Comparison of methods for identification of microbial communities in book collections: Culture-dependent (sequencing and MALDI-TOF MS) and culture-independent (Illumina MiSeq)

Kraková, Lucia; Šoltýs, Katarína; Otlewska, Anna; Pietrzak, Katarzyna; Purkrtová, Sabina; Savická, D.; Puškárová, Andrea; Bučková, Maria; Szemes, Tomáš; Budiš, Jaroslav; Demnerová, Kateřina; Gutarowska, Beata; Pangallo, Domenico

doi:10.1016/j.ibiod.2017.02.015

Cited by 60 publications

(45 citation statements)

References 36 publications

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“…A total of 13 DNA samples (6 from the mummy's surface, 3 from the internal organs, 1 from the skin crystal and 1 each from the chapel air, the sarcophagus air and the sarcophagus glass) were analysed by Illumina sequencing using the procedure given in Kraková et al (2018). The approach includes PCR amplification of the bacterial 16S rRNA gene V1-V4 region using primers 27f (5 0 -AGA GTT TGA TCC TGG CTC AG-3 0 ) and 685r (5 0 -TCT ACG CAT TTC ACC GCT AC-3 0 ) and amplification of the fungal 28S rRNA large-subunit D1/D2 region using the NL1/NL4 primer set (NL1: 5 0 -GCA TAT CAA TAA GCG GAG GAA AAG-3 0 ; NL4: 5 0 -GGT CCG TGT TTC AAG ACG G-3 0 ).…”

Section: Illumina Platform High-throughput Sequencingmentioning

confidence: 99%

The microbiomes of a XVIII century mummy from the castle of Krásna Hôrka (Slovakia) and its surrounding environment

Kraková

Šoltýs

Puškárová

et al. 2018

Environmental Microbiology

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This microbiological survey was performed to determine the conservation state of a mummy in the Slovak castle of Krásna Hôrka and its surrounding environment. Culture-dependent identification was coupled with biodegradation assays on keratin, gelatin and cellulose. Next Generation Sequencing (NGS) using Illumina platform was used for a deeper microbial investigation. Three environmental samples were collected: from the glass of the sarcophagus, from the air inside it, and from the air of the chapel where the mummy is located. Seven different samples were taken from mummy's surface: from the left ear, left-hand palm, left-hand nail, left instep, right hand, abdomen and mineral crystals embedded within the skin. Three internal organ samples, from the lung, pleura and stomach, were also included in this study. Together, the culture-dependent and culture-independent analyses revealed that the bacterial communities present had fewer taxa than the fungal ones. The mycobiome showed the largest variability and included Epicoccum nigrum, Penicillium spp., Alternaria spp., Aspergillus spp., Cladosporium spp. and Aureobasidium pullulans; many other Ascomycota and Basidiomycota genera were detected by NGS. The most interesting results came from the skin mineral crystals and the internal organs. The hydrolytic assays revealed those microorganisms which might be considered dangerous 'mummy pathogens'. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

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Section: Illumina Platform High-throughput Sequencingmentioning

confidence: 99%

The microbiomes of a XVIII century mummy from the castle of Krásna Hôrka (Slovakia) and its surrounding environment

Kraková

Šoltýs

Puškárová

et al. 2018

Environmental Microbiology

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“…The PCR product of the most common primer pair ITS1-ITS2 used for fungal identification (Iwen et al, 2002;Kõljalg et al, 2013) is too short and also too variable for truly universal primer design (von der Schulenburg et al, 2001). The low-throughput Sanger sequencing of the hypervariable D1-D2 region of 28S rRNA (Khot et al, 2009) or high-throughput Illumina sequencing of the transposon fragmented 28S rRNA (Kraková et al, 2018) still lacks the ability of precise fungal discrimination. The amplification and sequence of a large part of the ribosomal cluster in one fragment would be ideal.…”

Section: Microbial Communities' Analysismentioning

confidence: 99%

“…The bacteria of the group Propionibacterium/Cutibacterium are very frequently isolated from human skin, therefore is very likely that they have a human origin. Other bacteria of cutaneous origin, belonging to the genera Corynebacterium and Staphylococcus (Ramsey et al, 2016), present on the seal surface were also detected from several archive documents in the past (Puškárová et al, 2016;Kraková et al, 2018). Among these bacteria of presumed human origin Staphylococcus aureus previously showed the Pb resistance and sensitivity (Levinson et al, 1996) and evidenced the sorption of lead in the extracellular polymeric substance (Bhaskar and Bhosle, 2006).…”

Section: Microbial Communities' Analysismentioning

confidence: 99%

Lead soaps formation and biodiversity in a XVIII Century wax seal coloured with minium

Šoltýs

Planý

Biocca³

et al. 2019

Environmental Microbiology

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Summary A multidisciplinary approach was carried out in order to study the biodeterioration and the associated microbiome of a XVIII Century wax seal coloured with minium. A small wax seal fragment was observed by scanning electron microscopy combined with energy dispersive spectroscopy in non‐destructive mode. The same object was analysed by Raman and Fourier‐transform infrared spectroscopy. The identification of the microbiota growing on the seal was performed with both a culture‐dependent strategy, combined with hydrolytic assays, and high‐throughput sequencing using the MinION platform. The whole bacterial 16S rRNA gene and the fungal markers ITS and 28S rRNA were targeted. It was observed that the carnauba wax coloured with lead tetroxide (minium) was covered by a biofilm consisting of a network of filaments and other structures of microbial origin. The culture‐dependent and culture‐independent investigations showed the presence of a complex microbiota composed mainly by fungal members, which demonstrated interesting properties related to lipids and lead processing. The formation of lead soaps and secondary biogenic minerals was also described.

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“…Moreover, a contemporaneous collection of animal skins bound together provides a 4 remarkable biological resource, which may inform upon the husbandry of the animals and in turn shed 5 light on the assembly of the codex. The utility of parchment documents as a store of biological 6 information is confirmed by a number of molecular studies, which have successfully retrieved DNA 7 sequences from parchments and produced comparisons with modern reference populations of cattle, 8 sheep and goat [1][2][3][4]. These analyses have utilised isolated parchment fragments, which are then digested 9…”

Section: Introductionmentioning

confidence: 99%

“…11 12 In the light of the vast potential afforded by ancient manuscripts several authors are experimenting with 13 non-destructive sampling of documents. Whilst most of these methods involve some form of 14 spectroscopic analysis, novel approaches which release molecules from the surface, such as the use of 15 synthetic gel films [5,6] have been reported, and this work can be seen as part of a wider push to develop 16 sampling methods for material culture [7][8][9][10][11]. These studies also form part of an increasingly 17 sophisticated analysis of the conservation status of objects, which includes analyses of the microflora 18 within buildings and upon objects.…”

Section: Introductionmentioning

confidence: 99%

The York Gospels: a one thousand year biological palimpsest

Teasdale

Fiddyment

Vnouček

et al. 2017

Preprint

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26Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary 27 record but also a remarkable reservoir of biological information. Palaeographic and codicological 28 investigation can often locate and date these documents with remarkable precision. The York Gospels 29 (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel 30 books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) 31 sampling technique eZooMS, to include the analysis of DNA we report a cost effective and simple-to-use 32 biomolecular sampling technique. We apply this combined methodology to document for the first time a 33 rich palimpsest of biological information contained within the York Gospels, which has accumulated over 34 the 1,000 year lifespan of this cherished object that remains an active participant in the life of York 35Minster. This biological data provides insights into the decisions made in the selection of materials, the 36 construction of the codex and the use history of the object.

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Comparison of methods for identification of microbial communities in book collections: Culture-dependent (sequencing and MALDI-TOF MS) and culture-independent (Illumina MiSeq)

Cited by 60 publications

References 36 publications

The microbiomes of a XVIII century mummy from the castle of Krásna Hôrka (Slovakia) and its surrounding environment

The microbiomes of a XVIII century mummy from the castle of Krásna Hôrka (Slovakia) and its surrounding environment

Lead soaps formation and biodiversity in a XVIII Century wax seal coloured with minium

The York Gospels: a one thousand year biological palimpsest

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