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https://www.readbyqxmd.com/read/29134939/the-nursing-home-elder-microbiome-stability-and-associations-with-age-frailty-nutrition-and-physical-location
#1
John P Haran, Vanni Bucci, Protiva Dutta, Doyle Ward, Beth McCormick
PURPOSE: The microbiome from nursing home (NH) residents is marked by a loss in diversity that is associated with increased frailty. Our objective was to explore the associations of NH environment, frailty, nutritional status and residents' age to microbiome composition and potential metabolic function. METHODOLOGY: We conducted a prospective longitudinal cohort study of 23 residents, 65 years or older, from one NH that had four floors: two separate medical intensive floors and two floors with active elders...
November 14, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/29128932/atomic-force-microscopy-a-promising-tool-for-deciphering-the-pathogenic-mechanisms-of-fungi-in-cystic-fibrosis
#2
Stéphane Cuenot, Jean-Philippe Bouchara
During the past decades, atomic force microscopy (AFM) has emerged as a powerful tool in microbiology. Although most of the works concerned bacteria, AFM also permitted major breakthroughs in the understanding of physiology and pathogenic mechanisms of some fungal species associated with cystic fibrosis. Complementary to electron microscopies, AFM offers unprecedented insights to visualize the cell wall architecture and components through three-dimensional imaging with nanometer resolution and to follow their dynamic changes during cell growth and division or following the exposure to drugs and chemicals...
November 11, 2017: Mycopathologia
https://www.readbyqxmd.com/read/29128052/the-intestinal-microbiome-in-nonalcoholic-fatty-liver-disease
#3
REVIEW
Puneet Puri, Arun J Sanyal
Nonalcoholic fatty liver disease is the most common cause of chronic liver disease in North America and is growing as a cause of chronic liver disease in many other parts of the world as well. It has 2 principal clinical-pathologic phenotypes: (1) nonalcoholic fatty liver and (2) nonalcoholic steatohepatitis. The development of both phenotypes is tightly linked to excess body weight and insulin resistance. This review discusses the emerging tools for the analysis of the microbiome, their limitations, and the existing literature with respect to the intestinal microbiome and their role in nonalcoholic fatty liver...
February 2018: Clinics in Liver Disease
https://www.readbyqxmd.com/read/29122749/frontline-defenders-goblet-cell-mediators-dictate-host-microbe-interactions-in-the-intestinal-tract-during-health-and-disease
#4
Joannie M Allaire, Vijay Morampudi, Shauna Mary Crowley, Martin Stahl, Hongbing Yu, Kirandeep Bhullar, Leigh A Knodler, Brian Bressler, Kevan Jacobson, Bruce A Vallance
Goblet cells (GC)s are the predominant secretory epithelial cells lining the luminal surface of the mammalian gastrointestinal (GI) tract. Best known for their apical release of the mucin Muc2, which is critical in the formation of the intestinal mucus barrier, GCs have often been overlooked for their active contributions to intestinal protection and host defense. In part, this oversight reflects the limited tools available to study their function, but also because GCs have long been viewed as relatively passive players in promoting intestinal homeostasis and host defense...
November 9, 2017: American Journal of Physiology. Gastrointestinal and Liver Physiology
https://www.readbyqxmd.com/read/29106455/virapipe-scalable-parallel-pipeline-for-viral-metagenome-analysis-from-next-generation-sequencing-reads
#5
Altti Ilari Maarala, Zurab Bzhalava, Joakim Dillner, Keijo Heljanko, Davit Bzhalava
Motivation: Next Generation Sequencing (NGS) technology enables identification of microbial genomes from massive amount of human microbiomes more rapidly and cheaper than ever before. However, the traditional sequential genome analysis algorithms, tools, and platforms are inefficient for performing large-scale metagenomic studies on ever-growing sample data volumes. Currently, there is an urgent need for scalable analysis pipelines that enable harnessing all the power of parallel computation in computing clusters and in cloud computing environments...
November 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29063093/nmr-window-of-molecular-complexity-showing-homeostasis-in-superorganisms
#6
REVIEW
Jun Kikuchi, Shunji Yamada
NMR offers tremendous advantages in the analyses of molecular complexity, such as crude bio-fluids, bio-extracts, and intact cells and tissues. Here we introduce recent applications of NMR approaches, as well as next generation sequencing (NGS), for the evaluation of human and environmental health (i.e., maintenance of a homeostatic state) based on metabolic and microbial profiling and data science. We describe useful databases and web tools that are used to support these studies by facilitating the characterization of metabolites from complex NMR spectra...
October 24, 2017: Analyst
https://www.readbyqxmd.com/read/29056429/three-dimensional-microbiome-and-metabolome-cartography-of-a-diseased-human-lung
#7
Neha Garg, Mingxun Wang, Embriette Hyde, Ricardo R da Silva, Alexey V Melnik, Ivan Protsyuk, Amina Bouslimani, Yan Wei Lim, Richard Wong, Greg Humphrey, Gail Ackermann, Timothy Spivey, Sharon S Brouha, Nuno Bandeira, Grace Y Lin, Forest Rohwer, Douglas J Conrad, Theodore Alexandrov, Rob Knight, Pieter C Dorrestein
Our understanding of the spatial variation in the chemical and microbial makeup of an entire human organ remains limited, in part due to the size and heterogeneity of human organs and the complexity of the associated metabolome and microbiome. To address this challenge, we developed a workflow to enable the cartography of metabolomic and microbiome data onto a three-dimensional (3D) organ reconstruction built off radiological images. This enabled the direct visualization of the microbial and chemical makeup of a human lung from a cystic fibrosis patient...
November 8, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/29041965/enrichment-allows-identification-of-diverse-rare-elements-in-metagenomic-resistome-virulome-sequencing
#8
Noelle R Noyes, Maggie E Weinroth, Jennifer K Parker, Chris J Dean, Steven M Lakin, Robert A Raymond, Pablo Rovira, Enrique Doster, Zaid Abdo, Jennifer N Martin, Kenneth L Jones, Jaime Ruiz, Christina A Boucher, Keith E Belk, Paul S Morley
BACKGROUND: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements...
October 17, 2017: Microbiome
https://www.readbyqxmd.com/read/29038487/the-microbiome-beyond-the-horizon-of-ecological-and-evolutionary-theory
#9
REVIEW
Britt Koskella, Lindsay J Hall, C Jessica E Metcalf
The ecological and evolutionary study of community formation, diversity, and stability is rooted in general theory and reinforced by decades of system-specific empirical work. Deploying these ideas to study the assembly, complexity, and dynamics of microbial communities living in and on eukaryotes has proved seductive, but challenging. The success of this research endeavour depends on our capacity to observe and characterize the distributions, abundances, and functional traits of microbiota, representing an array of technical and analytical challenges...
October 16, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/29038470/trios-promising-in-silico-biomarkers-for-differentiating-the-effect-of-disease-on-the-human-microbiome-network
#10
Zhanshan Sam Ma, Dandan Ye
Recent advances in the HMP (human microbiome project) research have revealed profound implications of the human microbiome to our health and diseases. We postulated that there should be distinctive features associated with healthy and/or diseased microbiome networks. Following Occam's razor principle, we further hypothesized that triangle motifs or trios, arguably the simplest motif in a complex network of the human microbiome, should be sufficient to detect changes that occurred in the diseased microbiome...
October 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29036251/an-adhesive-patch-based-skin-biopsy-device-for-molecular-diagnostics-and-skin-microbiome-studies
#11
Zuxu Yao, Ronald Moy, Talisha Allen, Burkhard Jansen
INTRODUCTION: A number of diagnoses in clinical dermatology are currently histopathologically confirmed and this image recognition-based confirmation generally requires surgical biopsies. The increasing ability of molecular pathology to corroborate or correct a clinical diagnosis based on objective gene expression, mutation analysis, or molecular microbiome data is on the horizon and would be further supported by a tool or procedure to collect samples non-invasively. This study characterizes such a tool in form of a 'bladeless' adhesive patch-based skin biopsy device...
October 1, 2017: Journal of Drugs in Dermatology: JDD
https://www.readbyqxmd.com/read/29031890/changing-perspectives-in-atopic-dermatitis
#12
REVIEW
E Serra-Baldrich, J O de Frutos, I Jáuregui, J C Armario-Hita, J F Silvestre, L Herraez, A Martín-Santiago, A Valero, J Sastre
Atopic dermatitis (AD) is a multifaceted disease that involves a complex interplay between the skin and the immune system. The course of the disease depends strongly on the genetic background of the patient and on yet poorly-defined environmental factors. Changes in lifestyle could be behind the dramatic rise in the prevalence of AD across continents; including hygienic conditions, food, social habits, skin microbiome or exposure to a number of allergens. Although AD typically develops in childhood and disappears after a few years, in a relatively large number of patients it continues into adulthood...
October 11, 2017: Allergologia et Immunopathologia
https://www.readbyqxmd.com/read/29028892/nephele-a-cloud-platform-for-simplified-standardized-and-reproducible-microbiome-data-analysis
#13
Nick Weber, David Liou, Jennifer Dommer, Philip MacMenamin, Mariam Quiñones, Ian Misner, Andrew Oler, Joe Wan, Lewis Kim, Meghan Coakley McCarthy, Samuel Ezeji, Karlynn Noble, Darrell E Hurt
Motivation: Widespread interest in the study of the microbiome has resulted in data proliferation and the development of powerful computational tools. However, many scientific researchers lack the time, training, or infrastructure to work with large datasets or to install and use command line tools. Results: The National Institute of Allergy and Infectious Diseases (NIAID) has created Nephele, a cloud-based microbiome data analysis platform with standardized pipelines and a simple web interface for transforming raw data into biological insights...
September 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29021832/pharmacogenomics-in-the-treatment-of-mood-disorders-strategies-and-opportunities-for-personalized-psychiatry
#14
REVIEW
Azmeraw T Amare, Klaus Oliver Schubert, Bernhard T Baune
Personalized medicine (personalized psychiatry in a specific setting) is a new model towards individualized care, in which knowledge from genomics and other omic pillars (microbiome, epigenomes, proteome, and metabolome) will be combined with clinical data to guide efforts to new drug development and targeted prescription of the existing treatment options. In this review, we summarize pharmacogenomic studies in mood disorders that may lay the foundation towards personalized psychiatry. In addition, we have discussed the possible strategies to integrate data from omic pillars as a future path to personalized psychiatry...
September 2017: EPMA Journal
https://www.readbyqxmd.com/read/29019934/a-massively-parallel-sequence-similarity-search-for-metagenomic-sequencing-data
#15
Masanori Kakuta, Shuji Suzuki, Kazuki Izawa, Takashi Ishida, Yutaka Akiyama
Sequence similarity searches have been widely used in the analyses of metagenomic sequencing data. Finding homologous sequences in a reference database enables the estimation of taxonomic and functional characteristics of each query sequence. Because current metagenomic sequencing data consist of a large number of nucleotide sequences, the time required for sequence similarity searches account for a large proportion of the total time. This time-consuming step makes it difficult to perform large-scale analyses...
October 11, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29018846/antibiotics-and-specialized-metabolites-from-the-human-microbiota
#16
REVIEW
Walaa K Mousa, Bilal Athar, Nishanth J Merwin, Nathan A Magarvey
Covering: 2000 to 2017Decades of research on human microbiota have revealed much of their taxonomic diversity and established their direct link to health and disease. However, the breadth of bioactive natural products secreted by our microbial partners remains unknown. Of particular interest are antibiotics produced by our microbiota to ward off invasive pathogens. Members of the human microbiota exclusively produce evolved small molecules with selective antimicrobial activity against human pathogens. Herein, we expand upon the current knowledge concerning antibiotics derived from human microbiota and their distribution across body sites...
November 15, 2017: Natural Product Reports
https://www.readbyqxmd.com/read/28992056/a-world-of-opportunities-with-nanopore-sequencing
#17
Richard M Leggett, Matthew D Clark
Oxford Nanopore Technologies' MinION sequencer was launched in pre-release form in 2014 and represents an exciting new sequencing paradigm. The device offers multi-kilobase reads and a streamed mode of operation that allows processing of reads as they are generated. Crucially, it is an extremely compact device that is powered from the USB port of a laptop computer, enabling it to be taken out of the lab and facilitating previously impossible in-field sequencing experiments to be undertaken. Many of the initial publications concerning the platform focused on provision of tools to access and analyse the new sequence formats and then demonstrating the assembly of microbial genomes...
August 23, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28988258/moving-beyond-descriptions-of-diversity-clinical-and-research-implications-of-bacterial-imbalance-in-chronic-rhinosinusitis
#18
B Wagner Mackenzie, D W Waite, M Hoggard, M W Taylor, K Biswas, R G Douglas
Chronic rhinosinusitis (CRS) is a debilitating disease which affects 5-16% of the general population and involves long-term inflammation of the sinonasal cavity. While microbial involvement in the pathogenesis of CRS has long been suspected, the exact role of microbes remains unclear. Recent application of cultivation-independent, molecular methods has provided much new information, taking advantage of developments in both laboratory- and bioinformatics-based analyses. The aim of this mini-review is to present a variety of available bioinformatics approaches, such as data classification techniques and network analyses, with proven applications in other aspects of human microbiome health and disease research...
October 8, 2017: Rhinology
https://www.readbyqxmd.com/read/28985331/an-introductory-how-to-guide-for-incorporating-microbiome-research-into-integrative-and-comparative-biology
#19
Kevin D Kohl
Research on host-associated microbial communities has grown rapidly. Despite the great body of work, inclusion of microbiota-related questions into integrative and comparative biology is still lagging behind other disciplines. The purpose of this paper is to offer an introduction into the basic tools and techniques of host-microbe research. Specifically, what considerations should be made before embarking on such projects (types of samples, types of controls)? How is microbiome data analyzed and integrated with data measured from the hosts? How can researchers experimentally manipulate the microbiome? With this information, integrative and comparative biologists should be able to include host-microbe studies into their research and push the boundaries of both fields...
July 25, 2017: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/28976641/synthetic-biology-and-the-gut-microbiome
#20
REVIEW
Jennifer Dou, Matthew R Bennett
The gut microbiome plays a crucial role in maintaining human health. Functions performed by gastrointestinal microbes range from regulating metabolism to modulating immune and nervous system development. Scientists have attempted to exploit this importance through the development of engineered probiotics that are capable of producing and delivering small molecule therapeutics within the gut. However, existing synthetic probiotics are simplistic and fail to replicate the complexity and adaptability of native homeostatic mechanisms...
October 4, 2017: Biotechnology Journal
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