Biology subjects

Nemeth, T.

Publications and source records attributed to Nemeth, T..

6 recordsLinked to original sources

bioRxiv2026

Catcher in the rye: museomics reveals the identity of cereal remains recovered from a late nineteenth century antique furniture

Historical crop remains preserved in everyday objects are an underused archive of agrobiodiversity change, yet their degraded DNA resists conventional analysis. We recovered cereal grains and straws used as upholstery padding in a Central European settee dated to about 1870 to 1900. We identified and characterized the specimen by genome skimming. Damage-aware sequencing confirmed authentic historical DNA of modest, late nineteenth-century age. The assembled plastome placed the specimen securely within rye, and a genome-wide SNP panel of rye landraces resolved it inside cultivated Secale cereale subsp. cereale, closest to a Hungarian bred rye and a Slovak upland landrace and remote from wild or eastern lineages. Screening 192 stress-associated loci recovered the structural machinery of resistance, abiotic stress and aluminum tolerance pathways, while heading-date genotyping showed the Weining earliness allele at Hd2R already present. Divergence across 36 domestication sweep regions concentrated at a few improvement loci. Integrating these genomic signals with genebank passport data and an 1891 newspaper record, we interpret the specimen as a tall Central European rye at the threshold between landrace and improved variety. Historical crop material, read this way, preserves both genomes and the traces of human agricultural practice.

genomics↗

bioRxiv2025

Intracellular acidification by bacteria-derived valeric acid is a mechanism of trans-kingdom ecology against Candida parapsilosis colonization

In hematopoietic cell transplant patients, intestinal Candida parapsilosis expansion and translocation cause life-threatening candidemia, yet how commensal intestinal bacteria prevent Candida expansion remains incompletely defined. Here, we trained a machine learning model on supernatant metabolomic profiles of commensal bacteria to identify bacteria-derived inhibitors of fungal growth, with valeric and butyric acid as top hits. Experimental validation confirmed in silico predictions in three systems. First, in patient fecal samples, valeric and butyric acid levels inversely correlated with C. parapsilosis growth. Second, in vitro, valeric acid potently inhibited C. parapsilosis growth by causing intracellular acidification. Third, administration of glycerol valerate, and free or microencapsulated valeric acid blunted C. parapsilosis growth at murine intestinal sites where valeric acid could be detected. Thus, machine learning could identify a mechanistic driver of trans-kingdom ecology limiting C. parapsilosis intestinal expansion and may inform strategies to reduce patient risk of developing candidiasis during high-risk periods.

microbiology↗

bioRxiv2024

Clinical considerations on antimicrobial resistance potential of complex microbiological samples

Antimicrobial resistance (AMR) is one of our greatest public health challenges. Targeted use of antibiotics (AB) can reduce the occurrence and spread of AMR and boost the effectiveness of treatment. This requires knowledge of the antibiotic susceptibility (AS) of the pathogens involved in the disease. Therapeutic recommendations based on classical antibiotic susceptibility testing (AST) are based on the analysis of only a fraction of the bacteria present in the disease process. Next and third generation sequencing technologies allow the identification of antimicrobial resistance genes (ARGs) present in a bacterial community. Using this genomic approach, we can map the antimicrobial resistance potential (AMRP) of a complex, multi-bacterial microbial sample. The same approach can be used to identify antibiotics without any ARGs in the sample that interfere with their activity. Our paper summarises the clinical interpretation opportunities of genomic analysis results from 574 Escherichia coli strains and a complex microbiological sample from canine external otitis. In clinical metagenomics, AMRP may be an important approach to make AB therapy more targeted and effective. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/594174v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@d84733org.highwire.dtl.DTLVardef@12aa447org.highwire.dtl.DTLVardef@873811org.highwire.dtl.DTLVardef@1721aba_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

A One Health approach metagenomic study on the antimicrobial resistance traits of canine saliva

According to the One Health concept, physical proximity among pets and their owners facilitates the spread of various bacteria. Interspecies bacterial transfer media include canine saliva that can be transmitted by licking and biting. Antimicrobial resistance genes (ARGs) are the natural constituents of the bacterial genome. However, human activity can increase the prominence of ARGs. To assess factors that may affect the resistome of the canine oral cavity, the shotgun metagenomic sequencing dataset of 1830 canine saliva samples was bioinformatically analyzed and supplemented with survey results of the physical and behavioral traits of the dogs. Bacteriome and resistome associated with the canine saliva samples were described throughout the analysis. Moreover, the subset of higher public health ARGs and ESKAPE pathogen-related (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) higher public health ARGs were also collected. Further on, the set and subsets of ARGs were studied considering the surveyed traits of the sampled dogs. Overall, 318 ARG types reached sufficiently high detection rates. These ARGs can affect 31 antibiotic drug classes by various resistance mechanisms. ARGs against tetracyclines and cephalosporins appeared in the highest number of samples. However, surprisingly, another CIA group, peptides were represented by ARGs in the third-highest number of samples. Considering further ARG appearance rates in the samples, Critically Important Antimicrobials (CIAs, WHO), such as aminoglycosides, fluoroquinolones, or macrolides, were among the most frequently affected drug classes by higher public health risk ARGs and ESKAPE pathogen related higher public health risk ARGs. Bacteria in the saliva of white and diluted (merle, gray) color dogs and dogs characterized with decreased activity and decreased aggression more often harbored ARGs. Reduced playfulness could have been specifically associated with higher public health risk ARG presence. Even though the oral microbiome of the owners is unknown, One Health and public health implications of the close human-pet bonds and factors potentially underlying the rise in salivary ARG numbers should be considered, mostly in the light of the presence of ARGs affecting critically important drugs for human medicine.

genomics↗

bioRxiv2023

First animal source metagenome assembly of Lawsonella clevelandensis from canine external otitis

External otitis is one of the most common conditions in dogs to be presented to the veterinarian. Moreover, the disorder is often difficult to manage. The range and role of microorganisms involved in the pathogenesis are currently not fully understood. Therefore, the condition has been studied using third-generation sequencing (Oxford Nanopore Technology) to gain a more complete picture of the pathogens involved. Throughout the metagenome assembly of a sample harvested from the ear canal of an 11-year-old female Yorkshire terrier suffering from chronic external otitis, a genome of Lawsonella clevelandensis was compiled. To our knowledge, this result is the first of its type of animal origin. The outcome of the assembly (CP140010) is a single circular chromosome with a length of 1,878,509 bp, and 1,826 predicted protein-coding genes. No open reading frames associated with antimicrobial resistance could have been identified.

bioinformatics↗

bioRxiv2022

Canine saliva is a source of interspecies antimicrobial resistance gene transfer

While the One Health issues of intensive animal farming are commonly discussed, keeping companion animals is less associated with the interspecies headway of antimicrobial resistance. With the constant advance of veterinary standards, antibiotics are regularly applied in companion animal medicine. Due to the close coexsistance of dogs and humans, dog bites and other casual encounters with dog saliva (e.g. licking the owner) are common. According to our metagenome studies based on 26 new generation sequencing canine saliva datasets from 2020 and 2021 reposited in NCBI SRA by The 10,000 Dog Genome Consortium and the Broad Institute within Darwins Ark project, canine saliva is rich in bacteria with predictably transferable antimicrobial resistance genes (ARGs). In the genom of potentially pathogenic Bacteroides, Capnocytophaga, Corynebacterium, Fusobacterium, Pasteurella, Porphyromonas, Staphylococcus and Streptococcus species, that are some of the most relevant bacteria in dog bite infections, ARGs against aminoglycosides, carbapenems, cephalosporins, glycylcyclines, lincosamides, macrolides, oxazolidinone, penams, phenicols, pleuromutilins, streptogramins, sulfonamides and tetracyclines could be identfied. Several ARGs, including ones against amoxicillin-clavulanate, the most commonly applied antibiotic by dog bites, was predicted to be potentially transferable based on their association with mobile genetic elements (e.g. plasmids, phages, integrated mobile genetic elements). According to our findings canine saliva may be a source of transfer of ARG-rich bacteria, that can either colonize the human body or transport ARGs to the host bacteriota and thus can be considered as a risk in the spread of antimicrobial resistance.

genomics↗