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microbiome tool

Katherine R Amato
Research examining the gut microbiota is currently exploding, and results are providing new perspectives on human biology. Factors such as host diet and physiology influence the composition and function of the gut microbiota, which in turn affects human nutrition, health, and behavior via interactions with metabolism, the immune system, and the brain. These findings represent an exciting new twist on familiar topics, and as a result, gut microbiome research is likely to provide insight into unresolved biological mechanisms driving human health...
October 20, 2016: American Journal of Human Biology: the Official Journal of the Human Biology Council
Walter H Moos, Carl A Pinkert, Michael H Irwin, Douglas V Faller, Krishna Kodukula, Ioannis P Glavas, Kosta Steliou
Preclinical Research Approximately 2,500 years ago, Hippocrates used the word herpes as a medical term to describe lesions that appeared to creep or crawl on the skin, advocating heat as a possible treatment. During the last 50 years, pharmaceutical research has made great strides, and therapeutic options have expanded to include small molecule antiviral agents, protease inhibitors, preventive vaccines for a handful of the papillomaviruses, and even cures for hepatitis C virus infections. However, effective treatments for persistent and recurrent viral infections, particularly the highly prevalent herpesviruses, continue to represent a significant unmet medical need, affecting the majority of the world's population...
October 20, 2016: Drug Development Research
Sonja C Sawh, Santosh Deshpande, Sandy Jansen, Christopher J Reynaert, Philip M Jones
CONTEXT: Necrotizing enterocolitis (NEC) is the most frequent gastrointestinal emergency in neonates. The microbiome of the preterm gut may regulate the integrity of the intestinal mucosa. Probiotics may positively contribute to mucosal integrity, potentially reducing the risk of NEC in neonates. OBJECTIVE: To perform an updated systematic review and meta-analysis on the efficacy and safety of probiotics for the prevention of NEC in premature infants. DATA SOURCES: Structured searches were performed in: Medline, Embase, and the Cochrane Central Register of Controlled Trials (all via Ovid, from 2013 to January 2015)...
2016: PeerJ
Katherine A Dunn, Jessica Moore-Connors, Brad MacIntyre, Andrew Stadnyk, Nikhil A Thomas, Angela Noble, Gamal Mahdi, Mohsin Rashid, Anthony R Otley, Joseph P Bielawski, Johan Van Limbergen
BACKGROUND: Exclusive enteral nutrition (EEN) is a first-line therapy in pediatric Crohn's disease (CD) thought to induce remission through changes in the gut microbiome. With microbiome assessment largely focused on microbial taxonomy and diversity, it remains unclear to what extent EEN induces functional changes that thereby contribute to its therapeutic effect. METHODS: Fecal samples were collected from 15 pediatric CD patients prior to and after EEN treatment, as well as from 5 healthy controls...
November 2016: Inflammatory Bowel Diseases
I-Min A Chen, Victor M Markowitz, Ken Chu, Krishna Palaniappan, Ernest Szeto, Manoj Pillay, Anna Ratner, Jinghua Huang, Evan Andersen, Marcel Huntemann, Neha Varghese, Michalis Hadjithomas, Kristin Tennessen, Torben Nielsen, Natalia N Ivanova, Nikos C Kyrpides
The Integrated Microbial Genomes with Microbiome Samples (IMG/M: system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives...
October 13, 2016: Nucleic Acids Research
Katerina V-A Johnson, Philip W J Burnet
Studies on microbiome diversity are flooding the current literature, yet lessons from ecology clearly demonstrate that diversity is just one factor to consider when analyzing an ecosystem, along with its stability, structure and function. Measures of diversity may be a useful tool for interpreting metagenomic data but the question remains as to how informative they are and what insight they may provide into the state of the microbiome. A study utilizing mathematical modelling to investigate the ecological dynamics of microbial communities has shown that diversity and stability may not always be concomitant...
October 10, 2016: Gut Microbes
Elisabeth M Bik
Recent developments in sequencing methods and bioinformatics analysis tools have greatly enabled the culture-independent analysis of complex microbial communities associated with environmental samples, plants, and animals. This has led to a spectacular increase in the number of studies on both membership and functionalities of these hitherto invisible worlds, in particular those of the human microbiome. The wide variety in available microbiome tools and platforms can be overwhelming, and making sound conclusions from scientific research can be challenging...
September 2016: Yale Journal of Biology and Medicine
Samuel T Westreich, Ian Korf, David A Mills, Danielle G Lemay
BACKGROUND: Although metatranscriptomics-the study of diverse microbial population activity based on RNA-seq data-is rapidly growing in popularity, there are limited options for biologists to analyze this type of data. Current approaches for processing metatranscriptomes rely on restricted databases and a dedicated computing cluster, or metagenome-based approaches that have not been fully evaluated for processing metatranscriptomic datasets. We created a new bioinformatics pipeline, designed specifically for metatranscriptome dataset analysis, which runs in conjunction with Metagenome-RAST (MG-RAST) servers...
September 29, 2016: BMC Bioinformatics
Iain Dickinson, William Goodall-Copestake, Michael A S Thorne, Thomas Schlitt, Maria L Ávila-Jiménez, David A Pearce
Recent attempts to explore marine microbial diversity and the global marine microbiome have indicated a large proportion of previously unknown diversity. However, sequencing alone does not tell the whole story, as it relies heavily upon information that is already contained within sequence databases. In addition, microorganisms have been shown to present small-to-large scale biogeographical patterns worldwide, potentially making regional combinations of selection pressures unique. Here, we focus on the extremophile community in the boundary region located between the Polar Front and the Southern Antarctic Circumpolar Current in the Southern Ocean, to explore the potential of metagenomic approaches as a tool for bioprospecting in the search for novel functional activity based on targeted sampling efforts...
January 11, 2016: Microorganisms
Moreno Zolfo, Adrian Tett, Olivier Jousson, Claudio Donati, Nicola Segata
Metagenomic characterization of microbial communities has the potential to become a tool to identify pathogens in human samples. However, software tools able to extract strain-level typing information from metagenomic data are needed. Low-throughput molecular typing schema such as Multilocus Sequence Typing (MLST) are still widely used and provide a wealth of strain-level information that is currently not exploited by metagenomic methods. We introduce MetaMLST, a software tool that reconstructs the MLST loci of microorganisms present in microbial communities from metagenomic data...
September 19, 2016: Nucleic Acids Research
Jinxing Li, Soracha Thamphiwatana, Wenjuan Liu, Berta Esteban-Fernández de Ávila, Pavimol Angsantikul, Elodie Sandraz, Jianxing Wang, Tailin Xu, Fernando Soto, Valentin Ramez, Xiaolei Wang, Weiwei Gao, Liangfang Zhang, Joseph Wang
The gastrointestinal (GI) tract, which hosts hundreds of bacteria species, becomes the most exciting organ for the emerging microbiome research. Some of these GI microbes are hostile and cause a variety of diseases. These bacteria colonize in different segments of the GI tract dependent on the local physicochemical and biological factors. Therefore, selectively locating therapeutic or imaging agents to specific GI segments is of significant importance for studying gut microbiome and treating various GI-related diseases...
September 20, 2016: ACS Nano
Hannah M Salk, Whitney L Simon, Nathaniel D Lambert, Richard B Kennedy, Diane E Grill, Brian F Kabat, Gregory A Poland
Live attenuated influenza vaccine (LAIV) has demonstrated varying levels of efficacy against seasonal influenza; however, LAIV may be used as a tool to measure interactions between the human microbiome and a live, replicating virus. To increase our knowledge of this interaction, we measured changes to the nasal microbiome in subjects who received LAIV to determine if associations between influenza-specific IgA production and the nasal microbiome exist after immunization with a live virus vaccine. The anterior nares of 47 healthy subjects were swabbed pre- (Day 0) and post- (Days 7 and 28) LAIV administration, and nasal washes were conducted on Days 0 and 28...
2016: PloS One
Richard D Beger, Warwick Dunn, Michael A Schmidt, Steven S Gross, Jennifer A Kirwan, Marta Cascante, Lorraine Brennan, David S Wishart, Matej Oresic, Thomas Hankemeier, David I Broadhurst, Andrew N Lane, Karsten Suhre, Gabi Kastenmüller, Susan J Sumner, Ines Thiele, Oliver Fiehn, Rima Kaddurah-Daouk
INTRODUCTION BACKGROUND TO METABOLOMICS: Metabolomics is the comprehensive study of the metabolome, the repertoire of biochemicals (or small molecules) present in cells, tissues, and body fluids. The study of metabolism at the global or "-omics" level is a rapidly growing field that has the potential to have a profound impact upon medical practice. At the center of metabolomics, is the concept that a person's metabolic state provides a close representation of that individual's overall health status...
2016: Metabolomics: Official Journal of the Metabolomic Society
Araceli Muñoz-Garach, Cristina Diaz-Perdigones, Francisco J Tinahones
In recent years, many studies have related gut microbiome to development of highly prevalent diseases such as type 2 diabetes and obesity. Obesity itself is associated to changes in the composition of gut microbiome, with a trend to an overgrowth of microorganisms more efficiently obtaining energy from diet. There are several mechanisms that relate microbiota to the onset of insulin resistance and diabetes, including changes in bowel permeability, endotoxemia, interaction with bile acids, changes in the proportion of brown adipose tissue, and effects associated to use of drugs like metformin...
September 12, 2016: Endocrinología y Nutrición: órgano de la Sociedad Española de Endocrinología y Nutrición
Ana Lokmer, M Anouk Goedknegt, David W Thieltges, Dario Fiorentino, Sven Kuenzel, John F Baines, K Mathias Wegner
Unveiling the factors and processes that shape the dynamics of host associated microbial communities (microbiota) under natural conditions is an important part of understanding and predicting an organism's response to a changing environment. The microbiota is shaped by host (i.e., genetic) factors as well as by the biotic and abiotic environment. Studying natural variation of microbial community composition in multiple host genetic backgrounds across spatial as well as temporal scales represents a means to untangle this complex interplay...
2016: Frontiers in Microbiology
Pamela Ferretti, Stefania Farina, Mario Cristofolini, Giampiero Girolomoni, Adrian Tett, Nicola Segata
The skin is the largest organ in the human body and it is populated by a large diversity of microbes, most of which are co-evolved with the host and live in symbiotic harmony. There is increasing evidence that the skin microbiome plays a crucial role in the defence against pathogens, immune system training and homeostasis, and microbiome perturbations have been associated with pathological skin conditions. Studying the skin resident microbial community is thus essential to better understand the microbiome-host crosstalk and to associate its specific configurations with cutaneous diseases...
September 13, 2016: Experimental Dermatology
Débora P Paula, Benjamin Linard, Alex Crampton-Platt, Amrita Srivathsan, Martijn J T N Timmermans, Edison R Sujii, Carmen S S Pires, Lucas M Souza, David A Andow, Alfried P Vogler
Characterizing trophic networks is fundamental to many questions in ecology, but this typically requires painstaking efforts, especially to identify the diet of small generalist predators. Several attempts have been devoted to develop suitable molecular tools to determine predatory trophic interactions through gut content analysis, and the challenge has been to achieve simultaneously high taxonomic breadth and resolution. General and practical methods are still needed, preferably independent of PCR amplification of barcodes, to recover a broader range of interactions...
2016: PloS One
Deborah B Nelson, L Christie Rockwell, Morgan D Prioleau, Laura Goetzl
Recent assessments have examined the composition of bacterial communities influencing reproductive, pregnancy and infant health. The Microbiome Project has made great strides in sequencing the microbiome and identifying the vast communities of microorganisms that inhabit our bodies and much work continues to examine the individual contribution of bacteria on health and disease to inform future therapies. This review explores the current literature outlining the contribution of important bacteria on reproductive health among sexually active men and women, outlines gaps in current research to determine causal and interventional relationships, and suggests future research initiatives...
September 6, 2016: Anaerobe
Claudio Donati, Moreno Zolfo, Davide Albanese, Duy Tin Truong, Francesco Asnicar, Valerio Iebba, Duccio Cavalieri, Olivier Jousson, Carlotta De Filippo, Curtis Huttenhower, Nicola Segata
Microbial epidemiology and population genomics have previously been carried out near-exclusively for organisms grown in vitro. Metagenomics helps to overcome this limitation, but it is still challenging to achieve strain-level characterization of microorganisms from culture-independent data with sufficient resolution for epidemiological modelling. Here, we have developed multiple complementary approaches that can be combined to profile and track individual microbial strains. To specifically profile highly recombinant neisseriae from oral metagenomes, we integrated four metagenomic analysis techniques: single nucleotide polymorphisms in the clade's core genome, DNA uptake sequence signatures, metagenomic multilocus sequence typing and strain-specific marker genes...
2016: Nature Microbiology
Elizabeth Stulberg, Deborah Fravel, Lita M Proctor, David M Murray, Jonathan LoTempio, Linda Chrisey, Jay Garland, Kelly Goodwin, Joseph Graber, M Camille Harris, Scott Jackson, Michael Mishkind, D Marshall Porterfield, Angela Records
Genome-enabled technologies have supported a dramatic increase in our ability to study microbial communities in environments and hosts. Taking stock of previously funded microbiome research can help to identify common themes, under-represented areas and research priorities to consider moving forward. To assess the status of US microbiome research, a team of government scientists conducted an analysis of federally funded microbiome research. Microbiomes were defined as host-, ecosystem- or habitat-associated communities of microorganisms, and microbiome research was defined as those studies that emphasize community-level analyses using 'omics technologies...
2016: Nature Microbiology
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