Author

J. Nesme

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 7 Ecology· 2

Signature Assays, Organisms & Methods

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Assay:metagenomics· 6 Approach:experimental assay· 5 Research Focus:host-pathogen & immune response· 5 Organism:bacteria (other)· 3 Research Focus:cell type annotation· 2 Research Focus:ecology & biodiversity· 2 Organism:human· 2 Approach:statistical model· 2

Frequent Co-Authors

S. J. Sorensen· 7 shared J. Russel· 4 shared A. Dechesne· 2 shared B. F. Smets· 2 shared J. S. Madsen· 2 shared L. Li· 2 shared R. Pinilla-Redondo· 2 shared S. A. Shah· 2 shared

Activity by Year

2019-2023 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 23 mutual co-author links

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7 shared papersMicrobiology

S. J. Sorensen

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Author profile →

9 papers

Recent·Most cited

A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics

R. Eisenhofer, J. Nesme, L. Santos-Bay, A. Koziol, S. J. Sorensen, A. Alberdi, O. Aizpurua

The paper compares short-read, HiFi long-read, and hybrid sequencing strategies for genome-resolved metagenomics, finding each excels in different metrics like assembly quality, bin refinement, and mapping rate.

bioRxiv · Oct 4, 2023Microbiology

The role of plasmids in the gut microbiome during the first year of life

W. He, J. Russel, F. Klincke, J. Nesme, S. J. Sorensen

This study characterizes the acquisition and development of plasmids in the infant gut microbiome using longitudinal metagenomic data from 98 Swedish children.

bioRxiv · Apr 5, 2023 · PreprintMicrobiology

Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition

X. Li, A. Brejnrod, U. Trivedi, J. Russel, J. Thorsen, S. A. Shah, G. A. Vestergaard, M. A. Rasmussen, J. Nesme, H. Bisgaard, J. Stokholm, S. J. Sorensen

This study finds that antibiotic resistance gene co-localization is common in infants' gut microbiomes and linked to immature microbial composition.

bioRxiv · Feb 19, 2023Microbiology

CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids

R. Pinilla-Redondo, J. Russel, D. Mayo-Munoz, S. A. Shah, R. A. Garrett, J. Nesme, J. S. Madsen, P. C. Fineran, S. J. Soerensen

The paper investigates CRISPR-Cas systems on bacterial and archaeal plasmids, finding they are widespread, diverse, and involved in plasmid-plasmid conflicts.

bioRxiv · Jun 4, 2021Microbiology

Kin discrimination promotes horizontal gene transfer between unrelated strains in Bacillus subtilis

P. Stefanic, K. Belcijan, B. Kraigher, R. Kostanjsek, J. Nesme, j. Madsen, J. Kovac, S. J. Sorensen, M. Vos, I. Mandic-Mulec

This study shows that kin discrimination in B. subtilis promotes horizontal gene transfer between distantly related strains by inducing competence in recipients through a stress response.

bioRxiv · Mar 4, 2021 · PreprintMicrobiology

Extended spectrum β-lactamase and carbapenemase genes are substantially and sequentially reduced during conveyance and treatment of urban sewage

L. Li, J. Nesme, M. Quintela-Baluja, S. Balboa, S. Hashsham, M. R. Williams, Z. Yu, S. J. Sorensen, D. W. Graham, J. L. Romalde, A. Dechesne, B. F. Smets

The paper quantifies the reduction of antibiotic resistance genes during urban sewage conveyance and treatment, showing greater removal occurs during conveyance than treatment.

bioRxiv · Nov 12, 2020Ecology

Conjugative dissemination of plasmids in rapid sand filters: a trojan horse strategy to enhance pesticide degradation in groundwater treatment

R. Pinilla-Redondo, A. K. Olsen, J. Russel, L. E. de Vries, L. D. Christensen, S. Musovic, J. Nesme, S. J. Soerensen

bioRxiv · Mar 6, 2020 · PreprintMicrobiology

Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes

L. Li, A. Dechesne, J. S. Madsen, J. Nesme, S. J. Sorensen, B. F. Smets

This study shows that plasmids can persist in microbial communities by providing fitness benefits to multiple bacterial phylotypes, enabling long-term community-wide access to antibiotic resistance genes.

bioRxiv · Aug 28, 2019Ecology

Construction of simplified microbial consortia to degrade recalcitrant materials based on enrichment and dilution-to-extinction cultures

D. Kang, S. Jacquiod, J. Herschend, S. Wei, J. Nesme, S. J. Sorensen

This paper develops a method using enrichment and dilution-to-extinction cultures to construct simplified microbial consortia for keratinous waste degradation, showing they retain biodegradation efficiency.

bioRxiv · Jun 17, 2019Microbiology