keyword
MENU ▼
Read by QxMD icon Read
search

Microbiome bioinformatics

keyword
https://www.readbyqxmd.com/read/28934286/denitrification-potential-of-the-eastern-oyster-microbiome-using-a-16s-rrna-gene-based-metabolic-inference-approach
#1
Ann Arfken, Bongkeun Song, Jeff S Bowman, Michael Piehler
The eastern oyster (Crassostrea virginica) is a foundation species providing significant ecosystem services. However, the roles of oyster microbiomes have not been integrated into any of the services, particularly nitrogen removal through denitrification. We investigated the composition and denitrification potential of oyster microbiomes with an approach that combined 16S rRNA gene analysis, metabolic inference, qPCR of the nitrous oxide reductase gene (nosZ), and N2 flux measurements. Microbiomes of the oyster digestive gland, the oyster shell, and sediments adjacent to the oyster reef were examined based on next generation sequencing (NGS) of 16S rRNA gene amplicons...
2017: PloS One
https://www.readbyqxmd.com/read/28903732/a-comparison-of-sequencing-platforms-and-bioinformatics-pipelines-for-compositional-analysis-of-the-gut-microbiome
#2
Imane Allali, Jason W Arnold, Jeffrey Roach, Maria Belen Cadenas, Natasha Butz, Hosni M Hassan, Matthew Koci, Anne Ballou, Mary Mendoza, Rizwana Ali, M Andrea Azcarate-Peril
BACKGROUND: Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines...
September 13, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28875147/protected-sampling-is-preferable-in-bronchoscopic-studies-of-the-airway-microbiome
#3
Rune Grønseth, Christine Drengenes, Harald G Wiker, Solveig Tangedal, Yaxin Xue, Gunnar Reksten Husebø, Øistein Svanes, Sverre Lehmann, Marit Aardal, Tuyen Hoang, Tharmini Kalananthan, Einar Marius Hjellestad Martinsen, Elise Orvedal Leiten, Marianne Aanerud, Eli Nordeide, Ingvild Haaland, Inge Jonassen, Per Bakke, Tomas Eagan
The aim was to evaluate susceptibility of oropharyngeal contamination with various bronchoscopic sampling techniques. 67 patients with obstructive lung disease and 58 control subjects underwent bronchoscopy with small-volume lavage (SVL) through the working channel, protected bronchoalveolar lavage (PBAL) and bilateral protected specimen brush (PSB) sampling. Subjects also provided an oral wash (OW) sample, and negative control samples were gathered for each bronchoscopy procedure. DNA encoding bacterial 16S ribosomal RNA was sequenced and bioinformatically processed to cluster into operational taxonomic units (OTU), assign taxonomy and obtain measures of diversity...
July 2017: ERJ Open Research
https://www.readbyqxmd.com/read/28854168/commensal-bacteria-make-gpcr-ligands-that-mimic-human-signalling-molecules
#4
Louis J Cohen, Daria Esterhazy, Seong-Hwan Kim, Christophe Lemetre, Rhiannon R Aguilar, Emma A Gordon, Amanda J Pickard, Justin R Cross, Ana B Emiliano, Sun M Han, John Chu, Xavier Vila-Farres, Jeremy Kaplitt, Aneta Rogoz, Paula Y Calle, Craig Hunter, J Kipchirchir Bitok, Sean F Brady
Commensal bacteria are believed to have important roles in human health. The mechanisms by which they affect mammalian physiology remain poorly understood, but bacterial metabolites are likely to be key components of host interactions. Here we use bioinformatics and synthetic biology to mine the human microbiota for N-acyl amides that interact with G-protein-coupled receptors (GPCRs). We found that N-acyl amide synthase genes are enriched in gastrointestinal bacteria and the lipids that they encode interact with GPCRs that regulate gastrointestinal tract physiology...
August 30, 2017: Nature
https://www.readbyqxmd.com/read/28845973/human-microbiome-inspired-antibiotics-with-improved-%C3%AE-lactam-synergy-against-mdr-staphylococcus-aureus
#5
John Chu, Xavier Vila Farres, Daigo Inoyama, Ricardo Gallardo-Macias, Mark Jaskowski, Shruthi Satish, Joel Stephen Freundlich, Sean F Brady
The flippase MurJ is responsible for transporting the cell wall intermediate lipid II from the cytoplasm to the outside of the cell. While essential for the survival of bacteria it remains an underexploited target for antibacterial therapy. The humimycin antibiotics are lipid II flippase (MurJ) inhibitors that were synthesized based on bioinformatic predictions derived from secondary metabolite gene clusters found in the human microbiome. Here we describe an SAR campaign around humimycin A that produced humimycin 17S...
August 28, 2017: ACS Infectious Diseases
https://www.readbyqxmd.com/read/28838410/the-microbiome-in-crohn-s-disease-role-in-pathogenesis-and-role-of-microbiome-replacement-therapies
#6
REVIEW
Sahil Khanna, Laura E Raffals
Individuals with a genetic predisposition to Crohn's disease develop aberrant immune responses to environmental triggers. The gastrointestinal microbiota is increasingly recognized to play an important role in the development of Crohn's disease. Decrease in global gut microbial diversity and specific bacterial alterations have been implicated in Crohn's disease. Advances in sequencing techniques and bioinformatics and correlation with host genetics continue to improve insight into the structure and function of the microbial community and interactions with the host immune system...
September 2017: Gastroenterology Clinics of North America
https://www.readbyqxmd.com/read/28837129/large-scale-comparative-metagenomics-of-blastocystis-a-common-member-of-the-human-gut-microbiome
#7
Francesco Beghini, Edoardo Pasolli, Tin Duy Truong, Lorenza Putignani, Simone M Cacciò, Nicola Segata
The influence of unicellular eukaryotic microorganisms on human gut health and disease is still largely unexplored. Blastocystis spp. commonly colonize the gut, but its clinical significance and ecological role are currently unsettled. We have developed a high-sensitivity bioinformatic pipeline to detect Blastocystis subtypes (STs) from shotgun metagenomics, and applied it to 12 large data sets, comprising 1689 subjects of different geographic origin, disease status and lifestyle. We confirmed and extended previous observations on the high prevalence the microrganism in the population (14...
August 22, 2017: ISME Journal
https://www.readbyqxmd.com/read/28831186/the-ibd-interactome-an-integrated-view-of-aetiology-pathogenesis-and-therapy
#8
REVIEW
Heitor S P de Souza, Claudio Fiocchi, Dimitrios Iliopoulos
Crohn's disease and ulcerative colitis are prototypical complex diseases characterized by chronic and heterogeneous manifestations, induced by interacting environmental, genomic, microbial and immunological factors. These interactions result in an overwhelming complexity that cannot be tackled by studying the totality of each pathological component (an '-ome') in isolation without consideration of the interaction among all relevant -omes that yield an overall 'network effect'. The outcome of this effect is the 'IBD interactome', defined as a disease network in which dysregulation of individual -omes causes intestinal inflammation mediated by dysfunctional molecular modules...
August 23, 2017: Nature Reviews. Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28818754/daily-thanatomicrobiome-changes-in-soil-as-an-approach-of-postmortem-interval-estimation-an-ecological-perspective
#9
Joe Adserias-Garriga, Marta Hernández, Narciso M Quijada, David Rodríguez Lázaro, Dawnie Steadman, Jesús Garcia-Gil
Understanding human decomposition is critical for its use in postmortem interval (PMI) estimation, having a significant impact on forensic investigations. In recognition of the need to establish the scientific basis for PMI estimation, several studies on decomposition have been carried out in the last years. The aims of the present study were: (i) to identify soil microbiota communities involved in human decomposition through high-throughput sequencing (HTS) of DNA sequences from the different bacteria, (ii) to monitor quantitatively and qualitatively the decay of such signature species, and (iii) to describe succesional changes in bacterial populations from the early putrefaction state until skeletonization...
September 2017: Forensic Science International
https://www.readbyqxmd.com/read/28812256/the-potential-for-emerging-microbiome-mediated-therapeutics-in-asthma
#10
REVIEW
Ayse Bilge Ozturk, Benjamin Arthur Turturice, David L Perkins, Patricia W Finn
PURPOSE OF REVIEW: In terms of immune regulating functions, analysis of the microbiome has led the development of therapeutic strategies that may be applicable to asthma management. This review summarizes the current literature on the gut and lung microbiota in asthma pathogenesis with a focus on the roles of innate molecules and new microbiome-mediated therapeutics. RECENT FINDINGS: Recent clinical and basic studies to date have identified several possible therapeutics that can target innate immunity and the microbiota in asthma...
August 10, 2017: Current Allergy and Asthma Reports
https://www.readbyqxmd.com/read/28793309/the-microbiome-in-urogenital-schistosomiasis-and-induced-bladder-pathologies
#11
Adewale S Adebayo, Mangesh Survayanshi, Shrikanth Bhute, Atinuke M Agunloye, Raphael D Isokpehi, Chiaka I Anumudu, Yogesh S Shouche
BACKGROUND: Human schistosomiasis is a highly prevalent neglected tropical disease (NTD) caused by Schistosoma species. Research on the molecular mechanisms influencing the outcomes of bladder infection by Schistosoma haematobium is urgently needed to develop new diagnostics, therapeutics and infection prevention strategies. The objective of the research study was to determine the microbiome features and changes in urine during urogenital schistosomiasis and induced bladder pathologies...
August 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28764865/rumen-microbiome-probiotics-and-fermentation-additives
#12
REVIEW
Joshua C McCann, Ahmed A Elolimy, Juan J Loor
Fermentation of a variety of feedstuffs by the ruminal microbiome is the distinctive feature of the ruminant digestive tract. The host derives energy and nutrients from microbiome activity; these organisms are essential to survival. Advances in DNA sequencing and bioinformatics have redefined the rumen microbial community. Current research seeks to connect our understanding of the rumen microbiome with nutritional strategies in ruminant livestock systems and their associated digestive disorders. These efforts align with a growing number of products designed to improve ruminal fermentation to benefit the overall efficiency of ruminant livestock production and health...
July 29, 2017: Veterinary Clinics of North America. Food Animal Practice
https://www.readbyqxmd.com/read/28750626/biogeographical-distribution-analysis-of-hydrocarbon-degrading-and-biosurfactant-producing-genes-suggests-that-near-equatorial-biomes-have-higher-abundance-of-genes-with-potential-for-bioremediation
#13
Jorge S Oliveira, Wydemberg J Araújo, Ricardo M Figueiredo, Rita C B Silva-Portela, Alaine de Brito Guerra, Sinara Carla da Silva Araújo, Carolina Minnicelli, Aline Cardoso Carlos, Ana Tereza Ribeiro de Vasconcelos, Ana Teresa Freitas, Lucymara F Agnez-Lima
BACKGROUND: Bacterial and Archaeal communities have a complex, symbiotic role in crude oil bioremediation. Their biosurfactants and degradation enzymes have been in the spotlight, mainly due to the awareness of ecosystem pollution caused by crude oil accidents and their use. Initially, the scientific community studied the role of individual microbial species by characterizing and optimizing their biosurfactant and oil degradation genes, studying their individual distribution. However, with the advances in genomics, in particular with the use of New-Generation-Sequencing and Metagenomics, it is now possible to have a macro view of the complex pathways related to the symbiotic degradation of hydrocarbons and surfactant production...
July 27, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28749657/deep-metaproteomics-approach-for-the-study-of-human-microbiomes
#14
Xu Zhang, Wendong Chen, Zhibin Ning, Janice Mayne, David Mack, Alain Stintzi, Ruijun Tian, Daniel Figeys
Host-microbiome interactions have been shown to play important roles in human health and diseases. Most of the current studies of the microbiome have been performed by genomic approaches through next-generation sequencing. Technologies, such as metaproteomics, for functional analysis of the microbiome are needed to better understand the intricate host-microbiome interactions. However, significant efforts to improve the depth and resolution of gut metaproteomics are still required. In this study, we combined an efficient sample preparation technique, high resolution mass spectrometry, and metaproteomic bioinformatics tools to perform ultradeep metaproteomic analysis of human gut microbiome from stool...
September 5, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28727425/database-and-bioinformatics-studies-of-probiotics
#15
REVIEW
Lin Tao, Bohua Wang, Yafen Zhong, Siok Hoon Pow, Xian Zeng, Chu Qin, Peng Zhang, Shangying Chen, Weidong He, Ying Tan, Hongxia Liu, Yuyang Jiang, Weiping Chen, Yu Zong Chen
Probiotics have been widely explored for health benefits, animal cares, and agricultural applications. Recent advances in microbiome, microbiota, and microbial dark matter research have fueled greater interests in and paved ways for the study of the mechanisms of probiotics and the discovery of new probiotics from uncharacterized microbial sources. A probiotics database named PROBIO was developed to facilitate these efforts and the need for the information on the known probiotics, which provides the comprehensive information about the probiotic functions of 448 marketed, 167 clinical trial/field trial, and 382 research probiotics for use or being studied for use in humans, animals, and plants...
September 6, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28718274/-microbiome-and-next-generation-sequencing
#16
REVIEW
A Suárez Moya
The human microbiome is an internal ecosystem that refers to the community of microorganisms that populate the human body. These microorganisms are essential to support his health, because the interaction between the host immune system and microorganisms, provide the host with protection against pathogens, and contributes to the preservation of health. Bacteriological culture has been the basis for traditional microbiology; however, most of the bacterial forms observed in nature cannot be isolated with laboratory culture methods...
July 17, 2017: Revista Española de Quimioterapia: Publicación Oficial de la Sociedad Española de Quimioterapia
https://www.readbyqxmd.com/read/28713344/outer-membrane-proteome-of-veillonella-parvula-a-diderm-firmicute-of-the-human-microbiome
#17
Daniel I Poppleton, Magalie Duchateau, Véronique Hourdel, Mariette Matondo, Jennifer Flechsler, Andreas Klingl, Christophe Beloin, Simonetta Gribaldo
Veillonella parvula is a biofilm-forming commensal found in the lungs, vagina, mouth, and gastro-intestinal tract of humans, yet it may develop into an opportunistic pathogen. Furthermore, the presence of Veillonella has been associated with the development of a healthy immune system in infants. Veillonella belongs to the Negativicutes, a diverse clade of bacteria that represent an evolutionary enigma: they phylogenetically belong to Gram-positive (monoderm) Firmicutes yet maintain an outer membrane (OM) with lipopolysaccharide similar to classic Gram-negative (diderm) bacteria...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28706917/insights-into-study-design-and-statistical-analyses-in-translational-microbiome-studies
#18
REVIEW
Jyoti Shankar
Research questions in translational microbiome studies are substantially more complex than their counterparts in basic science. Robust study designs with appropriate statistical analysis frameworks are pivotal to the success of these translational studies. This review considers how study designs can account for heterogeneous phenotypes by adopting representative sampling schemes for recruiting the study population and making careful choices about the control population. Advantages and limitations of 16S profiling and whole-genome sequencing, the two primary techniques for measuring the microbiome, are discussed followed by an overview of bioinformatic processing of high-throughput sequencing data from these measurements...
June 2017: Annals of Translational Medicine
https://www.readbyqxmd.com/read/28686570/using-metagenomics-to-connect-microbial-community-biodiversity-and-functions
#19
Lucas William Mendes, Lucas Peres Palma Braga, Acacio Aparecido Navarrete, Dennis Goss de Souza, Genivaldo Gueiros Zacarias Silva, Siu Mui Tsai
Microbes constitute about a third of the Earth's biomass and are composed by an enormous genetic diversity. In a majority of environments the microbial communities play crucial roles for the ecosystem functioning, where a drastic biodiversity alteration or loss could lead to negative effects on the environment and sustainability. A central goal in microbiome studies is to elucidate the relation between microbial diversity to functions. A better understanding of the relation diversity-function would increase the ability to manipulate that diversity to improve plant and animal health and also setting conservation priorities...
July 6, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28682460/strategies-for-managing-rival-bacterial-communities-lessons-from-burying-beetles
#20
Ana Duarte, Martin Welch, Chris Swannack, Josef Wagner, Rebecca M Kilner
The role of bacteria in animal development, ecology and evolution is increasingly well understood, yet little is known of how animal behaviour affects bacterial communities. Animals that benefit from defending a key resource from microbial competitors are likely to evolve behaviours to control or manipulate the animal's associated external microbiota. We describe four possible mechanisms by which animals could gain a competitive edge by disrupting a rival bacterial community: "weeding," "seeding," "replanting" and "preserving...
July 6, 2017: Journal of Animal Ecology
keyword
keyword
45810
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"