Biology subjects

Muurinen, J.

Publications and source records attributed to Muurinen, J..

3 recordsLinked to original sources

bioRxiv2026

Antibiotic Resistomes And Microbial Communities In The 18th-Century Urban Settlement And Slaughterhouse Environment

Antimicrobial resistance (AMR) is an ancient and natural phenomenon, yet it now poses a critical threat to global health. Human activities, particularly animal husbandry, have shaped microbial evolution by creating manure-rich environments that promote interactions between environmental and host-associated bacteria and facilitate horizontal gene transfer. Here, we investigated dormant, potential antibiotic-producing bacteria, microbial communities, and their AMR genes and mobile genetic elements in 18th-century preindustrial slaughterhouse surroundings excavated in Turku, Finland. By combining cultivation, genomic analyses, metagenomic sequencing, and ancient DNA authentication methods, we reconstructed preindustrial microbiomes and resistomes to better understand the early ecology and evolution of AMR, and to explore the role of antibiotic-producing bacteria in the emergence of AMR. Our results reveal putative ancestral forms of resistance mechanisms only recently characterized, such as fosfomycin thiol transferase fosI, plasmid-associated tmexCD-toprJ efflux pumps conferring resistance to last-resource antibiotic tigecycline, as well as sequences related to mobility of AMR genes. These findings demonstrate that key AMR elements were already present prior to widespread antibiotic use, reflecting their long-term environmental origins.

microbiology↗

bioRxiv2026

Bio-based fertilizers shape soil microbiome, resistome and mobilome through metabolism of antibiotic-producing Streptomyces

Streptomyces are abundant soil inhabitants with extensive secondary metabolism and antibiotic resistance traits. Yet, their ecological role in shaping soil antibiotic resistome dynamics remains understudied. Here, we investigated how two different bio-based fertilizers harbouring Streptomyces shaped soil resistome and mobilome by combining genome analysis of eight Streptomyces isolates to metagenomic profiling of soils before fertilization, within 48 hours after fertilizer application, and six weeks after. Streptomyces genomes showed linkages among antibiotic resistance genes, carbohydrate-active enzymes, and antibiotic-production-associated biosynthetic gene clusters, connecting resistance and biosynthesis to broader metabolic strategies. Relationships between carbon degradation and biosynthesis associated with specific enzyme families, indicating that carbon availability shapes secondary metabolism. We confirmed experimentally that antibacterial potential varied with carbon source, suggesting that microbial activity during manufacturing of the bio-based fertilizers may create localized selection pressures before fertilizers enter the soil. Fertilization with the studied materials induced modest but consistent shifts in resistome and mobilome without major changes in dominant taxa or overall bacterial abundances, indicating functional reorganization within soil communities. Diversity of antibiotic resistance genes and mobile genetic elements increased, whereas abundance changes were small. Mobile genetic element composition showed stronger responses that were associated with fertilizer inputs, Streptomyces abundance, and taxa linked to faecal and resistance sources. Together, our results show that bio-based fertilizers shape soil resistome primarily through ecological restructuring of resident soil communities, while carbon-dependent microbial activity within fertilizers may enrich resistance. These factors should be considered in manufacturing of bio-based fertilizer as well as in designing agricultural practices.

microbiology↗

bioRxiv2020

Swine Growth Promotion with Antibiotics or Alternatives Increases Antibiotic Resistance Gene Mobility Potential in the Fecal Microbiome

Even though the use of antibiotics for food-producing animals may contribute to the emergence of antimicrobial resistance, antibiotics are still used as growth promoters. Due to consumer and regulatory pressures, the use of alternatives to antibiotics as growth promoters is increasing, thus more information is needed on their capability to disseminate antimicrobial resistance compared to antibiotics. We investigated the impacts of carbadox (antibiotic), copper sulfate and zinc oxide (metals) and mushroom powder (natural product) on the pig fecal resistome and microbiome. Antibiotic resistance gene (ARG) and mobile genetic element (MGE) abundances were measured using a high-throughput qPCR array with 382 primer pairs. Bacterial community composition was determined by 16S rRNA gene sequencing. More ARGs co-occurred with MGEs in the growth promoter group samples than in the control group samples. Community composition could not be linked to resistome in the growth promoter group samples, indicating a potential decoupling of ARGs and phylogeny. Additionally, machine-learning methods aided in defining the community and resistome differences in response to treatments. Since increased ARG mobility potential was the primary response to the dietary additives used in this study, we suggest that ARG mobility should be considered when designing antimicrobial use policies and antimicrobial resistance surveillances.

microbiology↗