davy Vanden Broeck, John-Paul Bogers, Gilbert Donders
Objective: To characterize the vaginal microbiome and the rate of sexually transmitted infections (STIs) in the women of Príncipe (São Tomé and Príncipe). Methods: Cross-sectional study of 100 consecutive women, invited for a free appointment and cervical cancer screening. A vaginal slide (wet mount microscopy) and a cervical sample (ThinPrep®) (Pap test, high risk human papillomavirus [HR-HPV], N . gonorrhea [NG], T . vaginalis [TV], and C . trachomatis [CT]) were obtained...
2017: Infectious Diseases in Obstetrics and Gynecology
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