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Gut microbiota dysbiosis in adolescent depression: a comparative analysis with adult depression and healthy adolescent.

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Paper

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The authors' code

Java · 65 lines · 1.7 KB · GPL-2.0

  1. /*
  2. * ClassificationResult.java
  3. *
  4. * Copyright 2006 Michigan State University Board of Trustees
  5. *
  6. * Created on October 29, 2003, 4:51 PM
  7. */
  8. package edu.msu.cme.rdp.classifier;
  10. import edu.msu.cme.rdp.classifier.utils.HierarchyVersion;
  11. import edu.msu.cme.rdp.readseq.readers.Sequence;
  12. import java.util.List;
  14. /**
  15. * This class holds the classification results for a query sequence.
  16. * @author wangqion
  17. */
  18. public class ClassificationResult {
  20. Sequence pSeq;
  21. List<RankAssignment> assignments;
  22. HierarchyVersion hVersion;
  23. boolean reverse;
  25. /** Creates a new instance of ClassificationResult.
  26. * This class holds the classification results for a query sequence.
  27. */
  28. public ClassificationResult(Sequence p, boolean reverse, List<RankAssignment> a, HierarchyVersion version) {
  29. pSeq = p;
  30. assignments = a;
  31. hVersion = version;
  32. this.reverse = reverse;
  33. }
  35. /**
  36. * Returns the query sequence
  37. */
  38. public Sequence getSequence() {
  39. return pSeq;
  40. }
  42. /**
  43. * Returns a list of RankAssignments. The assignments are returned in
  44. * the order of taxonomic ranks, from the highest to the lowest.
  45. */
  46. public List<RankAssignment> getAssignments() {
  47. return assignments;
  48. }
  50. /** Returns the training set number of the taxonomy hierarchy from of the training file.
  51. */
  52. public int getTrainsetNo() {
  53. return hVersion.getTrainsetNo();
  54. }
  56. /** Returns the version of the taxonomy hierarchy from of the training file.
  57. */
  58. public HierarchyVersion getHierarchyTrainsetNo() {
  59. return hVersion;
  60. }
  62. public boolean isReverse() {
  63. return reverse;
  64. }
  65. }

ClassificationResult.java at commit 9ff2c6f, under GPL-2.0 · at the source

Overview

Authors: Yongchun Ma1, Liyuan Luo1, Huichao Li1, YuXin Zhou1, Shasha Xiang2,3, Xiaohong Liu2, Xuan Zhu2
  1. Department of Sleep Medicine, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
  2. School of Food Science and Bioengineering, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
  3. Weifang Elbe Biotechnology Co., Ltd., Weifang, China
Institutions: Tongde Hospital of Zhejiang Province (China); Zhejiang Gongshang University (China)
Journal: Frontiers in microbiology, volume 17, article 1849097
Dates: received 7 April 2026; accepted 18 June 2026; published online 9 July 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.3389/fmicb.2026.1849097 · PMID 42495140 · PMCID PMC13393218 · OpenAlex W7167820535
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), depression (population), developmental (subfield)
Methods: Statistics, Machine learning
Keywords: adolescent depression, gut microbiota' microbiota-gut-brain axis, full-length 16S rRNA, gut microbiota, age-conserved, adolescent-specific
Topic: Gut microbiota and health (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Citations: not cited yet (Europe PMC); 51 references in the paper

Abstract

Introduction: Adolescent depression differs substantially from adult depression in neurodevelopmental and pathophysiological aspects, with gut microbiota dysbiosis recognized as a key regulator via the microbiota-gut-brain axis. Nevertheless, the age-specific microbial and metabolic signatures of adolescent depression remain poorly defined.

Methods: 125 participants including 33 adolescents with depression, 62 adults with depression, and 30 healthy adolescent controls were recruited. Full-length 16S rRNA gene sequencing was applied to profile gut microbial composition and functional metabolism.

Results: Alpha diversity was markedly reduced in adolescents with depression relative to healthy adolescent, whereas no significant difference was observed between adolescent and adult depression. PCoA and age-adjusted PERMANOVA revealed distinct microbial community separation across the three groups, with disease status contributing substantially to community divergence. A significant Group × Age interaction indicated that depression may exerted age-dependent effects on gut microbiota. At the genus level, 19 differential taxa were identified between depressed and healthy adolescents, with Akkermansia, Faecalibacterium, Prevotella, and Roseburia depleted, while only Eubacterium hallii group was enriched. Four genera differed between adolescent and adult depression, and 3 genera exhibited obvious age-interaction patterns, suggesting that adolescent depression disrupts microbial developmental trajectories and induces an adult-like dysbiotic phenotype. A Random Forest diagnostic model based on differential bacterial biomarkers achieved achieved promising exploratory performance in distinguishing depressed adolescents from healthy controls (5-CV AUC = 0.966), but failed to differentiate adolescent from adult depression. PICRUSt2 prediction further revealed that gut microbiota metabolism alterations in depression are primarily driven by depressive status.

Discussion: Our findings reveal both age-conserved and adolescent-specific microbial signatures, providing candidate microbial signatures and hypothesis-generating functional insights.

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

Repository

Its files are read in the Code ↔ Paper reader above.

rdpstaff/classifier

License: GPL-2.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 9ff2c6f769c0988927b7fc73dd165df906099a01, 29 December 2020
Languages: Java (104)
Size: 137 files, 104 scripts
Software Heritage: archived
Found in: the text, “16S rRNA gene sequencing and analysis”
Holds: README, license file, tests
Not found: CITATION.cff, environment file, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
106 files
At the source: github.com/rdpstaff/classifier

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;
  • 104 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • 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 availability statement

The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.

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

Versions

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, pages, dates, 7 authors, 6 keywords, 51 references.

Cite

This paper

Ma, Y., Luo, L., Li, H., Zhou, Y., Xiang, S., Liu, X., & Zhu, X. (2026). Gut microbiota dysbiosis in adolescent depression: a comparative analysis with adult depression and healthy adolescent. Frontiers in microbiology, 17, 1849097. https://doi.org/10.3389/fmicb.2026.1849097

BibTeX

@article{ma2026gut,
author = {Ma, Yongchun and Luo, Liyuan and Li, Huichao and Zhou, YuXin and Xiang, Shasha and Liu, Xiaohong and Zhu, Xuan},
title = {{Gut microbiota dysbiosis in adolescent depression: a comparative analysis with adult depression and healthy adolescent}},
journal = {Frontiers in microbiology},
year = {2026},
month = jul,
volume = {17},
pages = {1849097},
publisher = {Frontiers Media SA},
issn = {1664-302X},
doi = {10.3389/fmicb.2026.1849097},
url = {https://doi.org/10.3389/fmicb.2026.1849097},
pmid = {42495140},
pmcid = {PMC13393218}
}

RIS

TY - JOUR
AU - Ma, Yongchun
AU - Luo, Liyuan
AU - Li, Huichao
AU - Zhou, YuXin
AU - Xiang, Shasha
AU - Liu, Xiaohong
AU - Zhu, Xuan
TI - Gut microbiota dysbiosis in adolescent depression: a comparative analysis with adult depression and healthy adolescent
T2 - Frontiers in microbiology
J2 - Front Microbiol
PY - 2026
DA - 2026/07/09
VL - 17
SP - 1849097
SN - 1664-302X
PB - Frontiers Media SA
DO - 10.3389/fmicb.2026.1849097
UR - https://doi.org/10.3389/fmicb.2026.1849097
LA - en
ER -

CSL-JSON

{
"id": "10.3389/fmicb.2026.1849097",
"type": "article-journal",
"title": "Gut microbiota dysbiosis in adolescent depression: a comparative analysis with adult depression and healthy adolescent",
"container-title": "Frontiers in microbiology",
"author": [
{
"family": "Ma",
"given": "Yongchun"
},
{
"family": "Luo",
"given": "Liyuan"
},
{
"family": "Li",
"given": "Huichao"
},
{
"family": "Zhou",
"given": "YuXin"
},
{
"family": "Xiang",
"given": "Shasha"
},
{
"family": "Liu",
"given": "Xiaohong"
},
{
"family": "Zhu",
"given": "Xuan"
}
],
"container-title-short": "Front Microbiol",
"volume": "17",
"page": "1849097",
"DOI": "10.3389/fmicb.2026.1849097",
"PMID": "42495140",
"PMCID": "PMC13393218",
"ISSN": "1664-302X",
"publisher": "Frontiers Media SA",
"URL": "https://doi.org/10.3389/fmicb.2026.1849097",
"language": "en",
"issued": {
"date-parts": [
[
2026,
7,
9
]
]
}
}

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