Biology subjects

Eggers, S.

Publications and source records attributed to Eggers, S..

3 recordsLinked to original sources

bioRxiv2025

Evolutionary history and recurrent host adaptation in ancient Salmonella enterica

Salmonella enterica subsp. enterica is an extremely diverse bacterial pathogen causing frequent infections and foodborne disease among human populations. More than 1500 different bacterial strains (serovars) have been described, many with a wide host range. A small number of serovars are adapted to infect specific hosts: of these, serovars Typhi and Paratyphi A, B, and C cause primate-specific systemic infections (typhoid and paratyphoid fever). Although Paratyphi C is one of the rarest human-specific serovars today, it was once widespread, and all ancient Salmonella genomes published to date belong to or are ancestral to this lineage. Here, we present 53 new ancient Salmonella genomes spanning Eurasia and dating between 3500 BCE and 1300 CE. This rich genomic dataset allows us to reconstruct the evolutionary history of this pathogen in unprecedented detail. We identify multiple extinct prehistoric lineages that caused infections throughout Eurasia. Multiple lineage replacement events are observed throughout prehistoric and historic times, and Bayesian phylogenetic analysis is used to date and identify host adaptation events within this lineage. We find that host-adapted sublineages Paratyphi C, Choleraesuis, and Typhisuis continued to evolve host specificity independently from each other. We reconstruct signals of convergent host adaptation in the studied lineages and other host-adapted strains by analysing shared pseudogenes and recurrent gene gain and loss events. This analysis demonstrates a role for host interactions as a particular target of selection, highlighting the gradual adaptation of this S. enterica lineage to humans that coincides with the intensification of animal husbandry in pastoralist and sedentary farming societies.

genetics↗

bioRxiv2025

Zinc and Cobalt exposure influence Akkermansia muciniphila growth and short-chain fatty acid metabolism

Akkermansia muciniphila is a probiotic bacterium that has been proposed as a potential intervention for depression. A. muciniphila is a common mucin degrader, producing short fatty chain acids (SCFAs), including acetate, butyrate, and propionate, which can help regulate mood via the gut-brain axis. However, the interplay between A. muciniphila and other neuroactive environmental exposures is unclear. The objective of this study was to assess the effects of Zn and Co exposure, individually and together, on A. muciniphila growth and SCFA production. Minimum Inhibitory Concentration (MIC) was calculated for each metal, and sub-MIC exposure testing at high and low levels was conducted with single and combined metals. Growth curves were measured for each exposure condition, and SCFAs were measured using liquid chromatography-mass spectroscopy. Growth and SCFA production were compared between exposures and controls using paired t-tests and linear regression models. All p-values were corrected using FDR adjustments (q-values). A. muciniphila was tolerant to both metal exposures, with MICs at 750mg/L for Zn and 4,000 mg/L for Co. Growth at 24-and 48-hours was only significantly reduced upon exposure to high levels of Co, alone and in combination with Zn. Production of propionate significantly increased with high and low Zn exposures alone and in combination with low Co exposure (q-values <0.01), and significantly decreased with high Co exposure alone and in combination with Zn (q-values <0.01). Overall, A. muciniphila was metal tolerant, supporting its use as a probiotic in the presence of other neuroactive metal exposures.

microbiology↗

bioRxiv2025

Primary tumor microbiomes predict distant metastasis of colorectal cancer

Metastasis causes most cancer-related deaths in colorectal carcinoma (CRC), and microbiome markers may have prognostic value. We hypothesized that primary tumor microbiomes predict distant metastases. We analyzed 5-year metastasis-free survival (MFS) in a retrospective cohort of 900 ORIEN CRC tumor microbiomes (RNAseq). ORIEN findings were validated on an independent cohort using 16S rDNA sequencing and pathobiont-specific qPCR. Microbiome alpha diversity was higher in primary tumors than metastases and positively correlated with metastasis risk. Microbiome beta diversity distinguished primary vs. metastasis and predicted 5-year MFS. High primary tumor abundance of B. fragilis and low F. nucleatum were associated with short MFS. Enterobacteriaceae, including E. coli, were enriched in metastases. qPCR identified increased enterotoxigenic B. fragilis and pks+ E. coli detection in CRC metastasizers. Microbial co-occurrence analysis identified a 3-species clique that predicts metastasis (OR 1.9 [1.4-2.6]). Results suggest that primary tumor microbiomes and specific pathobionts are precision markers for metastasis risk.

cancer biology↗