OSCR

Non-concussive head impacts sustained during American football correlate with changes in gut microbiome diversity and composition.

Code ↔ Paper

12 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 12 matches
  1. [1] § Materials and methods › Fecal sample collection lifestyle questionnaires ↔ TBI_CLR.Rmd, lines 30–80 · score 0.82 · miceRanger, Bristol Stool, orthopedic injury, illness, nicotine, vomiting
  2. [2] § Materials and methods › Fecal sample collection lifestyle questionnaires ↔ TBI_Microbiome_R.Rmd, lines 31–83 · score 0.82 · miceRanger, Bristol Stool, orthopedic injury, illness, nicotine, vomiting
  3. [3] § Results › Bray-Curtis dissimilarity increases three days following substantial head impact exposure ↔ TBI Microbiome.ipynb, lines 1033–1165 · score 0.73 · 72–96 hours, 0–24 hours, Bray Curtis Dissimilarity, 48–72 hours, head impact, Nemenyi
  4. [4] § Results › Bray-Curtis dissimilarity increases three days following substantial head impact exposure ↔ TBI_Microbiome.ipynb, lines 978–1109 · score 0.73 · 72–96 hours, 0–24 hours, Bray Curtis Dissimilarity, 48–72 hours, head impact, Nemenyi
  5. [5] § Results › Bray-Curtis dissimilarity increases three days following substantial head impact exposure ↔ TBI Microbiome.ipynb, lines 1033–1165 · score 0.68 · 72–96 hours, 0–24 hour, Bray Curtis Dissimilarity, 48–72, head impact, Nemenyi
  6. [6] § Results › Bray-Curtis dissimilarity increases three days following substantial head impact exposure ↔ TBI_Microbiome.ipynb, lines 978–1109 · score 0.68 · 72–96 hours, 0–24 hour, Bray Curtis Dissimilarity, 48–72, head impact, Nemenyi
  7. [7] § Materials and methods › Data analysis – Data slicing and repeated-measures analysis ↔ TBI Microbiome.ipynb, lines 920–1029 · score 0.57 · post hoc pairwise, Rank, ANOVA, Nemenyi, Friedman, microbial
  8. [8] § Materials and methods › Data analysis – Data slicing and repeated-measures analysis ↔ TBI_Microbiome.ipynb, lines 865–974 · score 0.57 · post hoc pairwise, Rank, ANOVA, Nemenyi, Friedman, microbial
  9. [9] § Materials and methods › Data processing – Taxonomic data ↔ TBI Microbiome.ipynb, lines 273–291 · score 0.55 · Silva V4, classifier provided, taxonomic, sequence, microbial
  10. [10] § Materials and methods › Data processing – Taxonomic data ↔ TBI_Microbiome.ipynb, lines 280–298 · score 0.55 · Silva V4, classifier provided, taxonomic, sequence, microbial
  11. [11] § Results › Gut microbiome composition changes 48–72 hours post head impact ↔ TBI_CLR.Rmd, lines 251–321 · score 0.55 · CLR, circumstances, Orthopedic, caffeine, Coriobacteriales, sleep
  12. [12] § Results › Gut microbiome composition changes 48–72 hours post head impact ↔ TBI_Microbiome_R.Rmd, lines 312–385 · score 0.51 · circumstances, Orthopedic, caffeine, Coriobacteriales, sleep, Verrucomicrobiales

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The authors' code

Jupyter notebook · 1,633 lines · 216 KB · no license · 4 matches

The registry keeps no copy of this file: its repository has no license, so its authors keep all their rights to it. Your browser shows it from its source, with JavaScript.

It can be read at the source: TBI Microbiome.ipynb.

Overview

Authors: Zachary J. Pelland1, Aziz Zafar2,3, Ahmet A. Ay2,3, Kenneth Douglas Belanger2
ORCID iDs: Zachary J. Pelland, Kenneth Douglas Belanger
  1. Program in Neuroscience, Colgate University, Hamilton, New York, United States of America
  2. Department of Biology, Colgate University, Hamilton, New York, United States of America
  3. Department of Mathematics, Colgate University, Hamilton, New York, United States of America
Institutions: Colgate University (United States)
Journal: PloS one, volume 21, issue 5, article e0345651
Dates: received 7 October 2025; accepted 9 March 2026; published online 6 May 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1371/journal.pone.0345651 · PMID 42090386 · PMCID PMC13148679 · OpenAlex W7160403358
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), traumatic brain injury (population), clinical / translational (subfield)
Methods: Statistics
MeSH: Brain Concussion*, Football*, Gastrointestinal Microbiome*, Athletes, Humans, Male, United States, Young Adult (* major topic)
Journal subjects: Biology and Life Sciences, Microbiology, Medical Microbiology, Microbiome, Genetics, Genomics, Microbial Genomics, Psychology, Behavior, Recreation, Sports, Social Sciences, Sports Science, Immunology, Immune Response, Inflammation, Medicine and Health Sciences, Clinical Medicine, Signs and Symptoms, Pharmacology, Drugs, Analgesics, NSAIDs, Pain management, Critical Care and Emergency Medicine, Trauma Medicine, Traumatic Injury, Neurotrauma, Traumatic Brain Injury, Organisms, Bacteria, Gut Bacteria, Ruminococcus, Anatomy, Head, Physiology, Physiological Processes, Sleep
Topic: Traumatic Brain Injury Research (Epidemiology, Medicine), according to OpenAlex
Funding: Colgate University (N/A)
Citations: cited by 1 paper (Europe PMC); 70 references in the paper

Abstract

Non-concussive head impacts (NHIs) are a significant health concern among at-risk groups, including athletes and military personnel. NHIs are hits to the head or head acceleration events (HAEs) that do not generate clinically detectable symptoms and are unlikely to meet diagnostic criteria for mild traumatic brain injury (mTBI). The composition of the gut microbiota influences many aspects of health and wellness and can be altered by TBIs and by brain-related diseases and disorders; however, microbiome alterations have not previously been linked to NHIs. We investigated whether NHIs in a cohort of American football players correlate with acute and long-term changes in the gut microbiome. This study monitored head impact exposure, gut microbiome composition, and a breadth of clinical and behavioral factors in a cohort of collegiate American football players across a competition season. Both short- and long-term changes in the microbiome were analyzed for correlation with head impact events and mathematical modeling was used to examine the contribution of NHIs and other clinical factors to these changes. We observe that NHI exposure correlates with changes in microbial diversity and composition three days following a head impact event. Furthermore, the athletes’ gut microbiomes change significantly across the season, with evidence from mixed-effects modeling indicating that the cumulative effects of NHIs contribute to this change. Our results provide strong evidence for a link between NHIs and changes in the diversity and composition of the gut microbiome. The outcomes of this study emphasize the importance of careful monitoring of head impacts, including those that do not generate clinical symptoms.

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

Repository

Its files are read in the Code ↔ Paper reader above, with 12 matches between paragraphs and lines of code.

aziz-zafar/TBI-Microbiome

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: d13d3d7c12fa1833180f138096ba1848f150c08e, 27 January 2026
Languages: Jupyter (2), R (2), Python (1)
Size: 8 files, 5 scripts
Software Heritage: not archived
Found in: “Data Availability”
Holds: README, 4 notebooks
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Matplotlib (3 files), NumPy (3 files), pandas (3 files), SciPy (3 files), car (2 files), ggplot2 (2 files), igraph (2 files), lme4 (2 files), lmerTest (2 files), scikit-learn (2 files), seaborn (2 files), tidyverse (2 files), scikit-posthocs (1 file), statsmodels (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
6 files, not copied: shown from their source

OSCR keeps no copy of these files: this repository has no license that allows it. The reader above shows each one from its source, fetched by your browser at commit d13d3d7, when its fingerprint is the one OSCR verified. How this works.

At the source: github.com/aziz-zafar/TBI-Microbiome

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:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 5 scripts, each with its path and the digest of its content;
  • 12 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

Data links

Data Availability

Raw 16S rRNA sequences generated in this study are available via the NCBI BioProject database under accession number PRJNA1111907 (http://www.ncbi.nlm.nih.gov/bioproject/1111907). All metadata and the code used for data processing and statistical analyses are available on this GitHub repository: https://github.com/aziz-zafar/TBI-Microbiome.

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, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 4 authors, 8 MeSH terms, 1 funder, 68 references.

Cite

This paper

Pelland, Z. J., Zafar, A., Ay, A. A., & Belanger, K. D. (2026). Non-concussive head impacts sustained during American football correlate with changes in gut microbiome diversity and composition. PloS one, 21(5), e0345651. https://doi.org/10.1371/journal.pone.0345651

BibTeX

@article{pelland2026non,
author = {Pelland, Zachary J. and Zafar, Aziz and Ay, Ahmet A. and Belanger, Kenneth Douglas},
title = {{Non-concussive head impacts sustained during American football correlate with changes in gut microbiome diversity and composition}},
journal = {PloS one},
year = {2026},
month = may,
volume = {21},
number = {5},
pages = {e0345651},
publisher = {PLOS},
issn = {1932-6203},
doi = {10.1371/journal.pone.0345651},
url = {https://doi.org/10.1371/journal.pone.0345651},
pmid = {42090386},
pmcid = {PMC13148679}
}

RIS

TY - JOUR
AU - Pelland, Zachary J.
AU - Zafar, Aziz
AU - Ay, Ahmet A.
AU - Belanger, Kenneth Douglas
TI - Non-concussive head impacts sustained during American football correlate with changes in gut microbiome diversity and composition
T2 - PloS one
J2 - PLoS One
PY - 2026
DA - 2026/05/06
VL - 21
IS - 5
SP - e0345651
SN - 1932-6203
PB - PLOS
DO - 10.1371/journal.pone.0345651
UR - https://doi.org/10.1371/journal.pone.0345651
LA - en
ER -

CSL-JSON

{
"id": "10.1371/journal.pone.0345651",
"type": "article-journal",
"title": "Non-concussive head impacts sustained during American football correlate with changes in gut microbiome diversity and composition",
"container-title": "PloS one",
"author": [
{
"family": "Pelland",
"given": "Zachary J."
},
{
"family": "Zafar",
"given": "Aziz"
},
{
"family": "Ay",
"given": "Ahmet A."
},
{
"family": "Belanger",
"given": "Kenneth Douglas"
}
],
"container-title-short": "PLoS One",
"volume": "21",
"issue": "5",
"page": "e0345651",
"DOI": "10.1371/journal.pone.0345651",
"PMID": "42090386",
"PMCID": "PMC13148679",
"ISSN": "1932-6203",
"publisher": "PLOS",
"URL": "https://doi.org/10.1371/journal.pone.0345651",
"language": "en",
"issued": {
"date-parts": [
[
2026,
5,
6
]
]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.1093/braincomms/fcag176 [code]
Tau topography subtypes account for clinical heterogeneity and longitudinal trajectories in early-onset Alzheimer's disease.
Journal: Brain communications
In common: car, lmerTest, lme4, 9 other tools, clinical / translational
[2] doi:10.1016/j.nicl.2026.104012 [code]
Structural-functional multilayer brain network properties and outcome of combined repetitive transcranial magnetic stimulation and psychotherapy for obsessive-compulsive disorder.
Journal: NeuroImage. Clinical
In common: car, lmerTest, lme4, 9 other tools
[3] doi:10.1162/imag.a.105 [code]
Right posterior theta reflects human parahippocampal phase resetting by salient cues during goal-directed navigation
Journal: —
In common: car, lmerTest, lme4, 8 other tools
[4] doi:10.3389/fnhum.2026.1839961 [code]
Developmental stability of task-rest neural efficiency in youth using a threat and cognitive control task.
Journal: Frontiers in human neuroscience
In common: car, lmerTest, lme4, 8 other tools
[5] doi:10.1126/sciadv.adz6517 [code]
Corticosterone-linked microglial activity underpins sexually dimorphic neuroplasticity after ketamine anesthesia.
Journal: Science advances
In common: scikit-posthocs, lme4, statsmodels, 8 other tools
[6] doi:10.1093/bioinformatics/btag592 [code]
Network-based stratification of allele-specific expression reveals patient subgroups in Huntington's disease.
Journal: Bioinformatics (Oxford, England)
In common: car, igraph, lme4, 8 other tools
[7] doi:10.1002/hbm.70534 [code]
Longitudinal Multimodal Neuroimaging After Traumatic Brain Injury.
Journal: Human brain mapping
In common: lmerTest, lme4, statsmodels, 7 other tools, traumatic brain injury, clinical / translational
[8] doi:10.1038/s41597-026-07350-9 [code]
An open multi-center MEG-EEG dataset for studying conscious visual perception.
Journal: Scientific data
In common: car, lmerTest, statsmodels, 8 other tools
[9] doi:10.1038/s41597-026-07377-y [code]
An open-access multi-site fMRI dataset for investigating conscious visual perception.
Journal: Scientific data
In common: car, lmerTest, statsmodels, 8 other tools
[10] doi:10.1038/s42003-026-10957-8 [code]
Brain defence by the extracellular matrix protein Cochlin.
Journal: Communications biology
In common: igraph, lme4, statsmodels, 8 other tools

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: questions and error reports about this paper and its code, from signed-in readers and its authors. It opens with sign-in.

Reproductions: reports from readers who ran the authors' code: what they reproduced, with which environment, commit and data. It opens with sign-in.

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.