PhylOPDb: a 16S rRNA oligonucleotide probe database for prokaryotic identification

Jaziri, Faouzi; Parisot, Nicolas; Abid, Anis; Denonfoux, Jérémie; Ribière, Céline; Gasc, Cyrielle; Boucher, Delphine; Brugère, Jean-François; Mahul, Antoine; Hill, David R.C.; Peyretaillade, Éric; Peyret, Pierre

doi:10.1093/database/bau036

Cited by 21 publications

(16 citation statements)

References 38 publications

(39 reference statements)

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“…The limited phylogenetic coverage of nanoSIMS might be overcome in the future by the steadily growing databases on species or phylum-specific probes [Cole et al, 2014;Jaziri et al, 2014] or by coupling nanoSIMS with microarrays (CHIP-SIP) [Mayali et al, 2012].…”

Section: Methods Developments In Sip Techniquesmentioning

confidence: 99%

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

et al. 2016

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Stable isotope probing (SIP) techniques have become state-of-the-art in microbial ecology over the last 10 years, allowing for the targeted detection and identification of organisms, metabolic pathways and elemental fluxes active in specific processes within complex microbial communities. For studying anaerobic hydrocarbon-degrading microbial communities, four stable isotope techniques have been used so far: DNA/RNA-SIP, PLFA (phospholipid-derived fatty acids)-SIP, protein-SIP, and single-cell-SIP by nanoSIMS (nanoscale secondary ion mass spectrometry) or confocal Raman microscopy. DNA/RNA-SIP techniques are most frequently applied due to their most meaningful phylogenetic resolution. Especially using ¹³C-labeled benzene and toluene as model substrates, many new hydrocarbon degraders have been identified by SIP under various electron acceptor conditions. This has extended the current perspective of the true diversity of anaerobic hydrocarbon degraders relevant in the environment. Syntrophic hydrocarbon degradation was found to be a common mechanism for various electron acceptors. Fundamental concepts and recent advances in SIP are reflected here. A discussion is presented concerning how these techniques generate direct insights into intrinsic hydrocarbon degrader populations in environmental systems and how useful they are for more integrated approaches in the monitoring of contaminated sites and for bioremediation.

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Section: Methods Developments In Sip Techniquesmentioning

confidence: 99%

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

et al. 2016

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“…It involves the enrichment of the target gene fragments out of a complex environmental genomic mixture, without PCR biases and direct metagenome sequencing limitations. The success of a gene capture experiment in environmental microbiology strongly depends on the high-quality probe set encompassing variant specific and explorative probes to reveal novelties coupled to adapted databases (Jaziri et al 2014). Additionally, this innovative strategy for microbial ecology allows recovering of large DNA fragments, therefore extending beyond the initial targeted biomarker gene sequence and thus facilitating the discovery of new genes or genomic organizations.…”

Section: Sequence Enrichment By Solution Hybrid Selection Capture Methodsmentioning

confidence: 99%

Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions

Chaudhary

Gaci

Borrel

et al. 2015

Appl Microbiol Biotechnol

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Until recently, human gut microbiota was believed to be colonized by few methanogenic archaeal species. Much higher microbial diversity within the human gut was revealed by the use of molecular approaches as compared to routine microbiological techniques, but still, a lot remains unknown. Molecular techniques has the advantage of being rapid, reproducible, and can be highly discriminative as compared to conventional culturing methods. Some of them provide both qualitative and quantitative information. However, the choice of method should be taken with care to avoid biases. The advent of next-generation sequencing gives much deeper information from which functional and ecological hypotheses can be drawn. In this review, molecular techniques that are currently used together with their possible future developments to study gut methanogenic communities are indicated along with their limitations and difficulties that are encountered during their implementation. Moreover, the high amount of metagenomics data from the human gut microbiome indicate that this environment could be a paradigm for new directions in methanogen diversity studies and help to develop new approaches for other environments as well. Concerning humans, this should help us to better understand the possible association of methanogens with some of the diseased conditions and their peculiar distribution among age groups in human.

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“…The double-labeled universal 16S rRNA probe allows for the unbiased detection of all bacterial species present within tissue and can provide valuable insight into how pathogens and the microbiota spatially interact with mucosal surfaces in disease and healthy states. Using resources such as probeBase, PhylOPDb or the PROBE_DESIGN tool of the ARB software package for the selection or design of species or genera-specific 16S or 23S rRNA probes, this protocol can be adapted for the detection of specific bacterial species or genera within tissue 15,21,22 . An important future direction for this method is multiplexing using species-or genera-specific probes labeled with different, discrete fluorophores for evaluation of microbial diversity within the bladder mucosa.…”

Section: Discussionmentioning

confidence: 99%

Detection of Tissue-resident Bacteria in Bladder Biopsies by 16S rRNA Fluorescence In Situ Hybridization

Neugent¹,

Gadhvi²,

Palmer³

et al. 2019

JoVE

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Visualization of the interaction of bacteria with host mucosal surfaces and tissues can provide valuable insight into mechanisms of pathogenesis. While visualization of bacterial pathogens in animal models of infection can rely on bacterial strains engineered to express fluorescent proteins such as GFP, visualization of bacteria within the mucosa of biopsies or tissue obtained from human patients requires an unbiased method. Here, we describe an efficient method for the detection of tissue-associated bacteria in human biopsy sections. This method utilizes fluorescent in situ hybridization (FISH) with a fluorescently labeled universal oligonucleotide probe for 16S rRNA to label tissue-associated bacteria within bladder biopsy sections acquired from patients suffering from recurrent urinary tract infection. Through use of a universal 16S rRNA probe, bacteria can be detected without prior knowledge of species, genera, or biochemical characteristics, such as lipopolysaccharide (LPS), that would be required for detection by immunofluorescence experiments. We describe a complete protocol for 16S rRNA FISH from biopsy fixation to imaging by confocal microscopy. This protocol can be adapted for use in almost any type of tissue and represents a powerful tool for the unbiased visualization of clinically-relevant bacterial-host interactions in patient tissue. Furthermore, using species or genera-specific probes, this protocol can be adapted for the detection of specific bacterial pathogens within patient tissue.

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PhylOPDb: a 16S rRNA oligonucleotide probe database for prokaryotic identification

Cited by 21 publications

References 38 publications

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions

Detection of Tissue-resident Bacteria in Bladder Biopsies by 16S rRNA Fluorescence In Situ Hybridization

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