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Microbial bioinformatics

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https://www.readbyqxmd.com/read/28731467/uncultivated-microbes-in-need-of-their-own-taxonomy
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
https://www.readbyqxmd.com/read/28682460/strategies-for-managing-rival-bacterial-communities-lessons-from-burying-beetles
#10
Ana Duarte, Martin Welch, Chris Swannack, Josef Wagner, Rebecca M Kilner
1.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. 2.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
https://www.readbyqxmd.com/read/28680972/non-toxin-producing-bacillus-cereus-strains-belonging-to-the-b-%C3%A2-anthracis-clade-isolated-from-the-international-space-station
#11
Kasthuri Venkateswaran, Nitin K Singh, Aleksandra Checinska Sielaff, Robert K Pope, Nicholas H Bergman, Sandra P van Tongeren, Nisha B Patel, Paul A Lawson, Masataka Satomi, Charles H D Williamson, Jason W Sahl, Paul Keim, Duane Pierson, Jay Perry
In an ongoing Microbial Observatory investigation of the International Space Station (ISS), 11 Bacillus strains (2 from the Kibo Japanese experimental module, 4 from the U.S. segment, and 5 from the Russian module) were isolated and their whole genomes were sequenced. A comparative analysis of the 16S rRNA gene sequences of these isolates showed the highest similarity (>99%) to the Bacillus anthracis-B. cereus-B. thuringiensis group. The fatty acid composition, polar lipid profile, peptidoglycan type, and matrix-assisted laser desorption ionization-time of flight profiles were consistent with the B...
May 2017: MSystems
https://www.readbyqxmd.com/read/28669592/personalized-microbiome-dynamics-cytometric-fingerprints-for-routine-diagnostics
#12
REVIEW
Christin Koch, Susann Müller
Microbiomes convoy human life in countless ways. They are an essential part of the human body and interact with its host in countless ways. Currently, extensive microbiome analyses assessing the microbiomes' composition and functions based on sequencing information are still far away from being routine analyses due to the complexity of applied techniques and data analysis, their time demand as well as high costs. With the growing demand for on-time community assessment and monitoring of its dynamic behavior with high resolution, alternative high-throughput methods such as microbial community flow cytometry come into focus...
June 29, 2017: Molecular Aspects of Medicine
https://www.readbyqxmd.com/read/28666129/microbial-community-profiling-of-fresh-basil-and-pitfalls-in-taxonomic-assignment-of-enterobacterial-pathogenic-species-based-upon-16s-rrna-amplicon-sequencing
#13
Siele Ceuppens, Dieter De Coninck, Nadine Bottledoorn, Filip Van Nieuwerburgh, Mieke Uyttendaele
Application of 16S rRNA (gene) amplicon sequencing on food samples is increasingly applied for assessing microbial diversity but may as unintended advantage also enable simultaneous detection of any human pathogens without a priori definition. In the present study high-throughput next-generation sequencing (NGS) of the V1-V2-V3 regions of the 16S rRNA gene was applied to identify the bacteria present on fresh basil leaves. However, results were strongly impacted by variations in the bioinformatics analysis pipelines (MEGAN, SILVAngs, QIIME and MG-RAST), including the database choice (Greengenes, RDP and M5RNA) and the annotation algorithm (best hit, representative hit and lowest common ancestor)...
June 17, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28663049/challenges-and-perspectives-of-metaproteomic-data-analysis
#14
Robert Heyer, Kay Schallert, Roman Zoun, Beatrice Becher, Gunter Saake, Dirk Benndorf
In nature microorganisms live in complex microbial communities. Comprehensive taxonomic and functional knowledge about microbial communities supports medical and technical application such as fecal diagnostics as well as operation of biogas plants or waste water treatment plants. Furthermore, microbial communities are crucial for the global carbon and nitrogen cycle in soil and in the ocean. Among the methods available for investigation of microbial communities, metaproteomics can approximate the activity of microorganisms by investigating the protein content of a sample...
June 26, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28655556/comparison-of-two-bioinformatics-tools-used-to-characterize-the-microbial-diversity-and-predictive-functional-attributes-of-microbial-mats-from-lake-obersee-antarctica
#15
Hyunmin Koo, Joseph A Hakim, Casey D Morrow, Peter G Eipers, Alfonso Davila, Dale T Andersen, Asim K Bej
In this study, using NextGen sequencing of the collective 16S rRNA genes obtained from two sets of samples collected from Lake Obersee, Antarctica, we compared and contrasted two bioinformatics tools, PICRUSt and Tax4Fun. We then developed an R script to assess the taxonomic and predictive functional profiles of the microbial communities within the samples. Taxa such as Pseudoxanthomonas, Planctomycetaceae, Cyanobacteria Subsection III, Nitrosomonadaceae, Leptothrix, and Rhodobacter were exclusively identified by Tax4Fun that uses SILVA database; whereas PICRUSt that uses Greengenes database uniquely identified Pirellulaceae, Gemmatimonadetes A1-B1, Pseudanabaena, Salinibacterium and Sinobacteraceae...
June 24, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28649474/using-high-throughput-sequencing-of-its2-to-describe-symbiodinium-metacommunities-in-st-john-us-virgin-islands
#16
Ross Cunning, Ruth D Gates, Peter J Edmunds
Symbiotic microalgae (Symbiodinium spp.) strongly influence the performance and stress-tolerance of their coral hosts, making the analysis of Symbiodinium communities in corals (and metacommunities on reefs) advantageous for many aspects of coral reef research. High-throughput sequencing of ITS2 nrDNA offers unprecedented scale in describing these communities, yet high intragenomic variability at this locus complicates the resolution of biologically meaningful diversity. Here, we demonstrate that generating operational taxonomic units by clustering ITS2 sequences at 97% similarity within, but not across, samples collapses sequence diversity that is more likely to be intragenomic, while preserving diversity that is more likely interspecific...
2017: PeerJ
https://www.readbyqxmd.com/read/28648489/pyrosequencing-analysis-of-cryogenically-ground-samples-from-primary-and-secondary-persistent-endodontic-infections
#17
Cangül Keskin, Ebru Özsezer Demiryürek, Ertan Emek Onuk
INTRODUCTION: This study aimed to characterize the microbial communities of primary and secondary/persistent endodontic infections using high-throughput pyrosequencing from the pulverized samples. METHODS: The roots of 20 extracted human teeth with primary endodontic infection and 20 teeth with secondary/persistent endodontic infection were collected. The outer surfaces of the roots were disinfected, and whole roots were cryopulverized. 16S amplicon pyrosequencing data from the DNA extracted from the pulverized root powders were obtained, and microorganism abundance and diversity were calculated...
June 22, 2017: Journal of Endodontics
https://www.readbyqxmd.com/read/28648396/25-years-of-serving-the-community-with-ribosomal-rna-gene-reference-databases-and-tools
#18
Frank Oliver Glöckner, Pelin Yilmaz, Christian Quast, Jan Gerken, Alan Beccati, Andreea Ciuprina, Gerrit Bruns, Pablo Yarza, Jörg Peplies, Ralf Westram, Wolfgang Ludwig
SILVA (lat. forest) is a comprehensive web resource, providing services around up to date, high-quality datasets of aligned ribosomal RNA gene (rDNA) sequences from the Bacteria, Archaea, and Eukaryota domains. SILVA dates back to the year 1991 when Dr. Wolfgang Ludwig from the Technical University Munich started the integrated software workbench ARB (lat. tree) to support high-quality phylogenetic inference and taxonomy based on the SSU and LSU rDNA marker genes. At that time, the ARB project maintained both, the sequence reference datasets and the software package for data analysis...
June 22, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28637810/mcclintock-an-integrated-pipeline-for-detecting-transposable-element-insertions-in-whole-genome-shotgun-sequencing-data
#19
Michael G Nelson, Raquel S Linheiro, Casey M Bergman
Transposable element (TE) insertions are among the most challenging type of variants to detect in genomic data because of their repetitive nature and complex mechanisms of replication. Nevertheless, the recent availability of large resequencing datasets has spurred development of many new methods to detect TE insertions in whole genome shotgun sequences. Here we report an integrated bioinformatics pipeline for the detection of TE insertions in whole genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods...
June 21, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28637301/eden-evolutionary-dynamics-within-environments
#20
Philipp C Münch, Bärbel Stecher, Alice C McHardy
Summary: Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data...
June 16, 2017: Bioinformatics
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