A Comparison of Three Different Bioinformatics Analyses of the 16S –23S rRNA Encoding Region for Bacterial Identification

Discussion Until now, the main tool used for bacterial identification based on NGS of the 16S–23S rRNA encoding region was de novo assembly followed by BLASTN on NCBI database (Sabat et al., 2017), however, there was no evidence that it would be the most accurate and/or fastest method available. The de novo assembly and BLASTN is the only approach of the three that works at the contig level, and both the OTU clustering and mapping are performed at the read level. Using the NCBI database for these two last approaches would have resulted in odd results, since the NCBI database includes sequences that do not belong to the 16S–23S rRNA encoding region, but that due to the small read length, would have homology with our reads and would have resulted in the creation of bizarre OTUs and mapping results. The OTU clustering and mapping approaches are usually used when a database containing the sequences of interest are known, hence the need for the creation of a 16S-ITS-23S rDNA database. Therefore, in this study, we first assessed the use of an in-house developed and curated 16S–23S rRNA encoding region database for the NGS data analysis compared to the NCBI database. Secondly, we compared three different NGS data analysis approaches, de novo assembly and BLAST, OTU clustering, and mapping in terms of their capacity to accurately and efficiently identify bacterial species using the in-house developed 16S–23S rRNA encoding region database. The results show tha...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research

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Authors: Sabet Sarvestani F, Azarpira N Abstract Heart and cerebral infarctions, as two important ischemic diseases, lead to the death of tissues due to inadequate blood supply and high mortality worldwide. These statuses are started via blockage of vessels and depletion of oxygen and nutrients which affected these areas. After reperfusion and restoration of oxygen supply, more severe injury was mediated by multifaceted cascades of inflammation and oxidative stress. microRNAs (miRNAs) as the regulator of biological and pathological pathways can adjust these conditions by interaction with their targets. Also, miRNAs...
Source: Immunological Investigations - Category: Allergy & Immunology Tags: Immunol Invest Source Type: research
CONCLUSIONS: Xyloglucan/gelose plus ORS was effective and safe in treating acute diarrhea in children. PMID: 33028102 [PubMed - as supplied by publisher]
Source: Expert Review of Gastroenterology and Hepatology - Category: Gastroenterology Tags: Expert Rev Gastroenterol Hepatol Source Type: research
CONCLUSION: In this study, no influence of tear substitutes containing different viscosities of hyaluronic acid on the measurement results of optical coherence tomography could be determined. Therefore, 0.1%, 0.2% and 0.3% hyaluronic acid can be applied to the patient to improve the corneal surface before the examination with optical coherence tomography, without influencing the measurement results of optical coherence tomography. PMID: 33036058 [PubMed - as supplied by publisher]
Source: Klinische Monatsblatter fur Augenheilkunde - Category: Opthalmology Tags: Klin Monbl Augenheilkd Source Type: research
Conclusions: (1) Data at our center suggests at least a regional implementation gap in GBS screening and IAP. (2) The decline in the resistance rate ofE. coli for all antimicrobial substances might indicate that the reduction of prenatal antibiotics use is beneficial and that neonatal antibiotic stewardship programs should include pregnant women as well.What is Known:• GBS screening and intrapartum antibiotic prophylaxis led to a 32%-reduction in GBS disease in Germany with a 0.75 (92:122) ratio of early-onset disease to late-onset disease in 2009–2010.• Prenatal antibiotic use might increase the risk of E....
Source: European Journal of Pediatrics - Category: Pediatrics Source Type: research
Abstract Trace metals concentrations of 25 elements were determined for 22 subcomponents of biodegradable and non-biodegradable waste samples representing the United States municipal solid waste (MSW) stream collected during three separate waste sorts. The subcomponent trace metal concentrations and estimated composition results were used to predict trace metal concentrations present in the overall MSW stream along with MSW compost and waste to energy (WTE) ash, which were compared to health-based standards (i.e., US EPA regional screening levels) and to values previously reported in the literature. These estimate...
Source: Chemosphere - Category: Chemistry Authors: Tags: Chemosphere Source Type: research
Boosting the sensitivity of in vitroβ-lactam allergy diagnostic tests. Chem Commun (Camb). 2020 Oct 14;56(80):11973-11976 Authors: Peña-Mendizabal E, Morais S, Maquieira Á Abstract The synthesis of structurally new haptens and the development of suitable antigens are essential for boosting the sensitivity of drug allergy diagnostic testing. Unprecedented structural antigens for benzylpenicillin and amoxicillin are characterised and evaluated in a cohort of 70 subjects with a turnkey solution based on consumer electronics. PMID: 33033809 [PubMed - in process]
Source: Chemical Communications - Category: Chemistry Authors: Tags: Chem Commun (Camb) Source Type: research
Publication date: Available online 9 October 2020Source: NeuropsychologiaAuthor(s): Erin L. Meier, Shannon M. Sheppard, Emily B. Goldberg, Catherine R. Head, Delaney M. Ubellacker, Alexandra Walker, Argye E. Hillis
Source: Neuropsychologia - Category: Neurology Source Type: research
Publication date: Available online 9 October 2020Source: Neurología (English Edition)Author(s): J.P. Martínez-Barbero, P. Tomás-Muñoz, R. Martínez-Moreno
Source: Neurologia - Category: Neurology Source Type: research
Authors: Mantero V, Rigamonti A, Basilico P, Sangalli D, Scaccabarozzi C, Salmaggi A PMID: 33029982 [PubMed]
Source: Journal of Clinical Neurology - Category: Neurology Tags: J Clin Neurol Source Type: research
Authors: Kargiotis O, Safouris A, Psychogios K, Chondrogianni M, Andrikopoulou A, Theodorou A, Magoufis G, Stamboulis E, Tsivgoulis G PMID: 33029978 [PubMed]
Source: Journal of Clinical Neurology - Category: Neurology Tags: J Clin Neurol Source Type: research
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