PEOPLEMohamed Sarhan

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Mohamed Sarhan

Senior Researcher
Institute for Biomedicine

Senior Researcher
Institute for Mummy Studies

T +39 0471 055 785

mohamed.sarhan@eurac.edu

https://orcid.org/0000-0003-0904-976X

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About

Mohamed Sabry Sarhan is a microbiologist studying ancient DNA (aDNA), metagenomics, and microbiome evolution, with a particular emphasis on fungal genomics and metagenomic classification. He develops and applies advanced computational and molecular approaches for the detection, taxonomic classification, and strain-level characterization of microbes in both ancient and modern metagenomic contexts, aiming to understand evolutionary history and ecological diversity of microbes over time. A central aspect of his work involves de novo assembly of ancient and modern metagenomic DNA.

External Links:

Google Scholar: https://scholar.google.com/citations?user=cLUbbJkAAAAJ
LinkedIn: https://www.linkedin.com/in/mohamed-s-sarhan-46ab05109/
BlueSky: https://bsky.app/profile/msabrysarhan.bsky.social
ResearchGate: https://www.researchgate.net/profile/Mohamed-Sarhan
Web of Science: https://www.webofscience.com/wos/author/record/48706857

Scientific Publications

Journal article2026

De novo assembly of complete circular mitochondrial genomes from 2,695 fungal species

Sarhan MS, Abdalrahem A, Maixner F, Fuchsberger C

Christian Fuchsberger, Mohamed Sarhan, Frank Maixner

Progetto: Centro Multi-Omics per Alimenti e Salute, Mining and Dining - Le abitudini alimentari dei minatori preistorici del sale

Fungal mitochondrial genomes are critical for understanding phylogenetics, evolution, and ecology of the Kingdom Fungi, yet they remain underrepresented in public databases. To address this, we developed a workflow to recover mitochondrial genomes from 12,902 fungal short read sequencing data housed in the Sequence Read Archive (SRA) records, assembling complete circular genomes from 2,695 species. This effort expanded fungal mitochondrial genome diversity by nearly 2.3X particularly in understudied phyla such as Mucoromycota (11X increase) and Zoopagomycota (8X increase). The new dataset contains novel yet undescribed mitochondrial genomes at numerous taxonomic levels, including 15 classes, 64 orders, 178 families, and 544 genera. Taxonomic analysis revealed broad ecological representation among the top-assembled species, including human pathogens (e.g., Cryptococcus tetragattii), plant pathogens (e.g., Melampsora larici-populina), edible mushrooms (e.g., Suillus luteus), and industrial fungi. By leveraging the not yet fully exploited SRA sequencing data, this study fills critical gaps in fungal mitochondrial genomics, tripling the currently known mitochondrial genome diversity of the Kingdom Fungi, and provides an extensive resource for phylogenetic and evolutionary research.

DOI Fonte

DOI: 10.1038/s41597-025-06447-x

Journal article2026

The Iceman’s microbiome: unveiling millennia of microbial diversity and continuity

Sarhan MS, Samadelli M, Zink A, Maixner F

Marco Samadelli, Mohamed Sarhan, Frank Maixner, Albert Zink

Background The Iceman mummy, a 5300-year-old natural alpine glacier mummy, provides a unique opportunity to study ancient microbial ecosystems. However, disentangling the mummy’s endogenous microbiome from modern environmental contaminants introduced during three decades of conservation remains a significant challenge. Results By integrating culture-dependent and culture-independent approaches, including amplicon sequencing, shotgun metagenomics and de novo metagenomic assembly, as well as isolate-level genomics, we performed a comprehensive characterization of the Iceman’s microbial landscape. We identified three distinct microbial drivers: endogenous post-mortem succession, ancient glacier-derived relicts, and modern anthropogenic introduction. Metagenomic analysis of internal tissues revealed anaerobic bacteria, including ancient gut taxa, including such as Romboutsia hominis, Clostridium moniliforme, Eubacterium sp., Ruminococcus bromii, Kineothrix sp., Treponema succinifaciens, Enterousia sp., and Huintestinicola butyrica. These taxa, characterized by ancient DNA (aDNA) damage profiles (C to T deamination frequency), show high similarity to ancestral, non-Westernized human gut communities, providing a rare baseline for Copper Age intestinal ecosystems. Conversely, we identified a shift in the external mycobiome, marked by the recent proliferation of psychrophilic yeasts, including Glaciozyma watsonii, Mrakia robertii, Phenoliferia glacialis, and Goffeauzyma sp. While internal bacterial communities remained stable, these external yeast populations showed increased relative abundance and reduced DNA damage signatures between 2010 and 2019, indicating active, modern colonization. Furthermore, strain-level analysis of Pseudomonas sp. 5C2 confirmed that specific environmental strains have successfully colonized the mummy, persisting across multiple tissue sites with minimal genetic divergence.

Conclusions Our study demonstrates that the Iceman is not a static relic but a dynamic biological interface. The coexistence of ancient, endogenous gut microbes and modern, psychrophilic colonizers highlights the potential for ongoing microbial activity even at sub-zero temperatures. These findings underscore that maintaining strict environmental parameters is essential to prevent these specialized microbial communities from transitioning from latent persistence to active microorganisms.

DOI

DOI: 10.1186/s40168-026-02417-6

Journal article2025

Human mitochondrial DNA in public metagenomes: Opportunity or privacy threat?

Sarhan MS, Antonello G, Weissensteiner H, Mengoni C, Mascalzoni D, Waldron L, Segata N, Fuchsberger C

Deborah Mascalzoni, Christian Fuchsberger, Mohamed Sarhan

Human DNA is unavoidably present in metagenomic analyses of human microbiomes. While current protocols remove human DNA before submission to public repositories, mitochondrial DNA (mtDNA) has been overlooked and frequently persists. We discuss the privacy risks and research opportunities associated with mtDNA, urging consideration by the scientific, ethics, and legal communities.

DOI

DOI: 10.1016/j.cell.2025.03.023

Journal article2025

Systematic mediation and interaction analyses of kidney function genetic loci in a general population study

Ghasemi-Semeskandeh D, Emmert D, König E, Foco L, Gögele M, Sarhan MS, Barin L, Fujii R,

Cristian Pattaro, Martin Gögele, Luisa Foco, Peter P. Pramstaller, David Emmert, Christian Fuchsberger, Eva König, Mohamed Sarhan

Progetto: Formazione multidisciplinare sulla malattia renale cronica: dai modificatori genetici all'individuazione di farmaci

Chronic kidney disease (CKD) is a complex disease affecting >10% of the global population, with large between- and within-continent variability reflecting major environmental determinants. To identify molecular targets for treatment and prevention, genome-wide association study meta-analyses (GWAMAs) of CKD-defining traits have identified hundreds of genetic loci in aggregated population samples. However, while GWAMAs estimate the average allelic effect across studies, single population studies may be relevant to unravel specific mechanisms. To assess whether a study sample from a specific population could extend existing knowledge on kidney function genetics, we selected 147 kidney function relevant loci identified by a large GWAMA, assessing their association with the glomerular filtration rate estimated from serum creatinine (eGFRcrea) in 10,146 participants to the Cooperative Health Research In South Tyrol (CHRIS) study, conducted in an Alpine region where thyroid dysfunction is common. We identified associations with single nucleotide polymorphisms (SNPs) at 11 loci, showing up-to-5.4 times larger effect sizes than in the corresponding GWAMA, not explainable by allele frequency differences. Systematic mediation analysis across 70 quantitative traits identified serum magnesium and the activated partial thromboplastin time as partial mediators of the eGFRcrea associations at SHROOM3 and SLC34A1, respectively. Given that free triiodothyronine and thyroxine acted as effect modifiers across all loci, we conducted SNP-by-thyroid stimulating hormone (TSH) interaction analyses, identifying significant interactions at STC1: SNPs had larger effects on eGFRcrea at higher TSH levels, possibly reflecting stanniocalcin-1 autocrine and paracrine role. Individual population studies can help characterize genetic associations. The interplay between phenotypes at SHROOM3 and SLC34A1 and the role of thyroid function as a genetic effect modifier warrant further investigations.

DOI

DOI: 10.1371/journal.pone.0323057

Internet2024

Taxonize-gb: A tool for filtering GenBank non-redundant databases based on taxonomy [preprint]

Sarhan MS, Filosi M, Maixner F, Fuchsberger C

Christian Fuchsberger, Frank Maixner, Mohamed Sarhan

Analyzing taxonomic diversity and identification in diverse ecological samples has become a crucial routine in various research and industrial fields. While DNA barcoding marker-gene approaches were once prevalent, the decreasing costs of next-generation sequencing have made metagenomic shotgun sequencing more popular and feasible. In contrast to DNA-barcoding, metagenomic shotgun sequencing offers possibilities for in-depth characterization of structural and functional diversity. However, analysis of such data is still considered a hurdle due to absence of taxa-specific databases. Here we present taxonize-gb, a command-line software tool to extract GenBank non-redundant nucleotide and protein databases, related to one or more input taxonomy identifier. Our tool allows the creation of taxa-specific reference databases tailored to specific research questions, which reduces search times and therefore represents a practical solution for researchers analyzing large metagenomic data on regular basis. Taxonize-gb is an open-source command-line Python-based tool freely available for installation at https://pypi.org/project/taxonize-gb/ and on GitHub https://github.com/msabrysarhan/taxonize_genbank. It is released under Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0).

DOI Fonte

DOI: 10.1101/2024.03.22.586347

Journal article2023

A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland

Sarhan M, Wurst C, Tzankov A, Bircher AJ, Wittig H, Briellmann T, Augsburger M, Hotz G,

Christina Wurst, Frank Maixner, Mohamed Sarhan, Albert Zink

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

Background: In 1975, the mummified body of a female has been found in the Franciscan church in Basel, Switzerland. Molecular and genealogic analyses unveiled her identity as Anna Catharina Bischoff (ACB), a member of the upper class of post-reformed Basel, who died at the age of 68 years, in 1787. The reason behind her death is still a mystery, especially that toxicological analyses revealed high levels of mercury, a common treatment against infections at that time, in different body organs. The computed tomography (CT) and histological analysis showed bone lesions in the femurs, the rib cage, and the skull, which refers to a potential syphilis case.
Results: Although we could not detect any molecular signs of the syphilis-causing pathogen Treponema pallidum subsp. pallidum, we realized high prevalence of a nontuberculous mycobacterium (NTM) species in brain tissue sample. The genome analysis of this NTM displayed richness of virulence genes and toxins, and similarity to other infectious NTM, known to infect immunocompromised patients. In addition, it displayed potential resistance to mercury compounds, which might indicate a selective advantage against the applied treatment. This suggests that ACB might have suffered from an atypical mycobacteriosis during her life, which could explain the mummy’s bone lesion and high mercury concentrations.
Conclusions: The study of this mummy exemplifies the importance of employing differential diagnostic approaches in paleopathological analysis, by combining classical anthropological, radiological, histological, and toxicological observations with molecular analysis. It represents a proof-of-concept for the discovery of not-yet-described ancient pathogens in well-preserved specimens, using de novo metagenomic assembly.

DOI

DOI: 10.1186/s12915-022-01509-7

Journal article2023

Molekulargenetische Untersuchung einer Mumie

Wurst C, Sarhan SM, Maixner F, Zink A

Christina Wurst, Frank Maixner, Mohamed Sarhan, Albert Zink

Progetto: Valutazione dei collegamenti mancanti nell'aterogenesi, attraverso la paleogenetica, la tomografia computerizzata e l’analisi degli isotopi stabili.

By applying Next Generation Sequencing (NGS) methods to ancient human remains, we can learn a lot about our own past. These methods not only allow us to analyse highly fragmented ancient DNA molecules,
but also give us a tool for their ancient authentication. An example of what is possible by using NGS methods in paleogenetics is shown here with the “Lady of the Barfüsser Church”, where both ancient human
and microbial DNA was studied.

DOI Fonte

DOI: 10.1007/s12268-023-1982-z

Journal article2022

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,

Giovanna Cipollini, Mohamed Sarhan, Frank Maixner, Albert Zink

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

1. Nucleic acid extraction from complex environmental and ancient tissue material is prone to co-extract inhibitory substances that make further molecular analysis difficult or impossible. This co-extraction occurs in both solid-phase and liquid-phase/organic nucleic acid extraction protocols. Currently, the widely used method to overcome inhibition includes the addition of bovine serum albumin (BSA) to the downstream enzymatic reactions or the dilution of the nucleic acid extracts. BSA, however, seems to reduce the inhibitory effect of certain compounds only, and excessive dilution may change the original DNA composition.
2. In this study, we introduce an innovative new method using linear polyacrylamide (LPA) to efficiently precipitate and purify nucleic acids extracted from complex environmental and ancient tissue samples in one working step. The LPA method replaces the precipitation step in classic liquid-phase/organic extraction protocols or can be easily applied as an additional post-extraction step on impure DNA extracts. As a proof of concept, we experimented with this method on different ancient human mummy samples (bones, soft tissues and gut contents) from different time periods (5000 BC–1800 AD), as well as on complex environmental samples (e.g. soil, activated sludge and animal faeces) known to contain inhibitory compounds.

3. We demonstrated that LPA precipitates nucleic acids, even in an aqueous ethanol solution without the addition of chaotropic salts, resulting in the recovery of highly pure DNA from all tested samples that displayed inhibition with previously published extraction protocols. Compared to the current, most widely
used silica-based extraction method for ancient and sedimentary DNA, our LPA method resulted in comparable DNA qualities and overall DNA compositions (human endogenous content and microbial diversity).
4. In conclusion, our LPA method with its high purifying capacity provides an important alternative to the commonly used DNA extraction protocols in the environmental and ancient DNA (aDNA) fields.

DOI Fonte

DOI: 10.1111/2041-210X.13772

Journal article2021

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

Mohamed Sarhan, Frank Maixner, Albert Zink

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

Recent studies have demonstrated the potential to recover ancient human mitochondrial DNA and nuclear DNA from cave sediments. However, the source of such sedimentary ancient DNA is still under discussion. Here we report the case of a Bronze Age human skeleton, found in a limestone cave, which was covered with layers of calcite stone deposits. By analyzing samples representing bones and stone deposits from this cave, we were able to: i) reconstruct the full human mitochondrial genome from the bones and the stones (same
haplotype); ii) determine the sex of the individual; iii) reconstruct six ancient bacterial and archaeal genomes; and finally iv) demonstrate better ancient DNA preservation in the stones than in the bones. Thereby, we demonstrate the direct diffusion of human DNA from bones into the surrounding environment and show the potential to reconstruct ancient microbial genomes from such cave deposits, which represent an additional paleoarcheological archive resource.

DOI

DOI: 10.1016/j.isci.2021.103397

Journal article2021

From Gene Mapping to Gene Editing, A Guide from the Arabidopsis Research

El‐Soda M, Sarhan MS

Mohamed Sarhan

Gene mapping aims to identify the causal genetic factors underlying any trait of interest. To map those genetic factors, three main pre-requisites are required, i.e. traits measured on quantitative scales, segregating populations, and linkage maps. Quantitative traits are controlled by many genes and can be collected by screening segregating populations, which either can be immortal populations or large collections of natural homozygous inbred accessions. Genetic polymorphisms within each of those population types can be investigated using advanced sequencing technologies or polymerase chain reaction (PCR)-based molecular markers that can be grouped and presented as linkage maps, which represent chromosomes. The mapping process itself can be achieved by traditional quantitative trait loci (QTL) mapping or association mapping, which accelerate mutant and gene discovery. Traditionally, the identified mutants or genes can be used to generate new plants with improved or desirable features through crossing or selection that are laborious and time-consuming. An effective, precise, and rapid alternative to target and modify the identified mutants or genes is through gene-editing technologies. The three most common genome-editing technologies are Zinc finger nucleases (ZFN), transcription activator- like effector nucleases (TALEN), and clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) nuclease. Experience gained with the model plant Arabidopsis thaliana will be the focus of this article.

DOI Fonte

DOI: 10.1002/9781119312994.apr0765

Journal article2021

Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period

Maixner F, Sarhan MS, Huang KD, Tett A, Schoenafinger A, Zingale S, Blanco-Mıguez A, Manghi P,

Stefania Zingale, Mohamed Sarhan, Frank Maixner, Albert Zink

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

We subjected human paleofeces dating from the Bronze Age to the Baroque period (18th century AD) to indepth microscopic, metagenomic, and proteomic analyses. The paleofeces were preserved in the underground salt mines of the UNESCO World Heritage site of Hallstatt in Austria. This allowed us to reconstruct the diet of the former population and gain insights into their ancient gutmicrobiome composition. Our dietary survey identified bran and glumes of different cereals as some of the most prevalent plant fragments. This highly fibrous, carbohydrate-rich diet was supplemented with proteins from broad beans and occasionally with fruits, nuts, or animal food products. Due to these traditional dietary habits, all ancient miners up to the Baroque period have gut microbiome structures akin to modern non-Westernized individuals whose diets are also mainly composed of unprocessed foods and fresh fruits and vegetables. This may indicate a shift in the gut community composition of modern Westernized populations due to quite recent dietary and lifestyle changes. When we extended our microbial survey to fungi present in the paleofeces, in one of the Iron Age samples, we observed a high abundance of Penicillium roqueforti and Saccharomyces cerevisiae DNA. Genome-wide analysis indicates that both fungi were involved in food fermentation and provides the first molecular evidence for blue cheese and beer consumption in Iron Age Europe.

DOI Fonte

DOI: 10.1016/j.cub.2021.09.031

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Journal article2026

The Iceman’s microbiome: unveiling millennia of microbial diversity and continuity

Sarhan MS, Samadelli M, Zink A, Maixner F

Marco Samadelli, Mohamed Sarhan, Frank Maixner, Albert Zink

DOI

DOI: 10.1186/s40168-026-02417-6

Mohamed Sarhan

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Scientific Publications

De novo assembly of complete circular mitochondrial genomes from 2,695 fungal species

The Iceman’s microbiome: unveiling millennia of microbial diversity and continuity

Human mitochondrial DNA in public metagenomes: Opportunity or privacy threat?

Systematic mediation and interaction analyses of kidney function genetic loci in a general population study

Taxonize-gb: A tool for filtering GenBank non-redundant databases based on taxonomy [preprint]

A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland

Molekulargenetische Untersuchung einer Mumie

Linear polyacrylamide is highly efficient in precipitating and purifying environmental and ancient DNA

Ancient DNA diffuses from human bones to cave stones

From Gene Mapping to Gene Editing, A Guide from the Arabidopsis Research

Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period

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Scientific Publications

De novo assembly of complete circular mitochondrial genomes from 2,695 fungal species

The Iceman’s microbiome: unveiling millennia of microbial diversity and continuity

Human mitochondrial DNA in public metagenomes: Opportunity or privacy threat?

Systematic mediation and interaction analyses of kidney function genetic loci in a general population study

Taxonize-gb: A tool for filtering GenBank non-redundant databases based on taxonomy [preprint]

A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland

Molekulargenetische Untersuchung einer Mumie

Linear polyacrylamide is highly efficient in precipitating and purifying environmental and ancient DNA

Ancient DNA diffuses from human bones to cave stones

From Gene Mapping to Gene Editing, A Guide from the Arabidopsis Research

Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period