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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.
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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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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.
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Speck, Mark D., and Stuart P. Donachie. "Widespread Oceanospirillaceae Bacteria inPoritesspp." Journal of Marine Biology 2012 (2012): 1–7. http://dx.doi.org/10.1155/2012/746720.
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We present evidence that a clade of bacteria in the Oceanospirillaceae is widely distributed inPoritesspp. and other hermatypic corals.Bacteria16S rDNA clone libraries were prepared from community genomic DNA extracted fromPorites compressaandPorites lobatasurface mucus and adjacent seawater collected along a line transect off Maui. Phylogenetic affiliations of operational taxonomic units (OTUs) defined at the 97% level of nucleotide identity varied within and between the respectivePoritesspp. along the transect and differed from those in the seawater. One OTU (C7-A01), however, occurred in all mucus samples from bothPoritesspecies. C7-A01c affiliates with a clade of uncultivatedOceanospirillum-like bacteria; the nearest neighbors of this OTU have been reported only in the surface mucus layer ofPoritesspp. and other stony corals, in reef-dwelling invertebrates, and the corallivorous six-banded angelfish,Pomacanthus sexstriatus.
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Can, Mehmet, and Osman Gürsoy. "Clustering 16S rRNA for OTU prediction: A similarity based method." Heritage and Sustainable Development 1, no. 2 (2019): 78–83. http://dx.doi.org/10.37868/hsd.v1i2.4.
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To study the phylogeny and taxonomy of samples from complex environments Next-generation sequencing (NGS)-based 16S rRNA sequencing , which has been successfully used jointly with the PCR amplification and NGS technology. First step for many downstream analyses is clustering 16S rRNA sequences into operational taxonomic units (OTUs). Heuristic clustering is one of the most widely employed approaches for generating OTUs in which one or more seed sequences to represent each cluster are selected. In this work we chose five random seeds for each cluster from a genes library, and we present a novel distance measure to cluster bacteria in the sample. Artificially created sets of 16S rRNA genes selected from databases are successfully clustered with more than %98 accuracy, sensitivity, and specificity.
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Frøslev, Tobias, Thomas Jeppesen, Tim Robertson, and Dmitry Schigel. "eDNA Metabarcoding Data in the Global Biodiversity Information Facility (GBIF)." Biodiversity Information Science and Standards 7 (August 7, 2023): e110672. https://doi.org/10.3897/biss.7.110672.
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The Global Biodiversity Information Facility (GBIF) is an international network and data infrastructure that provides free and open access to biodiversity data from around the world, enabling scientists, policymakers, and the public to explore and analyze information about the Earth's living organisms. Originally developing at a distance from GBIF, metabarcoding of DNA has become a standard tool for detecting species in bulk samples or environmental samples such as soil, water, and air. Raw sequence data (fastq files) are often shared and deposited in dedicated repositories. Seen from a biodiversity documenting perspective, raw sequences have limited value, as several steps of bioinformatic processing and filtering are needed to arrive at a credible set of sequences that can be interpreted by comparing to a sequence reference database. Most often, such interpretated DNA metabarcoding data come in the shape a table with abundances of so-called Amplicon Sequence Variants (ASV) or Operational Taxonomic Units (OTU) across samples—a so-called ASV/OTU table—and some associated files, e.g., spatiotemporal and other sample metadata, and taxonomic inferences of sequences. In this session we present GBIF state-of-work and plans for developing and improving publishing and standardisation of OTU table-like biodiversity data for easier and broader reuse, including a prototype tool using the OTU table as a publishing model, mapping this research-familiar data format to the Darwin Core standard (Darwin Core Task Group 2009).
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House, Geoffrey L., Saliya Ekanayake, Yang Ruan, et al. "Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering." Applied and Environmental Microbiology 82, no. 16 (2016): 4921–30. http://dx.doi.org/10.1128/aem.00816-16.
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ABSTRACTArbuscular mycorrhizal (AM) fungi form mutualisms with plant roots that increase plant growth and shape plant communities. Each AM fungal cell contains a large amount of genetic diversity, but it is unclear if this diversity varies across evolutionary lineages. We found that sequence variation in the nuclear large-subunit (LSU) rRNA gene from 29 isolates representing 21 AM fungal species generally assorted into genus- and species-level clades, with the exception of species of the generaClaroideoglomusandEntrophospora. However, there were significant differences in the levels of sequence variation across the phylogeny and between genera, indicating that it is an evolutionarily constrained trait in AM fungi. These consistent patterns of sequence variation across both phylogenetic and taxonomic groups pose challenges to interpreting operational taxonomic units (OTUs) as approximations of species-level groups of AM fungi. We demonstrate that the OTUs produced by five sequence clustering methods using 97% or equivalent sequence similarity thresholds failed to match the expected species of AM fungi, although OTUs from AbundantOTU, CD-HIT-OTU, and CROP corresponded better to species than did OTUs from mothur or UPARSE. This lack of OTU-to-species correspondence resulted both from sequences of one species being split into multiple OTUs and from sequences of multiple species being lumped into the same OTU. The OTU richness therefore will not reliably correspond to the AM fungal species richness in environmental samples. Conservatively, this error can overestimate species richness by 4-fold or underestimate richness by one-half, and the direction of this error will depend on the genera represented in the sample.IMPORTANCEArbuscular mycorrhizal (AM) fungi form important mutualisms with the roots of most plant species. Individual AM fungi are genetically diverse, but it is unclear whether the level of this diversity differs among evolutionary lineages. We found that the amount of sequence variation in an rRNA gene that is commonly used to identify AM fungal species varied significantly between evolutionary groups that correspond to different genera, with the exception of two genera that are genetically indistinguishable from each other. When we clustered groups of similar sequences into operational taxonomic units (OTUs) using five different clustering methods, these patterns of sequence variation caused the number of OTUs to either over- or underestimate the actual number of AM fungal species, depending on the genus. Our results indicate that OTU-based inferences about AM fungal species composition from environmental sequences can be improved if they take these taxonomically structured patterns of sequence variation into account.
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Cornejo, Melitza, Krizia Pretell, Akemy Arévalo, Yacory Sernaqué, and Eric Mialhe. "Culture/Co-Culture Dependent and Independent Identification of Bacterial Communities along a Chronosequence of Spontaneous Reclamation on Gold Mine Spoils in Peru." Advanced Materials Research 1130 (November 2015): 589–93. http://dx.doi.org/10.4028/www.scientific.net/amr.1130.589.
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Cyanide leaching is currently the dominant process used by the mineral industry to extract gold and silver minerals. Cyanide is a nitrogen compound toxic for most living organisms. Many microorganisms are able to tolerate and degrade cyanide and its derivatives. In this study, were considered bacteria from soil and water samples corresponding to a chronological sequence (up to 5 years) of spontaneous cyanide bioremediation in a gold mining area (La Libertad Region, Peru). Culture dependent molecular identifications, based on 16S rDNA amplification and sequencing, were performed for bacteria isolated on agar media. Co-culture dependent molecular identifications were performed through 16S rDNA targeted metagenomics based on Next generation Sequencing with DNA directly extracted from the co-cultures in order to determine bacteria species unable to grow individually on agar media. Culture independent identifications were similarly performed through 16S rDNA targeted metagenomics from DNA directly extracted from water or soil samples in order to establish their respective global microbiota. Concerning cyanide contaminated soils, more than one hundred operational taxonomic units (OTU) were identified by metagenomics with only 30% species co-cultivable in broth medium and 82 isolated strains, in particularPseudomonasspp. The global microbiota in non-contaminated soils was markedly different. Concerning cyanide contaminated waters, about one hundred operational taxonomic units (OTU) were identified by metagenomics with only 30% species co-cultivable in broth medium. The most frequently identified species belong toAlcaligenes, Alkalibacterium, Bacillus, PaenibacillusandSerratia. Bacteria isolated and co-cultivated from contaminated waters and soils are currently analyzed as candidates for cyanide bioremediation.
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Gorrasi, Susanna, Marcella Pasqualetti, Barbara Muñoz-Palazon, et al. "Comparison of the Peel-Associated Epiphytic Bacteria of Anthocyanin-Rich “Sun Black” and Wild-Type Tomatoes under Organic and Conventional Farming." Microorganisms 10, no. 11 (2022): 2240. http://dx.doi.org/10.3390/microorganisms10112240.
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Tomatoes are among the most consumed vegetables worldwide and represent a source of health-beneficial substances. Our study represents the first investigating the peel-associated epiphytic bacteria of red and purple (anthocyanin-rich) tomatoes subjected to organic and conventional farming systems. Proteobacteria was the dominant phylum (relative abundances 79–91%) in all experimental conditions. Enterobacteriaceae represented a large fraction (39.3–47.5%) of the communities, with Buttiauxella and Atlantibacter as the most represented genera. The core microbiota was composed of 59 operational taxonomic units (OTUs), including the majority of the most abundant ones. The occurrence of the most abundant OTUs differed among the experimental conditions. OTU 1 (Buttiauxella), OTU 2 (Enterobacteriales), and OTU 6 (Bacillales) were higher in red and purple tomatoes grown under organic farming. OTU 5 (Acinetobacter) had the highest abundance in red tomatoes subjected to organic farming. OTU 3 (Atlantibacter) was among the major OTUs in red tomatoes under both farming conditions. OTU 7 (Clavibacter) and OTU 8 (Enterobacteriaceae) had abundances ≥1% only in red tomatoes grown under conventional farming. PCA and clustering analysis highlighted a high similarity between the bacterial communities of red and purple tomatoes grown under organic farming. Furthermore, the bacterial communities of purple tomatoes grown under organic farming showed the lowest diversity and evenness. This work paves the way to understand the role of nutritional superior tomato genotypes, combined with organic farming, to modulate the presence of beneficial/harmful bacteria and supply healthier foods within a sustainable agriculture.
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Zerva, Ioanna, Nikolaos Remmas, and Spyridon Ntougias. "Biocatalyst Potential of Cellulose-Degrading Microorganisms Isolated from Orange Juice Processing Waste." Beverages 5, no. 1 (2019): 21. http://dx.doi.org/10.3390/beverages5010021.
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Cellulases can be applied as macerating and peeling enzymes in the orange juice processing industry. In this work, indigenous cellulose-degrading microorganisms were isolated from orange juice processing waste through successive enrichment procedures using carboxymethyl cellulose (CMC) as the sole carbon source. A total of 24 microbial isolates were screened for their ability to grow in CMC liquid medium, resulting in the selection of seven isolates. The latter were further assessed by determining their endo-1,4-β-d-glucanase, exo-1,4-β-d-glucanase, and β-1,4-d-glucosidase activities, of which their respective activities were as high as 3.89, 10.67, and 10.69 U/mg protein. All cellulose-degraders selected belonged to the genus Paenibacillus, although to distinct operational taxonomic units related to P. xylanexedens, P. tundrae, and P. pabuli (operational taxonomic unit—OTU#1) and to P. wynnii, P. odorifer, and P. donghaensis (OTU#2) spectrum. Regarding the cellulase activities of the orange juice processing waste, endo-1,4-β-d-glucanase activity (4.00 ± 0.11 U/g) was exerted only extracellularly, whereas exo-1,4-β-d-glucanase (2.60 ± 0.19 U/g) and β-1,4-d-glucosidase (5.69 ± 0.23 U/g) activities were exhibited both extracellularly and intracellularly. In conclusion, orange juice processing waste can be considered as a valuable source for the isolation of cellulose-degrading microbiota with potential uses in beverage industry, solid state fermentation and energy production.
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Anderson, Michael, and Joshua Habiger. "Characterization and Identification of Productivity-Associated Rhizobacteria in Wheat." Applied and Environmental Microbiology 78, no. 12 (2012): 4434–46. http://dx.doi.org/10.1128/aem.07466-11.
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ABSTRACTThe rhizosphere is populated by a numerous and diverse array of rhizobacteria, and many impact productivity in largely unknown ways. Here we characterize the rhizobacterial community in a wheat variety categorized according to shoot biomass using 16S rRNA pyrosequencing abundance data. Plants were grown in homogenized field soil under greenhouse conditions, and DNA was extracted and pyrosequenced, resulting in 29,007 quality sequences. Operational taxonomic units (OTUs) that were significantly associated with biomass productivity were identified using an exact test adjusted for the false-discovery rate. The productivity deviation expressed as a percentage of the total mean square for regression (PMSR) was determined for each OTU. Out of 719 OTUs, 42 showed significant positive associations and 39 showed significant negative associations (qvalue, ≤0.05). OTUs with the greatest net positive associations, by genus, were as follows:Duganella, OTU 43 and OTU 3;Janthinobacterium, OTU 278;Pseudomonas, OTU 588; andCellvibrio, OTU 1847. Those with negative associations were as follows:Bacteria, OTU 273;Chryseobacterium, OTU 508;Proteobacteria, OTU 249; andEnterobacter, OTU 357. Shoot biomass productivity was strongly correlated with the balance between the overall abundances of positive- and negative-productivity-associated OTUs. High-productivity rhizospheres contained 9.2 significant positives for every negatively associated rhizobacterium, while low-productivity rhizospheres showed 2.3 significant negatives for every positively associated rhizobacterium. Overall rhizobacterial community diversity as measured by the Chao1, Shannon, and Simpson indexes was nonlinearly related to productivity, closely fitting a wavelike cubic equation. We conclude that shoot biomass productivity is strongly related to the ratio of positive- to negative-productivity-associated rhizobacteria in the rhizosphere. This study identifies significant OTUs composing the productive and unproductive rhizobacterial communities.
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Ceballos-Escalera, Angelina, John Richards, Maria Belen Arias, Daegan J. G. Inward, and Alfried P. Vogler. "Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers." MycoKeys 88 (March 8, 2022): 1–33. http://dx.doi.org/10.3897/mycokeys.88.77106.
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Full taxonomic characterisation of fungal communities is necessary for establishing ecological associations and early detection of pathogens and invasive species. Complex communities of fungi are regularly characterised by metabarcoding using the Internal Transcribed Spacer (ITS) and the Large-Subunit (LSU) gene of the rRNA locus, but reliance on a single short sequence fragment limits the confidence of identification. Here we link metabarcoding from the ITS2 and LSU D1-D2 regions to characterise fungal communities associated with bark beetles (Scolytinae), the likely vectors of several tree pathogens. Both markers revealed similar patterns of overall species richness and response to key variables (beetle species, forest type), but identification against the respective reference databases using various taxonomic classifiers revealed poor resolution towards lower taxonomic levels, especially the species level. Thus, Operational Taxonomic Units (OTUs) could not be linked via taxonomic classifiers across ITS and LSU fragments. However, using phylogenetic trees (focused on the epidemiologically important Sordariomycetes) we placed OTUs obtained with either marker relative to reference sequences of the entire rRNA cistron that includes both loci and demonstrated the largely similar phylogenetic distribution of ITS and LSU-derived OTUs. Sensitivity analysis of congruence in both markers suggested the biologically most defensible threshold values for OTU delimitation in Sordariomycetes to be 98% for ITS2 and 99% for LSU D1-D2. Studies of fungal communities using the canonical ITS barcode require corroboration across additional loci. Phylogenetic analysis of OTU sequences aligned to the full rRNA cistron shows higher success rate and greater accuracy of species identification compared to probabilistic taxonomic classifiers.
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Ceballos-Escalera, Angelina, John Richards, Maria Belen Arias, Daegan J. G. Inward, and Alfried P. Vogler. "Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers." MycoKeys 88 (March 8, 2022): 1–33. https://doi.org/10.3897/mycokeys.88.77106.
Full textAbstract:
Full taxonomic characterisation of fungal communities is necessary for establishing ecological associations and early detection of pathogens and invasive species. Complex communities of fungi are regularly characterised by metabarcoding using the Internal Transcribed Spacer (ITS) and the Large-Subunit (LSU) gene of the rRNA locus, but reliance on a single short sequence fragment limits the confidence of identification. Here we link metabarcoding from the ITS2 and LSU D1-D2 regions to characterise fungal communities associated with bark beetles (Scolytinae), the likely vectors of several tree pathogens. Both markers revealed similar patterns of overall species richness and response to key variables (beetle species, forest type), but identification against the respective reference databases using various taxonomic classifiers revealed poor resolution towards lower taxonomic levels, especially the species level. Thus, Operational Taxonomic Units (OTUs) could not be linked via taxonomic classifiers across ITS and LSU fragments. However, using phylogenetic trees (focused on the epidemiologically important Sordariomycetes) we placed OTUs obtained with either marker relative to reference sequences of the entire rRNA cistron that includes both loci and demonstrated the largely similar phylogenetic distribution of ITS and LSU-derived OTUs. Sensitivity analysis of congruence in both markers suggested the biologically most defensible threshold values for OTU delimitation in Sordariomycetes to be 98% for ITS2 and 99% for LSU D1-D2. Studies of fungal communities using the canonical ITS barcode require corroboration across additional loci. Phylogenetic analysis of OTU sequences aligned to the full rRNA cistron shows higher success rate and greater accuracy of species identification compared to probabilistic taxonomic classifiers.
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Zavadska, Daryna, Nicolas Henry, Adrià Auladell, Cédric Berney, and Daniel J. Richter. "Diverse patterns of correspondence between protist metabarcodes and protist metagenome-assembled genomes." PLOS ONE 19, no. 6 (2024): e0303697. http://dx.doi.org/10.1371/journal.pone.0303697.
Full textAbstract:
Two common approaches to study the composition of environmental protist communities are metabarcoding and metagenomics. Raw metabarcoding data are usually processed into Operational Taxonomic Units (OTUs) or amplicon sequence variants (ASVs) through clustering or denoising approaches, respectively. Analogous approaches are used to assemble metagenomic reads into metagenome-assembled genomes (MAGs). Understanding the correspondence between the data produced by these two approaches can help to integrate information between the datasets and to explain how metabarcoding OTUs and MAGs are related with the underlying biological entities they are hypothesised to represent. MAGs do not contain the commonly used barcoding loci, therefore sequence homology approaches cannot be used to match OTUs and MAGs. We made an attempt to match V9 metabarcoding OTUs from the 18S rRNA gene (V9 OTUs) and MAGs from the Tara Oceans expedition based on the correspondence of their relative abundances across the same set of samples. We evaluated several metrics for detecting correspondence between features in these two datasets and developed controls to filter artefacts of data structure and processing. After selecting the best-performing metrics, ranking the V9 OTU/MAG matches by their proportionality/correlation coefficients and applying a set of selection criteria, we identified candidate matches between V9 OTUs and MAGs. In some cases, V9 OTUs and MAGs could be matched with a one-to-one correspondence, implying that they likely represent the same underlying biological entity. More generally, matches we observed could be classified into 4 scenarios: one V9 OTU matches many MAGs; many V9 OTUs match many MAGs; many V9 OTUs match one MAG; one V9 OTU matches one MAG. Notably, we found some instances in which different OTU-MAG matches from the same taxonomic group were not classified in the same scenario, with all four scenarios possible even within the same taxonomic group, illustrating that factors beyond taxonomic lineage influence the relationship between OTUs and MAGs. Overall, each scenario produces a different interpretation of V9 OTUs, MAGs and how they compare in terms of the genomic and ecological diversity they represent.
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Torok, Valeria A., Gwen E. Allison, Nigel J. Percy, Kathy Ophel-Keller, and Robert J. Hughes. "Influence of Antimicrobial Feed Additives on Broiler Commensal Posthatch Gut Microbiota Development and Performance." Applied and Environmental Microbiology 77, no. 10 (2011): 3380–90. http://dx.doi.org/10.1128/aem.02300-10.
Full textAbstract:
ABSTRACTThe effects of avilamycin, zinc bacitracin, and flavophospholipol on broiler gut microbial community colonization and bird performance in the first 17 days posthatch were investigated. Significant differences in gut microbiota associated with gut section, dietary treatment, and age were identified by terminal restriction fragment length polymorphism (T-RFLP), although no performance-related differences between dietary treatments were detected. Similar age-related shifts in the gut microbiota were identified regardless of diet but varied between the ilea and ceca. Interbird variabilities in ileal bacterial communities were reduced (3 to 7 days posthatch) in chicks fed with feed containing antimicrobial agents. Avilamycin and flavophospholipol had the most consistent effect on gut microbial communities. Operational taxonomic units (OTU) linked to changes in gut microbiota in birds on antimicrobial-supplemented diets were characterized and identified. Some OTUs could be identified to the species level; however, the majority could be only tentatively classified to the genus, family, order, or domain level. OTUs 140 to 146 (Lachnospiraceae), OTU 186/188 (Lactobacillus johnsonii), OTU 220 (Lachnospiraceae), OTUs 284 to 288 (unclassified bacterial spp. orRuminococcaceae), OTU 296/298 (unclassified bacterium orClostridiales), and OTU 480/482 (Oxalobacteraceae) were less prevalent in the guts of chicks fed antimicrobial-supplemented diets. OTU 178/180 (Lactobacillus crispatus), OTU 152 (Lactobacillus reuterior unclassifiedClostridiales), OTU 198/200 (Subdoligranulumspp.), and OTU 490/492 (unclassified bacterium orEnterobacteriaceae) were less prevalent in the gut of chicks raised on the antimicrobial-free diet. The identification of key bacterial species influenced by antimicrobial-supplemented feed immediately posthatch may assist in the formulation of diets that facilitate beneficial gut microbial colonization and, hence, the development of alternatives to current antimicrobial agents in feed for sustainable poultry production.
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Dai, Mulan, Chantal Hamel, Marc St. Arnaud, et al. "Arbuscular mycorrhizal fungi assemblages in Chernozem great groups revealed by massively parallel pyrosequencing." Canadian Journal of Microbiology 58, no. 1 (2012): 81–92. http://dx.doi.org/10.1139/w11-111.
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The arbuscular mycorrhizal (AM) fungal resources present in wheat fields of the Canadian Prairie were explored using 454 pyrosequencing. Of the 33 dominant AM fungal operational taxonomic units (OTUs) found in the 76 wheat fields surveyed at anthesis in 2009, 14 clustered as Funneliformis – Rhizophagus, 16 as Claroideoglomus, and 3 as Diversisporales. An OTU of Funneliformis mosseae and one OTU of Diversisporales each accounted for approximately 16% of all AM fungal OTUs. The former was ubiquitous, and the latter was mainly restricted to the Black and Dark Brown Chernozems. AM fungal OTU community composition was better explained by the Chernozem great groups (P = 0.044) than by measured soil properties. Fifty-two percent of the AM fungal OTUs were unrelated to measured soil properties. Black Chernozems hosted the largest AM fungal OTU diversity and almost twice the number of AM fungal sequences seen in Dark Brown Chernozems, the great group ranking second for AM fungal sequence abundance. Brown Chernozems hosted the lowest AM fungal abundance and an AM fungal diversity as low as that seen in Gray soils. We concluded that Black Chernozems are most conducive to AM fungal proliferation. AM fungi are generally distributed according to Chernozem great groups in the Canadian Prairie, although some taxa are evenly distributed in all soil groups.
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Hu, Haiyang, Yunli Liu, Yiqun Huang, Zhan Zhang, and Hongzhi Tang. "The Leaf Microbiome of Tobacco Plants across Eight Chinese Provinces." Microorganisms 10, no. 2 (2022): 450. http://dx.doi.org/10.3390/microorganisms10020450.
Full textAbstract:
Leaf microorganism communities play significant roles in the process of plant growth, but the microbiome profiling of crop leaves is still a relatively new research area. Here, we used 16S rDNA sequencing to profile the microbiomes of 78 primary dried tobacco leaf samples from 26 locations in eight Chinese provinces. Our analyses revealed that the national leaf microbial communities contain 4473 operational taxonomic units (OTU) representing 1234 species, but there is a small, national core microbiome with only 14 OTU representing nine species. The function of this core microbiome is related to processes including nitrogen fixation, detoxification of diverse pollutants, and heavy-metal reduction. The leaf microorganism communities are obviously affected by local environments but did not exhibit obvious relationships to single ecological factors (e.g., temperature, precipitation). Our findings enhance the understanding of microbial diversity of tobacco leaves, which could be utilized for a variety of bioprocess, agricultural, and environmental detoxification applications.
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Nishitani, Goh, Satoshi Nagai, Shiho Hayakawa, et al. "Multiple Plastids Collected by the Dinoflagellate Dinophysis mitra through Kleptoplastidy." Applied and Environmental Microbiology 78, no. 3 (2011): 813–21. http://dx.doi.org/10.1128/aem.06544-11.
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ABSTRACTKleptoplastidy is the retention of plastids obtained from ingested algal prey, which may remain temporarily functional and be used for photosynthesis by the predator. We showed that the marine dinoflagellateDinophysis mitrahas great kleptoplastid diversity. We obtained 308 plastidrbcLsequences by gene cloning from 14D. mitracells and 102 operational taxonomic units (OTUs). Most sequences were new in the genetic database and positioned within Haptophyceae (227 sequences [73.7%], 80 OTUs [78.4%]), particularly within the genusChrysochromulina. Others were closely related to Prasinophyceae (16 sequences [5.2%], 5 OTUs [4.9%]), Dictyochophyceae (14 sequences [4.5%], 5 OTUs [4.9%]), Pelagophyceae (14 sequences [4.5%], 1 OTU [1.0%]), Bolidophyceae (3 sequences [1.0%], 1 OTU [1.0%]), and Bacillariophyceae (1 sequence [0.3%], 1 OTU [1.0%]); however, 33 sequences (10.8%) as 9 OTUs (8.8%) were not closely clustered with any particular group. Only six sequences were identical to those ofChrysochromulina simplex,Chrysochromulina hirta,Chrysochromulinasp. TKB8936,Micromonas pusillaNEPCC29,Micromonas pusillaCCMP491, and an unidentified diatom. Thus, we detected >100 different plastid sequences from 14D. mitracells, strongly suggesting kleptoplastidy and the need for mixotrophic prey such asLaboea,Tontonia, andStrombidium-like ciliates, which retain numerous symbiotic plastids from different origins, for propagation and plastid sequestration.
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Martynov, Alexander V., T. Sivaruban, Dmitry M. Palatov, et al. "Contribution to the knowledge of Teloganodidae (Ephemeroptera, Ephemerelloidea) of India." ZooKeys 1113 (July 18, 2022): 167–97. http://dx.doi.org/10.3897/zookeys.1113.85448.
Full textAbstract:
Two new species of Dudgeodes Sartori, 2008 and a new species of Teloganodes Eaton, 1882 are described from India; they are Dudgeodes selvakumari Martynov & Palatov, sp. nov. from Himalayan region (Uttarakhand), Dudgeodes molinerii Sivaruban, Martynov, Srinivasan, Barathy & Isack, sp. nov., and Teloganodes barathyae Sivaruban, Martynov, Srinivasan & Isack, sp. nov. from the Tamil Nadu part of the Western Ghats. Thus, for now, the Teloganodidae fauna of India includes 11 species. Dudgeodes selvakumarisp. nov. appears to be significantly extend northward the known distribution of Dudgeodes. Partial COI sequences were used as an initial clustering method to show the relationships of D. selvakumarisp. nov. with other sequenced operational taxonomic units (OTU) of the genus.
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Bruno, Laura, Daniela Billi, Simona Bellezza, and Patrizia Albertano. "Cytomorphological and Genetic Characterization of Troglobitic Leptolyngbya Strains Isolated from Roman Hypogea." Applied and Environmental Microbiology 75, no. 3 (2008): 608–17. http://dx.doi.org/10.1128/aem.01183-08.
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ABSTRACT Six Leptolyngbya strains, isolated from the archaeological surfaces of hypogean sites, were phenotypically and genetically characterized by light and electron microscopy and 16S rRNA gene and 16S-23S internally transcribed spacer (ITS) sequencing. Three phycoerythrin-rich (red) and three phycocyanin-rich (green) isolates were assigned to different operational taxonomic units (OTUs). Among the green isolates, one strain showed an OTU intraspecific variation due to differences in the ITS sequences and genomic polymorphism. Within the ITS sequence, variable regions, conserved domains and tRNAIle and tRNAAla genes showed high sequence identity among the phylotypes. Together, these data indicated a relatedness of the six strains to other Leptolyngbya from subaerophytic and geothermal environments and allowed the definition of novel Leptolyngbya OTUs.
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Martynov, Alexander V., T. Sivaruban, Dmitry M. Palatov, et al. "Contribution to the knowledge of Teloganodidae (Ephemeroptera, Ephemerelloidea) of India." ZooKeys 1113 (July 18, 2022): 167–97. https://doi.org/10.3897/zookeys.1113.85448.
Full textAbstract:
Two new species of Dudgeodes Sartori, 2008 and a new species of Teloganodes Eaton, 1882 are described from India; they are Dudgeodes selvakumari Martynov & Palatov, sp. nov. from Himalayan region (Uttarakhand), Dudgeodes molinerii Sivaruban, Martynov, Srinivasan, Barathy & Isack, sp. nov., and Teloganodes barathyae Sivaruban, Martynov, Srinivasan & Isack, sp. nov. from the Tamil Nadu part of the Western Ghats. Thus, for now, the Teloganodidae fauna of India includes 11 species. Dudgeodes selvakumari sp. nov. appears to be significantly extend northward the known distribution of Dudgeodes. Partial COI sequences were used as an initial clustering method to show the relationships of D. selvakumari sp. nov. with other sequenced operational taxonomic units (OTU) of the genus.
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Chiarello, Marlène, Mark McCauley, Sébastien Villéger, and Colin R. Jackson. "Ranking the biases: The choice of OTUs vs. ASVs in 16S rRNA amplicon data analysis has stronger effects on diversity measures than rarefaction and OTU identity threshold." PLOS ONE 17, no. 2 (2022): e0264443. http://dx.doi.org/10.1371/journal.pone.0264443.
Full textAbstract:
Advances in the analysis of amplicon sequence datasets have introduced a methodological shift in how research teams investigate microbial biodiversity, away from sequence identity-based clustering (producing Operational Taxonomic Units, OTUs) to denoising methods (producing amplicon sequence variants, ASVs). While denoising methods have several inherent properties that make them desirable compared to clustering-based methods, questions remain as to the influence that these pipelines have on the ecological patterns being assessed, especially when compared to other methodological choices made when processing data (e.g. rarefaction) and computing diversity indices. We compared the respective influences of two widely used methods, namely DADA2 (a denoising method) vs. Mothur (a clustering method) on 16S rRNA gene amplicon datasets (hypervariable region v4), and compared such effects to the rarefaction of the community table and OTU identity threshold (97% vs. 99%) on the ecological signals detected. We used a dataset comprising freshwater invertebrate (three Unionidae species) gut and environmental (sediment, seston) communities sampled in six rivers in the southeastern USA. We ranked the respective effects of each methodological choice on alpha and beta diversity, and taxonomic composition. The choice of the pipeline significantly influenced alpha and beta diversities and changed the ecological signal detected, especially on presence/absence indices such as the richness index and unweighted Unifrac. Interestingly, the discrepancy between OTU and ASV-based diversity metrics could be attenuated by the use of rarefaction. The identification of major classes and genera also revealed significant discrepancies across pipelines. Compared to the pipeline’s effect, OTU threshold and rarefaction had a minimal impact on all measurements.
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Fukasawa, Yu, Kimiyo Matsukura, Yoko Ando, et al. "Relative importance of climate, vegetation, and spatial factors in the community and functional composition of wood-inhabiting fungi in discontinuously distributed subalpine spruce forests." Canadian Journal of Forest Research 51, no. 7 (2021): 1029–38. http://dx.doi.org/10.1139/cjfr-2020-0344.
Full textAbstract:
Wood-inhabiting fungi are critically important for the decomposition of coarse woody debris (CWD). To evaluate the relative importance of climate, vegetation, and spatial factors in the functional composition of fungal communities that inhabit CWD in discontinuously distributed subalpine Hondo spruce (Picea jezoensis (Sieb. & Zucc.) Carr. var. hondoensis (Mayr) Rehder) forests, a metabarcoding analysis was conducted on spruce deadwood samples obtained from six subalpine forests in central Japan using a high-throughput DNA sequencing technique. We detected 454 fungal operational taxonomic units (OTUs) from 67 spruce CWDs and determined that spatial factors explained a larger fraction of community variation than environmental (climate and vegetation) factors at all six study sites. However, environmental factors explained a larger fraction than spatial factors if we excluded data from one site that is geographically distant from other study sites. The OTU number and the occurrence of brown-rot fungi were positively associated with mean annual temperature and negatively associated with mean annual precipitation. Similarly, the principal component of forest vegetation significantly affected the OTU number and occurrence of brown-rot fungi. Precipitation seasonality was positively associated with the OTU number of undefined saprotrophs. These results suggest that fungal OTUs belonging to different functional groups respond differently to environmental variables.
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Preheim, Sarah P., Allison R. Perrotta, Antonio M. Martin-Platero, Anika Gupta, and Eric J. Alm. "Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit." Applied and Environmental Microbiology 79, no. 21 (2013): 6593–603. http://dx.doi.org/10.1128/aem.00342-13.
Full textAbstract:
ABSTRACT16S rRNA sequencing, commonly used to survey microbial communities, begins by grouping individual reads into operational taxonomic units (OTUs). There are two major challenges in calling OTUs: identifying bacterial population boundaries and differentiating true diversity from sequencing errors. Current approaches to identifying taxonomic groups or eliminating sequencing errors rely on sequence data alone, but both of these activities could be informed by the distribution of sequences across samples. Here, we show that using the distribution of sequences across samples can help identify population boundaries even in noisy sequence data. The logic underlying our approach is that bacteria in different populations will often be highly correlated in their abundance across different samples. Conversely, 16S rRNA sequences derived from the same population, whether slightly different copies in the same organism, variation of the 16S rRNA gene within a population, or sequences generated randomly in error, will have the same underlying distribution across sampled environments. We present a simple OTU-calling algorithm (distribution-based clustering) that uses both genetic distance and the distribution of sequences across samples and demonstrate that it is more accurate than other methods at grouping reads into OTUs in a mock community. Distribution-based clustering also performs well on environmental samples: it is sensitive enough to differentiate between OTUs that differ by a single base pair yet predicts fewer overall OTUs than most other methods. The program can decrease the total number of OTUs with redundant information and improve the power of many downstream analyses to describe biologically relevant trends.
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Bi, Yuewei, Qianyu Yang, Jiao Li, et al. "The Gut Microbiota and Inflammatory Factors in Pediatric Appendicitis." Disease Markers 2022 (July 7, 2022): 1–11. http://dx.doi.org/10.1155/2022/1059445.
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Background. The study analyzed gut microflora’s composition and investigated the associations between the associations between gut dysbiosis and inflammatory indicators in pediatric patients with acute appendicitis. Methods. High-throughput sequencing and bioinformatics analysis were used to investigate the composition and diversity of gut microflora in 20 pediatric patients with acute appendicitis and 11 healthy children. Endpoints measured were operational taxonomic units (OTU) of gut microflora. The OTU and its abundance analysis, sample diversity analysis, principal component analysis of samples, differential analysis, and analysis of biomarkers were performed. Results. Overall fecal microbial richness and diversity were similar in patients and controls. Yet richness within the group of Bilophila, Eggerthella, Clostridium, Parvimonas, Megasphaera, Atopobium, Phascolarctobacterium, Adlercreutzia, Barnesiella, Klebsiella, Enterococcus, and Prevotella genera was higher in patients. Adlercreutzia was significantly positively correlated with IL-10, while the three other genera, comprising Klebsiella, Adlercreutzia, and Prevotella, were positively correlated with B cells level. Conclusion. Gut microbiome components are significantly different in pediatric patients with acute appendicitis and healthy children. The differential abundance of some genera is correlated with the production of inflammatory markers in appendicitis.
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Zhang, Shirley L., Lei Bai, Namni Goel, et al. "Human and rat gut microbiome composition is maintained following sleep restriction." Proceedings of the National Academy of Sciences 114, no. 8 (2017): E1564—E1571. http://dx.doi.org/10.1073/pnas.1620673114.
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Insufficient sleep increasingly characterizes modern society, contributing to a host of serious medical problems. Loss of sleep is associated with metabolic diseases such as obesity and diabetes, cardiovascular disorders, and neurological and cognitive impairments. Shifts in gut microbiome composition have also been associated with the same pathologies; therefore, we hypothesized that sleep restriction may perturb the gut microbiome to contribute to a disease state. In this study, we examined the fecal microbiome by using a cross-species approach in both rat and human studies of sleep restriction. We used DNA from hypervariable regions (V1-V2) of 16S bacteria rRNA to define operational taxonomic units (OTUs) of the microbiome. Although the OTU richness of the microbiome is decreased by sleep restriction in rats, major microbial populations are not altered. Only a single OTU, TM7-3a, was found to increase with sleep restriction of rats. In the human microbiome, we find no overt changes in the richness or composition induced by sleep restriction. Together, these results suggest that the microbiome is largely resistant to changes during sleep restriction.
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Flores-Mireles, Ana L., Stephen C. Winans, and Gina Holguin. "Molecular Characterization of Diazotrophic and Denitrifying Bacteria Associated with Mangrove Roots." Applied and Environmental Microbiology 73, no. 22 (2007): 7308–21. http://dx.doi.org/10.1128/aem.01892-06.
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ABSTRACT An analysis of the molecular diversity of N2 fixers and denitrifiers associated with mangrove roots was performed using terminal restriction length polymorphism (T-RFLP) of nifH (N2 fixation) and nirS and nirK (denitrification), and the compositions and structures of these communities among three sites were compared. The number of operational taxonomic units (OTU) for nifH was higher than that for nirK or nirS at all three sites. Site 3, which had the highest organic matter and sand content in the rhizosphere sediment, as well as the lowest pore water oxygen concentration, had the highest nifH diversity. Principal component analysis of biogeochemical parameters identified soil texture, organic matter content, pore water oxygen concentration, and salinity as the main variables that differentiated the sites. Nonmetric multidimensional scaling (MDS) analyses of the T-RFLP data using the Bray-Curtis coefficient, group analyses, and pairwise comparisons between the sites clearly separated the OTU of site 3 from those of sites 1 and 2. For nirS, there were statistically significant differences in the composition of OTU among the sites, but the variability was less than for nifH. OTU defined on the basis of nirK were highly similar, and the three sites were not clearly separated on the basis of these sequences. The phylogenetic trees of nifH, nirK, and nirS showed that most of the cloned sequences were more similar to sequences from the rhizosphere isolates than to those from known strains or from other environments.
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J., K. Ebigwai, A. Egbe A., L. Nyannanyo B., and A. Ngele B. "Pollen Album of Rhizophora Members in Nigeria and Its Taxonomic Implications." Journal of Agriculture and Ecology Research International 12, no. 3 (2017): 1–10. https://doi.org/10.9734/JAERI/2017/33497.
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Pollen samples of <em>Rhizophora</em> individuals in Nigeria Niger Delta were conducted to generate a pollen album. Samples were collected in permanent plots in Koko, Ogidigben (Delta State), Akakumama, Nembe (Bayelsa State), Olupiri-Epelema, Ugwede (Rivers State), Ikwe, Opolom (Akwa Ibom State), Adiabo Ukanabio and Esighi (Cross River State) between 2013 - 2016. A total of three hundred and sixty four (364) <em>Rhizophora</em> pollen samples were obtained from the sea water-land interfaces to 604 meters inland (maximum <em>Rhizophora</em> occurrence landward). The samples were prepared using standard Erdtmanian methods. The result showed the presence of five different shapes of tricolporate pollen. The exine sculptures were baculate, rugulate, striate and reticulate while the pollen shapes were either sub prolate, prolate or oblate. The polar shapes were circular in Operational Taxonomic Units (OTUs) 1 and 4, triangular in OTUs 2 and 3 and trilobate in OTU5. The grain arrangements for all five OTUs were monad. When this data was normalized and converted to numerical taxonomy using Euclidean distance, a loose relationship was observed between OTUs 1 and 2 suggesting distinct species. Although, OTUs 3, 4 and 5 showed statistical difference (0.05 confidence limit) among themselves, analysis revealed no statistical difference to OTU 1 and 2, implying them as subtypes of either OTU. The finding is in contrast to the widely held notion that only three putative <em>Rhizophora</em> species exist in Nigeria. Edaphic and genetic research of the two inferred species and three subtypes should be conducted.
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Urakawa, Hidetoshi, Kumiko Kita-Tsukamoto, and Kouichi Ohwada. "Restriction fragment length polymorphism analysis of psychrophilic and psychrotrophic Vibrio and Photobacterium from the north-western Pacific Ocean and Otsuchi Bay, Japan." Canadian Journal of Microbiology 45, no. 1 (1999): 67–76. http://dx.doi.org/10.1139/w98-128.
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Typing and identification of 60 marine psychrophilic and psychrotrophic vibrios isolated from the north-western Pacific Ocean and coastal environment of Japan were performed by restriction fragment length polymorphism analysis on the basis of polymerase chain reaction amplified 16S rDNA. We obtained 15 operational taxonomic units (OTUs) by digestion with four restriction endonucleases (HhaI, DdeI, RsaI, and Sau3AI); four large groups were obtained from the neighbor-joining method. Significant differences were observed in OTU composition between isolates from the deep sea and coastal areas. Vibrio marinus and Photobacterium species were the dominant culturable vibrios in the deep sea areas, while Vibrio splendidus like species were the dominant culturable vibrios in a coastal area of Japan.Key words: restriction analysis, Vibrio, Photobacterium, Vibrio marinus (Moritella marina), Vibrio splendidus.
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Cheng, Xiuqin, Abulajiang Tuoheti, Xiaobang Huang, and Xingzhi Gu. "High-Throughput Sequencing Investigation of Bacterial Diversity in Chronic Suppurative Otitis Media and Middle Ear Cholesteatoma." Evidence-Based Complementary and Alternative Medicine 2022 (September 19, 2022): 1–9. http://dx.doi.org/10.1155/2022/9616582.
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Background. Chronic otitis media is a common middle ear disease in otolaryngology. Bacterial infection is considered as the cause of the disease, but relying on conventional bacterial cultures can be problematic for identifying specific pathogens. Current research suggests that bacteria in microbial communities can only be identified by rDNA sequencing of bacteria. Methods. This cross-sectional study utilized broad-range PCR amplification of 16S rRNA genes with clone analysis to compare bacterial diversity in lesions from 6 patients with chronic suppurative otitis media (CSOM) and 10 patients with cholesteatoma of middle ear lesions. Bacteria were analyzed at the levels of phylum, order, family, genus, and species. Results. The age and sex difference between the patients with chronic suppurative otitis media and the patients with middle ear cholesteatoma were comparable ( P > 0.05 ). Bacterial species abundance and species diversity were greater in cholesteatoma of the middle ear lesions than in CSOM lesions. The total number of detected operational taxonomic units (OTU) was 838, comprising 788 OTU detected in cholesteatoma pathological tissues, 230 in CSOM pathological tissues, and 180 OTU common to both groups. Proteus is a major part of CSOM (99.46%, P = 0.000321 ). The phyla detected in the Cholesteatoma samples were Proteus (Proteobacteria) (35.77%), thikum (Firmicutes) (44.21%, P = 0.001071 ), and Actinomycetes (Actinobacteria) (16.66%, P = 0.032464 ). At all bacterial taxonomic levels, the epithelial tissue of middle ear cholesteatoma was complex in terms of bacterial diversity, covering many Gram-positive and Gram-negative bacteria, likely related to bacterial microbiome formation. In contrast, the bacteriology of the CSOM lesions was relatively simple at all taxonomic levels, with all sequences characterized as belonging to Gram-negative bacteria. Conclusion. Our results suggest that persistent middle ear cholesteatoma infection may be a microbial flora disorder related to conditional pathogenic bacteria rather than a single bacterial infectious disease. The pathogen is relatively single in the diseased tissue of chronic suppurative otitis media, which is the main reason for its effective antiinfection treatment.
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Goulpeau, Arnaud, Benoit Penel, Marie-Eugénie Maggia, et al. "OTU Delimitation with Earthworm DNA Barcodes: A Comparison of Methods." Diversity 14, no. 10 (2022): 866. http://dx.doi.org/10.3390/d14100866.
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Although DNA barcodes-based operational taxonomic units (OTUs) are increasingly used in earthworm research, the relative efficiency of the different methods available to delimit them has not yet been tested on a comprehensive dataset. For this study, we used three datasets containing 651, 2304 and 4773 COI barcodes of earthworms from French Guiana, respectively, to compare five of these methods: two phylogenetic methods—namely Poisson Tree Processes (PTP) and General Mixed Yule Coalescence (GMYC)—and three distance matrix methods—namely Refined Single Linkage (RESL, used for assigning Barcode Index Numbers in the Barcode of Life Data systems), Automatic Barcode Gap Discovery (ABGD), and Assemble Species by Automatic Partitioning (ASAP). We found that phylogenetic approaches are less suitable for delineating OTUs from DNA barcodes in earthworms, especially for large sets of sequences. The computation times are unreasonable, they often fail to converge, and they also show a strong tendency to oversplit species. Among distance-based methods, RESL also has a clear tendency to oversplitting, while ABGD and ASAP are less prone to mismatches and have short computation times. ASAP requires less a priori knowledge for model parameterisation than AGBD, provides efficient graphical outputs, and has a much lower tendency to generate mismatches.
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Palau, Montserrat, Núria Piqué, André M. Comeau, et al. "Detection of Helicobacter pylori Microevolution and Multiple Infection from Gastric Biopsies by Housekeeping Gene Amplicon Sequencing." Pathogens 9, no. 2 (2020): 97. http://dx.doi.org/10.3390/pathogens9020097.
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Despite the great efforts devoted to research on Helicobacter pylori, the prevalence of single-strain infection or H. pylori mixed infection and its implications in the mode of transmission of this bacterium are still controversial. In this study, we explored the usefulness of housekeeping gene amplicon sequencing in the detection of H. pylori microevolution and multiple infections. DNA was extracted from five gastric biopsies from four patients infected with distinct histopathological diagnoses. PCR amplification of six H. pylori-specific housekeeping genes was then assessed on each sample. Optimal results were obtained for the cgt and luxS genes, which were selected for amplicon sequencing. A total of 11,833 cgt and 403 luxS amplicon sequences were obtained, 2042 and 112 of which were unique sequences, respectively. All cgt and luxS sequences were clustered at 97% to 9 and 13 operational taxonomic units (OTUs), respectively. For each sample from a different patient, a single OTU comprised the majority of sequences in both genes, but more than one OTU was detected in all samples. These results suggest that multiple infections with a predominant strain together with other minority strains are the main way by which H. pylori colonizes the human stomach.
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He, Zichen, Takeshi Naganuma, Ryosuke Nakai, Satoshi Imura, Megumu Tsujimoto, and Peter Convey. "Microbiomic Analysis of Bacteria Associated with Rock Tripe Lichens in Continental and Maritime Antarctic Regions." Journal of Fungi 8, no. 8 (2022): 817. http://dx.doi.org/10.3390/jof8080817.
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Increased research attention is being given to bacterial diversity associated with lichens. Rock tripe lichens (Umbilicariaceae) were collected from two distinct Antarctic biological regions, the continental region near the Japanese Antarctic station (Syowa Station) and the maritime Antarctic South Orkney Islands (Signy Island), in order to compare their bacterial floras and potential metabolism. Bulk DNA extracted from the lichen samples was used to amplify the 18S rRNA gene and the V3-V4 region of the 16S rRNA gene, whose amplicons were Sanger- and MiSeq-sequenced, respectively. The fungal and algal partners represented members of the ascomycete genus Umbilicaria and the green algal genus Trebouxia, based on 18S rRNA gene sequences. The V3-V4 sequences were grouped into operational taxonomic units (OTUs), which were assigned to eight bacterial phyla, Acidobacteriota, Actinomyceota, Armatimonadota, Bacteroidota, Cyanobacteria, Deinococcota, Pseudomonadota and the candidate phylum Saccharibacteria (also known as TM7), commonly present in all samples. The OTU floras of the two biological regions were clearly distinct, with regional biomarker genera, such as Mucilaginibacter and Gluconacetobacter, respectively. The OTU-based metabolism analysis predicted higher membrane transport activities in the maritime Antarctic OTUs, probably influenced by the sampling area’s warmer maritime climatic setting.
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Álvarez-Solís, José David, María del Rosario Cardoso-Villanueva, Beatriz Xoconostle-Cázares, Martín Eduardo Sánchez-García, José Luis Barragán-Soriano, and Jesús Pérez-Moreno. "Bacterial community structure associated with roots of Pinus montezumae Lamb. inoculated with edible ectomycorrhizal fungi and mycorrhizal helper bacteria." Mexican journal of biotechnology 9, no. 3 (2024): 1–19. http://dx.doi.org/10.29267/mxjb.2024.9.3.1.
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Tree roots are associated with a high diversity of microorganisms that play key roles in soil fertility and plant nutrition and health. Here we examine the composition and diversity of bacterial community in ectomycorrhizal root (ECR) and their ectomycorrhizosphere (EMR) of the Neotropical tree Pinus montezumae inoculated with Laccaria laccata and Hebeloma mesophaeum, applied alone or co-inoculated with Azospirillum brasilense. For this, we used a 16S rRNA gene metabarcoding-sequencing approach in samples of ECR and EMR that were collected nine-months after inoculation in greenhouse. A total of 943 Operational Taxonomic Units (OTU) were differentiated and grouped in 32 bacterial phyla. The most abundant phyla were Proteobacteria (67%) and Actinobacteria (20.7%). Bacterial communities were structured in ECR and EMR (Anosim, R=0.77, P≤0.005), and were more diverse in EMR than ECR (Shannon-Weaver of 4.2 and 3.6, and Simpson inverse of 33.7 and 16.7, respectively). The abundance of Pseudomonas, Actinoplanes and Salinibacterium were promoted with L. laccata, while with H. mesophaeum an OTU from Burkholderiaceae was prominent. Our results showed that the ectomycorrhizal fungi strongly shaped the composition of the bacterial communities associated with roots of P. montezumae.
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Dixon, T. J., S. I. Mortimer, and B. J. Norris. "16S rRNA gene microbial analysis of the skin of fleece rot resistant and susceptible sheep." Australian Journal of Agricultural Research 58, no. 7 (2007): 739. http://dx.doi.org/10.1071/ar06273.
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Fleece rot is a bacterial dermatitis that follows prolonged wetting of the sheep’s skin, and a major pre-disposing condition to body strike in the Australian Merino. Several studies have examined bacterial load of the fleece in relation to fleece rot using traditional culture-based techniques focussing on only a few bacterial species. We examined the natural bacterial diversity of the healthy sheep skin and changes that occurred in fleece-rot resistant and susceptible animals during fleece rot development. Presented is a preliminary molecular genetic analysis of the bacterial ecology of the sheep skin. Eight 16S rRNA gene libraries were constructed from susceptible and resistant sheep both before and after onset of the disease following induction by simulated rainfall. Approximately 75% of the sequences obtained in this study have not been previously identified in fleece-rot studies. Four operational taxonomic units (OTU; groups of >97% sequence similarity) of major interest were present on susceptible animals and absent from resistant animals. Data on these OTU expand current knowledge of bacteria involved in inflammation and wounding of sheep skin tissue, and provide direction for future research that may lead to new treatment options for fleece rot and body strike.
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Macher, Jan-Niklas, Till-Hendrik Macher, and Florian Leese. "Combining NCBI and BOLD databases for OTU assignment in metabarcoding and metagenomic datasets: The BOLD_NCBI _Merger." Metabarcoding and Metagenomics 1 (December 15, 2017): e22262. https://doi.org/10.3897/mbmg.1.22262.
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Metabarcoding and metagenomic approaches are becoming routine techniquesfor use in biodiversity assessment and in ecological studies. The assignment of taxonomic information to millions of sequences obtained via high-throughput sequencing is challenging, as many DNA reference libraries are lacking information on certain taxonomic groups and can contain erroneous sequences. Combining different reference databases is therefore a promising approach for maximising taxonomic coverage and reliability of results. The "BOLD_NCBI_Merger" bash script is introduced, which combines sequence data obtained from the National Centre for Biotechnology Information (NCBI) GenBank and the Barcode of Life Database (BOLD) and prepares it for taxonomic assignment with the software MEGAN.
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Zhang, Han-Bo, Chan-Wen Xu, Miao-Miao Wang, Tao Li, and Zhi-Wei Zhao. "Quantitatively evaluating mistaken clone assignments by RFLP analysis of 16S rRNA genes: a case study." Canadian Journal of Microbiology 54, no. 6 (2008): 479–82. http://dx.doi.org/10.1139/w08-031.
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We quantitatively evaluated the errors of clone assignment based on the restriction fragment length polymorphism (RFLP) pattern of 16S rRNA genes. Eighty clones were randomly selected from a 16S rRNA gene library and were categorized into 35 operational taxonomic units (OTU) based on their indistinguishable enzyme restriction patterns of 3 tetrameric restriction enzymes RsaI, BsuRI, and HinfI. All of these clones were then sequenced and were reassigned into 36–53 OTUs using the DOTUR program when sequence similarities of 95%–100% were used. The number of the identically assigned clones ranged from 53 to 61 and the percentage varied from 66.3% to 76.3%. The Shannon–Weaver index for the bacterial community observed by RFLP analysis was 2.75, equal to that estimated by DOTUR at a 97% sequence similarity. Compared with clones assigned with the DOTUR program at a 97% sequence similarity, only 61 clones (76.3%) were correctly assigned by RFLP analysis. Six clones (7.5%) were assigned mistakenly at the phylum level, and the positions of 13 clones (16.2%) were phylogenetically different at a lower taxonomic rank.
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Machado, Karine Borges, Cíntia Pelegrineti Targueta, Adriana Maria Antunes, et al. "Diversity patterns of planktonic microeukaryote communities in tropical floodplain lakes based on 18S rDNA gene sequences." Journal of Plankton Research 41, no. 3 (2019): 241–56. http://dx.doi.org/10.1093/plankt/fbz019.
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AbstractThe aquatic microbiota plays key roles in ecosystem processes; however, the mechanisms that influence their biogeographic patterns are not yet fully understood. Using high-throughput 18S rDNA gene sequencing, we investigated the composition of planktonic microeukaryotes (organisms sampled using a 68-μm plankton net) in 27 floodplain lakes of the Araguaia River, central Brazil and explored the influence of environmental and spatial factors for communities considering taxonomic and trophic groups. Of the 807 operational taxonomic units (OTUs) observed, Chlorophyta and Charophyta were the groups with greater abundance. Beta diversity was high, and the similarity of communities decreased as the geographic distance increased. We found a shared explanation between environmental and spatial predictors for total and autotrophic microbiota. Environmental variables influence only mixotrophic microbiota. These results suggest an OTU turnover along the floodplain and a spatially structured composition. This spatial pattern can be derived from the association with extrinsic factors, such as spatially structured environmental variables, that generate spatial dependence. However, the relationship between the composition of microbiota and environmental conditions is still unclear.
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Jeske, Jan Torsten, and Claudia Gallert. "Microbiome Analysis via OTU and ASV-Based Pipelines—A Comparative Interpretation of Ecological Data in WWTP Systems." Bioengineering 9, no. 4 (2022): 146. http://dx.doi.org/10.3390/bioengineering9040146.
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Linking community composition and ecosystem function via the cultivation-independent analysis of marker genes, e.g., the 16S rRNA gene, is a staple of microbial ecology and dependent disciplines. The certainty of results, independent of the bioinformatic handling, is imperative for any advances made within the field. In this work, thermophilic anaerobic co-digestion experimental data, together with primary and waste-activated sludge prokaryotic community data, were analyzed with two pipelines that apply different principles when dealing with technical, sequencing, and PCR biases. One pipeline (VSEARCH) employs clustering methods, generating individual operational taxonomic units (OTUs), while the other (DADA2) is based on sequencing error correction algorithms and generates exact amplicon sequence variants (ASVs). The outcomes of both pipelines were compared within the framework of ecological-driven data analysis. Both pipelines provided comparable results that would generally allow for the same interpretations. Yet, the two approaches also delivered community compositions that differed between 6.75% and 10.81% between pipelines. Inconsistencies were also observed linked to biologically driven variability in the samples, which affected the two pipelines differently. These pipeline-dependent differences in taxonomic assignment could lead to different conclusions and interfere with any downstream analysis made for such mis- or not-identified species, e.g., network analysis or predictions of their respective ecosystem service.
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Segawa, Takahiro, and Nozomu Takeuchi. "Cyanobacterial communities on Qiyi glacier, Qilian Shan, China." Annals of Glaciology 51, no. 56 (2010): 135–44. http://dx.doi.org/10.3189/172756411795932047.
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AbstractCyanobacterial communities on a glacier in the Qilian Shan, western China, were investigated using microscopic as well as 16S rRNA and internal transcribed spacer gene analyses. Microscopy revealed that there were abundant cyanobacteria on the entire glacier surface and their community consisted mainly of three morphological types. Low-cycle 16S rRNA gene sequences from six clone libraries were grouped into a total of eight cyanobacterial operational taxonomic units (OTUs), defined as 16S rRNA sequences with similarity of 99%. Although the cyanobacterial community based on morphological types displayed no significant differences among the study sites on the glacier, the community based on OTU groups varied among sites. This inconsistency may be due to simple morphology which might hide a large genetic variability. Phylogenetic analysis revealed that the OTU groups included the orders Oscillatoriales, Chroococcales and unclassified, and the majority of OTUs were Oscillatoriales. From the source environments of the cyanobacterial 16S rRNA gene sequences of each OTU on the glacier estimated by BLAST search (>97% similarity), 39.9% were from soil, 38.2% from fresh water and 1.7% from snow and ice environments. Based on geographical records in the database, all cyanobacterial OTUs were matched to those recorded from the Arctic and Antarctica. The results suggest that the cyanobacterial communities on the glacier are common in cold regions of the world and are likely not to be specialized members of the snow and ice biota but also inhabitants of soil and freshwater environments.
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Wu, Qingzhong, Joy E. M. Watts, Kevin R. Sowers, and Harold D. May. "Identification of a Bacterium That Specifically Catalyzes the Reductive Dechlorination of Polychlorinated Biphenyls with Doubly Flanked Chlorines." Applied and Environmental Microbiology 68, no. 2 (2002): 807–12. http://dx.doi.org/10.1128/aem.68.2.807-812.2002.
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ABSTRACT A microorganism whose growth is linked to the dechlorination of polychlorinated biphenyls (PCBs) with doubly flanked chlorines was identified. Identification was made by reductive analysis of community 16S ribosomal DNA (rDNA) sequences from a culture enriched in the presence of 2,3,4,5-tetrachlorobiphenyl (2,3,4,5-CB), which was dechlorinated at the para position. Denaturing gradient gel electrophoresis (DGGE) analysis of total 16S rDNA extracted from the culture led to identification of three operational taxonomic units (OTUs 1, 2, and 3). OTU 1 was always detected when 2,3,4,5-CB or other congeners with doubly flanked chlorines were present and dechlorinated. Only OTUs 2 and 3 were detected in the absence of PCBs and when other PCBs (i.e., PCBs lacking doubly flanked chlorines) were not dechlorinated. Partial sequences of OTUs 2 and 3 exhibited 98.2% similarity to the sequence of “Desulfovibrio caledoniensis” (accession no. DCU53465 ). A sulfate-reducing vibrio isolated from the culture generated OTUs 2 and 3. This organism could not dechlorinate 2,3,4,5-CB. From these results we concluded that OTU 1 represents the dechlorinating bacterium growing in a coculture with a Desulfovibrio sp. The 16S rDNA sequence of OTU 1 is most similar to the 16S rDNA sequence of bacterium o-17 (89% similarity), an ortho-PCB-dechlorinating bacterium. The PCB dechlorinator, designated bacterium DF-1, reductively dechlorinates congeners with doubly flanked chlorines when it is supplied with formate or H2-CO2 (80:20).
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Yoneda, Momoka, Hiroki Ameno, Ayaka Nishimura, Kohei Tabuchi, Yuki Hatano, and Takashi Osono. "Diversity of ligninolytic ascomycete fungi associated with the bleached leaf litter in subtropical and temperate forests." AIMS Microbiology 10, no. 4 (2024): 973–85. http://dx.doi.org/10.3934/microbiol.2024042.
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<p>Little is known regarding the diversity patterns of Xylariaceae and Hypoxylaceae (Ascomycota) fungi taking part in the lignin decomposition of leaf litter from different tree species and under different climatic regions. The alpha and beta diversity of Xylariaceae and Hypoxylaceae fungi was investigated on bleached leaf litter from nine subtropical and cool temperate tree species in Japan. A total of 248 fungal isolates, obtained from 480 leaves from the nine tree species, were classified into 43 operational taxonomic units (OTUs) with a 97% similarity threshold and were assigned to nine genera of Xylariaceae and Hypoxylaceae. There was no overlap of fungal OTUs between subtropical and cool temperate trees. The mean number of fungal OTUs was generally higher in subtropical than cool temperate trees, whereas rarefaction curves depicting the numbers of OTU with respect to the number of leaves from which fungi were isolated were less steep in subtropical trees than in cool temperate trees, reflecting the dominance of major OTUs in the subtropical trees and indicating a higher species richness in cool temperate regions. Nonmetric multidimensional scaling showed general overlaps of fungal OTU compositions among tree species in the respective climatic regions, and one-way permutational multivariate analysis of variance indicated that the OTU composition was not significantly different between the tree species. These results suggest a wide host range and some geographic and climatic structures of distribution of these ligninolytic fungi.</p>
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Tapolczai, Kálmán, François Keck, Valentin Vasselon, et al. "Strategies for the bioinformatic treatment of high-throughput sequencing data for diatom studies and bioassessment." ARPHA Conference Abstracts 4 (March 4, 2021): e65047. https://doi.org/10.3897/aca.4.e65047.
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Diatom biomonitoring and ecological studies can greatly benefit from DNA metabarcoding compared to conventional microscopical analysis by potentially providing more reliable and accurate data in a cost- and time-efficient way. A conventional strategy for the bioinformatic treatment of sequencing data involves the clustering of quality filtered sequences into Operational Taxonomic Units (OTUs) based on a global sequence similarity, and their assignment to taxonomy using a reference library. Then, the obtained species lists of the successfully assigned taxa are used for subsequent analyses or quality index calculation. However, the high diversity of bioinformatic methods and parameters make inter-studies comparison difficult, especially because OTUs are specific to a given study. Clustering sequences into OTUs aims to reduce the biasing effect of sequencing artefacts and to reach an approximate species level delimitation at the price of potentially grouping together sequences with different ecology. A similar bias occurs when sequences that differ from each other by their ecological preference are assigned to the same taxa. The incompleteness of reference libraries can further introduce a bias by not taking into account unassigned sequences, thus losing the ecological information they possess. In order to overcome these biases, our studies tested new approaches on <em>de novo</em> developed diatom indices based on periphytic samples collected from streams in France and Hungary. Index development was performed with the <em>leave-one-out cross validation </em> (LOOCV) technique by building a model on a training dataset containing <em>n-1</em> samples and testing it on the remaining test sample. Test values were correlated with a reference environmental gradient. The model was based on the calculation of optimum and tolerance of taxonomic units along the reference gradient and a modified Zelinka-Marvan diatom index equation. Taxonomic units tested in the studies were morphospecies, OTUs (95% similarity threshold), Individual Sequence Units (ISUs, via minimal bioinformatic quality filtering) and Exact Sequence Variants (ESVs, via DADA2 denoising algorithm).The "clustering-free" approach (ISU- and ESV-based indices) performed better than the OTU-based one, providing a fine taxonomic resolution where the ecological difference on genetically close sequence variants could be detected. Thus, these indices are more adapted to a standardized and comparable routine bioassessment. The "taxonomy-free" approach revealed the ecological preferences for those molecular taxonomic units (ISUs/ESVs) that otherwise either (i) would have been assigned to the same taxa due to genetic similarity, or (ii) would not have been recognized because of their absence from the reference libraries. However, we also found that taxonomic information cannot be neglected in ecological studies when the presence of organisms under particular environmental conditions is to be explained or interpreted e.g. via the traits they possess. New types of clustering methods are welcome in the future of biomonitoring where the delimitation of taxonomic units should be refined based on a higher emphasis on their ecology rather than on morphological or genetical criteria.