ANCIENT PATHOGENS

Analisi molecolare del microbioma e di malattie infettive in reperti antichi umani - dalla diagnosi basata sulla “Capture-Sequencing” alla caratterizzazione metagenomica.

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  • Project duration: December 2012 - December 2022
  • Project status: ongoing
  • Funding:
    Internal funding EURAC (Project)
  • Total project budget: 530.000,00 €

La caratterizzazione molecolare dei patogeni nei reperti antichi umani, costituisce un interessante ed innovativo campo di ricerca, contribuendo allo studio della storia e della evoluzione  delle malattie infettive. L´analisi istologica e la caratterizzazione mediante  PCR sono gli approcci diagnostici comunemente utilizzati. Le  moderne tecniche "high-throughput sequencing” permettono di analizzare il DNA antico con metodiche innovative; ad esempio e`stato sequenziato il primo genoma completo dell`agente infettivo, Yersinia pestis, responsabile della “morte nera”. Tuttavia, in paleomicrobiologia si presentano non poche difficolta´metodologiche, come problemi di amplificazione, PCR, dovuti a DNA altamente degradati o lo sviluppo di sistemi  bioinformatici per la valutazione di complessi dati metagenomici per patogeni antichi. Lo scopo di questo progetto sara´quello di migliorare l´individuazione mediante analisi del DNA  dei patogeni in reperti antichi umani. Sara´possibile ottimizzare  l´approccio diagnostico basato sull`amplificazione del DNA (PCR) grazie alla possibilita`offerta dall´EURAC, Istituto per le mummie e l` ìceman, di aver accesso ad una grande varieta´ di tessuti con possibili casi di infezione da tubercolosi, Brucellosi e malaria. Inoltre, in collaborazone con Vienna, sono in corso analisi dei dati ottenuti  dall`Iceman con appoccio  metagenomico , per definire una base informatica per la caratterizzazione de novo di patogeni , individuabili dai dataset metagenomici dei reperti antichi umani.

Publications
Linear polyacrylamide is highly efficient in precipitating and purifying environmental and ancient DNA
Maixner F, Mitterer C, Jäger HY, Sarhan MS, Valverde G, Lücker S, Piombino-Mascali D, Szikossy I, Molnár E, Pálfi G, Pap I, Cipollini G, Zink A (2021)
Articolo su rivista
Methods in Ecology and Evolution

https://doi.org/10.1111/2041-210X.13772

Verification of tuberculosis infection among Vác mummies (18th century CE, Hungary) based on lipid biomarker profiling with a new HPLC-HESI-MS approach
Váradi OA, Rakk D, Spekker O, Terhes G, Urbán E, Berthon W, Pap I, Szikossy I, Maixner F, Zink A, Vágvólgyi C, Donoghue H, Minnikin D, Szekeres A, Pálfi G (2021)
Articolo su rivista
Tuberculosis

Ulteriori informazioni: https://doi.org/10.1016/j.tube.2020.102037

https://doi.org/10.1016/j.tube.2020.102037

https://hdl.handle.net/10863/16368

Reconstruction of ancient microbial genomes from the human gut
Wibowo MC, Yang Z, Borry M, Hübner A, Huang KD, Tierney BT, Zimmerman S, Barajas-Olmos F, Contreras-Cubas C, García-Ortiz H, Martínez-Hernández A, Luber JM, Kirstahler P, Blohm T, Smiley FE, Arnold R, Ballal SA, Pamp SJ, Russ J, Maixner F, Rota-Stabelli O, Segata N, Reinhard K, Orozco L, Warinner C, Snow M, LeBlanc S, Kostic AD (2021)
Articolo su rivista
Nature

Ulteriori informazioni: https://www.nature.com/articles/s41586-021-03532-0

https://doi.org/10.1038/s41586-021-03532-0

https://hdl.handle.net/10863/17191

Ancient DNA analysis of rare genetic bone disorders
Maixner F, Gresky J, Zink A (2021)
Articolo su rivista
International Journal of Paleopathology

Ulteriori informazioni: https://doi.org/10.1016/j.ijpp.2021.04.009

https://doi.org/10.1016/j.ijpp.2021.04.009

https://hdl.handle.net/10863/17193

Molecular and microscopic analysis of human paleofeces from the salt mines in Hallstatt, Austria, provide precious insights into dietary habits and gut microbiome composition of Iron Age miners
Maixner F, Sarhan MS, Huang KD, Tett A, Schoenafinger A, Zingale S, Blanco-Míguez A, Manghi P, Cemper-Kiesslich J, Rosendahl W, Kusebauch U, Morrone SR, Hoopmann MR, Rota-Stabelli O, Rattei T, Moritz RL, Oeggl K, Segata N, Zink A, Reschreiter H, Kowarik K (2021)
Presentazione

Conference: ISBA9| 9TH INTERNATIONAL SYMPOSIUM ON BIOMOLECULAR ARCHAEOLOGY | Toulouse : 1.6.2021 - 4.6.2021

https://hdl.handle.net/10863/18542

Recovery of ancient human- and microbial DNA from cave bones and-sediments
Sarhan M, Lehmkuhl A, Wieland G, Franken M, Zink A, Maixner F (2021)
Presentazione

Conference: Bioinformatics Virtual Coordination Network Virtual Conference| Holistic Bioinformatic Approaches used in Microbiome Research | : 7.6.2021 - 11.6.2021

https://hdl.handle.net/10863/18947

Ancient DNA diffuses from human bones to cave stones
Sarhan MS, Lehmkuhl A, Straub R, Tett A, Wieland G, Francken M, Zink A, Maixner F (2021)
Articolo su rivista
iScience

https://doi.org/10.1016/j.isci.2021.103397

https://hdl.handle.net/10863/20140

Analysis of 1,321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structures and subspecies functional adaptations
Karcher N, Pasolli E, Asnicar F, Huang K, Tett A, Manara S, Armanini F, Bain D, Duncan SH, Louis P, Zolfo M, Manghi P, Raffaetà R, Rota-Stabelli O, Collado MC, Zeller G, Falush D, Maixner F, Walker AW, Huttenhower C, Segata N (2020)
Articolo su rivista
Genome Biology

https://doi.org/10.1186/s13059-020-02042-y

https://hdl.handle.net/10863/14778

Lipid biomarker based verification of TB infection in mother’s and daughter’s mummified human remains (Vác Mummy Collection, 18th century, CE, Hungary)
Váradia OA, Szikossy I, Spekkera O, Rakk D, Terhes G, Urbán E, Berthon W, Pap I, Maixner F, Zink A, Vágvölgyi C, Donoghue HD, Minnikin DE, Pálfi´G, Szekeres A (2020)
Articolo su rivista
Acta Biologica Szegediensis

Ulteriori informazioni: http://abs.bibl.u-szeged.hu/index.php/abs

https://doi.org/10.14232/abs.2020.2.99-109

https://hdl.handle.net/10863/16814

The Prevotella copri complex comprises four distinct clades that are underrepresented in Westernized populations
Tett A, Huang KD, Asnicar F, Fehlner-Peach H, Pasolli E, Karcher N, Armanini F, Manghi P, Bonham K, Zolfo M, De Filippis F, Magnabosco C, Bonneau R, Lusingu R, Amuasi J, Reinhard K, Rattei T, Boulund F, Engstrand L, Zink A, Collado MC, Littman DR, Eibach D, Ercolini D, Rota-Stabelli O, Huttenhower C, Maixner F, Segata N (2019)
Articolo su rivista
Cell Host & Microbe

https://doi.org/10.1016/j.chom.2019.08.018

https://hdl.handle.net/10863/11462

Molecular Reconstruction of the Diet in Human Stool Samples
Maixner F (2019)
Articolo su rivista
mSystems

https://doi.org/10.1128/mSystems.00634-19

https://hdl.handle.net/10863/12257

Helicobacter pylori in ancient human remains
Maixner F, Thorell K, Granehäll L, Linz B, Moodley Y, Rattei T, Engstrand L, Zink A (2019)
Articolo su rivista
World Journal of Gastroenterology

Ulteriori informazioni: https://www.wjgnet.com/1007-9327/full/v25/i42/6289.htm

https://doi.org/10.3748/wjg.v25.i42.6289

https://hdl.handle.net/10863/12256

The Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals
Maixner F, Turaev D, Cazenave-Gassiot A, Janko M, Krause-Kyora B, Hoopmann MR, Kusebauch U, Sartain M, Guerriero G, O'Sullivan N, Teasdale M, Cipollini G, Paladin A, Mattiangeli V, Samadelli M, Putzer A, Tecchiati U, Meissen J, Palazoglu M, Rausch P, Lösch S, Kim BJ, Baines JF, Gostner P, An HJ, Malfertheiner P, Egarter-Vigl E, Stark RW, Keller A, Bishop D, Wenk M, Engstrand L, Moritz RL, Bradley DG, Fiehn O, Nebel A, Oeggl K, Doble P, Franke A, Rattei T, Grimm R, Zink A (2018)
Articolo su rivista
Current Biology

https://doi.org/10.1016/j.cub.2018.05.067

https://hdl.handle.net/10863/6829

The comparative study of two extraction methods for ancient DNA: silica suspension method and ultracentrifugal concentrator method
Lee EJ, Maixner F, Zink A (2018)
Articolo su rivista
Analytical Science & Technology

https://doi.org/10.5806/AST.2018.31.2.65

https://hdl.handle.net/10863/6824

miRNAs in ancient tissue specimens of the Tyrolean Iceman
Keller A, Kreis S, Leidinger P, Maixner F, Ludwig N, Backes C, Galata V, Guerriero G, Fehlmann T, Franke A, Meder B, Zink A, Meese E (2017)
Articolo su rivista
Molecular Biology and Evolution

https://doi.org/10.1093/molbev/msw291

https://hdl.handle.net/10863/7334

Tuberculosis in early medieval Switzerland: osteological and molecular evidence from Courroux
Cooper C, Fellner R, Heubi O, Maixner F, Zink A, Lösch S (2016)
Articolo su rivista
Swiss Medical Weekly

https://doi.org/10.4414/smw.2016.14269

https://hdl.handle.net/10863/6670

The 5300-year-old Helicobacter pylori genome of the Iceman
Maixner F, Krause-Kyora B, Turaev D, Herbig A, Hoopmann MR, Hallows JL, Kusebauch U, Vigl EE, Malfertheiner P, Megraud F, O'Sullivan N, Cipollini G, Coia V, Samadelli M, Engstrand L, Linz B, Moritz RL, Grimm R, Krause J, Nebel A, Moodley Y, Rattei T, Zink A (2016)
Articolo su rivista
Science

https://doi.org/10.1126/science.aad2545

https://hdl.handle.net/10863/6124

Our partners

University College Dublin, School of Archeology

Reiss-Engelhorn-Museen Mannheim

Max Planck Institute for the Science of Human History

Department of Biological Anthropology, University of Szeged, Dugonics Ter, Szeged, Hungary

Medizinische Universität Wien, Forensische Medizin, Fachbereich Forensische Anthropologie

Centre for Translational Microbiome Research (CTMR), Karolinska Institute, Stockholm, Sweden

University of Vienna, CUBE - Division of Computational Systems Biology, Department of Microbiology ...

Universita degli Studi di Firenze, Facultà di Medicina e Chirurgia

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MummyLabs

Potenziamento e centralizzazione delle infrastrutture di laboratorio dell´Istituto per lo Studio ...

Duration: December 2017 - July 2022Funding: FESR (EU funding / Project)

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