application of high-throughput sequencing methods for...
TRANSCRIPT
Application of high-throughput sequencing methods for microbial biodiversity
analyses in research of archaeological textiles.
Probable cause of death of the people buried in the west crypt
of St. Anne Chapel in the Castle of the Teutonic Order in Malbork.
Magdalena Dyda1, Anna Makulec2, Monika Stachurska2, Andrzej Gołembnik3, Przemysław Decewicz1,4, Krzysztof Romaniuk4, Łukasz Dziewit4, Łukasz Drewniak1,5
Archaeological objects are often found in a very bad state of preservation, i.a.
due to long-term exposure to microbial activity. Although the presence of
microorganisms on such artifacts is generally recognized, their identification is
rarely performed. Disturbingly, the latest studies in this area indicate that many
of the investigated strains are potential human pathogens, constituting a health
risk for the conservators and archaeologists. Therefore, the identification of
microorganisms colonizing archaeological sites and objects should become a
standard procedure. However, to efficiently assess the biodiversity of such
communities, also with respect to the possible human pathogens, adaptation of
the available metagenomics methods may be required.
ResultsIntroduction
Fig. 1. Archaeological exploration of St. Anne’s Chapel,
textiles excavation and conservation
Materials and methods
• High-throughput sequencing may be a quasi-forensic method for
identification of pathogens that may have caused death of the people
buried centuries ago.
• Metagenomics analyses not only enable the characterization of
microbial communities, but they may also indicate the contamination
of archeological objects with potential pathogens.
• The use of next-generation sequencing technology allows for reliable
and complete identification of bacteria and fungi, even if they are
difficult to cultivate using conventional microbiological methods.
Conclusions
Aim
The aim of the study was to analyse the biodiversity of bacteria and fungi
in the textiles collected during archaeological works in the Castle of the
Teutonic Order in Malbork.
Microorganism identification
Samples were taken from the textiles found in two tombs in the west crypt of St. Anne
chapel in the Castle of the Teutonic Order in Malbork (Fig. 1 and 2). Total DNA was isolated
and purified from the collected samples, followed by amplification and sequencing of the
V3-V4 region of the 16S rRNA gene for Bacteria and ITS1 region of the ITS gene for Fungi.
Illumina MiSeq technology was used for sequencing of each amplicon.
1Research and Development for Life Sciences Ltd., Warsaw, Poland; *[email protected] of Fine Arts in Warsaw, Department of Conservation and Restoration of Textiles, Warsaw, Poland
3Incedo3D, Warsaw, Poland4University of Warsaw, Faculty of Biology, Department of Bacterial Genetics, Warsaw, Poland
5University of Warsaw, Faculty of Biology, Laboratory of Environmental Pollution Analysis Warsaw, Poland
Fig. 2. Biodiversity of Bacteria in samples of textiles collected from 2 graves.
0% 20% 40% 60% 80% 100%
Mycobacterium Chitinophaga Pedobacter Virgibacillus
Clostridium Sporanaerobacter Phenylobacterium Mesorhizobium
Sphingomonas Sphingopyxis Ralstonia Escherichia
Steroidobacter Rhodanobacter Other Unspecified
1st grave
2nd grave
Percentage composition of bacterial genus identified across samples in graves.
Data for genus which constituted more than 1% in overall compositions.
Two additional and artificial groups were created to include the genus with abundance
lower than the threshold (Other) and the ones with unspecified (i.e. ‘f__’) or uncertain (i.e. ‘Incertae_sedis’) taxonomic position assigned (Unspecified).
Percentage composition of fungal genus identified across samples in graves.
Data for genus which constituted more than 1% in overall compositions.
Two additional and artificial groups were created to include the genus with abundance
lower than the threshold (Other) and the ones with unspecified (i.e. ‘f__’) or uncertain (i.e. ‘Incertae_sedis’) taxonomic position assigned (Unspecified).
0% 20% 40% 60% 80% 100%
Aspergillus Penicillium Spiromastix Oidiodendron
Pseudogymnoascus Engyodontium Other Unspecified
1st grave
2nd grave
Fig. 3. Biodiversity of Fungi in samples of textiles collected from 2 graves.
The genetic analysis of archeological textiles were founded by the company RDLS Ltd. Research and Development for Life Sciences - spin-off company of the University of Warsaw.
Research and restoration works including conservation of archeological textiles were conducted within the framework of program “Conservation and building works in the complex of the Holy Virgin Church in the Castle Museum in Malbork“ co-financed by the European Economic Area (EEA) Financial Mechanism 2009 – 2014 and Norwegian Financial Mechanism
RDLS sp. z o.o. to pierwsza spółka typu spin-off Uniwersytetu
Warszawskiego, założona przez uznanych ekspertów z zakresu mikrobiologii
środowiskowej. Naszym celem jest znajdywanie komercyjnego zastosowania dla
wynalazków z zakresu bioremediacji i biodegradacji, a także prowadzenie
działalności usługowej związanej z monitoringiem środowiskowym. Dzięki
współpracy z Uniwersytetem Warszawskim możliwe jest wykorzystywanie
specjalistycznej aparatury badawczej oraz stały kontakt z wybitnymi specjalistami
z dziedziny mikrobiologii, genetyki oraz biochemii.
Jeden z działów spółki zajmuje się usługami dla muzeów oraz innych instytucji
zajmujących się ochroną obiektów zabytkowych, archiwaliów, konserwacją i
restauracją dzieł sztuki, archeologią. Dzięki interdyscyplinarnemu zespołowi
oferujemy pełen pakiet usług: od ustalenia przyczyny zmian obserwowanych na
obiekcie (w tym identyfikację mikroorganizmów czy owadów) po rekomendacje
dotyczące działań naprawczych lub stabilizujących. Współpracujemy z różnymi
instytucjami zarówno na zasadach komercyjnych jak i w ramach projektów
naukowych.
Szczegóły dotyczące naszej działalności znajdą Państwo na stronie www.rdls.pl
RDLS sp. z o.o.ul. Ilji Miecznikowa 1/5a
02-096 Warszawa
tel.: 22 554 19 07 lub 786 28 44 96
e-mail: [email protected]
RDLS Ltd. is spin-off company of the University of Warsaw,
established by the renown experts in environmental
microbiology. Our main goal is to commercialize innovative
solutions and invention in the fields of bioremediation and
biodegradation, as well as providing high quality services in
environmental monitoring. Thanks to close ties to the
University of Warsaw we stay in touch with cutting-edge
technology and seasoned experts in microbiology and
genetics.
For museums, art collectors and national heritage sites,
RDLS Ltd. offers solutions for biodeterioration detection and
preservation. We offer a complete array of services from the
microorganism identification to recommendation of possible
solution aimed at either recovery or suppression of the
biodegradation.
For further information please visit our web site: www.rdls.eu