Biology subjects

Klassen, L.

Publications and source records attributed to Klassen, L..

4 recordsLinked to original sources

bioRxiv2026

A near-ubiquitous plasmid characterises Second Pandemic Yersinia pestis

Yersinia pestis, the causative agent of plague, crippled population across Eurasia in three well-described historical pandemics: The Justinianic plague (541-780), the Second Pandemic (1346-1840) and the Third Pandemic (1894-). The Second Pandemic was the deadliest, with the Black Death (1346-1351) killing up to 60% of Europe's population, far exceeding the population mortality of the Third pandemic, despite few genomic differences between their plague strains. To identify unique genetic variation that could help explain the high death toll of the Second Plague pandemic, we used variation-graph based pan-genomics on a large dataset of 110 new and 12 published shotgun sequenced ancient plague genomes to comprehensively characterise the pangenome diversity of the Second Pandemic plague. Our pangenomic approach revealed the presence of a cryptic 34kb plasmid, pTP33, in almost all strains from the Second Pandemic, but undetectable in all other ancient strains. We find that pTP33 is a phage-plasmid-like derived element with homologues in Enterobacterales bacteria with established insect- or invertebrate-associated lifestyle phases. Our results suggest that pTP33 widened the range and infectivity of vector species available for plague transmission, consistent with reported effects on biofilm formation and bacterial retention. We hypothesise that pTP33 broadened the vector range of Y. pestis beyond the classical rat/flea cycle, facilitating the establishment of new rodent-ectoparasite plague reservoirs, which, critically, increased the risk of flea- or lice-mediated plague transmission between humans. Taken together, our findings offer a biological explanation for differences in transmission dynamics and population mortality between the Second and Third plague pandemics.

genomics↗

bioRxiv2024

Microbial alginate foraging is conserved in geographically and taxonomically distinct ruminant microbiomes

Seaweed plays a crucial role in carbon cycling and is expected to be a valuable resource for sustainable biomass, with applications in biofuel production, human nutrition, and animal feed. Although seaweed has historically been used as a feed source for livestock grazing near coastlines, the process by which it is digested in the rumen remains unknown. Here, we show how the brown algae Saccharina latissima is catabolized in the rumen ecosystem of two different species using in vivo and in vitro experimental systems. We determined that the ruminal decomposition of alginate, a prominent component of the brown algae cell wall, requires microbial catabolic pathways complete with alginate lyases and transport proteins. Evidence of digestion was obtained through a combination of animal models, bacterial imaging, multilayered meta-omics, and enzyme biochemistry. The evolution of and implications for acquisition of alginate utilization loci within geographically and taxonomically distinct ruminants are considered. Graphical abstractSaccharina latissima is a brown alga commonly found in the North Atlantic, Arctic and Pacific oceans. S. latissima was collected from the west coast and Canada and Norway for microbiome studies. Alginate constitutes a substantial portion of the cell wall of S. latissima (SL), and its digestion requires a specific set of enzymes, alginate lyases. We investigated if and how S. latissima is metabolized in geographically distinct rumen ecosystems through in vivo lamb feeding experiments (2.5 and 5% inclusion, DM basis) and in vitro cattle-based rumen simulation technique, RUSITEC, experiments (up to 50% inclusion). Evidence supporting ruminal degradation of alginate was explored using a combination of multilayered meta-omics, physiology (fluorescently labelled S. latissima hot water extracts (FLA-SLAT)) and biochemical characterization of PL6 alginate lyases. O_FIG O_LINKSMALLFIG WIDTH=161 HEIGHT=200 SRC="FIGDIR/small/628917v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@eebe40org.highwire.dtl.DTLVardef@c6fb8org.highwire.dtl.DTLVardef@7a9b1borg.highwire.dtl.DTLVardef@15d30d7_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2022

Genetic risk for Multiple Sclerosis originated in Pastoralist Steppe populations

Multiple sclerosis (MS) is a modern neuro-inflammatory and -degenerative disease, which is most prevalent in Northern Europe. Whilst it is known that inherited risk to MS is located within or within close proximity to immune genes, it is unknown when, where and how this genetic risk originated 1. By using the largest ancient genome dataset from the Stone Age 2, along with new Medieval and post-Medieval genomes, we show that many of the genetic risk variants for MS rose to higher frequency among pastoralists located on the Pontic Steppe, and were brought into Europe by the Yamnaya-related migration approximately 5,000 years ago. We further show that these MS-associated immunogenetic variants underwent positive selection both within the Steppe population, and later in Europe, likely driven by pathogenic challenges coinciding with dietary, lifestyle, and population density changes. This study highlights the critical importance of this period as a determinant of modern immune responses and its subsequent impact on the risk of developing MS in a changing environment.

evolutionary biology↗

bioRxiv2020

Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria

Gut microbiomes have vast catabolic potential and are essential to host health and nutrition. An in-depth understanding of the metabolic pathways in these ecosystems will enable us to design treatments (i.e. prebiotics) that influence microbiome structure and enhance host physiology. Currently, the investigation of metabolic pathways relies on inferences derived from metagenomics or in vitro cultivations, however, novel approaches targeting specific cell physiologies can illuminate the functional potential encoded within microbial (meta)genomes to accurately assess metabolic abilities. Here, we present a multi-faceted study using complimentary next-generation physiology and omics approaches to characterize the microbial adaptation to a prebiotic in the rumen ecosystem. Using fluorescently labeled polysaccharides, we identified bacteria that actively metabolize a glycan prebiotic in the rumen microbiome ex vivo. Subsequently, we characterized strain-level variability in carbohydrate utilization systems and predict metabolic strategies of isolated bovine-adapted strains of Bacteroides thetaiotaomicron using comparative whole genome sequencing, RNA-Seq, and carbohydrate-active enzyme fingerprinting.

microbiology↗