OSCR

Dynamics of early gut microbiota maturation in extremely preterm infants and neurodevelopment at 2 years of age in a probiotic intervention trial.

Code ↔ Paper

3 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 3 matches · 2 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § STAR★Methods › Method details › Two years follow-up ↔ multiqc/templates/default/assets/js/packages/showdown.min.js, the whole file · a weak match · score 0.60 · ping, speech, hearing, walking, national, child
  2. [2] § STAR★Methods › Quantification and statistical analysis ↔ R/data_sanity_check.R, lines 1–134 · score 0.56 · mia, mixed, taxonomic, pairwise, genus, ANCOM
  3. [3] § STAR★Methods › Quantification and statistical analysis ↔ multiqc/templates/default/assets/js/packages/plotly-3.1.2.custom.min.js, the whole file · a weak match · score 0.55 · variance, linear, DA, transformation, NY, absolute

Paper

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The authors' code

JavaScript · 3 lines · 73 KB · GPL-3.0 · 1 match

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showdown.min.js at commit dc565eb, under GPL-3.0 · at the source

Overview

  1. Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
  2. Crown Princess Victoria Children’s Hospital, University Hospital, Linköping, Sweden
  3. Clinical Department of Pediatrics, Vrinnevi Hospital, Norrköping, Sweden
  4. Department of Bioscience, University of Vic – Central University of Catalonia, Vic, Spain
  5. Institut de Recerca i Innovació en Ciències de la Vida i de la Salut a la Catalunya Central (IRIS-CC), Vic, Spain
  6. Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
Journal: iScience, volume 29, issue 5, article 115802
Dates: received 2 October 2025; accepted 15 April 2026; published online 20 April 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1016/j.isci.2026.115802 · PMID 42111202 · PMCID PMC13157099 · OpenAlex W7154966463
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: human (organism)
Methods: Statistics, Machine learning, fMRI & imaging, Smoothing, state filtering, decompositions
Keywords: Health sciences, Medicine, Microbiology, Neuroscience
Topic: Infant Nutrition and Health (Nutrition and Dietetics, Nursing), according to OpenAlex
Funding: Region Östergötland; Swedish Society for Medical Research; Swedish Society of Medicine; Ekhaga Foundation; Swedish Research Council; BioGaia AB
Citations: cited by 1 paper (Europe PMC); 77 references in the paper

Abstract

Preterm birth is associated with a high risk of long-term neurological deficits. Although research underscores the role of the gut microbiome in the gut-brain axis, the mechanisms of neurodevelopmental impairment remain elusive. In this prospective observational study (PROPEL), we evaluated whether early gut microbiota development and Limosilactobacillus reuteri supplementation to extremely preterm infants with extremely low birth weight (EPT-ELBW) are associated with neurodevelopment at 2 years. Gut microbiota was characterized by 16S sequencing, and neurodevelopment was assessed by Bayley-III score. Microbiota composition constellations and lower microbial diversity, but not single bacteria, are associated with impaired neurodevelopment. Microbial maturation over the first month was discriminative for motor development, with higher abundance of E. coli and Enterococcus relative to Cutibacterium associated with impairment. L. reuteri supplementation did not seem to affect neurodevelopment via the gut microbiome. In conclusion, dynamics of gut microbiota maturation during early life may impact neurodevelopment in EPT-ELBW infants.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above, with 3 matches between paragraphs and lines of code.

magge30/PROPEL-2y-neurodevelopment

License: none: the authors keep all their rights
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: 3d1b337f65a0fd2c2b39cc3b20ee59d529aa63b9, 3 February 2026
Languages: R (8)
Size: 13 files, 8 scripts
Software Heritage: not archived
Found in: “Data and code availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ggpubr (2 files), tidyverse (2 files), caret (1 file), data.table (1 file), DESeq2 (1 file), ggplot2 (1 file), lme4 (1 file), multcomp (1 file), reshape2 (1 file), rstatix (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
9 files

ewels/MultiQC

License: GPL-3.0
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: dc565eb9eef7b22a289ab7eec78e5efb6bf297c3, 28 September 2026
Languages: Python (647), JavaScript (75), Shell (1)
Size: 1,215 files, 723 scripts
Software Heritage: not archived
Found in: the resources table
Holds: README, license file, CITATION.cff, environment (Dockerfile, flake.nix, pyproject.toml, setup.py), tests, continuous integration, documentation
Tools: NumPy (14 files), Plotly (8 files), Pillow (2 files)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
725 files

FrederickHuangLin/ANCOMBC

License: none: the authors keep all their rights
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: dc4febdf59badb3a8dfe0c767ef2186323c2199a, 18 September 2026
Languages: R (27)
Size: 46 files, 27 scripts
Software Heritage: archived
Found in: the resources table
Holds: README, environment (DESCRIPTION), tests, documentation, 6 notebooks
Not found: license file, CITATION.cff, continuous integration
Tools: lme4 (6 files), tidyverse (5 files), lmerTest (4 files), multcomp (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
28 files

chanw0/SparseMCMM

License: other
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: c46959840f9b286b036a3231c2a25d5dd4c28ca2, 28 January 2026
Languages: R (11)
Size: 26 files, 11 scripts
Software Heritage: not archived
Found in: the resources table
Holds: README, license file, environment (DESCRIPTION), tests, documentation
Not found: CITATION.cff, continuous integration
Tools: tidyverse (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
14 files

thelovelab/tximport

License: none: the authors keep all their rights
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: 2c532670e2f58139a7ebc3a57fd2ccf22d5b8cdf, 28 September 2026
Languages: R (18)
Size: 31 files, 18 scripts
Software Heritage: not archived
Found in: the resources table
Holds: README, environment (DESCRIPTION), tests, documentation, 1 notebook
Not found: license file, CITATION.cff, continuous integration
Tools: tidyverse (11 files), DESeq2 (1 file), edgeR (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
19 files

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 5 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 787 scripts, each with its path and the digest of its content;
  • 3 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data and code availability

The 16S rRNA dataset generated in this study is available at the European Nucleotide Archive: PRJEB36531 https://www.ebi.ac.uk/ena/browser/view/PRJEB36531.

The anonymized coded data have been made available at https://github.com/magge30/PROPEL-2y-neurodevelopment.git

All original code has been deposited at https://github.com/magge30/PROPEL-2y-neurodevelopment.git and is publicly available.

Any additional information required to reanalyze the data reported in this study is available from the lead contact upon request.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 4 keywords, 6 funders, 77 references.

Cite

This paper

Abrahamsson, T., Wejryd, E., Pujolassos, M., Calle, M. L., Sverremark-Ekström, E., Jenmalm, M. C., & Martí, M. (2026). Dynamics of early gut microbiota maturation in extremely preterm infants and neurodevelopment at 2 years of age in a probiotic intervention trial. iScience, 29(5), 115802. https://doi.org/10.1016/j.isci.2026.115802

BibTeX

@article{abrahamsson2026dynamics,
author = {Abrahamsson, Thomas and Wejryd, Erik and Pujolassos, Meritxell and Calle, M Luz and Sverremark-Ekström, Eva and Jenmalm, Maria C and Martí, Magalí},
title = {{Dynamics of early gut microbiota maturation in extremely preterm infants and neurodevelopment at 2 years of age in a probiotic intervention trial}},
journal = {iScience},
year = {2026},
month = apr,
volume = {29},
number = {5},
pages = {115802},
publisher = {Elsevier},
issn = {2589-0042},
doi = {10.1016/j.isci.2026.115802},
url = {https://doi.org/10.1016/j.isci.2026.115802},
pmid = {42111202},
pmcid = {PMC13157099}
}

RIS

TY - JOUR
AU - Abrahamsson, Thomas
AU - Wejryd, Erik
AU - Pujolassos, Meritxell
AU - Calle, M Luz
AU - Sverremark-Ekström, Eva
AU - Jenmalm, Maria C
AU - Martí, Magalí
TI - Dynamics of early gut microbiota maturation in extremely preterm infants and neurodevelopment at 2 years of age in a probiotic intervention trial
T2 - iScience
J2 - iScience
PY - 2026
DA - 2026/04/20
VL - 29
IS - 5
SP - 115802
SN - 2589-0042
PB - Elsevier
DO - 10.1016/j.isci.2026.115802
UR - https://doi.org/10.1016/j.isci.2026.115802
LA - en
ER -

CSL-JSON

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