Biology subjects

Brons, J. K.

Publications and source records attributed to Brons, J. K..

4 recordsLinked to original sources

bioRxiv2026

An expanded urine culturing workflow to cultivate and characterize diverse urobiome isolates

Despite increased recognition of the diverse resident microbiome of the urinary tract (i.e., the urobiome) in postmenopausal women, the roles and functions of these microbes remain largely unknown. Further empirical research is needed to understand the physiology, interactions, and antibiotic resistance evolution of urobiome members with pathogenic potential. However, experimental work relies on viable, culturable isolates. Standard urine culturing practices are designed for identifying a narrow set of known urinary microbes, and are thus poorly suited for cultivating taxa from the resident urobiome. Here we expand the urine culturing toolkit to reliably recover diverse urobiome taxa for downstream empirical research. Urine samples collected from postmenopausal women with recurrent urinary tract infections were shipped at ambient temperature to a central point for culturing. Microbial viability was maintained using boric acid preservative tubes during multi-day transport of sample aliquots. Selective media incubated under specialized conditions were used to promote recovery of diverse urobiome members, including fastidious taxa. Under 5% CO2 -enriched atmospheric conditions and with longer incubation times, we leveraged a chromogenic agar (UTIC) to further differentiate isolates based on colony color and morphology. We evaluated the workflow for its ability to isolate and characterize urobiome taxa, as determined by morphological differentiation and taxonomic identification. Across 108 urine samples, 6.3 {+/-} 3.2 distinct isolates were recovered, with no detectable relationship between sample shipment duration and isolate richness. On chromogenic agar, colony growth and color intensity was improved with CO2 -enriched atmospheric conditions and extended incubation times. We identified diverse taxa that are typically underrepresented in standard diagnostic culture and provide novel morphological characterizations for members of the genera Actinotignum, Aerococcus, Facklamia, Lactobacillus, Latilactobacillus, Limosilactobacillus, and Streptococcus species, which have not been previously described on UTIC chromogenic agar. Using this novel workflow, we recovered a diverse collection of urobiome isolates from urine samples shipped over multiple days. We also demonstrated the utility of a chromogenic agar for the visual differentiation of key urobiome taxa. While sequencing approaches have enhanced our understanding of urobiome composition, culturing is needed to investigate microbial interactions, virulence mechanisms, and antimicrobial susceptibility. This protocol adds to the growing toolkit for the cultivation of diverse urobiome isolates needed to support downstream empirical studies and advance urinary tract infection research.

microbiology↗

bioRxiv2025

Curated high-quality genomes of 39 diverse halophilic archaea

Archaea are widespread and ecologically important microorganisms, yet our understanding of their physiology and evolution is constrained by the limited number of complete genome assemblies available. Haloarchaea have emerged as model organisms for archaeal cell biology, virus-host interactions, and biotechnology. Despite their prominence in hypersaline environments and their potential for industrial applications, high-quality reference genomes remain scarce. Here, we present chromosome-level assemblies for 39 cultivable haloarchaeal strains for which no complete genomes were previously available. Using Oxford Nanopore sequencing, we obtained near-complete assemblies, with 38 strains resolving into single closed chromosomes and additional replicons such as plasmids captured largely in full. These genomes expand the available genomic resources for five haloarchaeal genera and provide a framework for comparative analyses of archaeal metabolism, genome organization, and mobile genetic elements. Given that many of these strains are natural hosts to diverse archaeal viruses, the genomes also represent a critical resource for advancing studies of virus-host interactions in archaea. Beyond fundamental insights into archaeal cell biology and evolution, this dataset will support the development of haloarchaeal model systems and facilitate the exploration of their biomolecules for biotechnological applications.

microbiology↗

bioRxiv2025

De novo whole genome assembly of the globally invasive green shore crab Carcinus maenas (Linnaeus, 1758) via long-read Oxford Nanopore MinION sequencing

Invasive species are rapidly reshaping aquatic ecosystems worldwide at an accelerating pace, with profound ecological and economic impacts. Many crustacean species have demonstrated invasive potential or are already well-established invaders. The green shore crab, Carcinus maenas, native to Europe and North Africa, is one of the most successful global marine invaders and is now present on six continents. Although the role of genomics in invasion science is increasingly recognized, genomic resources for brachyuran crabs remain limited, including the notable absence of a reference genome for C. maenas. Here we report on a de novo whole genome assembly of C. maenas via long-read Oxford Nanopore Technology sequencing. The assembly spans 1.09 Gbp across 21,887 scaffolds (N50 = 15 Mbp) with a BUSCO completeness of 98.4%, providing a high-quality resource for future genomic analyses. Additionally, we provide a detailed protocol for obtaining high-quality DNA to successfully sequence brachyuran crabs using a long-read approach, including strategies to address nanopore blockage issues. This new resource expands available genomic data for the species-rich infraorder Brachyura, and provides a valuable foundation for understanding the genetic factors underlying the global invasion success of C. maenas, supporting future research in marine invasion genomics.

genomics↗

bioRxiv2024

Community context influences the conjugation efficiency of E. coli

In urinary tract infections different bacteria can live in a polymicrobial community, it is unknown how such community members affect the conjugation rate of uropathogenic Escherichia coli. We investigated the influence of the polymicrobial urinary tract infection (UTI) community context on the conjugation rate of E. coli isolates in artificial urine medium. Pairwise conjugation rate experiments were conducted between a donor E. coli strain containing pOXA-48 and six uropathogenic E. coli isolates in the presence and absence of five community members to elucidate their effect on the rate of conjugation. We found that the basal conjugation rates in the absence of community members are genotype dependent. Interestingly, bacterial interactions have an overall positive effect on E. coli conjugation rates. Particularly Gram-positive enterococcal species were found to enhance the conjugation rates of most uropathogenic E. coli isolates. We hypothesize that the nature and co-culture of the interactions is important for these increased conjugation rates in AUM.

ecology↗