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Multi-omics profiling reveals gut microbiome signatures associated with cognitive decline in Alzheimer's disease.

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The authors' code

R · 56 lines · 4.1 KB · no license

  1. source ~/.bashrc_all
  2. ls list > sample.list
  3. klab_metaqc list -i 02clean_data -s sample.list -t F2
  4. cat sample.list | awk '{print $1}' > 11
  5. #cat sample.list | awk -F "/" '{print $1}' > 11
  6. #sed -i 's/.clean//g' 11;
  7. paste 11 sample_clean.list | awk -F "\t" '{print $1 "\t" $3}' > sample_clean.list.s
  8. mkdir 0.3_all_bins
  9. nohup Bin_as_binning.sh -s sample_clean.list.s -o 0.3_all_bins/0.3.1_bin_results -t 25 &
  10. nohup Bin_as_binning_vagina.sh -s sample_clean.list.s -o 0.3_all_bins/0.3.1_bin_results -t 40 &
  11. cd 0.3_all_bins/0.3.1_bin_results/03_binning/10_final_bin
  12. cat D*/*cm.s > all_final_50_5.cm.s
  13. more all_final_50_5.cm.s | awk -F "\t" '$3>80 && $4<5' > all_80_5_bins_cm.s
  14. mkdir ../0.4_all_80_5_bins
  15. cat all_80_5_bins_cm.s | awk -F "\t" '{print $1}' > all_80_5_bins_cm_names
  16. mkdir bins_80_5
  17. cat all_80_5_bins_cm_names | parallel -j 50 cp S*/*links/{}.fa ./bins_80_5
  18. mv bins_80_5/ all_80_5_bins_cm.s ../0.4_all_80_5_bins/
  19. mv 0.4_all_80_5_bins ../../../
  20. source activate galah
  21. readlink -f 0.4_all_80_5_bins/bins_80_5/* > all_bins_80_5.path
  22. galah cluster --ani 95 --min-aligned-fraction 30 --output-cluster-definition all_bins_80_5.cls.tsv -t 32 --genome-fasta-list all_bins_80_5.path
  23. less -S all_bins_80_5.cls.tsv | perl -a -F"\t" -lne '@F[0]=~/.*\/(.*?).fa/; $o1=$1; @F[1]=~/.*\/(.*?).fa/; $o2=$1; print "$o1\t$o2" ' | sort -k1 | perl -a -F"\t" -lne 'BEGIN{$n=""; $c=0}; if(@F[0] ne $n){ $c++; $n=@F[0]}; $o="SGB.".$c; print "$_\t$o" ' | csvtk join -t -T -H -f"2;1" - all_80_5_bins_cm.s | perl -a -F"\t" -lne '$score=@F[4]-5*@F[5]; print "$_\t$score" ' | sort -t $'\t' -k1,1 -k9,9nr -k7,7nr | perl -a -F"\t" -lne 'BEGIN{$n="";}; if(@F[0] ne $n){$o="Rep_genome"; $n=@F[0]}else{$o="Member"}; print "$_\t$o" ' > all_bins_80_5.cls.rep
  24. mkdir bins_80_5_links
  25. ln -s /ddnstor/imau_sunzhihong/userdata/data_mat/mat_meta/Postbiotics_diar/0.4_all_80_5_bins/bins_80_5/* /ddnstor/imau_sunzhihong/userdata/data_mat/mat_meta/Postbiotics_diar/0.4_all_80_5_bins/bins_80_5_links
  26. mkdir rep_genome
  27. grep Rep all_bins_80_5.cls.rep | cut -f2,3 | perl -lane 'print "cp -d /ddnstor/imau_sunzhihong/userdata/data_mat/mat_meta/mouse_micro_recovery_20211223/0.4_all_80_5_bins.renamed/@F[0].fa rep_genome/@F[1].fa" ' | rush {} -j 5
  28. grep Rep all_bins_80_5.cls.rep | cut -f2,3 | perl -lane 'print "cp -d /ddnstor/imau_sunzhihong/imau_zhaofy/10_mice_japen/0.4_all_80_5_bins/bins_80_5/@F[0].fa rep_genome/@F[1].fa" ' | rush {} -j 5
  29. grep Rep all_bins_80_5.cls.rep | cut -f2,3 | perl -lane 'print "cp -d /ddnstor/imau_sunzhihong/imau_zhaofy/22_zhangsheng/1.0_huxi/0.3_all_bins/0.4_all_80_5_bins/bins_80_5_links/@F[0].fa rep_genome/@F[1].fa" ' | rush {} -j 5
  30. mkdir ../0.5_all_SGBs
  31. cd ..
  32. mv rep_genome 0.5_all_SGBs
  33. cd rep_genome
  34. mkdir ../../0.6_all_SGBs/all_SGBs_bins/
  35. ls -d *fa | parallel -j 30 cp {} ../../0.6_all_SGBs/all_SGBs_bins/
  36. mkdir 0.6_all_SGBs_abundance
  37. Bin_abundance.sh -s final_sample.list.s -r /ddnstor/imau_sunzhihong/userdata/data_mat/meta_item/diarrhea/0.5_all_SGBs/rep_genome -o 0.6_all_SGBs_abundance -t 32
  38. for i in `ls -d *coverm.abundance`; do less ${i} | cut -f 1,2 > ${i}_v1; done
  39. csvtk join -t -T *v1 > all_sample_abundance
  40. less -S all_sample_abundance | sed 's/.rep.sort Relative Abundance (%)//g' > all_sample_abundance_1
  41. rm -rf all_sample_abundance; mv all_sample_abundance_1 all_sample_abundance
  42. for i in `ls -d *coverm.abundance`; do less ${i} | cut -f 1,3 > ${i}_v2; done
  43. csvtk join -t -T *v2 > all_sample_rpkm
  44. less -S all_sample_rpkm | sed 's/.rep.sort RPKM//g' > all_sample_rpkm_1
  45. rm -rf all_sample_rpkm
  46. mv all_sample_rpkm_1 all_sample_rpkm
  47. mkdir 0.7_SGBs_fastani
  48. cd 0.7_SGBs_fastani
  49. mkdir -p 0.7.1_fastANI
  50. cd ../0.5_all_SGBs/
  51. ls -d *fa | parallel -j 50 gzip {}
  52. ls -d *.gz | parallel echo /ddnstor/imau_sunzhihong/userdata/data_mat/meta_item/diarrhea/0.5_all_SGBs/rep_genome/{} '>>' ../../0.7_SGBs_fastani/0.7.1_fastANI/own_list
  53. cp /ddnstor/imau_sunzhihong/imau_zhaofy/10_mice_japen/0.7_SGBs_fastani/0.7.1_fastANI/ref_list.tsv ./
  54. Bin_get_gtdb_annotation.sh -l own_list -o new
  55. fastANI --ql own_list --refList ref_list.tsv --visualize --matrix -o GTDB_query -t 136
  56. get_besthits.sh GTDB_query > GTDB_best_query

Metagenomic-data-assembly-and-analysis.r at commit 9e8bee5, no license · at the source

Overview

Authors: Zhixin Zhao1, Feiyan Zhao1, Mengdi Zhang1,2, Jiaqi Sun1, Xiaoyan Wang1, Jing lou3, Ruizhi She3, Lai-Yu Kwok1, Zhihong Sun1, Weizhong Huangfu3, Bilige Menghe1
  1. Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
  2. College of Pharmacy, Inner Mongolia Medical University, Hohhot, Inner Mongolia 010110, China
  3. Inner Mongolia Medical University Affiliated Hospital (Inner Mongolia Autonomous Region Cardiovascular Research Institute), Hohhot, Inner Mongolia 010030, China
Institutions: Inner Mongolia Agricultural University (China); Inner Mongolia Medical University (China)
Journal: iScience, volume 29, issue 8, article 116622
Dates: received 1 December 2025; accepted 15 June 2026; published online 14 July 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1016/j.isci.2026.116622 · PMID 42519007 · PMCID PMC13382586 · OpenAlex W7168240013
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), human (organism), Alzheimer's / dementia (population), clinical / translational (subfield)
Methods: Connectivity, Statistics, Machine learning, Smoothing, state filtering, decompositions
Keywords: bacteriophage, biomarker, cognitive dysfunction, dysbiosis, gastrointestinal microbiome, metabolomics, microbiota-gut-brain axis
Topic: Gut microbiota and health (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: National Key Research and Development Program of China (2024YFA1307002); National Natural Science Foundation of China (National Science Foundation of China) (32325040, U25A20733); Natural Science Foundation of Inner Mongolia (2024LHMS08011); Inner Mongolia Medical University (YKD2021MS016, 2023NYFYLHYB009)
Citations: not cited yet (Europe PMC); 68 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repositories

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ngdc.cncb.ac.cn/gsa

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: the link answers
Software Heritage: not checked
Found in: “Data and code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
At the source: ngdc.cncb.ac.cn/gsa

shenx08/Metagenomic-data-assembly-and-analysis

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 9e8bee53b73a2fd5e1b7df5a5f623dbe194692bd, 12 December 2025
Languages: R (1)
Size: 2 files, 1 script
Software Heritage: not archived
Found in: “Data and code availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
2 files
At the source: github.com/shenx08/Metagenomic-data-assembly-and-analysis

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

Tracing map

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  • 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 1 script, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
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Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

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Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

Read it in the paper: doi.org/10.1016/j.isci.2026.116622.

Versions

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 11 authors, 7 keywords, 4 funders, 67 references.

Cite

This paper

Zhao, Z., Zhao, F., Zhang, M., Sun, J., Wang, X., lou, J., She, R., Kwok, L.-Y., Sun, Z., Huangfu, W., & Menghe, B. (2026). Multi-omics profiling reveals gut microbiome signatures associated with cognitive decline in Alzheimer's disease. iScience, 29(8), 116622. https://doi.org/10.1016/j.isci.2026.116622

BibTeX

@article{zhao2026multi,
author = {Zhao, Zhixin and Zhao, Feiyan and Zhang, Mengdi and Sun, Jiaqi and Wang, Xiaoyan and lou, Jing and She, Ruizhi and Kwok, Lai-Yu and Sun, Zhihong and Huangfu, Weizhong and Menghe, Bilige},
title = {{Multi-omics profiling reveals gut microbiome signatures associated with cognitive decline in Alzheimer's disease}},
journal = {iScience},
year = {2026},
month = jul,
volume = {29},
number = {8},
pages = {116622},
publisher = {Elsevier},
issn = {2589-0042},
doi = {10.1016/j.isci.2026.116622},
url = {https://doi.org/10.1016/j.isci.2026.116622},
pmid = {42519007},
pmcid = {PMC13382586}
}

RIS

TY - JOUR
AU - Zhao, Zhixin
AU - Zhao, Feiyan
AU - Zhang, Mengdi
AU - Sun, Jiaqi
AU - Wang, Xiaoyan
AU - lou, Jing
AU - She, Ruizhi
AU - Kwok, Lai-Yu
AU - Sun, Zhihong
AU - Huangfu, Weizhong
AU - Menghe, Bilige
TI - Multi-omics profiling reveals gut microbiome signatures associated with cognitive decline in Alzheimer's disease
T2 - iScience
J2 - iScience
PY - 2026
DA - 2026/07/14
VL - 29
IS - 8
SP - 116622
SN - 2589-0042
PB - Elsevier
DO - 10.1016/j.isci.2026.116622
UR - https://doi.org/10.1016/j.isci.2026.116622
LA - en
ER -

CSL-JSON

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