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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CONCLUSION: App-based facial training offers attractive opportunities to motivate patients for improved adherence to treatment, which could hypothetically lead to a better outcome. Evaluation of this question is planned in a clinical trial after completion of the development. PMID: 32495061 [PubMed - as supplied by publisher]
Source: HNO - Category: ENT & OMF Tags: HNO Source Type: research
Authors: Yousefi A, Nasehi S, Arshi S, Nabavi M, Bemanian MH, Shokri S, Seif F, Khoshmirsafa M, Saeedi Y, Rajabian B, Mahjoub F, Sadeghian M, Talachian E, Fallahpour M PMID: 32496031 [PubMed - as supplied by publisher]
Source: European Annals of Allergy and Clinical Immunology - Category: Allergy & Immunology Tags: Eur Ann Allergy Clin Immunol Source Type: research
Authors: Skander D, Allenova A, Maurer M, Kolkhir P PMID: 32496030 [PubMed - as supplied by publisher]
Source: European Annals of Allergy and Clinical Immunology - Category: Allergy & Immunology Tags: Eur Ann Allergy Clin Immunol Source Type: research
CONCLUSION: Structural prevention measures in addition to behavioral measures enable a reduction of the cancer risk caused by UV radiation. The aim must be to establish these measures nationwide for the entire population. PMID: 32494842 [PubMed - as supplied by publisher]
Source: Der Hautarzt: Zeitschrift fur Dermatologie, Venerologie, und verwandte Gebiete - Category: Dermatology Tags: Hautarzt Source Type: research
CONCLUSIONS: Early detection of MRSA colonization and eradication are necessary for rehabilitation. Management of skin diseases due to infectious diseases within the framework of OD is presented. PMID: 32494841 [PubMed - as supplied by publisher]
Source: Der Hautarzt: Zeitschrift fur Dermatologie, Venerologie, und verwandte Gebiete - Category: Dermatology Tags: Hautarzt Source Type: research
CONCLUSIONS: The most important factor when considering an orthopedic surgery applicant was how well the applicant performed on an audition rotation, followed by their United States Medical Licensing Examination scores. Grit has become an important consideration in resident selection. PMID: 32495837 [PubMed - as supplied by publisher]
Source: Military Medicine - Category: International Medicine & Public Health Tags: Mil Med Source Type: research
CONCLUSIONS: Although statistical significance was not reached, the efficacy of prasugrel was potentially different between stroke subtypes, warranting further studies. PMID: 32493881 [PubMed - as supplied by publisher]
Source: Journal of Atherosclerosis and Thrombosis - Category: Cardiology Tags: J Atheroscler Thromb Source Type: research
Researchers in the United Kingdom have put an abrupt stop to an arm of their Covid-19 trial that involves the antimalarial drug hydroxychloroquine.
Source: CNN.com - Health - Category: Consumer Health News Source Type: news
Conclusion: Direct compression of ICA is rare complication of pituitary apoplexy, which caused cerebral ischemia. Conventional angiography should be necessary for accurate diagnosis and prompt surgical decompression should be the treatment of choice. PMID: 32494388 [PubMed]
Source: Surgical Neurology International - Category: Neurosurgery Tags: Surg Neurol Int Source Type: research
Conclusion: Significant consensus in the perception of complications was observed in most of the analyzed scenarios for both LA and NA. However, within the LA data, responses to different clinical scenarios varied. PMID: 32494370 [PubMed]
Source: Surgical Neurology International - Category: Neurosurgery Tags: Surg Neurol Int Source Type: research
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