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https://www.readbyqxmd.com/read/28437450/esprit-forest-parallel-clustering-of-massive-amplicon-sequence-data-in-subquadratic-time
#1
Yunpeng Cai, Wei Zheng, Jin Yao, Yujie Yang, Volker Mai, Qi Mao, Yijun Sun
The rapid development of sequencing technology has led to an explosive accumulation of genomic sequence data. Clustering is often the first step to perform in sequence analy- sis, and hierarchical clustering is one of the most commonly used approaches for this purpose. However, it is currently computationally expensive to perform hierarchical clustering of extremely large sequence datasets due to its quadratic time and space complexities. In this paper we developed a new algorithm called ESPRIT-Forest for parallel hierarchical clustering of sequences...
April 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28391505/bacterial-communities-on-facial-skin-of-teenage-and-elderly-thai-females
#2
Naraporn Somboonna, Alisa Wilantho, Chutika Srisuttiyakorn, Anunchai Assawamakin, Sissades Tongsima
The Human Microbiome Project was first established to understand the roles of human-associated microbes to human health and disease. This study presents preliminary findings of Thai female facial skin microbiome using three pooled samples from groups of skin microbiome profiles, namely (1) healthy and (2) acne-prone young adults (teenage.hea and teenage.acn) and (3) healthy elderly adults (elderly.hea) based on standard dermatological criteria. These samples were sequenced using 454-pyrosequencing targeting 16S rRNA (V3-V4 regions)...
April 8, 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/28383789/salivary-microbiome-of-an-urban-indian-cohort-and-patterns-linked-to-subclinical-inflammation
#3
Aneesha Acharya, Yuki Chan, Supriya Kheur, Mohit Kheur, D Gopalakrishnan, R M Watt, Nikos Mattheos
OBJECTIVE: To profile salivary microbiomes of an urban-living, healthy Indian cohort and explore associations with proinflammatory status. METHODS: 51 clinically healthy Indian subjects' salivary microbiomes were analyzed using 16S rRNA Illumina MiSeq sequencing. Community distribution was compared with salivary data from the Human Microbiome Project (HMP). Indian subjects were clustered using microbiome based 'partitioning along medoids' (PAM) and relationships of interleukin 1 beta levels with community composition were analyzed...
April 6, 2017: Oral Diseases
https://www.readbyqxmd.com/read/28375407/hot-topics-in-primary-care-role-of-the-microbiome-in-disease-implications-for-treatment-of-irritable-bowel-syndrome
#4
REVIEW
Brian E Lacy
Dietary and some other treatments for IBS are supported by a growing body of evidence, much of which comes from programs such as the Human Microbiome Project and Human Gut Microbiome Initiative, which were intended to identify and characterize microorganisms found in association with both healthy and diseased humans. These programs used state-of-the-art technology to characterize the human microbiome from multiple body sites. This evidence indicates that the gut microbiome plays an important role in IBS and some other gastrointestinal (GI) disorders...
April 2017: Journal of Family Practice
https://www.readbyqxmd.com/read/28357466/-fundamentals-of-the-microbiome
#5
P R Steinhagen, D C Baumgart
Until the middle of the 20th century, clinical microbiology was limited to bacterial cultures enabling the detection of pathogenic microorganisms. Knowledge about the mutual relationship between humans and microorganisms has increased slowly. With the introduction of culture-independent analysis methods, comprehensive cataloging of the human microbiome was possible for the first time. Since then, compositional changes in relation to diseases have been studied. The goals of the Human Microbiome Project and MetaHIT include comparative studies of healthy and diseased individuals...
March 29, 2017: Der Internist
https://www.readbyqxmd.com/read/28216014/the-conserved-phylogeny-of-blood-microbiome
#6
Malay Bhattacharyya, Tuhin Ghosh, Sujit Shankar, Namrata Tomar
The proliferation and intensification of diseases have forced every researcher to take actions for a robust understanding of the organisms. This demands deep knowledge about the cells and tissues in an organ and its entire surroundings, more precisely the microbiome community which involves viruses, bacteria, archaea, among others. They play an important role in the function of our body, and act both as a deterrent as well as shelter for diseases. Therefore, it is pertinent to study the relation within the microbiome in a human body...
February 12, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28178947/an-integrative-bayesian-dirichlet-multinomial-regression-model-for-the-analysis-of-taxonomic-abundances-in-microbiome-data
#7
W Duncan Wadsworth, Raffaele Argiento, Michele Guindani, Jessica Galloway-Pena, Samuel A Shelbourne, Marina Vannucci
BACKGROUND: The Human Microbiome has been variously associated with the immune-regulatory mechanisms involved in the prevention or development of many non-infectious human diseases such as autoimmunity, allergy and cancer. Integrative approaches which aim at associating the composition of the human microbiome with other available information, such as clinical covariates and environmental predictors, are paramount to develop a more complete understanding of the role of microbiome in disease development...
February 8, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28146577/blood-microbiome-quantity-and-the-hyperdynamic-circulation-in-decompensated-cirrhotic-patients
#8
Daniela Traykova, Beacher Schneider, Mario Chojkier, Martina Buck
BACKGROUND: Recently, a complex microbiome was comprehensibly characterized in the serum and ascitic fluid of cirrhotic patients. In the current study, we investigated for the first time the induction of inflammatory pathways and Nitric Oxide, as well as the systemic hemodynamics in conjunction with the blood microbiome in a Child-Pugh class B cirrhotic cohort. METHODS AND FINDINGS: We used the Intestinal Infections Microbial DNA qPCR Array to screen for 53 bacterial DNA from the gut in the blood...
2017: PloS One
https://www.readbyqxmd.com/read/28125088/motivations-of-participants-in-the-citizen-science-of-microbiomics-data-from-the-british-gut-project
#9
Lorenzo Del Savio, Barbara Prainsack, Alena Buyx
PURPOSE: The establishment of databases for research in human microbiomics is dependent on the recruitment of sufficient numbers and diversity of participants. Factors that support or impede participant recruitment in studies of this type have not yet been studied. METHODS: We report the results of a survey aimed at establishing the motivations of participants in the British Gut Project, a research project that relies on volunteers to provide samples and to help fund the project...
January 26, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28111075/discovery-of-reactive-microbiota-derived-metabolites-that-inhibit-host-proteases
#10
Chun-Jun Guo, Fang-Yuan Chang, Thomas P Wyche, Keriann M Backus, Timothy M Acker, Masanori Funabashi, Mao Taketani, Mohamed S Donia, Stephen Nayfach, Katherine S Pollard, Charles S Craik, Benjamin F Cravatt, Jon Clardy, Christopher A Voigt, Michael A Fischbach
The gut microbiota modulate host biology in numerous ways, but little is known about the molecular mediators of these interactions. Previously, we found a widely distributed family of nonribosomal peptide synthetase gene clusters in gut bacteria. Here, by expressing a subset of these clusters in Escherichia coli or Bacillus subtilis, we show that they encode pyrazinones and dihydropyrazinones. At least one of the 47 clusters is present in 88% of the National Institutes of Health Human Microbiome Project (NIH HMP) stool samples, and they are transcribed under conditions of host colonization...
January 26, 2017: Cell
https://www.readbyqxmd.com/read/28063079/the-thyroid-the-eyes-and-the-gut-a-possible-connection
#11
REVIEW
D Covelli, M Ludgate
INTRODUCTION: Graves' disease (GD) is an autoimmune disorder responsible for 60-90% of thyrotoxicosis, with an incidence of 1 to 2 cases per 1000 population per year in England. Graves' orbitopathy (GO) is the most frequent extrathyroidal manifestation, not provoked directly by abnormal thyroid hormone levels, but by the consequence of the underlying autoimmune process. The aetiology of autoimmune disorders is due to an interplay between susceptibility genes and environmental factors, such as infections and stress...
January 7, 2017: Journal of Endocrinological Investigation
https://www.readbyqxmd.com/read/28028549/ssunique-detecting-sequence-novelty-in-microbiome-surveys
#12
Michael D J Lynch, Josh D Neufeld
High-throughput sequencing of small-subunit (SSU) rRNA genes has revolutionized understanding of microbial communities and facilitated investigations into ecological dynamics at unprecedented scales. Such extensive SSU rRNA gene sequence libraries, constructed from DNA extracts of environmental or host-associated samples, often contain a substantial proportion of unclassified sequences, many representing organisms with novel taxonomy (taxonomic "blind spots") and potentially unique ecology. Indeed, these novel taxonomic lineages are associated with so-called microbial "dark matter," which is the genomic potential of these lineages...
November 2016: MSystems
https://www.readbyqxmd.com/read/28025198/dace-a-scalable-dp-means-algorithm-for-clustering-extremely-large-sequence-data
#13
Linhao Jiang, Yichao Dong, Ning Chen, Ting Chen
Motivation: Advancements in next-generation sequencing technology have produced large amounts of reads at low cost in a short time. In metagenomics, 16S and 18S rRNA gene have been widely used as marker genes to profile diversity of microorganisms in environmental samples. Through clustering of sequencing reads we can determine both number of OTUs and their relative abundance. In many applications, clustering of very large sequencing data with high efficiency and accuracy is essential for downstream analysis...
March 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28005908/a-machine-learning-approach-for-using-the-postmortem-skin-microbiome-to-estimate-the-postmortem-interval
#14
Hunter R Johnson, Donovan D Trinidad, Stephania Guzman, Zenab Khan, James V Parziale, Jennifer M DeBruyn, Nathan H Lents
Research on the human microbiome, the microbiota that live in, on, and around the human person, has revolutionized our understanding of the complex interactions between microbial life and human health and disease. The microbiome may also provide a valuable tool in forensic death investigations by helping to reveal the postmortem interval (PMI) of a decedent that is discovered after an unknown amount of time since death. Current methods of estimating PMI for cadavers discovered in uncontrolled, unstudied environments have substantial limitations, some of which may be overcome through the use of microbial indicators...
2016: PloS One
https://www.readbyqxmd.com/read/27913230/effects-of-combined-oral-contraceptives-depot-medroxyprogesterone-acetate-and-the-levonorgestrel-releasing-intrauterine-system-on-the-vaginal-microbiome
#15
J Paul Brooks, David J Edwards, Diana L Blithe, Jennifer M Fettweis, Myrna G Serrano, Nihar U Sheth, Jerome F Strauss, Gregory A Buck, Kimberly K Jefferson
OBJECTIVES: Prior studies suggest that the composition of the vaginal microbiome may positively or negatively affect susceptibility to sexually transmitted infections (STIs) and bacterial vaginosis (BV). Some female hormonal contraceptive methods also appear to positively or negatively influence STI transmission and BV. Therefore, changes in the vaginal microbiome that are associated with different contraceptive methods may explain, in part, effects on STI transmission and BV. STUDY DESIGN: We performed a retrospective study of 16S rRNA gene survey data of vaginal samples from a subset of participants from the Human Vaginal Microbiome Project at Virginia Commonwealth University...
April 2017: Contraception
https://www.readbyqxmd.com/read/27899504/gene-function-analysis-in-the-ubiquitous-human-commensal-and-pathogen-malassezia-genus
#16
Giuseppe Ianiri, Anna F Averette, Joanne M Kingsbury, Joseph Heitman, Alexander Idnurm
The genus Malassezia includes 14 species that are found on the skin of humans and animals and are associated with a number of diseases. Recent genome sequencing projects have defined the gene content of all 14 species; however, to date, genetic manipulation has not been possible for any species within this genus. Here, we develop and then optimize molecular tools for the transformation of Malassezia furfur and Malassezia sympodialis using Agrobacterium tumefaciens delivery of transfer DNA (T-DNA) molecules...
November 29, 2016: MBio
https://www.readbyqxmd.com/read/27887570/metamis-a-metagenomic-microbial-interaction-simulator-based-on-microbial-community-profiles
#17
Grace Tzun-Wen Shaw, Yueh-Yang Pao, Daryi Wang
BACKGROUND: The complexity and dynamics of microbial communities are major factors in the ecology of a system. With the NGS technique, metagenomics data provides a new way to explore microbial interactions. Lotka-Volterra models, which have been widely used to infer animal interactions in dynamic systems, have recently been applied to the analysis of metagenomic data. RESULTS: In this paper, we present the Lotka-Volterra model based tool, the Metagenomic Microbial Interacticon Simulator (MetaMIS), which is designed to analyze the time series data of microbial community profiles...
November 25, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27822556/impact-of-sample-type-and-dna-isolation-procedure-on-genomic-inference-of-microbiome-composition
#18
Berith E Knudsen, Lasse Bergmark, Patrick Munk, Oksana Lukjancenko, Anders Priemé, Frank M Aarestrup, Sünje J Pamp
Explorations of complex microbiomes using genomics greatly enhance our understanding about their diversity, biogeography, and function. The isolation of DNA from microbiome specimens is a key prerequisite for such examinations, but challenges remain in obtaining sufficient DNA quantities required for certain sequencing approaches, achieving accurate genomic inference of microbiome composition, and facilitating comparability of findings across specimen types and sequencing projects. These aspects are particularly relevant for the genomics-based global surveillance of infectious agents and antimicrobial resistance from different reservoirs...
September 2016: MSystems
https://www.readbyqxmd.com/read/27822524/from-sample-to-multi-omics-conclusions-in-under-48-hours
#19
Robert A Quinn, Jose A Navas-Molina, Embriette R Hyde, Se Jin Song, Yoshiki Vázquez-Baeza, Greg Humphrey, James Gaffney, Jeremiah J Minich, Alexey V Melnik, Jakob Herschend, Jeff DeReus, Austin Durant, Rachel J Dutton, Mahdieh Khosroheidari, Clifford Green, Ricardo da Silva, Pieter C Dorrestein, Rob Knight
Multi-omics methods have greatly advanced our understanding of the biological organism and its microbial associates. However, they are not routinely used in clinical or industrial applications, due to the length of time required to generate and analyze omics data. Here, we applied a novel integrated omics pipeline for the analysis of human and environmental samples in under 48 h. Human subjects that ferment their own foods provided swab samples from skin, feces, oral cavity, fermented foods, and household surfaces to assess the impact of home food fermentation on their microbial and chemical ecology...
March 2016: MSystems
https://www.readbyqxmd.com/read/27822521/geography-and-location-are-the-primary-drivers-of-office-microbiome-composition
#20
John Chase, Jennifer Fouquier, Mahnaz Zare, Derek L Sonderegger, Rob Knight, Scott T Kelley, Jeffrey Siegel, J Gregory Caporaso
In the United States, humans spend the majority of their time indoors, where they are exposed to the microbiome of the built environment (BE) they inhabit. Despite the ubiquity of microbes in BEs and their potential impacts on health and building materials, basic questions about the microbiology of these environments remain unanswered. We present a study on the impacts of geography, material type, human interaction, location in a room, seasonal variation, and indoor and microenvironmental parameters on bacterial communities in offices...
March 2016: MSystems
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