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Microbiome programming

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https://www.readbyqxmd.com/read/29333363/creating-a-multi-center-rare-disease-consortium-the-consortium-of-eosinophilic-gastrointestinal-disease-researchers-cegir
#1
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
#2
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
#3
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
https://www.readbyqxmd.com/read/29221568/nutritional-programming-by-glucocorticoids-in-breast-milk-targets-mechanisms-and-possible-implications
#4
REVIEW
Jonneke J Hollanders, Annemieke C Heijboer, Bibian van der Voorn, Joost Rotteveel, Martijn J J Finken
Vertical transmission of glucocorticoids via breast milk might pose a mechanism through which lactating women could prepare their infants for the postnatal environment. The primary source of breast-milk glucocorticoids is probably the systemic circulation. Research from our group showed that milk cortisol and cortisone concentrations follow the diurnal rhythm of maternal hypothalamus-pituitary-adrenal axis activity, with a higher abundance of cortisone compared to cortisol. Measurement of breast-milk glucocorticoid concentrations is challenging due to possible cross-reactivity with progestagens and sex steroids, which are severely elevated during pregnancy and after parturition...
August 2017: Best Practice & Research. Clinical Endocrinology & Metabolism
https://www.readbyqxmd.com/read/29212440/constax-a-tool-for-improved-taxonomic-resolution-of-environmental-fungal-its-sequences
#5
Kristi Gdanetz, Gian Maria Niccolò Benucci, Natalie Vande Pol, Gregory Bonito
BACKGROUND: One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, functional and biological information of microbial communities cannot be inferred or interpreted. The internal transcribed spacer (ITS) region of the ribosomal DNA is the conventional marker region for fungal community studies. While bioinformatics pipelines that cluster reads into OTUs have received much attention in the literature, less attention has been given to the taxonomic classification of these sequences, upon which biological inference is dependent...
December 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29172724/distribution-and-diversity-of-ocular-microbial-communities-in-diabetic-patients-compared-with-healthy-subjects
#6
Baknoon Ham, Hyung Bin Hwang, Sang Hoon Jung, Sungyul Chang, Kui Dong Kang, Man Jae Kwon
PURPOSE: The aim of this study was to identify differences in the major (core vs. variable) microbial genera of human subjects with and without diabetes. METHODS: Bacterial 16S rRNA genes obtained from conjunctival swabs of 19 healthy subjects and 30 diabetic patients were sequenced using the Illumina MiSeq platform, and the sequencing data were analyzed using QIIME 1.9.1. To elucidate the microbial diversity in the ocular surface (OS), test programs from various bioinformatics domains were used...
November 27, 2017: Current Eye Research
https://www.readbyqxmd.com/read/29152318/gut-microbiota-composition-may-relate-to-weight-loss-rate-in-obese-pet-dogs
#7
Ida N Kieler, Shamrulazhar Shamzir Kamal, Anne D Vitger, Dennis S Nielsen, Charlotte Lauridsen, Charlotte R Bjornvad
Obese dogs seem to have a different gut microbiome (GM) composition compared to lean dogs, and in humans, GM composition may negatively impact the ability to lose weight in some individuals. The purpose of this study was to investigate the interaction between exercise, weight-loss and the composition of GM in dogs. Eighteen obese pet dogs were recruited for a 12-week weight-loss intervention. All dogs were fed restrictively with a commercial high-protein/high-fibre dry diet, and eight of these dogs were enrolled in an exercise program in addition to the diet intervention...
November 2017: Veterinary Medicine and Science
https://www.readbyqxmd.com/read/29106820/development-and-function-of-the-mucosal-immune-system-in-the-upper-respiratory-tract-of-neonatal-calves
#8
Rahwa Osman, Nilusha Malmuthuge, Patricia Gonzalez-Cano, Philip Griebel
Respiratory infections remain the second most common cause of clinical disease and mortality in newborn calves, which has led to increased interest in using vaccines early in life to mitigate this risk. Intranasal vaccination of neonatal calves can be an effective strategy to circumvent vaccine interference by maternal antibody, but this raises questions regarding onset of immune competence in the upper respiratory tract (URT) following birth. Little is known, however, about the development and function of mucosa-associated lymphoid tissue (MALT) in the URT of newborn calves and what factors, including the commensal microbiome, contribute to this early development...
November 6, 2017: Annual Review of Animal Biosciences
https://www.readbyqxmd.com/read/29104426/popmarker-identifying-phylogenetic-markers-at-the-population-level
#9
REVIEW
Huei-Mien Ke, Chun-Ping Yu, Yu-Ching Liu, Isheng J Tsai
As phylogenomic approach becomes a common practice for constructing true bacterial phylogenies, it has become apparent that single molecular markers such as 16S ribosomal DNA often lead to misclassification of species. In this study, we present a program called Popmarker that uses the true species phylogeny and identifies a minimum set of molecular markers reflecting the bacterial evolution history and phylogenetic relationship at the resolution of populations. Popmarker ranks the proteome according to the correlation of whole species tree or subtree branch length against orthologous sequence distances...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29083070/breastfeeding-and-autoimmunity-programing-health-from-the-beginning
#10
REVIEW
Vânia Vieira Borba, Kassem Sharif, Yehuda Shoenfeld
Breast milk is not only a completely adapted nutrition source for the newborn but also an impressive array of immune-active molecules that afford protection against infections and shape mucosal immune responses. Decisive imprinting events might be modulated during the first months of life with potential health long-term effects, enhancing the importance of breastfeeding as a major influence on the immune system correct development and modifying disease susceptibility. The aim of this review was to clarify the link between breastfeeding and autoimmune diseases, inquiring the related mechanisms, based on data available in the literature...
October 30, 2017: American Journal of Reproductive Immunology: AJRI
https://www.readbyqxmd.com/read/29033938/early-life-nutritional-factors-and-mucosal-immunity-in-the-development-of-autoimmune-diabetes
#11
REVIEW
Ling Xiao, Belinda Van't Land, Wouter R P H van de Worp, Bernd Stahl, Gert Folkerts, Johan Garssen
Type 1 diabetes (T1D) is an immune-mediated disease with a strong genetic basis but might be influenced by non-genetic factors such as microbiome development that "programs" the immune system during early life as well. Factors influencing pathogenesis, including a leaky intestinal mucosal barrier, an aberrant gut microbiota composition, and altered immune responsiveness, offer potential targets for prevention and/or treatment of T1D through nutritional or pharmacologic means. In this review, nutritional approaches during early life in order to protect against T1D development have been discussed...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28980268/processing-and-analyzing-human-microbiome-data
#12
Xuan Zhu, Jian Wang, Cielito Reyes-Gibby, Sanjay Shete
The human microbiome is associated with complex disorders such as diabetes, cancer, obesity and cardiovascular disorders. Recent technological developments have allowed researchers to fully quantify the composition of the microbiome using culture-independent approaches, resulting in a large amount of microbiome data, which provide invaluable opportunities to assess the important contributions of the microbiome to human health and disease. In this chapter, we discuss and evaluate multiple statistical approaches for processing, summarizing, and analyzing microbiome data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28920414/metagenomic-analysis-of-bacterial-community-structure-and-diversity-of-lignocellulolytic-bacteria-in-vietnamese-native-goat-rumen
#13
Huyen Thi Do, Khoa Trong Dao, Viet Khanh Hoang Nguyen, Giang Ngoc Le, Phuong Thi Mai Nguyen, Lam Tung Le, Nguyet Thu Phung, Nico van Straalen, Dick Roelofs, Hai Nam Truong
Objective: In a previous study, analysis of Illumina sequenced metagenomic DNA data of bacteria in Vietnamese goats' rumen showed a high diversity of putative lignocellulolytic genes. In this study, taxonomy speculation of microbial community and lignocellulolytic bacteria population in the rumen was conducted to elucidate a role of bacterial structure for effective degradation of plant materials. Methods: The metagenomic data had been subjected into Basic Local Alignment Search Tool (BLASTX) algorithm and the National Center for Biotechnology Information (NCBI) non-redundant (NR) sequence database...
September 18, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28901864/prenatal-stress-enhances-susceptibility-to-allergic-diseases-of-offspring
#14
Maria Moustaki, Sophia Tsabouri, Kostas Priftis, Konstantinos Douros
BACKGROUND AND OBJECTIVES: Maternal prenatal stress (MPS) may result in a range of long-term consequences in the offspring among which is susceptibility to allergic diseases. This review presents the current knowledge on the pathways through which MPS may affect the fetus, and the existing evidence regarding the association between MPS and development of allergy in the offspring. RESULT AND DISCUSSION: A pivotal mediator triggered in response to stress is the release of glucocorticoids (GC)...
September 12, 2017: Endocrine, Metabolic & Immune Disorders Drug Targets
https://www.readbyqxmd.com/read/28894921/structural-and-functional-variability-in-root-associated-bacterial-microbiomes-of-cd-zn-hyperaccumulator-sedum-alfredii
#15
Jipeng Luo, Qi Tao, Keren Wu, Jinxing Li, Jie Qian, Yongchao Liang, Xiaoe Yang, Tingqiang Li
Interactions between roots and microbes affect plant's resistance to abiotic stress. However, the structural and functional variation of root-associated microbiomes and their effects on metal accumulation in hyperaccumulators remain poorly understood. Here, we characterize the root-associated microbiota of a hyperaccumulating (HP) and a non-hyperaccumulating (NHP) genotype of Sedum alfredii by 16S ribosomal RNA gene profiling. We show that distinct microbiomes are observed in four spatially separable compartments: the bulk soil, rhizosphere, rhizoplane, and endosphere...
November 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28889823/epigenetics-and-dohad-from-basics-to-birth-and-beyond
#16
T Bianco-Miotto, J M Craig, Y P Gasser, S J van Dijk, S E Ozanne
Developmental origins of health and disease (DOHaD) is the study of how the early life environment can impact the risk of chronic diseases from childhood to adulthood and the mechanisms involved. Epigenetic modifications such as DNA methylation, histone modifications and non-coding RNAs are involved in mediating how early life environment impacts later health. This review is a summary of the Epigenetics and DOHaD workshop held at the 2016 DOHaD Society of Australia and New Zealand Conference. Our extensive knowledge of how the early life environment impacts later risk for chronic disease would not have been possible without animal models...
September 11, 2017: Journal of Developmental Origins of Health and Disease
https://www.readbyqxmd.com/read/28879172/epigenetic-matters-the-link-between-early-nutrition-microbiome-and-long-term-health-development
#17
REVIEW
Flavia Indrio, Silvia Martini, Ruggiero Francavilla, Luigi Corvaglia, Fernanda Cristofori, Salvatore Andrea Mastrolia, Josef Neu, Samuli Rautava, Giovanna Russo Spena, Francesco Raimondi, Giuseppe Loverro
Epigenetic modifications are among the most important mechanisms by which environmental factors can influence early cellular differentiation and create new phenotypic traits during pregnancy and within the neonatal period without altering the deoxyribonucleic acid sequence. A number of antenatal and postnatal factors, such as maternal and neonatal nutrition, pollutant exposure, and the composition of microbiota, contribute to the establishment of epigenetic changes that can not only modulate the individual adaptation to the environment but also have an influence on lifelong health and disease by modifying inflammatory molecular pathways and the immune response...
2017: Frontiers in Pediatrics
https://www.readbyqxmd.com/read/28875499/the-intestinal-microbiota-determines-the-colitis-inducing-potential-of-t-bet-deficient-th-cells-in-mice
#18
Jakob Zimmermann, Pawel Durek, Anja A Kühl, Florian Schattenberg, Patrick Maschmeyer, Francesco Siracusa, Katrin Lehmann, Kerstin Westendorf, Melanie Weber, René Riedel, Susann Müller, Andreas Radbruch, Hyun-Dong Chang
Conflicting evidence has been provided as to whether induction of intestinal inflammation by adoptive transfer of naïve T cells into Rag(-/-) mice requires expression of the transcription factor T-bet by the T cells. Here, we formally show that the intestinal microbiota composition of the Rag(-/-) recipient determines whether or not T-bet-deficient Th cells can induce colitis and we have resolved the differences of the two microbiomes, permissive or non-permissive to T-bet-independent colitis. Our data highlight the dominance of the microbiota over particular T cell differentiation programs in the pathogenesis of chronic intestinal inflammation...
September 6, 2017: European Journal of Immunology
https://www.readbyqxmd.com/read/28855974/the-skin-microbiome-impact-of-modern-environments-on-skin-ecology-barrier-integrity-and-systemic-immune-programming
#19
REVIEW
Susan L Prescott, Danica-Lea Larcombe, Alan C Logan, Christina West, Wesley Burks, Luis Caraballo, Michael Levin, Eddie Van Etten, Pierre Horwitz, Anita Kozyrskyj, Dianne E Campbell
Skin barrier structure and function is essential to human health. Hitherto unrecognized functions of epidermal keratinocytes show that the skin plays an important role in adapting whole-body physiology to changing environments, including the capacity to produce a wide variety of hormones, neurotransmitters and cytokine that can potentially influence whole-body states, and quite possibly, even emotions. Skin microbiota play an integral role in the maturation and homeostatic regulation of keratinocytes and host immune networks with systemic implications...
2017: World Allergy Organization Journal
https://www.readbyqxmd.com/read/28822770/regulation-of-autoimmune-myocarditis-by-host-responses-to-the-microbiome
#20
Jobert G Barin, Monica V Talor, Nicola L Diny, SuFey Ong, Julie A Schaub, Elizabeth Gebremariam, Djahida Bedja, Guobao Chen, Hee Sun Choi, Xuezhou Hou, Lei Wu, Ashley B Cardamone, Daniel A Peterson, Noel R Rose, Daniela Čiháková
The extensive, diverse communities that constitute the microbiome are increasingly appreciated as important regulators of human health and disease through inflammatory, immune, and metabolic pathways. We sought to elucidate pathways by which microbiota contribute to inflammatory, autoimmune cardiac disease. We employed an animal model of experimental autoimmune myocarditis (EAM), which results in inflammatory and autoimmune pathophysiology and subsequent maladaptive cardiac remodeling and heart failure. Antibiotic dysbiosis protected mice from EAM and fibrotic cardiac dysfunction...
October 2017: Experimental and Molecular Pathology
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