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Systematic Cross-biospecimen Evaluation of DNA Extraction Kits for Long-and Short-read Multi-metagenomic Sequencing Studies

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Genomics, Proteomics & Bioinformatics 2022年第2期20卷 405-417页

作者： jacquel.ne rehner Georges Pierre Schmartz Laura Groeger Jan Dastbaz Nicole Ludwig Matthias Hannig Stefan Rupf Berthold Seitz Elias Flockerzi Tim Berger Matthias Christian Reichert Marcin Krawczyk Eckart Meese Christian Herr Robert Bals Soren L.Becker Andreas Keller Rolf Muller The IMAGIne Consortium Institute of Medical Microbiology and Hygiene Saarland UniversityD-66421 HomburgGermany Clinical Bioinformatics Saarland UniversityD-66123 SaarbruckenGermany Department of Human Genetics Saarland UniversityD-66421 HomburgGermany Helmholtz Institute for Pharmaceutical Research Saarland D-66123 SaarbruckenGermany Clinic of Operative Dentistry Periodontology and Preventive DentistrySaarland UniversityD-66421 HomburgGermany Department of Ophthalmology Saarland University Medical CenterD-66421 HomburgGermany Department of Medicine Ⅱ Saarland University Medical CenterD-66421 HomburgGermany Department of Internal Medicine V–Pulmonology AllergologyIntensive Care MedicineSaarland UniversityD-66421 HomburgGermany

High-quality DNA extraction is a crucial step in metagenomic *** by different isolation kits impairs the comparison across datasets.A trending topic is,however,the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with *** thus collected bile,stool,saliva,plaque,sputum,and conjunctival swab samples and performed DNA extraction with three commercial *** each combination of the specimen type and DNA extraction kit,20-gigabase(Gb)metagenomic data were generated using short-read *** profiles of the specimen types showed close proximity to each other,we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction *** kit outperformed all selected kits on every *** reached consistently good results using the Qiagen QiAamp DNA Microbiome *** on the specimen,our data indicate that over 10 Gb of sequencing data are required to achieve sufficient resolution,but DNA-based identification is superior to identification by mass ***,longread nanopore sequencing confirmed the results(correlation coefficient>0.98).Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.

关键词： Whole-genome analysis Comparative genomics Short-read sequencing Long-read sequencing DNA extraction Metagenomics

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Fungal endophytes in green coffee seeds

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菌物学报 2008年第1期27卷 75-84页

作者： Femando E. VEGA Francisco POSADA M. Catherine AIME Stephen W. PETERSON Stephen A. rehner Sustainable Perennial Crops Laboratory U. S. Department of Agriculture Agricultural Research Service Building 011A BARC-W Beltsville Maryland 20705 USA Centro Nacional de lnvestigaciones de Cafe CENICAFE Chinchina Caldas Colombia Department of Plant Pathology and Crop Physiology Louisiana State University AgCenter 302 Life Sciences Bldg. Baton Rouge LA 70803 USA Microbial Genomics and Bioprocessing Research Unit National Center for Agricultural Utilization Research U. S. Department of Agriculture Agricultural Research Service 1815 N. University St. Peoria IL 61604 USA Systematic Mycology and Microbiology Laboratory U. S. Department of Agriculture Agricultural Research Service Building 011A BARC-W Beltsville Maryland20705 USA

Green coffee seeds from Colombia, Guatemala, India, Kenya, Papua new Guinea, Puerto Rico and Vietnam were sampled for the presence of fungal endophytes. Stions of surface sterilized seeds were plated on yeast malt agar, and fungal growth was isolated for subsequent DNA extraction and sequencing. Several fungal genera were isolated, including Acremonium, Aspergillus, Eurotium, Fusarium, Gibberella, Penicillium, Pseudozyma and an undescribed clavicipitaceous species. The biological activities that these fungi might be playing in coffee seeds remain unknown, but in other plants some of the genera isolated have been reported to protect against plant pathogens.

关键词：咖啡种子内生真菌新记录

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