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Microbial bioinformatics

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https://www.readbyqxmd.com/read/28810907/schr%C3%A3-dinger-s-microbes-tools-for-distinguishing-the-living-from-the-dead-in-microbial-ecosystems
#1
REVIEW
Joanne B Emerson, Rachel I Adams, Clarisse M Betancourt Román, Brandon Brooks, David A Coil, Katherine Dahlhausen, Holly H Ganz, Erica M Hartmann, Tiffany Hsu, Nicholas B Justice, Ivan G Paulino-Lima, Julia C Luongo, Despoina S Lymperopoulou, Cinta Gomez-Silvan, Brooke Rothschild-Mancinelli, Melike Balk, Curtis Huttenhower, Andreas Nocker, Parag Vaishampayan, Lynn J Rothschild
While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms...
August 16, 2017: Microbiome
https://www.readbyqxmd.com/read/28807046/a-comprehensive-evaluation-of-the-sl1p-pipeline-for-16s-rrna-gene-sequencing-analysis
#2
Fiona J Whelan, Michael G Surette
BACKGROUND: Advances in next-generation sequencing technologies have allowed for detailed, molecular-based studies of microbial communities such as the human gut, soil, and ocean waters. Sequencing of the 16S rRNA gene, specific to prokaryotes, using universal PCR primers has become a common approach to studying the composition of these microbiota. However, the bioinformatic processing of the resulting millions of DNA sequences can be challenging, and a standardized protocol would aid in reproducible analyses...
August 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28803266/a-degradome-based-polymerase-chain-reaction-to-resolve-the-potential-of-environmental-samples-for-2-4-dichlorophenol-biodegradation
#3
Eslam S Ibrahim, Mona T Kashef, Tamer M Essam, Mohammed A Ramadan
A clean way to overcome environmental pollution is biodegradation. In this perspective, at the intersection of biodegradation and metagenomics, the degradome is defined as the totality of genes related to the biodegradation of a certain compound. It includes the genetic elements from both culturable and uncultured microorganisms. The possibility of assessing the biodegradation potential of an environmental samples, using a degradome-based polymerase chain reaction, was explored. 2,4-Dichlorophenol (2,4-DCP) was chosen as a model and the use of tfdB gene as a biodegradation marker was confirmed by bioinformatics study of TfdB protein...
August 12, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28769883/a-case-study-into-microbial-genome-assembly-gap-sequences-and-finishing-strategies
#4
Sagar M Utturkar, Dawn M Klingeman, Richard A Hurt, Steven D Brown
This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28764865/rumen-microbiome-probiotics-and-fermentation-additives
#5
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/28761933/insights-into-butyrate-production-in-a-controlled-fermentation-system-via-gene-predictions
#6
S Esquivel-Elizondo, Z E Ilhan, E I Garcia-Peña, R Krajmalnik-Brown
Butyrate is a common fatty acid produced in important fermentative systems, such as the human/animal gut and other H2 production systems. Despite its importance, there is little information on the partnerships between butyrate producers and other bacteria. The objective of this work was to uncover butyrate-producing microbial communities and possible metabolic routes in a controlled fermentation system aimed at butyrate production. The butyrogenic reactor was operated at 37°C and pH 5.5 with a hydraulic retention time of 31 h and a low hydrogen partial pressure (PH2)...
July 2017: MSystems
https://www.readbyqxmd.com/read/28761145/large-scale-differences-in-microbial-biodiversity-discovery-between-16s-amplicon-and-shotgun-sequencing
#7
Michael Tessler, Johannes S Neumann, Ebrahim Afshinnekoo, Michael Pineda, Rebecca Hersch, Luiz Felipe M Velho, Bianca T Segovia, Fabio A Lansac-Toha, Michael Lemke, Rob DeSalle, Christopher E Mason, Mercer R Brugler
Modern metagenomic environmental DNA studies are almost completely reliant on next-generation sequencing, making evaluations of these methods critical. We compare two next-generation sequencing techniques - amplicon and shotgun - on water samples across four of Brazil's major river floodplain systems (Amazon, Araguaia, Paraná, and Pantanal). Less than 50% of phyla identified via amplicon sequencing were recovered from shotgun sequencing, clearly challenging the dogma that mid-depth shotgun recovers more diversity than amplicon-based approaches...
July 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28751211/microbial-f-type-lectin-domains-with-affinity-for-blood-group-antigens
#8
Sonal Mahajan, Aasawari Khairnar, Ritika Bishnoi, T N C Ramya
F-type lectins are fucose binding lectins with characteristic fucose binding and calcium binding motifs. Although they occur with a selective distribution in viruses, prokaryotes and eukaryotes, most biochemical studies have focused on vertebrate F-type lectins. Recently, using sensitive bioinformatics search techniques on the non-redundant database, we had identified many microbial F-type lectin domains with diverse domain organizations. We report here the biochemical characterization of F-type lectin domains from Cyanobium sp...
July 24, 2017: Biochemical and Biophysical Research Communications
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
#9
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/a-deep-metaproteomics-approach-for-the-study-of-human-microbiomes
#10
Xu Zhang, Wendong Chen, Zhibin Ning, Janice Mayne, David R 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 ultra-deep metaproteomic analysis of human gut microbiome from stool...
July 27, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28733590/hypersaline-sapropels-act-as-hotspots-for-microbial-dark-matter
#11
Adrian-Ştefan Andrei, Andreea Baricz, Michael Scott Robeson, Manuela Raluca Păuşan, Tudor Tămaş, Cecilia Chiriac, Edina Szekeres, Lucian Barbu-Tudoran, Erika Andrea Levei, Cristian Coman, Mircea Podar, Horia Leonard Banciu
Present-day terrestrial analogue sites are crucial ground truth proxies for studying life in geochemical conditions close to those assumed to be present on early Earth or inferred to exist on other celestial bodies (e.g. Mars, Europa). Although hypersaline sapropels are border-of-life habitats with moderate occurrence, their microbiological and physicochemical characterization lags behind. Here, we study the diversity of life under low water activity by describing the prokaryotic communities from two disparate hypersaline sapropels (Transylvanian Basin, Romania) in relation to geochemical milieu and pore water chemistry, while inferring their role in carbon cycling by matching taxa to known taxon-specific biogeochemical functions...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28731467/uncultivated-microbes-in-need-of-their-own-taxonomy
#12
Konstantinos T Konstantinidis, Ramon Rosselló-Móra, Rudolf Amann
The great majority of microbial species remains uncultured, severely limiting their taxonomic characterization and thus communication among scientists. Although Candidatus was devised as a provisional category to classify uncultured taxa, it has not been widely accepted owing to technical limitations and lack of priority of Candidatus names in the official nomenclature. High-throughput sequencing provides the potential for data-rich taxonomic descriptions of uncultivated microbes, comparable in quality to those of cultured organisms...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28727425/the-database-and-bioinformatics-studies-of-probiotics
#13
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 of 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...
July 20, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28719833/in-silico-search-of-inhibitors-of-streptococcus-mutans-for-the-control-of-dental-plaque
#14
Rodrigo Ochoa, María Cecilia Martínez-Pabón, María Adelaida Arismendi-Echeverri, Willer Leandro Rendón-Osorio, Carlos Enrique Muskus-López
Biofilm is an extremely complex microbial community arranged in a matrix of polysaccharides and attached to a substrate. Its development is crucial in the pathophysiology of oral infections like dental caries, as well as in periodontal, pulp, and periapical diseases. Streptococcus mutans is one of the most effective microorganisms in lactic acid production of the dental biofilm. Identifying essential Streptococcus mutans proteins using bioinformatics methods helps to search for alternative therapies. To this end, the bacterial genomes of several Streptococcus mutans strains and representative strains of other cariogenic and non-cariogenic bacteria were analysed by identifying pathogenicity islands and alignments with other bacteria, and by detecting the exclusive genes of cariogenic species in comparison to the non-pathogenic ones...
July 1, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28718274/-microbiome-and-next-generation-sequencing
#15
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/28705636/a-review-of-bioinformatics-platforms-for-comparative-genomics-recent-developments-of-the-edgar-2-0-platform-and-its-utility-for-taxonomic-and-phylogenetic-studies
#16
J Yu, J Blom, S P Glaeser, S Jaenicke, T Juhre, O Rupp, O Schwengers, S Spänig, A Goesmann
The rapid development of next generation sequencing technology has greatly increased the amount of available microbial genomes. As a result of this development, there is a rising demand for fast and automated approaches in analyzing these genomes in a comparative way. Whole genome sequencing also bears a huge potential for obtaining a higher resolution in phylogenetic and taxonomic classification. During the last decade, several software tools and platforms have been developed in the field of comparative genomics...
July 10, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28690805/evaluating-hybridization-capture-with-rad-probes-as-a-tool-for-museum-genomics-with-historical-bird-specimens
#17
Ethan B Linck, Zachary R Hanna, Anna Sellas, John P Dumbacher
Laboratory techniques for high-throughput sequencing have enhanced our ability to generate DNA sequence data from millions of natural history specimens collected prior to the molecular era, but remain poorly tested at shallower evolutionary time scales. Hybridization capture using restriction site-associated DNA probes (hyRAD) is a recently developed method for population genomics with museum specimens. The hyRAD method employs fragments produced in a restriction site-associated double digestion as the basis for probes that capture orthologous loci in samples of interest...
July 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28690211/new-perspectives-on-dandruff-and-seborrheic-dermatitis-lessons-we-learned-from-bacterial-and-fungal-skin-microbiota
#18
Luciana Campos Paulino
The human body is inhabited by complex microbial communities, which positively impact different aspects of our health, and might also be related to the development of diseases. Progress in technologies, particularly sequencing methods and bioinformatics tools, has been crucial for the advances in this field. Microbial communities from skin can modulate immune response and protect the host against pathogens, and there are also data supporting their association with several skin conditions; including dandruff and seborrheic dermatitis...
June 1, 2017: European Journal of Dermatology: EJD
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/28683838/a-novel-ultra-high-throughput-16s-rrna-gene-amplicon-sequencing-library-preparation-method-for-the-illumina-hiseq-platform
#20
Eric J de Muinck, Pål Trosvik, Gregor D Gilfillan, Johannes R Hov, Arvind Y M Sundaram
BACKGROUND: Advances in sequencing technologies and bioinformatics have made the analysis of microbial communities almost routine. Nonetheless, the need remains to improve on the techniques used for gathering such data, including increasing throughput while lowering cost and benchmarking the techniques so that potential sources of bias can be better characterized. METHODS: We present a triple-index amplicon sequencing strategy to sequence large numbers of samples at significantly lower c ost and in a shorter timeframe compared to existing methods...
July 6, 2017: Microbiome
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