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https://www.readbyqxmd.com/read/28184370/metaproteomics-as-a-complementary-approach-to-gut-microbiota-in-health-and-disease
#1
REVIEW
Bernardo A Petriz, Octávio L Franco
Classic studies on phylotype profiling are limited to the identification of microbial constituents, where information is lacking about the molecular interaction of these bacterial communities with the host genome and the possible outcomes in host biology. A range of OMICs approaches have provided great progress linking the microbiota to health and disease. However, the investigation of this context through proteomic mass spectrometry-based tools is still being improved. Therefore, metaproteomics or community proteogenomics has emerged as a complementary approach to metagenomic data, as a field in proteomics aiming to perform large-scale characterization of proteins from environmental microbiota, such as the human gut...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28178051/urinary-microbiome-and-cytokine-levels-in-women-with-interstitial-cystitis
#2
Melinda G Abernethy, Amy Rosenfeld, James R White, Margaret G Mueller, Christina Lewicky-Gaupp, Kimberly Kenton
OBJECTIVE: To investigate differences in the urinary microbiome and cytokine levels between women with and without interstitial cystitis and to correlate differences with scores on standardized symptom severity scales and depression and anxiety screening tools. METHODS: Our cross-sectional study compared women presenting to a pelvic floor clinic and diagnosed with interstitial cystitis over a 6-month period with age-matched women in a control group from the same institution...
February 6, 2017: Obstetrics and Gynecology
https://www.readbyqxmd.com/read/28174962/dop053-the-fecal-microbiome-as-a-tool-for-monitoring-and-predicting-response-outcomes-in-ustekinumab-treated-anti-tnf%C3%AE-refractory-crohn-s-disease-patients-results-from-the-certifi-study
#3
M K Doherty, C Koumpouras, S E Telesco, C Monast, C Brodmerkel, P D Schloss
No abstract text is available yet for this article.
February 1, 2017: Journal of Crohn's & Colitis
https://www.readbyqxmd.com/read/28174737/metagenomic-characterization-of-microbial-communities-in-situ-within-the-deeper-layers-of-the-ileum-in-crohn-s-disease
#4
Chandra Sekhar Pedamallu, Ami S Bhatt, Susan Bullman, Sharyle Fowler, Samuel S Freeman, Jacqueline Durand, Joonil Jung, Fujiko Duke, Veronica Manzo, Diana Cai, Ashwin Ananthakrishnan, Akinyemi I Ojesina, Aruna Ramachandran, Dirk Gevers, Ramnik J Xavier, Atul K Bhan, Matthew Meyerson, Vijay Yajnik
BACKGROUND & AIMS: Microbial dysbiosis and aberrant host-microbe interactions in the gut are believed to contribute to the development and progression of Crohn's disease (CD). Microbiome studies in CD typically have focused on microbiota in feces or superficial mucosal layers of the colon because accessing DNA from deeper layers of the bowel is challenging. In this study, we analyzed the deep tissue microbiome in patients who underwent surgical resection of the small intestine. METHODS: Paraffin blocks were obtained from 12 CD patients undergoing ileocecal resection, and healthy ileum samples (inflammatory bowel disease-free controls) were obtained from 12 patients undergoing surgery for right-sided colon cancer...
September 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28167213/metagenomics-approach-to-the-study-of-the-gut-microbiome-structure-and-function-in-zebrafish-danio-rerio-fed-with-gluten-formulated-diet
#5
Hyunmin Koo, Joseph A Hakim, Mickie L Powell, Ranjit Kumar, Peter G Eipers, Casey D Morrow, Michael Crowley, Elliot J Lefkowitz, Stephen A Watts, Asim K Bej
In this study, we report the gut microbial composition and predictive functional profiles of zebrafish, Danio rerio, fed with a control formulated diet (CFD), and a gluten formulated diet (GFD) using metagenomics approach and bioinformatics tools. The microbial communities of the GFD-fed D. rerio displayed heightened abundances of Legionellales, Rhizobiaceae, and Rhodobacter, as compared to the CFD-fed counterparts. Predicted metagenomics of microbial communities (PICRUSt) in GFD-fed D. rerio showed KEGG functional categories corresponding to bile secretion, secondary bile acid biosynthesis, and the metabolism of glycine, serine, and threonine...
February 3, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28164855/from-culture-to-high-throughput-sequencing-and-beyond-a-layperson-s-guide-to-the-omics-and-diagnostic-potential-of-the-microbiome
#6
REVIEW
Paul W O'Toole, Burkhardt Flemer
Detailed knowledge of the community of organisms in the gut has become possible in recent years because of the development of culture-independent methods. Largely based on latest DNA sequencing platforms, it is now possible to establish the composition of the microbiota and the repertoire of biochemical functions it encodes. Variations in either or both of these parameters have been linked to intestinal and extraintestinal disease. This article summarizes how these methods are applied, with special reference to gastroenterology, and describes the achievements and future potential of microbiota analysis as a diagnostic tool...
March 2017: Gastroenterology Clinics of North America
https://www.readbyqxmd.com/read/28144631/studying-vertical-microbiome-transmission-from-mothers-to-infants-by-strain-level-metagenomic-profiling
#7
Francesco Asnicar, Serena Manara, Moreno Zolfo, Duy Tin Truong, Matthias Scholz, Federica Armanini, Pamela Ferretti, Valentina Gorfer, Anna Pedrotti, Adrian Tett, Nicola Segata
The gut microbiome becomes shaped in the first days of life and continues to increase its diversity during the first months. Links between the configuration of the infant gut microbiome and infant health are being shown, but a comprehensive strain-level assessment of microbes vertically transmitted from mother to infant is still missing. We collected fecal and breast milk samples from multiple mother-infant pairs during the first year of life and applied shotgun metagenomic sequencing followed by computational strain-level profiling...
January 2017: MSystems
https://www.readbyqxmd.com/read/28134778/toward-a-personalized-approach-in-prebiotics-research
#8
Moul Dey
Recent characterization of the human microbiome and its influences on health have led to dramatic conceptual shifts in dietary bioactives research. Prebiotic foods that include many dietary fibers and resistant starches are perceived as beneficial for maintaining a healthy gut microbiota. This article brings forward some current perspectives in prebiotic research to discuss why reporting of individual variations in response to interventions will be important to discern suitability of prebiotics as a disease prevention tool...
January 26, 2017: Nutrients
https://www.readbyqxmd.com/read/28134072/lessons-on-dietary-biomarkers-from-twin-studies
#9
Cristina Menni
Metabolomic and microbiome profiling are promising tools to identify biomarkers of food intake and health status. The individual's genetic makeup plays a significant role on health, metabolism, gut microbes and diet and twin studies provide unique opportunities to untangle gene-environment effects on complex phenotypes. This brief review discusses the value of twin studies in nutrition research with a particular focus on metabolomics and the gut microbiome. Although, the twin model is a powerful tool to segregate the genetic component, to date, very few studies combine the twin design and metabolomics/microbiome in nutritional sciences...
January 30, 2017: Proceedings of the Nutrition Society
https://www.readbyqxmd.com/read/28131442/the-human-gut-microbiome-as-source-of-innovation-for-health-which-physiological-and-therapeutic-outcomes-could-we-expect
#10
Joël Doré, Marie-Christine Multon, Jehan-Michel Béhier
From the moment of birth, each human being builds a microbe-host symbiosis which is key for the preservation of its health and well-being. This personal symbiotic coexistence is the result of progressive enrichments in microorganism diversity through external supplies. This diversity is nowadays massively overthrown by drastic changes related to clinical practice in birth management, environmental exposure, nutrition and healthcare behaviors. The last two generations have been the frame of massive modifications in life and food habits, with people being more and more sedentary, overfed and permeated with drugs and pollutants...
January 3, 2017: Thérapie
https://www.readbyqxmd.com/read/28125793/the-state-of-systems-genetics-in-2017
#11
Nitin S Baliga, Johan L M Björkegren, Jef D Boeke, Michael Boutros, Nigel P S Crawford, Aimée M Dudley, Charles R Farber, Allan Jones, Allan I Levey, Aldons J Lusis, H Craig Mak, Joseph H Nadeau, Marcus B Noyes, Enrico Petretto, Nicholas T Seyfried, Lars M Steinmetz, Sibylle C Vonesch
Cell Systems invited 16 experts to share their views on the field of systems genetics. In questions repeated in the headings, we asked them to define systems genetics, highlight its relevance to researchers outside the field, discuss what makes a strong systems genetics paper, and paint a picture of where the field is heading in the coming years. Their responses, ordered by the journal but otherwise unedited, make it clear that deciphering genotype to phenotype relationships is a central challenge of systems genetics and will require understanding how networks and higher-order properties of biological systems underlie complex traits...
January 25, 2017: Cell Systems
https://www.readbyqxmd.com/read/28125039/microbial-contribution-to-wine-aroma-and-its-intended-use-for-wine-quality-improvement
#12
REVIEW
Ignacio Belda, Javier Ruiz, Adelaida Esteban-Fernández, Eva Navascués, Domingo Marquina, Antonio Santos, M Victoria Moreno-Arribas
Wine is a complex matrix that includes components with different chemical natures, the volatile compounds being responsible for wine aroma quality. The microbial ecosystem of grapes and wine, including Saccharomyces and non-Saccharomyces yeasts, as well as lactic acid bacteria, is considered by winemakers and oenologists as a decisive factor influencing wine aroma and consumer's preferences. The challenges and opportunities emanating from the contribution of wine microbiome to the production of high quality wines are astounding...
January 24, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28122610/fast-and-simple-protein-alignment-guided-assembly-of-orthologous-gene-families-from-microbiome-sequencing-reads
#13
Daniel H Huson, Rewati Tappu, Adam L Bazinet, Chao Xie, Michael P Cummings, Kay Nieselt, Rohan Williams
BACKGROUND: Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem. However, for some questions, only specific genes of interest need to be assembled. This is then a gene-centric assembly where the goal is to assemble reads into contigs for a family of orthologous genes...
January 25, 2017: Microbiome
https://www.readbyqxmd.com/read/28114473/historical-perspective-on-the-rise-and-fall-and-rise-of-antibiotics-and-human-weight-gain
#14
Scott H Podolsky
In recent medical and popular literature, audiences have been asked to consider whether antibiotics have contributed to the rising obesity epidemic. Prominent magazines have stated that weight may be adversely affected by antibiotics that destroy existing microbiomes and replace them with less helpful ones. However, there is a long history of efforts to investigate the relationship between antibiotics and human weight gain. In the early 1950s, amid initial findings that low doses of antibiotics served as growth promoters in animal livestock, investigators explored the role of antibiotics as magic bullets for human malnutrition...
January 17, 2017: Annals of Internal Medicine
https://www.readbyqxmd.com/read/28114391/quantitative-comparison-of-abundance-structures-of-generalized-communities-from-b-cell-receptor-repertoires-to-microbiomes
#15
Mohammadkarim Saeedghalati, Farnoush Farahpour, Bettina Budeus, Anja Lange, Astrid M Westendorf, Marc Seifert, Ralf Küppers, Daniel Hoffmann
The community, the assemblage of organisms co-existing in a given space and time, has the potential to become one of the unifying concepts of biology, especially with the advent of high-throughput sequencing experiments that reveal genetic diversity exhaustively. In this spirit we show that a tool from community ecology, the Rank Abundance Distribution (RAD), can be turned by the new MaxRank normalization method into a generic, expressive descriptor for quantitative comparison of communities in many areas of biology...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28103917/a-fast-and-robust-protocol-for-metataxonomic-analysis-using-rnaseq-data
#16
Jeremy W Cox, Richard A Ballweg, Diana H Taft, Prakash Velayutham, David B Haslam, Aleksey Porollo
BACKGROUND: Metagenomics is a rapidly emerging field aimed to analyze microbial diversity and dynamics by studying the genomic content of the microbiota. Metataxonomics tools analyze high-throughput sequencing data, primarily from 16S rRNA gene sequencing and DNAseq, to identify microorganisms and viruses within a complex mixture. With the growing demand for analysis of the functional microbiome, metatranscriptome studies attract more interest. To make metatranscriptomic data sufficient for metataxonomics, new analytical workflows are needed to deal with sparse and taxonomically less informative sequencing data...
January 19, 2017: Microbiome
https://www.readbyqxmd.com/read/28098358/subclinical-alteration-of-the-cervical-vaginal-microbiome-in-women-with-idiopathic-infertility
#17
Giuseppina Campisciano, Fiorella Florian, Angela D'Eustacchio, David Stanković, Giuseppe Ricci, Manola Comar
Biomarkers have a wide application in research and clinic, they help to choose the correct treatment for diseases. Recent studies, addressing the vaginal microbiome using next generation sequencing (NGS), reported the involvement of bacterial species in infertility. We compared the vaginal microbiome of idiopathic infertility diagnosed women with that of healthy, non-idiopathic infertile and bacterial vaginosis affected women, to identify bacterial species suitable as biomarkers. Information on microorganisms was obtained from the V3-16S rDNA sequencing of cervical-vaginal fluids of 96 women using the Ion Torrent platform...
January 18, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28095889/evolution-of-gut-microbiota-composition-from-birth-to-24-weeks-in-the-infantmet-cohort
#18
Cian J Hill, Denise B Lynch, Kiera Murphy, Marynka Ulaszewska, Ian B Jeffery, Carol Anne O'Shea, Claire Watkins, Eugene Dempsey, Fulvio Mattivi, Kieran Touhy, R Paul Ross, C Anthony Ryan, Paul W O' Toole, Catherine Stanton
BACKGROUND: The gut is the most extensively studied niche of the human microbiome. The aim of this study was to characterise the initial gut microbiota development of a cohort of breastfed infants (n = 192) from 1 to 24 weeks of age. METHODS: V4-V5 region 16S rRNA amplicon Illumina sequencing and, in parallel, bacteriological culture. The metabolomic profile of infant urine at 4 weeks of age was also examined by LC-MS. RESULTS: Full-term (FT), spontaneous vaginally delivered (SVD) infants' microbiota remained stable at both phylum and genus levels during the 24-week period examined...
January 17, 2017: Microbiome
https://www.readbyqxmd.com/read/28080023/microbial-nanoscopy-breakthroughs-challenges-and-opportunities
#19
Yves F Dufrêne
Studying the structure, properties, and interactions of microbial cells is key to understanding the functions of the microbiome. Recent advances in nanotechnology have offered new tools to probe microbes at the single-molecule and single-cell levels. In this issue of ACS Nano, Kumar et al. present an atomic force microscopy method that is capable of imaging the nanoscale organization of bacterial proteins in native, curved membranes. This study represents an important step forward in the development of nanoscopy techniques for analyzing biological systems with large curvature and vertical dimensions, such as membrane vesicles and bacterial cells...
January 12, 2017: ACS Nano
https://www.readbyqxmd.com/read/28077565/mahmi-database-a-comprehensive-metahit-based-resource-for-the-study-of-the-mechanism-of-action-of-the-human-microbiota
#20
Aitor Blanco-Míguez, Alberto Gutiérrez-Jácome, Florentino Fdez-Riverola, Anália Lourenço, Borja Sánchez
The Mechanism of Action of the Human Microbiome (MAHMI) database is a unique resource that provides comprehensive information about the sequence of potential immunomodulatory and antiproliferative peptides encrypted in the proteins produced by the human gut microbiota. Currently, MAHMI database contains over 300 hundred million peptide entries, with detailed information about peptide sequence, sources and potential bioactivity. The reference peptide data section is curated manually by domain experts. The in silico peptide data section is populated automatically through the systematic processing of publicly available exoproteomes of the human microbiome...
2017: Database: the Journal of Biological Databases and Curation
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