Biology subjects

Reinhold, S.

Publications and source records attributed to Reinhold, S..

4 recordsLinked to original sources

bioRxiv2026

PIGSTI: a modular, reproducible pipeline for detecting species identity, pathogens, and microbes from animal palaeogenomic data

Ancient genomics has enabled discovery of diverse pathogens across various time periods, host species, and material types. However, existing palaeogenomic pipelines predominantly focus on screening data from human hosts, or do not incorporate microbial screening methodologies. We present PIGSTI (Pathogen anImal Genome Sequence ToolkIt), a bioinformatic pipeline specifically designed for both the initial screening and subsequent detection of pathogens in shotgun sequencing data from ancient animal remains. PIGSTI's integrated Snakemake workflow performs both host detection, genome mapping and pathogen identification, generating outputs suitable for population genetics and phylogenetic analyses. Testing on 952 newly sequenced and publicly available animal palaeogenomic datasets, we identified ~15 ancient zoonotic and animal pathogens with high confidence, including the first documented case of Rickettsia felis and Leptospira borgpetersenii in an ancient animal. Our results demonstrate PIGSTI's utility for screening pathogen diversity in ancient animal hosts and reconstructing historical host-pathogen relationships.

genomics↗

bioRxiv2025

Probing the zooarchaeological record across time and space for ancient pathogens

Zoonoses are among the greatest threats to human health, with many zoonotic pathogens believed to have emerged during prehistory. Palaeomicrobiological investigations of the zooarchaeological record hold potential to uncover the reservoirs, host ranges, and host adaptations of zoonotic pathogens but face challenges in identifying promising specimens and pathogen DNA preservation. We performed palaeopathological and genetic examinations of 346 skeletal elements from domesticated and wild animals collected from 34 Eurasian sites dating across the last six millennia. We identified 68 signatures of ancient (opportunistic) pathogens, including the important zoonotic pathogen Salmonella enterica, and found support that palaeopathological lesions provide guidance for specimen selection. For two pathogen species, Erysipelothrix rhusiopathiae and Streptococcus lutetiensis, we confirmed their ancient authenticity using phylogenetics, showcasing an approach to explore the relationship between ancient low-coverage genomes and their modern-day relatives. Our work presents a pathway to understanding prehistoric zoonotic diseases by integrating zooarchaeological, palaeopathological, and genetic data.

microbiology↗

bioRxiv2023

Modeling of lung-liver interaction during infection in a human microfluidic organ-on-a-chip

BackgroundInfections of the respiratory tract such as pneumonia or COVID-19 cause high mortality and morbidity worldwide. Organ-on-a-chip (OC) technologies have been developed in the last years to establish human-based disease models, to study basic disease mechanisms and to provide a tool to speed up drug development. The aim of this study was to establish a lung-liver microfluidic system to study the interaction of both organ modules during infection. MethodsA two organ (lung / liver) microfluidic system was established using primary human bronchial (HBECs) or alveolar type epithelial cells (ATC) for the lung module and Huh-7 cells for the liver module. Inactivated non typeable Haemophilus influenzae (NTHi) and Pseudomonas aeruginosa PAO1 (PAO1) were applied to the lung module. Secreted mediators were screened by dot-blot analysis and quantified. The effect of lung epithelial bacterial stimulation on the liver cell transcriptome was analyzed by mRNA sequencing. ResultsLung and liver cells established stable cultures in a circulatory microfluidic system. Activation of HBECs or ATCs with NTHi or PAO1 resulted in the secretion of multiple inflammatory mediators into the microfluidic medium including TNF-, monocyte chemotactic protein-1 (MCP-1) and macrophage inflammatory protein-3 (MIP-3). Addition of lung cells and application of bacterial onto the HBECs module resulted in the gross change of the transcriptome of the liver cell module. Gene ontology enrichment analysis showed the induction of various pathways involved in host defense, metabolisms, repair, and acute phase response. InterpretationIn conclusion, a two-organ lung/liver microfluidic system was established to study the interaction of the organ modules during infection. Mediators released from epithelial culture modules into the microfluidic circulation after exposure to bacterial pathogens significantly modify the gene expression patterns of liver cells. FundingThis research was funded by the German Federal Ministry of Education and Research (BMBF), 031L0153 VISION "Alternativmethoden zum Tierversuch" and the Dr. Rolf M. Schwiete Stiftung.

cell biology↗

bioRxiv2021

Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-Path Neolithic expansion to Western Europe

Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture arrays such as the 1240K, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240K capture, YMCA significantly improves the coverage and number of sites hit on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.

genetics↗