Page 21 - Read Online
P. 21
Li et al. Microbiome Res Rep 2024;3:26 https://dx.doi.org/10.20517/mrr.2023.57 Page 15 of 16
Genomics Institute [OGI-156 and OGI-149], the Natural Sciences and Engineering Research Council of
Canada [NSERC, grant No. 210034], and the Ontario Ministry of Economic Development and Innovation
[ORF-DIG-14405 and project 13440].
Conflicts of interest
Figeys D cofounded MedBiome, a clinical microbiomic company. Zhang X is an Editorial Board member of
the journal Microbiome Research Reports. All other authors declared that there are no conflicts of interest.
Ethical approval and consent to participate
The protocol for human stool sample collection (# 20160585-01 H) was approved by the Ottawa Health
Science Network Research Ethics Board at the Ottawa Hospital, Ottawa, Canada. Participants signed written
informed consent form to participate.
Consent for publication
Not applicable.
Copyright
© The Author(s) 2024.
REFERENCES
1. Maier L, Pruteanu M, Kuhn M, et al. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature 2018;555:623-8. DOI
PubMed PMC
2. Klünemann M, Andrejev S, Blasche S, et al. Bioaccumulation of therapeutic drugs by human gut bacteria. Nature 2021;597:533-8.
DOI PubMed PMC
3. Coyte KZ, Schluter J, Foster KR. The ecology of the microbiome: networks, competition, and stability. Science 2015;350:663-6. DOI
PubMed
4. The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 2012;486:207-
14. DOI PubMed PMC
5. Falony G, Joossens M, Vieira-Silva S, et al. Population-level analysis of gut microbiome variation. Science 2016;352:560-4. DOI
PubMed
6. Costea PI, Hildebrand F, Arumugam M, et al. Enterotypes in the landscape of gut microbial community composition. Nat Microbiol
2018;3:8-16. DOI PubMed PMC
7. Faith JJ, Guruge JL, Charbonneau M, et al. The long-term stability of the human gut microbiota. Science 2013;341:1237439. DOI
PubMed PMC
8. Shaw LP, Bassam H, Barnes CP, Walker AS, Klein N, Balloux F. Modelling microbiome recovery after antibiotics using a stability
landscape framework. ISME J 2019;13:1845-56. DOI PubMed PMC
9. Palleja A, Mikkelsen KH, Forslund SK, et al. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat
Microbiol 2018;3:1255-65. DOI PubMed
10. Jalili-Firoozinezhad S, Gazzaniga FS, Calamari EL, et al. A complex human gut microbiome cultured in an anaerobic intestine-on-a-
chip. Nat Biomed Eng 2019;3:520-31. DOI PubMed PMC
11. Wilmes P, Bond PL. The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed
community of prokaryotic microorganisms. Environ Microbiol 2004;6:911-20. DOI PubMed
12. Zhang X, Deeke SA, Ning Z, et al. Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle
proteins in pediatric inflammatory bowel disease. Nat Commun 2018;9:2873. DOI PubMed PMC
13. Lehmann T, Schallert K, Vilchez-Vargas R, et al. Metaproteomics of fecal samples of Crohn’s disease and Ulcerative Colitis. J
Proteomics 2019;201:93-103. DOI PubMed
14. Long S, Yang Y, Shen C, et al. Metaproteomics characterizes human gut microbiome function in colorectal cancer. NPJ Biofilms
Microbiomes 2020;6:14. DOI PubMed PMC
15. Zhong H, Ren H, Lu Y, et al. Distinct gut metagenomics and metaproteomics signatures in prediabetics and treatment-naïve type 2
diabetics. EBioMedicine 2019;47:373-83. DOI PubMed PMC
16. Chen Z, Li J, Gui S, et al. Comparative metaproteomics analysis shows altered fecal microbiota signatures in patients with major
depressive disorder. Neuroreport 2018;29:417-25. DOI PubMed
17. Thuy-Boun PS, Mehta S, Gruening B, et al. Metaproteomics analysis of SARS-CoV-2-infected patient samples reveals presence of
potential coinfecting microorganisms. J Proteome Res 2021;20:1451-4. DOI PubMed PMC

