taxonomic units
Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units
... Despite quantitative differences in microbial richness, ecological interpretation of our large bacterial and fungal community data set was robust to the use of ESVs versus 97% OTUs. Thus, even though there are good ...
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Three operational taxonomic units of Eimeria are common in Nigerian chickens and may undermine effective diagnosis of coccidiosis
... erational taxonomic units or OTUs x, y andz) circu- lating among poultry in Australia has added further complexity [9, 10], with two of these variants also de- tected recently in sub-Saharan Africa ...
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OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units
... ABSTRACT Assignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) is a computational bottleneck in the process of analyzing microbial communities. Although this has been an active area of ...
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The Relation Between The Soil Taxonomic Units Developed on The Geomorphic Units and Soil Fertility Status in The West Delta, Egypt.
... geomorphic units in ...soil taxonomic units developed on the geomorphic units and soil fertility ...the taxonomic units are: 1) Typic Haplocalcids , Typic Calcigypsids developed ...
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Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria
... Farrant, Gregory K., Doré, Hugo, Cornejo-Castillo, Francisco M., Partensky, Frédéric, Ratin, Morgane, Ostrowski, Martin, Pitt, Frances D., Wincker, Patrick, Scanlan, David J. , Iudicone, Daniele, Acinas, Silvia G. and ...
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New operational taxonomic units of Enterocytozoon in three marsupial species
... Exploring the genetic composition of Enterocytozoon bieneusi in animals and humans is important for under- standing transmission patterns of disease (enterocyto- zoonosis), and for its prevention and control. By ...
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mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences
... operational taxonomic units (OTU) with clustering approaches such as those of MOTHUR [5] or UCLUST [6] as implemented within packages such as QIIME ...
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Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity
... create replicates. We then used CL clustering to cluster all of the subsamples, as well as the full dataset, and combined the clustering results by representative OTU sequence (defined as the most abundant sequence in ...
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Autism spectrum disorder is associated with gut microbiota disorder in children
... Feces were collected from each subject, placed in a sterile stool container, frozen immediately in liquid nitrogen and stored at − 80 °C. Since fecal samples differed in their col- lection dates, total bacterial DNA was ...
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The decline of the turtle dove: dietary associations with body condition and competition with other columbids analysed using high-throughput sequencing.
... 143 taxonomic units, of which we classified 55% to species, another 34% to genus and the remaining 11% to ...of taxonomic units from natural arable plant species and a lower proportion of ...
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Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi
... operational taxonomic units (OTUs) could be detected in HMP stool samples and compared this to the rate of detection of new 16S rRNA gene OTUs using all samples that had at least 1,000 reads from each ...
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Insect assemblages in a native (kanuka Kunzea ericoides) and an invasive (gorse Ulex europaeus) shrubland
... Abstract: In New Zealand, the European shrub gorse (Ulex europaeus) is becoming the initial post-disturbance shrub, replacing the native myrtaceous manuka (Leptospermum scoparium) and kanuka (Kunzea ericoides) scrub in ...
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Alteration in gut microbiota associated with hepatitis B and non-hepatitis virus related hepatocellular carcinoma
... Illumina TruSeq DNA PCR-Free Library Preparation Kit (Illumina, USA) was used for generation of sequenc- ing libraries. QIIME software 1.9 package was used to analyze sequences (Quantitative Insights Into Microbial ...
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Bamboo lignocellulose degradation by gut symbiotic microbiota of the bamboo snout beetle Cyrtotrachelus buqueti
... operational taxonomic units; LDA: linear discriminant analysis; SEM: scanning electron microscopy; GHs: glycoside hydrolases; GTs: glycosyltransferases; CEs: carbohydrate esterases; CBMs: carbohydrate- ...
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A human gut phage catalog correlates the gut phageome with type 2 diabetes
... operational taxonomic units (pOTUs) and identification of large phage scaffolds ( n = 2567, ≥ 10 k) revealed a comprehensive human gut phageome with a substantial number of novel sequences encoding genes ...
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Assessment and management of inherent and dynamic soil properties for intensive agriculture in the North Island, New Zealand and Tasmania, Australia
... Chapter 2 – Examples of assessing inherent soil properties 2.1 Chapter outline 2.2 Map units and taxonomic units 2.3 Example 1 - The Te Puke district 2.4 Te Puke district soil profile ch[r] ...
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The prophylactic effects of BIFICO on the antibiotic-induced gut dysbiosis and gut microbiota
... The number of operational taxonomic units (OTUs) in the control group after antibiotic treatment was significantly reduced compared to that prior to treatment, while those of the regul[r] ...
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Articles
... (2008) to determine whether they displayed detectable pseudogene traits (Buhay 2009). As DNA barcoding is usually a distance-based approach, we constructed a neighbour- joining tree (BIONJ, Gascuel 1997) with ...
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The Barcode of Life Initiative: synopsis and prospective societal impacts of DNA barcoding of Fish
... insects. Taxonomic literature is often difficult to locate, and the description of a new species does not assure its future ...of taxonomic experts and resources allocated to taxonomy, impose a ...
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Bioinformatic Genome Comparisons for Taxonomic and Phylogenetic Assignments Using Aeromonas as a Test Case
... IMPORTANCE Improvements in DNA sequencing technologies have resulted in the ability to generate large numbers of high- quality draft genomes and led to a dramatic increase in the number of publically available genomes. ...
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