Strong pathogen competition in neonatal gut colonisation

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PROBIC/mGEMS v0.1.0

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Microbiome diversity protects against pathogens by nutrient blocking

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Intestinal colonization resistance in the context of environmental, host, and microbial determinants

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Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year

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Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly

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Themisto: a scalable colored k -mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes

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Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCATPreprint

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Evolutionary and functional history of the Escherichia coli K1 capsule

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Plasmid-driven strategies for clone success in Escherichia coli

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Genetic strategies for sex-biased persistence of gut microbes across human life

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Modulation of multidrug-resistant clone success in Escherichia coli populations: a longitudinal, multi-country, genomic and antibiotic usage cohort study

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Geographical variation in the incidence of colorectal cancer and urinary tract cancer is associated with population exposure to colibactin-producing Escherichia coli

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Neonatal Colonization With Antibiotic-Resistant Pathogens in Low- and Middle-Income Countries

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Microbiota-derived small molecule genotoxins: host interactions and ecological impact in the gut ecosystem

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Group 2 and 3 ABC-transporter-dependent capsular K-loci contribute significantly to variation in the estimated invasive potential of Escherichia coliPreprint

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A comparative study of the molecular characteristics of human uropathogenic Escherichia coli collected from two hospitals in Norway and France in 2019

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Impact of intestinal colonization by Gram-negative bacteria on the incidence of bloodstream infections and lethality in critically ill neonates

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Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study

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Analysis of ESAC-Net/EARS-Net Data from 29 EEA Countries for Spatiotemporal Associations Between Antimicrobial Use and Resistance—Implications for Antimicrobial Stewardship?

McSorley, J. C. (2025) · Antibiotics · doi:10.3390/antibiotics14040399 · Cited by 7 · see citing works

Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain

Kim, Y., Worby, C. J., Acharya, S., van Dijk, L. R., Alfonsetti, D., Gromko, Z., Azimzadeh, P. N., Dodson, K., Gerber, G. K., Hultgren, S. J., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-025-01983-z · Cited by 7 · see citing works

Basic reproduction number varies markedly between closely related pandemic Escherichia coli clones

Ojala, F., Pesonen, H., Gladstone, R. A., Mäklin, T., Tonkin‐Hill, G. Q., Marttinen, P., & Corander, J. (2025) · Nature Communications · doi:10.1038/s41467-025-65301-1 · Cited by 7 · see citing works

Identification of transporter-dependent capsular loci associated with the invasive potential of Escherichia coli

Gladstone, R. A., Pesonen, M., Pöntinen, A. K., Mäklin, T., MacAlasdair, N., Thorpe, H. A., Shao, Y., Mallawaarachchi, S., Arredondo-Alonso, S., Parcell, B. J., et al. (2026) · Nature Microbiology · doi:10.1038/s41564-026-02283-w · Cited by 7 · see citing works

Assembly processes of rare and abundant microbial taxa are closely related to bacterial and fungal functionality during desert vegetation reestablishment

Zhouchang, Y. U., Zhang, W., Pian, D. U. O., Zhang, Y., Xingfang, T. I. A. N., Lin, S. U. N., Gu, Y., Zhang, J., Jiaxing, S. O. N. G., Sailike, A., et al. (2024) · Pedosphere · doi:10.1016/j.pedsph.2024.03.004 · Cited by 7 · see citing works

Residence-colonization trade-off and niche differentiation enable the coexistence of Escherichia coli phylogroups in healthy humansPreprint

Morel‐Journel, T., Lehtinen, S., Cotto, O., Amia, R., Dion, S., Figueroa, C., Martinson, J. N. V., Ralaimazava, P., Clermont, O., Duval, X., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.10.552787 · Cited by 7 · see citing works

Plasmid-driven strategies for clone success in Escherichia coliPreprint

Arredondo-Alonso, S., Pöntinen, A. K., Gama, J. A., Gladstone, R. A., Harms, K., Tonkin‐Hill, G. Q., Thorpe, H. A., Simonsen, G. S., Norwegian E. coli BSI Study Group, Samuelsen, Ø., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.14.562336 · Cited by 7 · see citing works

Vaccines preventing neonatal sepsis: focus on Group B Streptococcus , Klebsiella pneumoniae and Escherichia coli to combat rising antimicrobial resistance

Micoli, F., Rondini, S., Scorza, F. B., & Adamo, R. (2026) · Expert Review of Vaccines · doi:10.1080/14760584.2026.2622690 · Cited by 6 · see citing works

Reference-Free Variant Calling with Local Graph Construction with ska lo (SKA)

Derelle, R., Madon, K. J., Hellewell, J., Rodríguez-Bouza, V., Arinaminpathy, N., Lalvani, A., Croucher, N. J., Harris, S. R., Lees, J. A., & Chindelevitch, L. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf077 · Cited by 6 · see citing works

Selection, Comparative Genomics, and Potential Probiotic Features of Escherichia coli 5C, a pks-Negative Strain Isolated from Healthy Infant Donor Feces

Di Pierro, F., Sagheddu, V., Galletti, S., Casaroli, A., Labrini, E., Soldi, S., Cazzaniga, M., Bertuccioli, A., Matera, M., Cavecchia, I., et al. (2026) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-025-10522-5 · Cited by 5 · see citing works

Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation

Xiang, X., Li, Y., Ye, J., Li, B., He, G., Zhu, M., Zhang, J., Zhang, B., Miao, M., & Yang, Y. (2025) · npj Biofilms and Microbiomes · doi:10.1038/s41522-025-00768-w · Cited by 5 · see citing works

Lactobacillus rhamnosus modulates murine neonatal gut microbiota and inflammation caused by pathogenic Escherichia coli

Xuan, H. M., Umar, S., Zhong, C., Yu, W., Ahmed, I., Wheatley, J. L., Sampath, V., & Chávez‐Bueno, S. (2024) · BMC Microbiology · doi:10.1186/s12866-024-03598-6 · Cited by 5 · see citing works

Microbiota and resistome dynamics in untreated and treated wastewater: A ten-month study leveraging RNA-probe capture and subspecies-level metagenomics

Lindstedt, K., Osińska, A. D., Bargheet, A., Sørum, H. R., Wick, R. R., Holt, K. E., Pettersen, V. K., Sundsfjord, A., & Wasteson, Y. (2025) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2025.140566 · Cited by 4 · see citing works

Synteny – a high throughput web tool to streamline causal gene prioritisation and provide insight into protein function

Cutler, H. B., Stöckli, J., Madsen, S., Masson, S. W. C., Fuller, O. K., Shum, T. B., & James, D. E. (2025) · Scientific Reports · doi:10.1038/s41598-025-28473-w · Cited by 5 · see citing works

First Fit Algorithm for Bin Packing

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Analysis of twelve genomes of the bacterium Kerstersia gyiorum from brown-throated sloths (Bradypus variegatus), the first from a non-human host

Carhuaricra, D., Gonzalez, I. H. L., Ramos, P. L., da Silva, A. M., & Setúbal, J. C. (2024) · PeerJ · doi:10.7717/peerj.17206 · Cited by 3 · see citing works

The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom

Hamilton, W. L., Coscione, S., Maes, M., Warne, B., Pike, L. J., Khokhar, F., Blane, B., Brown, N. M., Gouliouris, T., Dougan, G., et al. (2023) · Microbial Genomics · doi:10.1099/mgen.0.001122 · Cited by 1 · see citing works

Zooming into the structure of the microbiome

Murray, G. G. R., & Chaguza, C. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00834-6 · Cited by 2 · see citing works

Strain intrinsic properties and environmental constraints together shape Escherichia coli dynamics and diversity over a twenty-year human gut time seriesPreprint

Condamine, B., Morel‐Journel, T., Tesson, F., Royer, G., Magnan, M., Bernheim, A. G., Denamur, É., Blanquart, F., & Clermont, O. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.21.581337 · Cited by 2 · see citing works

High ward-level and within-sample diversity of Klebsiella pneumoniae on a Malawian neonatal unit revealed by single colony whole genome sequencing and post-enrichment metagenomicsPreprint

Pearse, O., Zuza, A. M., Lester, R., Mangochi, H., Siyabu, P., Tewesa, E., Edwards, T., Thomson, N. R., Feasey, N., Kawaza, K., et al. (2025) · medRxiv · doi:10.1101/2025.07.02.25330551 · Cited by 2 · see citing works

Mobile genetic elements: the hidden puppet masters underlying infant gut microbiome assembly?

Kreuze, K., Friman, V., & Vatanen, T. (2024) · Microbiome Research Reports · doi:10.20517/mrr.2024.51 · Cited by 1 · see citing works

Tracing the early bacterial settlers in preterm and very-low birth-weight infants: first report of microbiota dynamics in South American neonates

Vera, J., Ferreira, C. V., Moraes, M., & Riera, N. (2026) · Infection and Immunity · doi:10.1128/iai.00570-25 · Cited by 1 · see citing works

Exploring the Microbiome of Fermented Soy Products: Implications for Gut Health in ChinaPreprint

Xiang, X., Li, Y., Ye, J., Li, B., He, G., Zhu, M., Zhang, J., Zhang, B., Miao, M., & Yang, Y. (2024) · Research Square · doi:10.21203/rs.3.rs-4982604/v1 · Cited by 1 · see citing works

Co-evolution between colibactin production and resistance is linked to clonal expansions in Escherichia coliPreprint

Mäklin, T., Calland, J. K., Mallawaarachchi, S., Thorpe, H. A., Gladstone, R. A., & Corander, J. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.17.686825 · Cited by 1 · see citing works

Finding common connections

Santiago, M. F. M., & Raulo, A. (2023) · eLife · doi:10.7554/elife.89468

SciScore Report for version 3

(2023) · doi:10.1099/acmi.0.000541.v3.1

iThenticate Report for version 3

(2023) · doi:10.1099/acmi.0.000541.v3.2

Microbiome and Resistome Dynamics in Untreated and Treated Wastewater: A Ten-Month Study Leveraging Rna-Probe Capture and Subspecies-Level MetagenomicsPreprint

Lindstedt, K., Osińska, A. D., Bargheet, A., Sørum, H. R., Wick, R. R., Holt, K. E., Pettersen, V. K., Sundsfjord, A., & Wasteson, Y. (2025) · SSRN Electronic Journal · doi:10.2139/ssrn.5204333

Uncovering the genetic arsenal of a multidrug-resistant Escherichia coli MB641 strain from infected orthopaedic implants in a hospital setting

Abbas, S., Yasmin, A., & Kazmi, A. (2025) · Microbial Pathogenesis · doi:10.1016/j.micpath.2025.107854

Machine learning-based lineage prediction from antimicrobial susceptibility testing phenotypes for Escherichia coli sequence type 131 clade C surveillance across infection types

Ross, T. A., Pöntinen, A. K., Holsbø, E., Samuelsen, Ø., Hegstad, K., Kampffmeyer, M., Jukka, C., & Gladstone, R. A. (2026) · Microbial Genomics · doi:10.1099/mgen.0.001608

Sequence type and strain-level detection of Klebsiella pneumoniae in culture-enriched bacterial metagenomes: comparative performance of mSWEEP and StrainGE bioinformatic tools

Buczek, D. J., Kabir, W., Lindstedt, K., Mäklin, T., Thorpe, H. A., Suzuki, Y., Corander, J., Samuelsen, Ø., & Sundsfjord, A. (2026) · Microbial Genomics · doi:10.1099/mgen.0.001638

Whole-genome sequencing reveals inter-household networks of gut-colonising ESBL- producing Escherichia coli in two rural Malawian districtsPreprint

O’Ferrall, A. M., Lally, D., Makaula, P., Namacha, G., Lewis, J. M., Musicha, P., Goodman, R. N., Allman, E., Moyo, S. J., Waddington, C. S., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.11.705350

Barking up the microbiome tree: a multi-body-site characterization of maternal postpartum and pup early colonization dynamicsPreprint

Cohen, T. M., Cohen, A., Turjeman, S., Kuzi, S., Tal, S., & Koren, O. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.04.742690

Mapping the evolutionary path towards multi-drug resistance in the pandemic Escherichia coli ST131 lineage

Pöntinen, A. K., Trung, N. V., Mallawaarachchi, S., Gladstone, R. A., Kuronen, J., Samuelsen, Ø., Yen, H. X., Yen, P. L. K., Lan, N. P. H., Dung, N. T., et al. (2026) · Microbial Genomics · doi:10.1099/mgen.0.001795

Understanding Strain-level Dynamics in Gut Commensal-Pathogen-Host Interactions

DeVeaux, A. L. (2025) · Open Scholarship Institutional Repository (Washington University in St. Louis) · doi:10.7936/172e-9543

Functional and Genomic Analyses of Klebsiella Pneumoniae Population Dynamics in the Gastrointestinal Tract

Wardwell-Scott, L. (2015) · Digital Access to Scholarship at Harvard (DASH) (Harvard University)

Context-Dependent Competition in a Model Gut Bacterial Community

de Muinck, E. J., Stenseth, N. C., Sachse, D., Roost, J. V., Rønningen, K. S., Rudi, K., & Trosvik, P. (2013) · PLoS ONE · doi:10.1371/journal.pone.0067210 · Cited by 25 · see citing works

Escherichia coli Pathotypes Occupy Distinct Niches in the Mouse Intestine

(2016)

Competitive advantage of hypervirulent Group B Streptococcus for neonatal colonization revealed by metagenomic analysis of gut microbiotaPreprint

Alvarez, A., Oñate, F. P., Touak, G., Kennedy, S., Goffinet, F., Plainvert, C., Mandelbrot, L., Ehrlich, S. D., Poyart, C., & Tazi, A. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.18.733191