PALEOMİKROBİYOLOJİ: ARKEOLOJİDEN MİKROBİYOLOJİYE
Paleomikrobiyoloji, antik kalıntılardan elde edilen mikroorganizma kalıntıları üzerinde yapılan mikrobiyolojik çalışmaları içeren bir disiplindir. Arkeoloji Bilimi, az sayıdaki yazılı kaynaklarla ortaya konulanlar dışındaki boşlukları doldurmak ve tarihi sağlam temeller üzerine dayandırmak üzere ortaya çıkmış, eski çağlarda insanoğlunun elinden çıkan maddesel kültür (kültür varlıkları) kalıntılarını inceleyerek geçmişimi aydınlatmayı amaç edinen bir bilim dalıdır. Arkeolojik buluntulardan mikrobiyolojik bazı incelemelerle geçmişe ait bazı veriler elde edilmesine olanak sağlar hale gelmiştir. Geçmiş insan biyolojisi, yaşam yolları ve ortamları hakkında bilgi ortaya çıkarmak için arkeolojik buluntulardan antik ve antik mikroorganizmaların kullanılması ”arkeolojik mikrobiyoloji”, hücrelerin genetik materyali olan DNA, proteinler veya kimyasal belirteçler kullanılarak eski mikroorganizmaların incelenmesi ise “paleomikrobiyoloji” olarak isimlendirilir. Bu alan, arkeoloji ve mikrobiyolojiyi birleştirerek, geçmiş toplulukların mikrobiyel dünyasını anlamak için benzersiz bir bakış açısı sunar. Paleomikrobiyoloji, antik topluluklarda yaygın olan hastalıkları belirleyerek bu toplulukların sağlık durumu hakkında önemli bilgiler sağlar. Örneğin, tüberküloz ve çeşitli mikroorganizmaların antik kalıntılarda tespit edilmesi, bu hastalıkların tarih öncesi topluluklar arasında nasıl yayıldığını anlamamıza yardımcı olur. Mikroorganizma kalıntıları, antik göç hareketlerini ve farklı topluluklar arasındaki mikrobiyel etkileşimleri ortaya koymada kritik bir rol oynar. Göç ve ticaret yollarını belirleyerek, paleomikrobiyoloji, tarih boyunca farklı kültürler arasındaki etkileşimleri aydınlatır. Makale, paleomikrobiyolojinin arkeolojiye sağladığı önemli katkıları ve gelecek dönemlerdeki potansiyel etkilerini incelemektedir. Paleomikrobiyoloji, antik toplulukların sağlık durumu, hastalıkların yayılımı, tarımın evrimi ve göç hareketleri gibi konularda kapsamlı bilgiler sağlar. Antik kalıntılardan elde edilen mikroorganizma DNA'sı analizi, tarihsel süreçlerin ve mikrobiyel etkileşimlerin daha iyi anlaşılmasını sağlar. Ayrıca, gelecekteki teknolojik gelişmeler ve interdisipliner işbirliği ile birlikte, paleomikrobiyolojinin arkeoloji alanında daha da önemli bir rol oynaması beklenmektedir. Sonuç olarak, paleomikrobiyoloji, insanlık tarihine dair yeni bakış açıları sunan ve arkeoloji disipliniyle birlikte geçmişin mikrobiyel dünyasını keşfeden heyecan verici bir araştırma alanını temsil eder. Bu disiplinin ilerlemesi, antik toplulukların yaşam koşulları, sağlık durumları ve kültürel etkileşimleri hakkında daha derinlemesine bir anlayışa ulaşmamıza katkı sağlayacaktır.
PALEOMICROBIOLOGY: FROM ARCHEOLOGY TO MICROBIOLOGY
Paleomicrobiology is a discipline that involves microbiological studies on the remains of microorganisms from ancient ruins. Archaeology is a branch of science that has emerged to fill the gaps other than those revealed by a small number of written sources and to base history on solid foundations, and aims to illuminate the past by examining the remains of material culture (cultural assets) produced by human beings in ancient times. It has become possible to obtain some data from the past through some microbiological examinations from archaeological finds. The use of ancient and historical microorganisms from archaeological finds to reveal information about past human biology, life paths and environments is called "archaeological microbiology", and the study of ancient microorganisms using DNA, proteins or chemical markers, which are the genetic material of cells, is called "paleomicrobiology". By combining archaeology and microbiology, the field offers a unique perspective for understanding the microbial world of past communities. Paleomicrobiology identifies diseases that were common in ancient communities, providing important insights into the health status of these communities. For example, the detection of tuberculosis and various microorganisms in ancient remains helps us understand how these diseases spread among prehistoric communities. Microbial remains play a critical role in revealing ancient migratory movements and microbial interactions between different communities. By identifying migration and trade routes, paleomicrobiology illuminates interactions between different cultures throughout history. This article examines the important contributions of paleomicrobiology to archaeology and its potential impact for the future. Paleomicrobiology provides comprehensive insights into the health status of ancient communities, the spread of disease, the evolution of agriculture and migratory movements. The analysis of microbial DNA from ancient remains provides a better understanding of historical processes and microbial interactions. Furthermore, with future technological advances and interdisciplinary collaboration, paleomicrobiology is expected to play an even more important role in the field of archaeology. In conclusion, paleomicrobiology represents an exciting field of research that offers new insights into human history and explores the microbial world of the past in conjunction with the discipline of archaeology. The advancement of this discipline will contribute to a deeper understanding of the living conditions, health status and cultural interactions of ancient communities.
___
- Adamiak, J.- Otlewska, A.- Tafer, H.- Lopandic, K.- Gutarowska, B.- Sterflinger, K.- Piñar, G. (2018). “First
evaluation of the microbiome of built Cultural Heritage by using the Ion Torrent next generation sequencing
platform”, Int. Biodeterio,. Biodegrad, 131: 11–18.
- Anastasiou, E. and Mitchell, P. D. (2013). “Palaeopathology and genes: investigating the genetics of infectious
diseases in excavated human skeletal remains and mummies from past populations”, Gene, 528: 33–40.
- Blaser, M. J.- Chen, Y. and Reibman, J. (2008). “Does Helicobacter pylori protect against asthma and allergy?”
Gut 57: 561–567.
- Boast, A.P.- Weyrich, L. S.- Wood, J. R.- Metcalf, J. L.- Knight, R.- Cooper, A. (2018). “Coprolites reveal ecological
interactions lost with the extinction of New Zealand birds”, Proc Natl Acad Sci USA. Feb 13;115 (7): 1546-155.
- Bos, K. I.- Schuenemann, V. J.- Golding, G. B.- Burbano, H. A.- Waglechner, N.- Coombes, B. K.- McPhee, J. B.-
DeWitte, S. N.- Meyer, M.- Schmedes, S.- Wood, J.- Earn, D. J.- Herring, D.A.- Bauer, P.- Poinar, H. N.- Krause, J.
(2011). “A draft genome of Yersinia pestis from victims of the Black Death”, Nature, 478 (7370), 506-510.
- Breurec, S.- Guillard, B.- Hem, S.- Brisse, S.- Dieye, F. B.- Huerre, M.- Oung, C.- Raymond, J.- Tan, T.S.- Thiberge, J.
M.- Vong, S.- Monchy, D.- Linz, B. (2011). Evolutionary history of Helicobacter pylori sequences reflect past human
migrations in Southeast Asia, PLoS One. 6 (7): e22058.
- Brosch, R.- Gordon, S. V.- Marmiesse, M.- Brodin, P.- Buchrieser, C.- Eiglmeier, K.- Garnier, T.- Gutierrez, C.-
Hewinson, G.- Kremer, K.- Parsons, L. M.- Pym, A. S.- Samper, S.- van Soolingen, D.- Cole, S. T. (2002). “A new
evolutionary scenario for the Mycobacterium tuberculosis complex”, Proc Natl Acad Sci U S A. Mar 19; 99 (6):
3684-9.
- Burrell, A. S.- Disotell, T. R. and Bergey, C. M. (2015). “The use of museum specimens with high-throughput DNA
sequencers”, J Hum Evol, 79, 35–44.
- Chen, Y. and Blaser, M. J. (2008). Helicobacter pylori colonization is inversely associated with childhood asthma.
Journal of Infectious Diseases 198: 553–560.
- Comas I.- Coscolla, M.- Luo, T.- Borrell, S.- Holt, K.E.- Kato-Maeda, M.- Parkhill, J.- Malla, B.- Berg, S.- Thwaites, G.-
Yeboah-Manu, D.- Bothamley, G.- Mei, J.- Wei, L.- Bentley, S.- Harris, S. R.- Niemann, S.- Diel, R.- Aseffa, A.- Gao,
Q.- Young, D.- Gagneux, S. (2013). “Out-of-Africa migration and Neolithic coexpansion of Mycobacterium
tuberculosis with modern humans”, Nat Genet, Oct; 45 (10): 1176-82.
- Devault, A. M.- Golding, G. B.- Waglechner, N.- Enk, J. M.- Kuch, M.- Tien, J. H.- Shi, M.- Phil, M.- Fisman, D. N.-
Dhody, A. N.- Forrest, S.- Bos, K. I.- Earn, D .J. D.- Holmes, E.C. and Poinar, H. N. (2014). “Second-pandemic strain
of Vibrio cholerae from the philadelphia cholera outbreak of 1849”, N Engl J Med, 370: 334–340.
- Diniz, G.- Karakayalı, M.- Aycan, İ.- Ertürk, G.- Uysal, G. (2022). “Mikroorganizmaların Keşfi ve Mikrobiyolojinin
Tarihçesi”, İzmir Tıp Fak Derg, 1 (2) :49-55.
- Dominguez-Bello, M.G. and Blaser, M. J. (2011). “The human microbiota as a marker for migrations of individuals
and populations”, Annual Review of Anthropology 40: 451–474.
- Donoghue, H. D.- Spigelman, M.- Zias, J.- Gernaey-Child, A.M. and Minnikin, D. E. (1998). “Mycobacterium
tuberculosis complex DNA in calcified pleura from remains 1400 years old”, Lett Appl Microbiol, 27 (5), 265–269.
- Drancourt, Mm, Aboudharam, G., Signoli, M., Dutour, O. and Raoult, D. (1998). “Detection of 400-year-old Yersinia
pestis DNA in human dental pulp: an approach to the diagnosis of ancient septicemia”, Proceedings of the
National Academy of Sciences, 95(21),12637–12640.
- Duggan, A.T.- Perdomo, M. F.- Piombino-Mascali, D.- Marciniak, S.- Poinar, D.- Emery, M. V.- Buchmann, J. P.-
Duchêne, S.- Jankauskas, R.- Humphreys, M.- Golding, G. B.- Southon, J.- Devault, A.- Rouillard, J. M.- Sahl, J. W.-
Dutour, O.- Hedman, K.- Sajantila, A.- Smith, G. L.- Holmes, E. C. (2016). “Poinar HN. 17th Century Variola Virus
Reveals the Recent History of Smallpox”, Curr Biol, Dec 19; 26 (24): 3407-3412.
- Eisenhofer, R.- Anderson, A.- Dobney, K.- Cooper, A. -Weyrich, L. (2019). “Ancient Microbial DNA in Dental
Calculus: A New method for Studying Rapid Human Migration Events”, Journal of Island & Coastal Archaeology,
14: 149-162.
- Gamble, C. (2014). Arkeolojinin Temelleri, Aktüel Arkeoloji Yayınları, İstanbul.
- Gelabert, P.- Olalde, I.- de-Dios, T.- Civit, S.- Lalueza-Fox, C. (2017). “Malaria was a weak selective force in
ancient Europeans”, Sci Rep. May 3;7 (1): 1377.
- Gutarowska B.- Celikkol-Aydin S.- Bonifay, V. –Otlewska, A.- Aydin, E.- Oldham, A.L.- Brauer, J. I.- Duncan, K.E.-
Adamiak, J.- Sunner, J. A.- Beech, I. B. (2015). Metabolomic and high-throughput sequencing analysis-modern
approach for the assessment of biodeterioration of materials from historic buildings, Front Microbiol.
- Higuchi, R.- Bowman, B.- Freiberger, M.- Ryder, O. A. and Wilson, A. C. (1984). DNA sequences from the quagga,
an extinct member of the horse family. Nature, 312 (5991), 282-284.
- Jackson, P. J.- Hugh-Jones, M. E.- Adair, D. M.- Green, G.- Hill, K. K.- Kuske, C.R.- Grinberg, L. M.- Abramova, F. A.
and Keim, P. (1998). “PCR analysis of tissue samples from the 1979 Sverdlovsk anthrax victims: the presence of
multiple Bacillus anthracis strains in different victims”, Proc Natl Acad Sci U S A, 95(3), 1224-1229.
- Kalisz, H. M. (1988). “Microbial proteinases”, Adv Biochem Eng Biotechnol, 36: 1-65.
- Krause-Kyora B.- Susat, J.- Key, F. M.- Kühnert, D.- Bosse, E.- Immel, A.- Rinne, C.- Kornell, S. C.- Yepes, D.-
Franzenburg, S.- Heyne, H.O.- Meier, T.- Lösch, S.- Meller, H.- Friederich, S.- Nicklisch, N.- Alt, K. W.- Schreiber, S.-
Tholey, A.- Herbig, A.- Nebel, A.- Krause, J. (2018). Neolithic and medieval virus genomes reveal complex
evolution of hepatitis B. Elife, May 10;7:e36666.
- Kusters, J. G.- van Vliet, A. H. and Kuipers, E. J. (2006). “Pathogenesis of Helicobacter pylori infection”, Clinical
Microbiology Reviews 19: 449–490.
- Liu, Y.- Weyrich, L.S. and Llamas, B. (2020). “More arrows in the ancient DNA quiver: use of paleoepigenomes and
paleomicrobiomes to investigate animal adaptation to environment”, Molecular Biology and Evolution 37: 307–
319.
- Marciniak, S.- Prowse, T. L.- Herring, D. A.- Klunk, J.- Kuch, M.- Duggan, A.T.- Bondioli, L.- Holmes, E. C.- Poinar, H. N.
(2016). “Plasmodium falciparum malaria in 1st-2nd century CE southern Italy”, Curr Biol, Dec 5; 2 6 (23): R1220-
R1222.
- Metcalf, J.L.- Song, S. J.- Morton, J. T.- Weiss, S.- Seguin-Orlando, A.- Joly, F.- Feh, C.- Taberlet, P.- Coissac Amir,
A. E.- Willerslev, E.- Knight, R.- McKenzie, V.- Orlando L. (2017). Evaluating the impact of domestication and
captivity on the horse gut microbiome, Scientific Reports Nov 14; 7 (1): 15497.
- Moodley, Y.- Linz, B.- Bond, R. P.- Nieuwoudt, M.- Soodyall, H.- Schlebusch, C. M.- Bernhöft, S.- Hale J.- Suerbaum,
S.- Mugisha, L.- van der Merwe, S. W.- Achtman, M. (2012). “Age of the association between Helicobacter pylori
and man”, PLoS Pathog. 8 (5): e1002693.
- Mullis, K. B. and Faloona, F.A. (1987). “Specific synthesis of DNA in vitro via a polymerase-catalyzed chain
reaction”, Meth Enzymol, 155: 335–350.
- Mühlemann B.- Margaryan, A.- Damgaard, P.- Allentoft, M. E.- Vinner, L.- Hansen, A. J.- Weber, A.- Bazaliiskii, V. I.-
Molak, M.- Arneborg, J.- Bogdanowicz, W.- Falys, C.- Sablin M.- Smrčka, V. Sten, S.- Tashbaeva, K.- Lynnerup, N.-
Sikora, M.- Smith, D. J.- Fouchier, R. A. M. (2018). “Ancient human parvovirus b19 in Eurasia reveals its long-term
association with humans”, PNAS 115: 7557–7562.
- Ottoni, C.- Guellil, M.- Ozga, A. T.- Stone, A. C.- Kersten, O.- Bramanti, B.- Porcier, S.- van Neer, W. (2019).
Metagenomic analysis of dental calculus in ancient Egyptian baboons, Sci Rep. Dec 23; 9 (1): 19637.
- Ozga, A.T.- Gilby, I.- Nockerts, R. S.- Wilson, M. L.- Puseyi, A. and Stone, A. C. (2019). Oral microbiome diversity in
chimpanzees from Gombe National Park. Scientific Reports 9: 17354.
- Özbilen, S. (2020). “Arkeoloji; Geçmiş, Zaman ve Kuram”, Uluslararası Eskiçağ Tarihi Araştırmaları Dergisi, 2/1: 41 -
65.
- Priscu, J. C.- Adams, E. E.- Lyons, W. B.- Voytek, M. A.- Mogk, D. W.- Brown, R. L.- McKay, C. P.- Takacs, C. D.- Welch,
K. A.- Wolf, C. F.- Kirshtein, J. D. and Avci, R. (1999). “Geomicrobiology of subglacial ice above Lake Vostok,
Antarctica”, Science, 286 (5447), 2141-2144.
- Rasmussen, S.- Allentoft, M. E.- Nielsen, K.- Orlando, L.- Sikora, M.- Sjögren, K.G.- Pedersen, A. G.- Schubert, M.-
van Dam, A.- Kapel, C. M.- Nielsen, H. B.- Brunak, S.- Avetisyan, P.- Epimakhov, A.- Khalyapin, M. V.- Gnuni, A.-
Kriiska, A.- Lasak, I.- Metspalu, M.- Moiseyev, V. (2015). “Early divergent strains of Yersinia pestis in Eurasia 5,000
years ago”, Cell, 163 (3): 571-582.
- Renfew, C.- Bahn, P. (2017). Arkeoloji: Kuramlar, Yöntemler ve Uygulama, Homer Kitapevi, İstanbul.
- Rivera-Perez, J. I.- Santiago-Rodriguez, T. M-, Toranzos, G. A. (2016). “Paleomicrobiology: a snapshot of ancient
microbes and approaches to forensic microbiology”, Microbiology Spectrum, 4( 4): 1-14.
- Salo, W. L.- Aufderheide, A. C.- Buikstra, J. and Holcomb, T. A. (1994). “Identification of Mycobacterium
tuberculosis DNA in a pre-Columbian Peruvian mummy”, Proc Natl Acad Sci USA, 91 (6): 2091-2094.
- Schopf, J. W. (2006). “Fossil evidence of Archaean life”, Philos Trans R Soc Lond B Biol Sci, 361: 869–885.
- Schuenemann, V. J.- Singh, P.- Mendum, T. A.- Krause-Kyora, B.- Jäger, G.- Bos, K. I., Herbig, A.- Economou, C.-
Benjak, A.- Busso, P.- Nebel, A.- Boldsen, J. L.- Kjellström, A.- Wu, H.- Stewart, G. R.- Taylor, G. M.- Bauer, P.- Lee, O.
Y.- Wu, H. H.- Minnikin, D.E.- Besra, G.S.- Tucker, K.- Roffey, S.- Sow, S. O.- Cole, S. T.- Nieselt, K.- Krause, J. (2013).
“Genome-wide comparison of medieval and modern Mycobacterium leprae”, Science, Jul 12;341 (6142): 179-83.
- Spigelman, M. and Lemma, E. (1993). “The use of the polymerase chain reaction (PCR) to detect Mycobacterium
tuberculosis in ancient skeletons”, International Journal of Osteoarchaeology, 3 (2): 137–143.
- Spyrou, M. A.- Keller, M.- Tukhbatova, R. I.- Scheib, C. L.- Nelson, E. and Andrades Valtueña, A. (2019).
“Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis
genomes”, Nat Commun, 10: 4470.
- Tito, R. Y.- Macmil, S.- Wiley, G.- Najar, F.- Cleeland, L.- Qu, C.- Wang, P.- Romagne, F.- Leonard, S.- Ruiz, A. J.-
Reinhard, K.- Roe, B. A. and Lewis, C. M. Jr. (2008). “Phylotyping and functional analysis of two ancient human
microbiomes”, PLoS One, 3(11) :e3703.
- Tsangaras, K. and Greenwood, A. D. (2012). “Museums and disease: using tissue archive and museum samples
to study pathogens”, Ann Anat, 194 (1): 58–73.
- Sevin, V. (1999). Arkeolojik Kazı Sistemi El Kitabı, Arkeoloji ve Sanat Yayınları, İstanbul.
- Vågene, Å. J.- Herbig, A.- Campana, M. G.- Robles García, N. M.- Warinner, C.- Sabin, S.- Spyrou, M. A.- Andrades
V. A.- Huson, D.- Tuross, N.- Bos, K. I. and Krause, J. (2018). “Salmonella enterica genomes from victims of a
major sixteenth-century epidemic in Mexico”, Nat Ecol Evol, 2 (3): 520-528.
- Wagner, D. M.- Klunk, J.- Harbeck, M.- Devault, A.- Waglechner, N.- Sahl, J. W.- Enk, J.- Birdsell, D. N.- Kuch, M.-
Lumibao, C.- Poinar, D.- Pearson, T.- Fourment, M.- Golding, B.- Riehm, J. M.- Earn, D. J.- Dewitte, S.- Rouillard, J.
M.- Grupe, G.- Wiechmann, I. (2014). “Yersinia pestis and the plague of Justinian 541-543 AD: a genomic
analysis”, Lancet Infect Dis, 14 (4): 319-326.
- Welker, F.- Duijm, E.- Gaag, K. J.- van der Geel, B.- van Knijff, P. De.- Leeuwen, J.- van Mol, D.- Plicht, J.- van der
Raes, N.- Reumer, J.- Gravendeel, B. (2014). “Analysis of coprolites from the extinct mountain goat Myotragus
balearicus”, Quaternary Research 81(1): 106–116.
- Weyrich, L. S. and Pérez, V. (2023). Archaeological Microbiology. In:Handbook of Archaeological Sciences,
Second Edition, Edited by A. Mark Pollard, Ruth Ann Armitage, and Cheryl A. Makarewicz. John Wiley & Sons Ltd.
Published 2023 by John Wiley & Sons Ltd.