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Microbiome programming

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...
March 19, 2018: Nature Microbiology
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
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 2, 2018: PLoS Pathogens
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
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 long-lastingly. 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-16V) until post-natal (PN) day 42 in a well-established rodent model for nutritional programming...
February 20, 2018: Diabetes, Obesity & Metabolism
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...
February 2, 2018: Journal of Pharmaceutical and Biomedical Analysis
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
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 U.S., 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 they may influence the severity of C. ribicola infection either directly by inhibiting pathogen growth or indirectly by inducing chemical defensive pathways in the tree...
February 1, 2018: Molecular Plant Pathology
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...
January 29, 2018: Proceedings of the National Academy of Sciences of the United States of America
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
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
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
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
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
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
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...
March 2018: Current Eye Research
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
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
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
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...
January 2018: American Journal of Reproductive Immunology: AJRI
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