Biology subjects

Franz, C. M. A. P.

Publications and source records attributed to Franz, C. M. A. P..

5 recordsLinked to original sources

bioRxiv2026

Danish profile of soft rot Pectobacteriaceae; A three-year field sampling study proving several clonal clades of soft rot isolates across diverse locations implicating a common origin

Soft rot Pectobacteriaceae (SRP) are among the most economically important plant pathogenic bacteria and are especially known to be problematic in potato production. The epidemiology of disease transmission has been investigated for almost a century, and several aspects have been highlighted as plausible infection routes. However, it is generally accepted that the major source of disease is the latently infected mother tuber, but several parameters are still influencing disease prevalence including contaminated equipment, soil water status as well as temperature. Management of the disease is limited to hygiene practices, dry storage and seed certification systems but several studies have also proven biocontrol agents such as bacteriophages (phages) as promising tools. Despite the severity of SRP on potato production, little is known about the genetic diversity of SRPs in Denmark, and since only few isolates are available, the possibility to design a broadly effective phage cocktail is limited. Here we describe a three-year field study utilizing an agri-citizen science approach where Danish farmers provided symptomatic potato plants or tubers, together with metadata such as date, location, potato variety and origin. By using whole genome sequencing (Illumina and Nanopore) together with metadata we were able to investigate and monitor the epidemiological disease spread across the country using 103 complete genomes, sampled across all three years. In this study we provide epidemiological evidence of disease origins and a suite of phages that could be used as a biocontrol tool for early disease intervention. Our results revealed several clonal clades across diverse locations (SNPs < 20) which strongly indicate common origin. A total of 17 Pectobacterium phages were tested and did target > 80% of clonal clades. Based on the clonality across the soft rot isolates we propose the possibility to set in early on using phages targeting strains relevant for soft rot development, with the possibility of a surveillance program together with customizing the phage preference.

microbiology↗

bioRxiv2025

Degradation of rutin and genistein and the effect on human bacterial fecal populations of obese and non-obese

This study re-evaluates the microbial degradation of rutin and genistein, emphasizing health-related metabotypes and novel degradation and transformation products of these compounds. In silico predictions and calculations were made to determine the molecular formulae of metabolites derived from precursor molecules by methylation, sulfation, and dehydroxylation. To validate these, anaerobic, ex vivo experiments were conducted with pooled fecal samples of obese and non-obese test persons (n=7 per group) over 48 hours, followed by 16S rRNA gene sequencing and semi-targeted high-resolution mass spectrometry analysis. We identified 46 rutin and 23 genistein metabolites, including novel methylated and sulfated derivatives. Microbial analysis revealed that the plant compounds influenced 34 bacterial families and 83 genera. Rutin inhibited obesity-associated genera while promoting butyrate-producing bacteria in BMI >40 samples, but reduced health-associated bifidobacteria and increased enterobacteria. Both compounds stimulated Eggerthella. These findings highlight significant microbial and metabolic shifts induced by plant-derived compounds, suggesting potential health implications.

microbiology↗

bioRxiv2025

Isolation of phages infecting the zoonotic pathogen Streptococcus suis reveals novel structural and genomic characteristics

Bacteriophage research has experienced a renaissance in recent years, owing to their therapeutic potential and versatility in biotechnology, particularly in combating antibiotic resistant-bacteria along the farm-to-fork continuum. However, certain pathogens remain underexplored as targets for phage therapy, including the zoonotic pathogen Streptococcus suis which causes infections in pigs and humans. Despite global efforts, the genome of only one infective S. suis phage has been described. Here, we report the isolation of two phages that infect S. suis: Bonnie and Clyde. The phages infect 58% of 100 S. suis strains tested, including representatives of seven different serotypes and thirteen known sequence types from diverse geographical origins. Clyde suppressed bacterial growth in vitro within two multi-strain mixes designed to simulate a polyclonal S. suis infection. Both phages demonstrated stability across various temperatures and pH levels, highlighting their potential to withstand storage conditions and maintain viability in delivery formulations. Genome comparisons revealed that neither phage shares significant nucleotide identity with any cultivated phages in the NCBI database and thereby represent novel species belonging to two distinct novel genera. This study is the first to investigate the adhesion devices of S. suis infecting phages. Structure prediction and analysis of adhesion devices with AlphaFold2 revealed two distinct lineages of S. suis phages: Streptococcus thermophilus-like (Bonnie) and S. suis-like (Clyde). The structural similarities between the adhesion devices of Bonnie and S. thermophilus phages, despite the lack of nucleotide similarity and differing ecological niches, suggest a common ancestor or convergent evolution, highlighting evolutionary links between pathogenic and non-pathogenic streptococcal species. These findings provide valuable insights into the genetic and phenotypic characteristics of phages that can infect S. suis, providing new data for the therapeutic application of phages in a One Health context.

microbiology↗

bioRxiv2022

CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice

Many prokaryotes harbor the adaptive CRISPR-Cas system, which stores small nucleotide fragments from previous invasions of nucleic acids via viruses or plasmids. This molecular archive blocks further invaders carrying identical or similar nucleotide sequences. However, very few of these systems have been experimentally confirmed to be active in gut bacteria. Here, we experimentally demonstrate that the type I-C CRISPR-Cas system of the prevalent gut bacterium Eggerthella lenta can specifically target and cleave foreign DNA in vitro by using a plasmid transformation assay. We also show that the CRISPR-Cas system acquires new immunities (spacers) from the genome of a virulent E. lenta phage using traditional phage-assays in vitro but also in vivo using gnotobiotic (GB) mice. An increased number of spacer acquisition events were observed when E. lenta was exposed to a low multiplicity of infection in vitro, and three phage genes were found to contain protospacer hotspots. Interestingly, much less new spacer acquisitions were detected in vivo than in vitro. Longitudinal analysis of phage-bacteria interactions showed sustained coexistence in the gut of GB mice, with phage abundance being approximately one log higher than the bacteria. Our findings show that while the type I-C CRISPR-Cas system is active in vitro and in vivo, a highly virulent phage in vitro was still able co-exist with its bacterial host in vivo. Taken altogether, our results suggest that the CRISPR-Cas defense system of E. lenta provides only partial immunity in the gut.

microbiology↗

bioRxiv2019

Isolation and characterisation of novel phages infecting Lactobacillus plantarum and proposal of a new genus, \"Silenusvirus\".

Bacteria of Lactobacillus sp. are very useful to humans. However, the biology and genomic diversity of their (bacterio)phage enemies remains understudied. Knowledge on Lactobacillus phage diversity should broaden to develop efficient phage control strategies. To this end, organic waste samples were screened for phages against two wine-related Lactobacillus plantarum strains. Isolates were shotgun sequenced and compared against the phage database and each other by phylogenetics and comparative genomics. The new isolates had only three distant relatives from the database but displayed a high overall degree of genomic similarity amongst them. The latter allowed for the use of one isolate as a representative to conduct transmission electron microscopy and structural protein sequencing, and to study phage adsorption and growth kinetics. The microscopy and proteomics tests confirmed the observed diversity of the new isolates and supported their classification to the family Siphoviridae and the proposal of the new phage genus \"Silenusvirus\".

microbiology↗