keyword
MENU ▼
Read by QxMD icon Read
search

human microbiome project

keyword
https://www.readbyqxmd.com/read/29378630/host-genetic-variation-and-its-microbiome-interactions-within-the-human-microbiome-project
#1
Raivo Kolde, Eric A Franzosa, Gholamali Rahnavard, Andrew Brantley Hall, Hera Vlamakis, Christine Stevens, Mark J Daly, Ramnik J Xavier, Curtis Huttenhower
BACKGROUND: Despite the increasing recognition that microbial communities within the human body are linked to health, we have an incomplete understanding of the environmental and molecular interactions that shape the composition of these communities. Although host genetic factors play a role in these interactions, these factors have remained relatively unexplored given the requirement for large population-based cohorts in which both genotyping and microbiome characterization have been performed...
January 29, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29373999/combining-16s-rrna-gene-variable-regions-enables-high-resolution-microbial-community-profiling
#2
Garold Fuks, Michael Elgart, Amnon Amir, Amit Zeisel, Peter J Turnbaugh, Yoav Soen, Noam Shental
BACKGROUND: Most of our knowledge about the remarkable microbial diversity on Earth comes from sequencing the 16S rRNA gene. The use of next-generation sequencing methods has increased sample number and sequencing depth, but the read length of the most widely used sequencing platforms today is quite short, requiring the researcher to choose a subset of the gene to sequence (typically 16-33% of the total length). Thus, many bacteria may share the same amplified region, and the resolution of profiling is inherently limited...
January 26, 2018: Microbiome
https://www.readbyqxmd.com/read/29340028/high-resolution-microbiome-profiling-uncovers-fusobacterium-nucleatum-lactobacillus-gasseri-johnsonii-and-lactobacillus-vaginalis-associated-to-oral-and-oropharyngeal-cancer-in-saliva-from-hpv-positive-and-hpv-negative-patients-treated-with-surgery-and-chemo
#3
Rafael Guerrero-Preston, James Robert White, Filipa Godoy-Vitorino, Arnold Rodríguez-Hilario, Kelvin Navarro, Herminio González, Christina Michailidi, Anne Jedlicka, Sierra Canapp, Jessica Bondy, Amanda Dziedzic, Barbara Mora-Lagos, Gustavo Rivera-Alvarez, Carmen Ili-Gangas, Priscilla Brebi-Mieville, William Westra, Wayne Koch, Hyunseok Kang, Luigi Marchionni, Young Kim, David Sidransky
Microbiome studies show altered microbiota in head and neck squamous cell carcinoma (HNSCC), both in terms of taxonomic composition and metabolic capacity. These studies utilized a traditional bioinformatics methodology, which allows for accurate taxonomic assignment down to the genus level, but cannot accurately resolve species level membership. We applied Resphera Insight, a high-resolution methodology for 16S rRNA taxonomic assignment that is able to provide species-level context in its assignments of 16S rRNA next generation sequencing (NGS) data...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29335008/multi-omics-differentially-classify-disease-state-and-treatment-outcome-in-pediatric-crohn-s-disease
#4
Gavin M Douglas, Richard Hansen, Casey M A Jones, Katherine A Dunn, André M Comeau, Joseph P Bielawski, Rachel Tayler, Emad M El-Omar, Richard K Russell, Georgina L Hold, Morgan G I Langille, Johan Van Limbergen
BACKGROUND: Crohn's disease (CD) has an unclear etiology, but there is growing evidence of a direct link with a dysbiotic microbiome. Many gut microbes have previously been associated with CD, but these have mainly been confounded with patients' ongoing treatments. Additionally, most analyses of CD patients' microbiomes have focused on microbes in stool samples, which yield different insights than profiling biopsy samples. RESULTS: We sequenced the 16S rRNA gene (16S) and carried out shotgun metagenomics (MGS) from the intestinal biopsies of 20 treatment-naïve CD and 20 control pediatric patients...
January 15, 2018: Microbiome
https://www.readbyqxmd.com/read/29311644/dynamics-of-metatranscription-in-the-inflammatory-bowel-disease-gut-microbiome
#5
Melanie Schirmer, Eric A Franzosa, Jason Lloyd-Price, Lauren J McIver, Randall Schwager, Tiffany W Poon, Ashwin N Ananthakrishnan, Elizabeth Andrews, Gildardo Barron, Kathleen Lake, Mahadev Prasad, Jenny Sauk, Betsy Stevens, Robin G Wilson, Jonathan Braun, Lee A Denson, Subra Kugathasan, Dermot P B McGovern, Hera Vlamakis, Ramnik J Xavier, Curtis Huttenhower
Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Genetic, environmental and microbial factors have been implicated in the onset and exacerbation of IBD. However, the mechanisms associating gut microbial dysbioses and aberrant immune responses remain largely unknown. The integrative Human Microbiome Project seeks to close these gaps by examining the dynamics of microbiome functionality in disease by profiling the gut microbiomes of >100 individuals sampled over a 1-year period...
January 8, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29282673/the-microbiome-gut-behavior-axis-crosstalk-between-the-gut-microbiome-and-oligodendrocytes-modulates-behavioral-responses
#6
REVIEW
Achilles Ntranos, Patrizia Casaccia
Environmental and dietary stimuli have always been implicated in brain development and behavioral responses. The gut, being the major portal of communication with the external environment, has recently been brought to the forefront of this interaction with the establishment of a gut-brain axis in health and disease. Moreover, recent breakthroughs in germ-free and antibiotic-treated mice have demonstrated the significant impact of the microbiome in modulating behavioral responses in mice and have established a more specific microbiome-gut-behavior axis...
December 27, 2017: Neurotherapeutics: the Journal of the American Society for Experimental NeuroTherapeutics
https://www.readbyqxmd.com/read/29281638/mplasso-inferring-microbial-association-networks-using-prior-microbial-knowledge
#7
Chieh Lo, Radu Marculescu
Due to the recent advances in high-throughput sequencing technologies, it becomes possible to directly analyze microbial communities in human body and environment. To understand how microbial communities adapt, develop, and interact with the human body and the surrounding environment, one of the fundamental challenges is to infer the interactions among different microbes. However, due to the compositional and high-dimensional nature of microbial data, statistical inference cannot offer reliable results. Consequently, new approaches that can accurately and robustly estimate the associations (putative interactions) among microbes are needed to analyze such compositional and high-dimensional data...
December 27, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29277868/comparative-metagenomics
#8
Andrew Maltez Thomas, Felipe Prata Lima, Livia Maria Silva Moura, Aline Maria da Silva, Emmanuel Dias-Neto, João C Setubal
Thanks in large part to newer, better, and cheaper DNA sequencing technologies, an enormous number of metagenomic sequence datasets have been and continue to be generated, covering a huge variety of environmental niches, including several different human body sites. Comparing these metagenomes and identifying their commonalities and differences is a challenging task, due not only to the large amounts of data, but also because there are several methodological considerations that need to be taken into account to ensure an appropriate and sound comparison between datasets...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29232932/adjuvant-probiotics-and-the-intestinal-microbiome-enhancing-vaccines-and-immunotherapy-outcomes
#9
REVIEW
Luis Vitetta, Emma Tali Saltzman, Michael Thomsen, Tessa Nikov, Sean Hall
Immune defence against pathogenic agents comprises the basic premise for the administration of vaccines. Vaccinations have hence prevented millions of infectious illnesses, hospitalizations and mortality. Acquired immunity comprises antibody and cell mediated responses and is characterized by its specificity and memory. Along a similar congruent yet diverse mode of disease prevention, the human host has negotiated from in utero and at birth with the intestinal commensal bacterial cohort to maintain local homeostasis in order to achieve immunological tolerance in the new born...
December 11, 2017: Vaccines
https://www.readbyqxmd.com/read/29196353/the-lung-microbiome-in-health-and-disease
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
keyword
keyword
112553
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"