Academic literature on the topic 'Operational taxonomic units (OTU)'
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Journal articles on the topic "Operational taxonomic units (OTU)"
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Ramette, Alban. "Quantitative Community Fingerprinting Methods for Estimating the Abundance of Operational Taxonomic Units in Natural Microbial Communities." Applied and Environmental Microbiology 75, no. 8 (2009): 2495–505. http://dx.doi.org/10.1128/aem.02409-08.
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ABSTRACT Molecular fingerprinting techniques offer great promise for analyzing changes in microbial community structure, especially when dealing with large number of samples. However, a serious limitation has been the lack of quantification offered by such techniques since the relative abundances of the identified operational taxonomic units (OTUs) in the original samples are not measured. A quantitative fingerprinting approach designated “qfingerprinting” is proposed here. This method involves serial dilutions of the sample of interest and further systematic fingerprinting of all dilution series. Using the ultimate dilutions for which OTU are still PCR amplifiable and taking into account peak size inaccuracy and peak reproducibility, the relative abundance of each OTU is then simultaneously determined over a scale spanning several orders of magnitude. The approach was illustrated by using a quantitative version of automated ribosomal intergenic spacer analysis (ARISA), here called qARISA. After validating the concept with a synthetic mixture of known DNA targets, qfingerprinting was applied to well-studied marine sediment samples to examine specific changes in OTU abundance associated with sediment depth. The new strategy represents a major advance for the detailed quantitative description of specific OTUs within complex communities. Further ecological applications of the new strategy are also proposed.
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Jackson, Matthew A., Jordana T. Bell, Tim D. Spector, and Claire J. Steves. "A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units." PeerJ 4 (August 30, 2016): e2341. http://dx.doi.org/10.7717/peerj.2341.
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A variety of methods are available to collapse 16S rRNA gene sequencing reads to the operational taxonomic units (OTUs) used in microbiome analyses. A number of studies have aimed to compare the quality of the resulting OTUs. However, in the absence of a standard method to define and enumerate the different taxa within a microbial community, existing comparisons have been unable to compare the ability of clustering methods to generate units that accurately represent functional taxonomic segregation. We have previously demonstrated heritability of the microbiome and we propose this as a measure of each methods’ ability to generate OTUs representing biologically relevant units. Our approach assumes that OTUs that best represent the functional units interacting with the hosts’ properties will produce the highest heritability estimates. Using 1,750 unselected individuals from the TwinsUK cohort, we compared 11 approaches to OTU clustering in heritability analyses. We find that de novo clustering methods produce more heritable OTUs than reference based approaches, with VSEARCH and SUMACLUST performing well. We also show that differences resulting from each clustering method are minimal once reads are collapsed by taxonomic assignment, although sample diversity estimates are clearly influenced by OTU clustering approach. These results should help the selection of sequence clustering methods in future microbiome studies, particularly for studies of human host-microbiome interactions.
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Westcott, Sarah L., and Patrick D. Schloss. "De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units." PeerJ 3 (December 8, 2015): e1487. http://dx.doi.org/10.7717/peerj.1487.
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Background.16S rRNA gene sequences are routinely assigned to operational taxonomic units (OTUs) that are then used to analyze complex microbial communities. A number of methods have been employed to carry out the assignment of 16S rRNA gene sequences to OTUs leading to confusion over which method is optimal. A recent study suggested that a clustering method should be selected based on its ability to generate stable OTU assignments that do not change as additional sequences are added to the dataset. In contrast, we contend that the quality of the OTU assignments, the ability of the method to properly represent the distances between the sequences, is more important.Methods.Our analysis implemented sixde novoclustering algorithms including the single linkage, complete linkage, average linkage, abundance-based greedy clustering, distance-based greedy clustering, and Swarm and the open and closed-reference methods. Using two previously published datasets we used the Matthew’s Correlation Coefficient (MCC) to assess the stability and quality of OTU assignments.Results.The stability of OTU assignments did not reflect the quality of the assignments. Depending on the dataset being analyzed, the average linkage and the distance and abundance-based greedy clustering methods generated OTUs that were more likely to represent the actual distances between sequences than the open and closed-reference methods. We also demonstrated that for the greedy algorithms VSEARCH produced assignments that were comparable to those produced by USEARCH making VSEARCH a viable free and open source alternative to USEARCH. Further interrogation of the reference-based methods indicated that when USEARCH or VSEARCH were used to identify the closest reference, the OTU assignments were sensitive to the order of the reference sequences because the reference sequences can be identical over the region being considered. More troubling was the observation that while both USEARCH and VSEARCH have a high level of sensitivity to detect reference sequences, the specificity of those matches was poor relative to the true best match.Discussion.Our analysis calls into question the quality and stability of OTU assignments generated by the open and closed-reference methods as implemented in current version of QIIME. This study demonstrates thatde novomethods are the optimal method of assigning sequences into OTUs and that the quality of these assignments needs to be assessed for multiple methods to identify the optimal clustering method for a particular dataset.
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Schloss, Patrick D., and Sarah L. Westcott. "Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis." Applied and Environmental Microbiology 77, no. 10 (2011): 3219–26. http://dx.doi.org/10.1128/aem.02810-10.
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ABSTRACTIn spite of technical advances that have provided increases in orders of magnitude in sequencing coverage, microbial ecologists still grapple with how to interpret the genetic diversity represented by the 16S rRNA gene. Two widely used approaches put sequences into bins based on either their similarity to reference sequences (i.e., phylotyping) or their similarity to other sequences in the community (i.e., operational taxonomic units [OTUs]). In the present study, we investigate three issues related to the interpretation and implementation of OTU-based methods. First, we confirm the conventional wisdom that it is impossible to create an accurate distance-based threshold for defining taxonomic levels and instead advocate for a consensus-based method of classifying OTUs. Second, using a taxonomic-independent approach, we show that the average neighbor clustering algorithm produces more robust OTUs than other hierarchical and heuristic clustering algorithms. Third, we demonstrate several steps to reduce the computational burden of forming OTUs without sacrificing the robustness of the OTU assignment. Finally, by blending these solutions, we propose a new heuristic that has a minimal effect on the robustness of OTUs and significantly reduces the necessary time and memory requirements. The ability to quickly and accurately assign sequences to OTUs and then obtain taxonomic information for those OTUs will greatly improve OTU-based analyses and overcome many of the challenges encountered with phylotype-based methods.
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Galimberti, Andrea, Martina Spada, Danilo Russo, et al. "Integrated Operational Taxonomic Units (IOTUs) in Echolocating Bats: A Bridge between Molecular and Traditional Taxonomy." PLoS ONE 7, no. 6 (2012): e40122. https://doi.org/10.5281/zenodo.13484858.
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(Uploaded by Plazi for the Bat Literature Project) Background: Nowadays, molecular techniques are widespread tools for the identification of biological entities. However, until very few years ago, their application to taxonomy provoked intense debates between traditional and molecular taxonomists. To prevent every kind of disagreement, it is essential to standardize taxonomic definitions. Along these lines, we introduced the concept of Integrated Operational Taxonomic Unit (IOTU). IOTUs come from the concept of Operational Taxonomic Unit (OTU) and paralleled the Molecular Operational Taxonomic Unit (MOTU). The latter is largely used as a standard in many molecular-based works (even if not always explicitly formalized). However, while MOTUs are assigned solely on molecular variation criteria, IOTUs are identified from patterns of molecular variation that are supported by at least one more taxonomic characteristic. Methodology/Principal Findings: We tested the use of IOTUs on the widest DNA barcoding dataset of Italian echolocating bats species ever assembled (i.e. 31 species, 209 samples). We identified 31 molecular entities, 26 of which corresponded to the morphologically assigned species, two MOTUs and three IOTUs. Interestingly, we found three IOTUs in Myotis nattereri, one of which is a newly described lineage found only in central and southern Italy. In addition, we found a level of molecular variability within four vespertilionid species deserving further analyses. According to our scheme two of them (i.e. M. bechsteinii and Plecotus auritus) should be ranked as unconfirmed candidate species (UCS). Conclusions/Significance: From a systematic point of view, IOTUs are more informative than the general concept of OTUs and the more recent MOTUs. According to information content, IOTUs are closer to species, although it is important to underline that IOTUs are not species. Overall, the use of a more precise panel of taxonomic entities increases the clarity in the systematic field and has the potential to fill the gaps between modern and traditional taxonomy.
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Galimberti, Andrea, Martina Spada, Danilo Russo, et al. "Integrated Operational Taxonomic Units (IOTUs) in Echolocating Bats: A Bridge between Molecular and Traditional Taxonomy." PLoS ONE 7, no. 6 (2012): e40122. https://doi.org/10.5281/zenodo.13484858.
Full textAbstract:
(Uploaded by Plazi for the Bat Literature Project) Background: Nowadays, molecular techniques are widespread tools for the identification of biological entities. However, until very few years ago, their application to taxonomy provoked intense debates between traditional and molecular taxonomists. To prevent every kind of disagreement, it is essential to standardize taxonomic definitions. Along these lines, we introduced the concept of Integrated Operational Taxonomic Unit (IOTU). IOTUs come from the concept of Operational Taxonomic Unit (OTU) and paralleled the Molecular Operational Taxonomic Unit (MOTU). The latter is largely used as a standard in many molecular-based works (even if not always explicitly formalized). However, while MOTUs are assigned solely on molecular variation criteria, IOTUs are identified from patterns of molecular variation that are supported by at least one more taxonomic characteristic. Methodology/Principal Findings: We tested the use of IOTUs on the widest DNA barcoding dataset of Italian echolocating bats species ever assembled (i.e. 31 species, 209 samples). We identified 31 molecular entities, 26 of which corresponded to the morphologically assigned species, two MOTUs and three IOTUs. Interestingly, we found three IOTUs in Myotis nattereri, one of which is a newly described lineage found only in central and southern Italy. In addition, we found a level of molecular variability within four vespertilionid species deserving further analyses. According to our scheme two of them (i.e. M. bechsteinii and Plecotus auritus) should be ranked as unconfirmed candidate species (UCS). Conclusions/Significance: From a systematic point of view, IOTUs are more informative than the general concept of OTUs and the more recent MOTUs. According to information content, IOTUs are closer to species, although it is important to underline that IOTUs are not species. Overall, the use of a more precise panel of taxonomic entities increases the clarity in the systematic field and has the potential to fill the gaps between modern and traditional taxonomy.
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Schloss, Patrick D., and Jo Handelsman. "Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness." Applied and Environmental Microbiology 71, no. 3 (2005): 1501–6. http://dx.doi.org/10.1128/aem.71.3.1501-1506.2005.
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ABSTRACT Although copious qualitative information describes the members of the diverse microbial communities on Earth, statistical approaches for quantifying and comparing the numbers and compositions of lineages in communities are lacking. We present a method that addresses the challenge of assigning sequences to operational taxonomic units (OTUs) based on the genetic distances between sequences. We developed a computer program, DOTUR, which assigns sequences to OTUs by using either the furthest, average, or nearest neighbor algorithm for each distance level. DOTUR uses the frequency at which each OTU is observed to construct rarefaction and collector's curves for various measures of richness and diversity. We analyzed 16S rRNA gene libraries derived from Scottish and Amazonian soils and the Sargasso Sea with DOTUR, which assigned sequences to OTUs rapidly and reliably based on the genetic distances between sequences and identified previous inconsistencies and errors in assigning sequences to OTUs. An analysis of the two 16S rRNA gene libraries from soil demonstrated that they do not contain enough sequences to support a claim that they contain different numbers of bacterial lineages with statistical confidence (P > 0.05), nor do they contain enough sequences to provide a robust estimate of species richness when an OTU is defined as containing sequences that are no more than 3% different from each other. In contrast, the richness of OTUs at the 3% level in the Sargasso Sea collection began to plateau after the sampling of 690 sequences. We anticipate that an equivalent extent of sampling for soil would require sampling more than 10,000 sequences, almost 100 times the size of typical sequence collections obtained from soil.
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Jackson, Matthew A., Ian B. Jeffery, Michelle Beaumont, et al. "Signatures of early frailty in the gut microbiota." Genome Medicine 8, no. 1 (2016): 8. https://doi.org/10.1186/s13073-016-0262-7.
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<strong>Background: </strong>Frailty is arguably the biggest problem associated with population ageing, and associates with gut microbiome composition in elderly and care-dependent individuals. Here we characterize frailty associations with the gut microbiota in a younger community dwelling population, to identify targets for intervention to encourage healthy ageing.<strong>Method: </strong>We analysed 16S rRNA gene sequence data derived from faecal samples obtained from 728 female twins. Frailty was quantified using a frailty index (FI). Mixed effects models were used to identify associations with diversity, operational taxonomic units (OTUs) and taxa. OTU associations were replicated in the Eldermet cohort. Phenotypes were correlated with modules of OTUs collapsed by co-occurrence.<strong>Results: </strong>Frailty negatively associated with alpha diversity of the gut microbiota. Models considering a number of covariates identified 637 OTUs associated with FI. Twenty-two OTU associations were significant independent of alpha diversity. Species more abundant with frailty included <i>Eubacterium dolichum</i> and <i>Eggerthella lenta</i>. A <i>Faecalibacterium prausnitzii</i> OTU was less abundant in frailer individuals, and retained significance in discordant twin analysis. Sixty OTU associations were replicated in the Eldermet cohort. OTU co-occurrence modules had mutually exclusive associations between frailty and alpha diversity.<strong>Conclusions: </strong>There was a striking negative association between frailty and gut microbiota diversity, underpinned by specific taxonomic associations. Whether these relationships are causal or consequential is unknown. Nevertheless, they represent targets for diagnostic surveillance, or for intervention studies to improve vitality in ageing.
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Park, Seunghyun, Hyun-soo Choi, Byunghan Lee, Jongsik Chun, Joong-Ho Won, and Sungroh Yoon. "hc-OTU: A Fast and Accurate Method for Clustering Operational Taxonomic Units Based on Homopolymer Compaction." IEEE/ACM Transactions on Computational Biology and Bioinformatics 15, no. 2 (2018): 441–51. http://dx.doi.org/10.1109/tcbb.2016.2535326.
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Juhel, Jean-Baptiste, Rizkie S. Utama, Virginie Marques, et al. "Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle." Proceedings of the Royal Society B: Biological Sciences 287, no. 1930 (2020): 20200248. http://dx.doi.org/10.1098/rspb.2020.0248.
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Environmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments, particularly for vertebrates in species-rich regions. However, this method requires the completeness of a reference database (i.e. a list of DNA sequences attached to each species), which is not currently achieved for many taxa and ecosystems. As an alternative, a range of operational taxonomic units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs provided by a limited eDNA sampling effort can predict regional species diversity is unknown. Here, by modelling OTU accumulation curves of eDNA seawater samples across the Coral Triangle, we obtained an asymptote reaching 1531 fish OTUs, while 1611 fish species are recorded in the region. We also accurately predict ( R ² = 0.92) the distribution of species richness among fish families from OTU-based asymptotes. Thus, the multi-model framework of OTU accumulation curves extends the use of eDNA metabarcoding in ecology, biogeography and conservation.
Dissertations / Theses on the topic "Operational taxonomic units (OTU)"
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Mann, Jenna D. "DNA barcodes and meiofaunal identification." Thesis, University of Edinburgh, 2010. http://hdl.handle.net/1842/4732.
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In recent years there has been a desire to definitively catalogue the life on our planet. In light of the increasing extinction rates that are driven by human activities, it is unlikely that this will be achieved using traditional methods. Whilst most organisms which have a body size of more than 1cm have been described, the vast majority of animal life is smaller than this, collectively known as meiofauna, and is yet to be catalogued. Meiofaunal organisms present a range of problems for traditional taxonomy. Firstly they are microscopic, meaning that morphological features are often difficult to resolve. Secondly these creatures often exhibit cryptic diversity meaning that different species often look the same. Thirdly, it is often the case that the organisms are poorly described in the literature making it very difficult to confirm identification, assuming that someone has already described it. It is possible, however, to obtain DNA sequences from these organisms. DNA barcoding, the use of short sequences of DNA to identify individuals, is now commonly used in a wide range of applications. It has been proposed that a single target gene should be sufficient to describe all organisms this way. Barcodes can be acquired from individuals or from bulk extractions from environmental samples. In the latter case, many of the sequences obtained are novel and unlikely to ever have a type specimen associated with them. When this is the case, assessing the diversity of a sample becomes a computational exercise. However, as yet, there is no agreed standard method adopted for analyzing the barcodes produced. Indeed most methods currently employed lack objectivity. This thesis investigates the efficiency of a range of gene targets and analysis methods for DNA barcoding, with an emphasis on meiofaunal organisms (nematodes, tardigrades and thrips). DNA barcodes were generated for up to three genes for each specimen. Sequences for each gene were analysed using two programs, MOTU_define.pl and DOTUR. These programs use different methods to assign sequences to operational taxonomic units (OTU), which were then compared. An objective method for analysing sequences such as MOTU_define.pl, which relies on only the information contained in the sequences, was found to be most suitable for designating taxa. It does not attempt to apply evolutionary models to the data, and then infer taxa from the derived data. In addition to barcoding, some samples were pre-processed using video capture and editing (VCE). This creates a virtual slide of a specimen so that a sequence can be linked to a morphological identification. VCE proved to be an efficient method to preserve morphological data from specimens.
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Tarlinton, Boyd. "Phylosymbiosis and the microbiome of the native Australian stingless bee Tetragonula carbonaria." Thesis, Queensland University of Technology, 2021. https://eprints.qut.edu.au/212693/1/Boyd_Tarlinton_Thesis.pdf.
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Tetragonula carbonaria (Smith 1854) is a native Australian stingless bee, hosting a diverse range of bacterial symbionts. T. carbonaria is used as a model to explore how relationships between host insects and the microbiome occur and can be detected within a single species, shedding light on how host-microbiome associations arise and are maintained across the corbiculate bees. Host-microbiome relationships are considered through the lens of phylosymbiosis. Methods for detecting phylosymbiosis are explored; different bioinformatics and statistical techniques are compared, with implications for future studies. Bayesian modelling is used to predict possible routes of acquisition of bee symbionts.
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Medina, Pons Francisco Javier. "Diversidad y funcionamiento de la comunidad epífita eucariota de las hojas de Posidonia oceanica." Doctoral thesis, Universitat de les Illes Balears, 2012. http://hdl.handle.net/10803/84119.
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Variability in the structure of the macroeukaryotic epiphytic fraction of Posidonia oceanica
leaves has been previously described under optical microscope or dissecting microscope
(classical microscopy approach). We tested the sensitivity of two molecular techniques
(Temperature gradient gel electrophoresis (TGGE) and small ribosomal subunit (SSU) clone
libraries), as an alternative to classical microscopy method, to detect variability in the structure
of that epiphytic assemblage. We also investigated the relationship between
diversity/composition of epiphytic macroalgae, the most diverse and abundant component of
the assemblage, and Nitrate reductase (NR) activity (as a measure of nitrogen assimilation
capacity from water column, which is an ecosystem key process). TGGE and SSU clone
libraries were able to monitor changes in the structure of that assemblage and overcame some
disadvantages of the classical microscopy approach, such as taxonomic impediment. In
addition, the composition of the assemblage suggested playing a relevant role in determining nitrogen assimilation rates.<br>La variabilidad en la estructura de la fracción epífita macroeucariota de las hojas de Posidonia
oceanica se ha estudiado previamente mediante microscopio óptico o lupa binocular
(aproximación clasica). Por un lado, se estudió la sensibilidad de dos técnicas moleculares
(electroforesis en geles de gradiente de temperatura (TGGE) y librerías de clones de los
genes de la subunidad pequeña del ribosoma (SSU), como alternativa al método clásico, en la
detección de variabilidad en la estructura de esa comunidad epífita. Por otro lado, se investigó
la relación entre la diversidad/composición de las macroalgas epífitas, el componente más
abundante y diverso de esta comunidad, y la actividad Nitrato reductasa (NR) (como una
medidad de la capacidad de asimilación de nitrógeno de la columna de agua, un proceso clave
en el ecosistema). El TGGE y las librerías de clones de los genes SSU eran capaces de
monitorizar los cambios en la estructura de esa comunidad y permitían evitar algunos
inconvenientes de la aproximacion clásica, tales como problemas a nivel de taxonomía.
Además, los resultados obtenidos sugerían que la composición de la comunidad juega un
papel relevante a la hora de determinar las tasas de asimilación de nitrógeno.<br>La variabilitat en l'estructura de la fracció epífita macroeucariota de les fulles de Posidonia
oceanica s'ha estudiat prèviament mitjançant microscopi òptic o lupa binocular (aproximació
clàssica). D'una banda, es va estudiar la sensibilitat de dues tècniques moleculars
(electroforesi en gels de gradient de temperatura (TGGE) i llibreries de clons dels gens de la
subunitat petita del ribosoma (SSU), com a alternativa al mètode clàssic, en la detecció de
variabilitat en l'estructura d'aquesta comunitat epífita. D'altra banda, es va investigar la relació
entre la diversitat/composició de les macroalgues epífites, el component més abundant i divers
d'aquesta comunitat, i l'activitat Nitrat reductasa (NR) (com una mesura de la capacitat d'
assimilació de nitrògen de la columna d'aigua, un proces clau en l'ecosistema). El TGGE i les
llibreries de clons dels gens SSU varen permetre monitoritzar els canvis en l'estructura
d'aquesta comunitat i evitaven alguns inconvenients de l'aproximacio clàssica, com ara
problemes a nivell de taxonomia. A més a més, els resultats obtinguts suggerien que la
composició de la comunitat juga un papel rellevant a l'hora de determinar les taxes
d'assimilació de nitrògen.
Books on the topic "Operational taxonomic units (OTU)"
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Taberlet, Pierre, Aurélie Bonin, Lucie Zinger, and Eric Coissac. DNA metabarcoding data analysis. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198767220.003.0008.
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DNA metabarcoding generates huge amounts of data containing noise introduced by molecular methods. Chapter 8 “DNA metabarcoding data analysis” discusses the analytic steps and available software to curate and evaluate DNA metabarcoding data prior to final ecological analyses. It provides command lines to perform primary analyses of Illumina sequencing data with the OBITools, ranging from read assignment to samples to the formation of molecular operational taxonomic units (MOTUs) and their assignment to a taxon through comparison against reference databases. Chapter 8 also develops several methods to further curate sequencing data from contaminants or dysfunctional PCRs by using DNA extraction, PCR, and sequencing blank controls as well as PCR/biological replicates. It also presents several classical analyses to ensure that the diversity of the sample or the study site is appropriately covered. Finally, this chapter considers what conclusions on biodiversity and ecological processes can be really drawn from metabarcoding data.
Book chapters on the topic "Operational taxonomic units (OTU)"
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Rosselló-Mora, Ramon, and Arantxa López-López. "The Least Common Denominator: Species or Operational Taxonomic Units?" In Accessing Uncultivated Microorganisms. ASM Press, 2014. http://dx.doi.org/10.1128/9781555815509.ch7.
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Guha, Subharup, and Somnath Datta. "A Bayesian Approach to Restoring the Duality Between Principal Components of a Distance Matrix and Operational Taxonomic Units in Microbiome Analyses." In Statistical Analysis of Microbiome Data. Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-73351-3_11.
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"Operational Taxonomic Unit (OTU)." In Encyclopedia of Genetics, Genomics, Proteomics and Informatics. Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6754-9_11891.
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"OTU (operational taxonomic unit)." In Encyclopedia of Genetics, Genomics, Proteomics and Informatics. Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6754-9_12016.
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Rowe, Graham, Michael Sweet, and Trevor J. C. Beebee. "Microbial ecology and metagenomics." In An Introduction to Molecular Ecology. Oxford University Press, 2017. http://dx.doi.org/10.1093/hesc/9780198716990.003.0011.
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This chapter explores microbial ecology and metagenomics. It notes the role of microbial communities in nature in line with outstanding issues in microbial ecology such as species identification, population dynamics, and community structure. Moreover, the chapter explains immunological and genomic approaches to microbial ecology. An example of which would be antibody identification. The chapter also discusses metagenomics in relation to ribosomal sequences and microbial ecology. The chapter looks at the genetic variability of bacteria species. It also discusses the phylogeography of viruses, bacteria, and fungi. DNA hybridization methods based on DNA microarray technology offer great promise on microbial identification and community analysis, especially where it is necessary to resolve closely related operational taxonomic units (OTU).
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Crandall, Keith A., and Alan R. Templeton. "Applications of intraspecific phylogenetics." In New Uses for New Phylogenies. Oxford University PressOxford, 1996. http://dx.doi.org/10.1093/oso/9780198549857.003.0006.
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Abstract Recent advances in population genetics theory, especially coalescent theory (Tavaré 1984; Watterson 1984; Ewens 1990; Hudson 1990), coupled with an explosion of molecular techniques have allowed detailed phylogenetic information at the population level. Such genealogical relationships are termed gene trees, allele trees, or haplotype trees (we use haplotype throughout this chapter) in which different haplotypes are the operational taxonomic units. Avise and colleagues were the first to utilize this powerful molecular phylogenetic approach for studies of population genetics, especially relating to biogeographic patterns (Avise et al. 1987; Avise 1989, 1994). Their approach explores qualitatively the relationship between lineage divergence and the extent of geographical partitioning among haplotypes.
Conference papers on the topic "Operational taxonomic units (OTU)"
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Wrangham, Jodi B., Joseph E. Penkala, Seth D’Imperio, Brent M. Peyton, and Kenneth G. Wunch. "Utilization of a 16S rRNA Gene Microarray to Analyze the Efficacy of Oil and Gas Industry Bacteria Culture Media." In CORROSION 2010. NACE International, 2010. https://doi.org/10.5006/c2010-10408.
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Abstract It is widely recognized that bacteria and archae are frequently contained within production fluids and can cause numerous problems and cost countless dollars to the oil and gas industries. Current techniques commonly employed to detect and enumerate these microorganisms and to test the efficacy of microbiocides focus on serial dilution culture methods. Unfortunately, culture-dependent methods allow for the growth of only a fraction of the field population present and do not support the growth of numerous potentially significant species. Currently, it is estimated that less than 15% of field populations can be cultivated by these means. In this study, genetic profile analyses of microbial communities present in produced water samples were compared to those that were derived from culturing that produced water using various commonly used growth media. Genetic analyses utilized a 16S rRNA gene microarray which can detect 8,741 OTUs (Operational Taxonomic Units) in a single test. As expected and in congruence with samples from other environments, cultivation-dependent techniques greatly underestimated the microbial diversity present. These results illustrate one of the fundamental problems of culture-dependent techniques: the large discrepancy between the microorganism population that is cultivated and detected in culture mediums and the population that is actually present in the oil and gas field environment.