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      Decoding the biological information contained in two ancient Slavonic parchment codices: an added historical value

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          Summary

          This study provides an example in the emerging field of biocodicology showing how metagenomics can help answer relevant questions that may contribute to a better understanding of the history of ancient manuscripts. To this end, two Slavonic codices dating from the 11th century were investigated through shotgun metagenomics. Endogenous DNA enabled to infer the animal origin of the skins used in the manufacture of the two codices, while nucleic sequences recovered from viruses were investigated for the first time in this material, opening up new possibilities in the field of biocodicology.

          In addition, the microbiomes colonizing the surface of the parchments served to determine their conservation status and their latent risk of deterioration. The saline environment provided by the parchments selected halophilic and halotolerant microorganisms, which are known to be responsible for the biodegradation of parchment. Species of Nocardiopsis, Gracilibacillus and Saccharopolyspora, but also members of the Aspergillaceae family were detected in this study, all possessing enzymatic capabilities for the biodeterioration of this material. Finally, a relative abundance of microorganisms originating from the human skin microbiome were identified, most probably related to the intensive manipulation of the manuscripts throughout the centuries, which should be taken with caution as they can be potential pathogens.

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          Most cited references65

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          STAR: ultrafast universal RNA-seq aligner.

          Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
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            Cutadapt removes adapter sequences from high-throughput sequencing reads

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              MetaPhlAn2 for enhanced metagenomic taxonomic profiling.

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                Author and article information

                Contributors
                guadalupe.pinar@boku.ac.at
                Journal
                Environ Microbiol
                Environ Microbiol
                10.1111/(ISSN)1462-2920
                EMI
                Environmental Microbiology
                John Wiley & Sons, Inc. (Hoboken, USA )
                1462-2912
                1462-2920
                29 May 2020
                August 2020
                : 22
                : 8 ( doiID: 10.1111/emi.v22.8 )
                : 3218-3233
                Affiliations
                [ 1 ] Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology University of Natural Resources and Life Sciences, Muthgasse 11, A‐1190 Vienna Austria
                [ 2 ] Institute of Science and Technology in Art (ISTA) Academy of Fine Arts Vienna Schillerplatz 3, A‐1010 Vienna Austria
                [ 3 ] Department of Slavonic Studies University of Vienna Spitalgasse 2‐4, Hof 3, A‐1090 Vienna Austria
                Author notes
                [*] [* ]For correspondence. *E‐mail guadalupe.pinar@ 123456boku.ac.at ; Tel. (+43) 1 47654 79862; Fax (+43) 1 47654 79009.
                Author information
                https://orcid.org/0000-0001-7881-8572
                Article
                EMI15064
                10.1111/1462-2920.15064
                7687136
                32400083
                a0eb415e-89db-4e08-8129-178ac05bc7a7
                © 2020 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 22 January 2020
                : 05 May 2020
                : 06 May 2020
                Page count
                Figures: 5, Tables: 2, Pages: 16, Words: 12049
                Funding
                Funded by: (FWF) , open-funder-registry 10.13039/501100002428;
                Funded by: Austrian Science Fund , open-funder-registry 10.13039/501100002428;
                Award ID: P29892
                Categories
                Research Article
                Research Articles
                Custom metadata
                2.0
                August 2020
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.9.4 mode:remove_FC converted:25.11.2020

                Microbiology & Virology
                Microbiology & Virology

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