Biology subjects

Krause, L.

Publications and source records attributed to Krause, L..

5 recordsLinked to original sources

bioRxiv2025

A molecular inventory of the faecal microbiomes of 23 marsupial species

Despite the recent expansion of culture-independent analyses of animal faecal microbiomes, many lineages remain understudied. Marsupials represent one such group, where despite their iconic status, direct sequencing-based analyses remain limited. Here we present a metagenomic and metabolomic exploration of the faecal microbiomes of 23 Diprotodontia marsupials, producing a reference set of 3,868 prokaryotic and 12,142 viral metagenome-assembled genomes, the majority (>80%) of which represent novel species. As with other animals, host phylogeny is the primary driver of microbiome composition, including distinct profiles for two eucalyptus folivore specialists (koalas and southern greater gliders), suggesting independent solutions to this challenging diet. Expansion of several bacterial and viral lineages were observed in these and other marsupial hosts that may provide adaptive benefits. Antimicrobial resistance genes were significantly more prevalent in captive than wild animals likely reflecting human interaction. This molecular dataset contributes to our ongoing understanding of animal faecal microbiomes. Impact statementDespite their ecological and evolutionary importance, marsupials remain underrepresented in microbiome research. Here, we present the most extensive faecal microbiome dataset to date for this group, encompassing metagenomic, metabolomic, and proximity ligation data from 23 marsupial species. As in other animals, we find the microbial community structure reflects the host species, and some marsupials carry expanded sets of certain microbial lineages indicative of within-host evolution. This work substantially expands the genomic landscape of host-associated microbes and viruses in a poorly studied mammalian clade. Data summaryRaw read data, prokaryotic MAGs [≥]50% complete with [≤]10% contamination are available via the European Nucleotide Archive under project PRJEB89408. The full set of viral genomes, clustered protein database and metabolite data (raw and processed) are available via https://doi.org/10.48610/14e37e9. Prokaryotic MAGs are also available via https://figshare.com/s/87443d80817f57aadc16.

microbiology↗

bioRxiv2025

A cytological framework of female meiosis in Arabidopsis

Female and male meiosis often differ in many aspects, such as their duration and the frequency as well as the positioning of crossovers. However, studying female meiosis is often very challenging and thus, much less is known about female versus male meiosis in many species including plants. To approach this gap, we have developed a live-cell imaging system for female meiocytes in Arabidopsis. This allowed us to obtain a temporally resolved cytological framework of female meiosis in the wildtype that serves as a guiding system for future studies. Here, we have applied this imaging system to study mutants in cyclin- dependent kinase inhibitors, in which a designated female meiocyte undergoes several mitotic divisions before entering meiosis. This enabled us to address when a meiocyte is committed to meiosis, a key question during reproductive development and in particular for the analysis of apomictic species in which meiosis is skipped. HighlightsEstablishment of a live-cell imaging system captures dynamic features of female meiosis. Identification of cytological landmarks ensures robust assignment of meiotic stages. Time-lapse imaging enables quantitative dissection of meiotic phases. Application of the framework reveals great plasticity in the commitment to meiosis.

cell biology↗

bioRxiv2024

A rational approach for the targeted discovery and characterisation of microbiome-derived therapeutics

The human gut microbiome is intrinsically involved in health and disease, representing a wealth of untapped therapeutic potential. Here, we demonstrate the utility and potential of a metagenome guided, large cohort-based approach for the rational selection of live biotherapeutics from the human gut. We applied this approach to Inflammatory Bowel Disease (IBD), identifying several lead candidates that were significantly depleted in individuals with IBD compared to healthy controls. Their therapeutic potential was assessed in preclinical models of IBD where they improved markers of disease pathology by reducing inflammation and promoting mucosal healing and wound repair. All leads had excellent safety profiles in silico and in vitro, and several additionally presented favourable manufacturing properties, supporting their progression into clinical trials. We believe that this rational approach will be generalisable to any disease state with underlying microbiome aetiology and will expedite the development of novel microbiome-derived therapeutics to improve human health.

microbiology↗

bioRxiv2023

Influences of chemotype and parental genotype on metabolic fingerprints of tansy plants uncovered by predictive metabolomics.

Intraspecific plant chemodiversity shapes plant-environment interactions. Within species, chemotypes can be defined according to variation in dominant specialised metabolites belonging to certain classes. Different ecological functions could be assigned to these distinct chemotypes. However, the roles of other metabolic variations and the parental genotype of the chemotypes remain poorly explored. Here, we first compared the capacity of terpenoid profiles and metabolic fingerprints to distinguish five chemotypes of common tansy (Tanacetum vulgare) and depict satellite metabolic differences. Metabolic fingerprints captured higher satellite variation while preserving the ability to define chemotypes. These satellite differences might influence plant performance and interactions with the environment. Next, to characterise the influence of the maternal genotype on chemodiversity, we performed variation partitioning and generalised linear modelling. Our findings revealed that maternal genotype was a higher source of chemical variation than chemotype. Predictive metabolomics unveiled 184 markers predicting maternal genotype with 89% accuracy. These markers included, among others, phenolics, whose functions in plant-environment interactions are well established. Hence, these findings place parental genotype at the forefront of intraspecific chemodiversity. We thus recommend considering this factor when comparing the ecology of various chemotypes. Besides, the combined inclusion of inherited and satellite metabolic variation in computational models may help connecting chemodiversity and evolutionary principles.

ecology↗

bioRxiv2021

Heat stress reveals the existence of a specialized variant of the pachytene checkpoint in meiosis of Arabidopsis thaliana

Plant growth and fertility strongly depend on environmental conditions such as temperature. Remarkably, temperature also influences meiotic recombination and thus, the current climate change will affect the genetic make-up of plants. To further understand temperature effects on meiosis, we have followed male meiocytes of Arabidopsis thaliana by live cell imaging under three different temperature regimes, at 21{degrees}C and at heat shock conditions of 30{degrees}C and 34{degrees}C as well as after an acclimatization phase of one week at 30{degrees}C. This work led to a cytological framework of meiotic progression at elevated temperature. We found that an increase to 30{degrees}C, sped up meiotic progression with specific phases being more amenable to heat than others. An acclimatization phase often moderated this effect. A sudden increase to 34{degrees}C promoted a faster progression of meiosis in early prophase compared to 21{degrees}C. However, the phase in which cross-overs maturate was found to be prolonged at 34{degrees}C. Interestingly, mutants involved in the recombination pathway did not show the extension of this phase at 34{degrees}C demonstrating that the delay is recombination dependent. Further analysis revealed the involvement of the ATM kinase in this prolongation indicating the existence of a specialized variant of the pachytene checkpoint in plants.

cell biology↗