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https://www.readbyqxmd.com/read/29196353/the-lung-microbiome-in-health-and-disease
#1
Miriam F Moffatt, William Ocm Cookson
The Human Microbiome Project began 10 years ago, leading to a significant growth in understanding of the role the human microbiome plays in health and disease. In this article, we explain with an emphasis on the lung, the origins of microbiome research. We discuss how 16S rRNA gene sequencing became the first major molecular tool to examine the bacterial communities present within the human body. We highlight the pitfalls of molecular-based studies, such as false findings resulting from contamination, and the limitations of 16S rRNA gene sequencing...
December 2017: Clinical Medicine: Journal of the Royal College of Physicians of London
https://www.readbyqxmd.com/read/29178920/the-gut-mycobiome-of-the-human-microbiome-project-healthy-cohort
#2
Andrea K Nash, Thomas A Auchtung, Matthew C Wong, Daniel P Smith, Jonathan R Gesell, Matthew C Ross, Christopher J Stewart, Ginger A Metcalf, Donna M Muzny, Richard A Gibbs, Nadim J Ajami, Joseph F Petrosino
BACKGROUND: Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene...
November 25, 2017: Microbiome
https://www.readbyqxmd.com/read/29177026/2-way-k-means-as-a-model-for-microbiome-samples
#3
Weston J Jackson, Ipsita Agarwal, Itsik Pe'er
Motivation. Microbiome sequencing allows defining clusters of samples with shared composition. However, this paradigm poorly accounts for samples whose composition is a mixture of cluster-characterizing ones and which therefore lie in between them in the cluster space. This paper addresses unsupervised learning of 2-way clusters. It defines a mixture model that allows 2-way cluster assignment and describes a variant of generalized k-means for learning such a model. We demonstrate applicability to microbial 16S rDNA sequencing data from the Human Vaginal Microbiome Project...
2017: Journal of Healthcare Engineering
https://www.readbyqxmd.com/read/29152585/total-lipopolysaccharide-from-the-human-gut-microbiome-silences-toll-like-receptor-signaling
#4
Eva d'Hennezel, Sahar Abubucker, Leon O Murphy, Thomas W Cullen
Cohabitation of microbial communities with the host enables the formation of a symbiotic relationship that maintains homeostasis in the gut and beyond. One prevailing model suggests that this relationship relies on the capacity of host cells and tissues to remain tolerant to the strong immune stimulation generated by the microbiota such as the activation of Toll-like receptor 4 (TLR4) pathways by lipopolysaccharide (LPS). Indeed, gut microbial LPS is thought to be one of the most potent activators of innate immune signaling and an important mediator of the microbiome's influence on host physiology...
November 2017: MSystems
https://www.readbyqxmd.com/read/29140991/a-bayesian-method-for-detecting-pairwise-associations-in-compositional-data
#5
Emma Schwager, Himel Mallick, Steffen Ventz, Curtis Huttenhower
Compositional data consist of vectors of proportions normalized to a constant sum from a basis of unobserved counts. The sum constraint makes inference on correlations between unconstrained features challenging due to the information loss from normalization. However, such correlations are of long-standing interest in fields including ecology. We propose a novel Bayesian framework (BAnOCC: Bayesian Analysis of Compositional Covariance) to estimate a sparse precision matrix through a LASSO prior. The resulting posterior, generated by MCMC sampling, allows uncertainty quantification of any function of the precision matrix, including the correlation matrix...
November 15, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29136663/phylogenic-inference-using-alignment-free-methods-for-applications-in-microbial-community-surveys-using-16s-rrna-gene
#6
Yifei Zhang, Alexander V Alekseyenko
The diversity of microbiota is best explored by understanding the phylogenetic structure of the microbial communities. Traditionally, sequence alignment has been used for phylogenetic inference. However, alignment-based approaches come with significant challenges and limitations when massive amounts of data are analyzed. In the recent decade, alignment-free approaches have enabled genome-scale phylogenetic inference. Here we evaluate three alignment-free methods: ACS, CVTree, and Kr for phylogenetic inference with 16s rRNA gene data...
2017: PloS One
https://www.readbyqxmd.com/read/29129355/a-metagenomic-approach-to-dissect-the-genetic-composition-of-enterotypes-in-han-chinese-and-two-muslim-groups
#7
Jing Li, Ruiqing Fu, Yajun Yang, Hans-Peter Horz, Yaqun Guan, Yan Lu, Haiyi Lou, Lei Tian, Shijie Zheng, Hongjiao Liu, Meng Shi, Kun Tang, Sijia Wang, Shuhua Xu
Distinct enterotypes have been observed in the human gut but little is known about the genetic basis of the microbiome. Moreover, it is not clear how many genetic differences exist between enterotypes within or between populations. In this study, both the 16S rRNA gene and the metagenomes of the gut microbiota were sequenced from 48 Han Chinese, 48 Kazaks, and 96 Uyghurs, and taxonomies were assigned after de novo assembly. Single nucleotide polymorphisms were also identified by referring to data from the Human Microbiome Project...
November 9, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29122007/pancreatic-cyst-fluid-harbors-a-unique-microbiome
#8
Shan Li, Gwenny M Fuhler, Nahush Bn, Tony Jose, Marco J Bruno, Maikel P Peppelenbosch, Sergey R Konstantinov
BACKGROUND: It is clear that specific intestinal bacteria are involved in the development of different premalignant conditions along the gastrointestinal tract. An analysis of the microbial constituents in the context of pancreatic cystic lesions has, however, as yet not been performed. This consideration prompted us to explore whether endoscopically obtained pancreatic cyst fluids (PCF) contain bacterial DNA and to determine the genera of bacteria present in such material. METHODS: Total DNA was isolated from 69 PCF samples...
November 9, 2017: Microbiome
https://www.readbyqxmd.com/read/29106667/microbiomedb-a-systems-biology-platform-for-integrating-mining-and-analyzing-microbiome-experiments
#9
Francislon S Oliveira, John Brestelli, Shon Cade, Jie Zheng, John Iodice, Steve Fischer, Cristina Aurrecoechea, Jessica C Kissinger, Brian P Brunk, Christian J Stoeckert, Gabriel R Fernandes, David S Roos, Daniel P Beiting
MicrobiomeDB (http://microbiomeDB.org) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to interrogate microbiome datasets. MicrobiomeDB was developed in collaboration with the Eukaryotic Pathogens Bioinformatics Resource Center (http://EuPathDB.org) and leverages the infrastructure and user interface of EuPathDB, which allows users to construct in silico experiments using an intuitive graphical 'strategy' approach. The current release of the database integrates microbial census data with sample details for nearly 14 000 samples originating from human, animal and environmental sources, including over 9000 samples from healthy human subjects in the Human Microbiome Project (http://portal...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29062070/new-opportunities-for-managing-acute-and-chronic-lung-infections
#10
REVIEW
William O C M Cookson, Michael J Cox, Miriam F Moffatt
Lung diseases caused by microbial infections affect hundreds of millions of children and adults throughout the world. In Western populations, the treatment of lung infections is a primary driver of antibiotic resistance. Traditional therapeutic strategies have been based on the premise that the healthy lung is sterile and that infections grow in a pristine environment. As a consequence, rapid advances in our understanding of the composition of the microbiota of the skin and bowel have not yet been matched by studies of the respiratory tree...
October 24, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/29038470/trios-promising-in-silico-biomarkers-for-differentiating-the-effect-of-disease-on-the-human-microbiome-network
#11
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/29031742/a-preliminary-examination-of-gut-microbiota-sleep-and-cognitive-flexibility-in-healthy-older-adults
#12
Jason R Anderson, Ian Carroll, M Andrea Azcarate-Peril, Amber D Rochette, Leslie J Heinberg, Christine Peat, Kristine Steffen, Lisa M Manderino, James Mitchell, John Gunstad
OBJECTIVES: Inadequate sleep increases the risk for age-related cognitive decline and recent work suggests a possible role of the gut microbiota in this phenomenon. Partial sleep deprivation alters the human gut microbiome, and its composition is associated with cognitive flexibility in animal models. Given these findings, we examined the possible relationship among the gut microbiome, sleep quality, and cognitive flexibility in a sample of healthy older adults. METHODS: Thirty-seven participants (age 64...
October 2017: Sleep Medicine
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/29022944/erratum-strains-functions-and-dynamics-in-the-expanded-human-microbiome-project
#14
Jason Lloyd-Price, Anup Mahurkar, Gholamali Rahnavard, Jonathan Crabtree, Joshua Orvis, A Brantley Hall, Arthur Brady, Heather H Creasy, Carrie McCracken, Michelle G Giglio, Daniel McDonald, Eric A Franzosa, Rob Knight, Owen White, Curtis Huttenhower
This corrects the article DOI: 10.1038/nature23889.
October 12, 2017: Nature
https://www.readbyqxmd.com/read/28967885/assessment-of-variation-in-microbial-community-amplicon-sequencing-by-the-microbiome-quality-control-mbqc-project-consortium
#15
Rashmi Sinha, Galeb Abu-Ali, Emily Vogtmann, Anthony A Fodor, Boyu Ren, Amnon Amir, Emma Schwager, Jonathan Crabtree, Siyuan Ma, Christian C Abnet, Rob Knight, Owen White, Curtis Huttenhower
In order for human microbiome studies to translate into actionable outcomes for health, meta-analysis of reproducible data from population-scale cohorts is needed. Achieving sufficient reproducibility in microbiome research has proven challenging. We report a baseline investigation of variability in taxonomic profiling for the Microbiome Quality Control (MBQC) project baseline study (MBQC-base). Blinded specimen sets from human stool, chemostats, and artificial microbial communities were sequenced by 15 laboratories and analyzed using nine bioinformatics protocols...
November 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28961122/clustering-and-integrating-of-heterogeneous-microbiome-data-by-joint-symmetric-nonnegative-matrix-factorization-with-laplacian-regularization
#16
Yuanyuan Ma, Xiaohua Hu, Tingting He, Xingpeng Jiang
Many datasets existed in the real world are often comprised of different representations or views which provide complementary information to each other. To integrate information from multiple views, data integration approaches such as nonnegative matrix factorization (NMF) have been developed to combine multiple heterogeneous data simultaneously to obtain a comprehensive representation. In this paper, we proposed a novel variant of symmetric nonnegative matrix factorization (SNMF), called Laplacian regularization based joint symmetric nonnegative matrix factorization (LJ-SNMF) for clustering multi-view data...
September 26, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28953883/strains-functions-and-dynamics-in-the-expanded-human-microbiome-project
#17
Jason Lloyd-Price, Anup Mahurkar, Gholamali Rahnavard, Jonathan Crabtree, Joshua Orvis, A Brantley Hall, Arthur Brady, Heather H Creasy, Carrie McCracken, Michelle G Giglio, Daniel McDonald, Eric A Franzosa, Rob Knight, Owen White, Curtis Huttenhower
The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, diversity, biogeography, and molecular function. The National Institutes of Health Human Microbiome Project has provided one of the broadest such characterizations so far. Here we introduce a second wave of data from the study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to provide new characterizations of microbiome personalization...
October 5, 2017: Nature
https://www.readbyqxmd.com/read/28915922/recent-urbanization-in-china-is-correlated-with-a-westernized-microbiome-encoding-increased-virulence-and-antibiotic-resistance-genes
#18
Kathryn Winglee, Annie Green Howard, Wei Sha, Raad Z Gharaibeh, Jiawu Liu, Donghui Jin, Anthony A Fodor, Penny Gordon-Larsen
BACKGROUND: Urbanization is associated with an increased risk for a number of diseases, including obesity, diabetes, and cancer, which all also show associations with the microbiome. While microbial community composition has been shown to vary across continents and in traditional versus Westernized societies, few studies have examined urban-rural differences in neighboring communities within a single country undergoing rapid urbanization. In this study, we compared the gut microbiome, plasma metabolome, dietary habits, and health biomarkers of rural and urban people from a single Chinese province...
September 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28846702/association-between-statin-use-the-vaginal-microbiome-and-gardnerella-vaginalis-vaginolysin-mediated-cytotoxicity
#19
Abdallah A Abdelmaksoud, Philippe H Girerd, Erin M Garcia, J Paul Brooks, Lauren M Leftwich, Nihar U Sheth, Steven P Bradley, Myrna G Serrano, Jennifer M Fettweis, Bernice Huang, Jerome F Strauss, Gregory A Buck, Kimberly K Jefferson
BACKGROUND: Bacterial vaginosis (BV) is the leading dysbiosis of the vaginal microbiome. The pathways leading towards the development of BV are not well understood. Gardnerella vaginalis is frequently associated with BV. G. vaginalis produces the cholesterol-dependent cytolysin (CDC), vaginolysin, which can lyse a variety of human cells and is thought to play a role in pathogenesis. Because membrane cholesterol is required for vaginolysin to function, and because HMG-CoA reductase inhibitors (statins) affect not only serum levels of cholesterol but membrane levels as well, we hypothesized that statins might affect the vaginal microbiome...
2017: PloS One
https://www.readbyqxmd.com/read/28842845/gut-microbiota-and-atherosclerosis
#20
REVIEW
Daniel Y Li, W H Wilson Tang
PURPOSE OF REVIEW: Studies in microbiota-mediated health risks have gained traction in recent years since the compilation of the Human Microbiome Project. No longer do we believe that our gut microbiota is an inert set of microorganisms that reside in the body without consequence. In this review, we discuss the recent findings which further our understanding of the connection between the gut microbiota and the atherosclerosis. RECENT FINDINGS: We evaluate studies which illustrate the current understanding of the relationship between infection, immunity, altered metabolism, and bacterial products such as immune activators or dietary metabolites and their contributions to the development of atherosclerosis...
August 25, 2017: Current Atherosclerosis Reports
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