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Gut microbiota in a Saudi population with chronic kidney disease
Afnan A Almuhanna, Chittibabu Vatte, Qian Guo, Tamer S Elsalamouni, Fahd A Al-Muhanna, Ameen M Aboalrihy, Hassan A Alhabib, Mohammed F Almomen, Rudaynah A Alali, Alawi H Habara, Mohammed A Alrubaish, Kaltham M Alfalah, Cyril Cyrus, Ibrahiem Saeed Abdul-Rahman, Brendan J Keating, Amein K Al-Ali, Chan Wang
Afnan A Almuhanna, Department of Radiology, King Fahd Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
Chittibabu Vatte, Alawi H Habara, Cyril Cyrus, Amein K Al-Ali, Department of Clinical Biochemistry, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
Qian Guo, Brendan J Keating, Division of Transplantation, Department of Surgery, New York University Langone Health, New York, NY 10016, United States
Tamer S Elsalamouni, Fahd A Al-Muhanna, Rudaynah A Alali, Kaltham M Alfalah, Ibrahiem Saeed Abdul-Rahman, Department of Internal Medicine, King Fahd Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
Ameen M Aboalrihy, Department of Internal Medicine, Qatif Health Network Eastern Province, Qatif 32654, Saudi Arabia
Hassan A Alhabib, Department of Internal Medicine, Jubail General Hospital, Jubail 35514, Saudi Arabia
Mohammed F Almomen, Department of Internal Medicine, King Fahd Hospital, Alahssa 31982, Saudi Arabia
Mohammed A Alrubaish, Department of Ophthalmology, King Fahd Hospital of University, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
Chan Wang, Division of Biostatistics, Department of Population Health, New York University Langone Health, New York, NY 10061, United States
Author contributions: Almuhanna AA, Elsalamouni TS, Al-Muhanna FA, Keating BJ, and Al-Ali AK contributed to conceptualization, funding, writing original manuscript and editing; Elsalamouni TS, Aboalrihy AM, Almomen MF, Alali RA, Alfalah KM, and Abdul-Rahman IS contributed to investigation and supervision; Vatte C, Guo Q, Habara AH, Cyrus C, and Al-Ali AK contributed to data curation, administration, visualization, analysis, and interpretation; and all authors thoroughly reviewed and endorsed the final manuscript.
Supported by the Deanship of scientific Research at Imam Abdulrahman Bin Faisal University, No. 2020-182-MED.
Institutional review board statement: This study was approved by the Medical Ethics Committee of Imam Abdulrahman Bin Faisal University, approval No. IRB-2020-01-277.
Informed consent statement: All the patients provided informed consent.
Conflict-of-interest statement: All the authors report no relevant conflicts of interest for this article.
STROBE statement: The authors have read the STROBE Statement-checklist of items, and the manuscript was prepared and revised according to the STROBE Statement-checklist of items.
Data sharing statement: The datasets generated during the current study are available in the European Variation Archive repository (
https://www.ebi.ac.uk/ena/browser/view/PRJEB105038), with accession number PRJEB105038. All requests for data can be sent to the corresponding author (Dr. Amein Al-Ali) and verified academic investigators will be granted full access.
Corresponding author: Amein K Al-Ali, PhD, Professor, Department of Clinical Biochemistry, Imam Abdulrahman Bin Faisal University, Building A72, Dammam 31441, Saudi Arabia.
aalali@iau.edu.sa
Received: December 30, 2025
Revised: February 7, 2026
Accepted: March 9, 2026
Published online: June 25, 2026
Processing time: 167 Days and 19.7 Hours
BACKGROUND
The gut microbiota (GM) plays an important role in chronic kidney disease (CKD) progression, and dialysis modalities can differentially impact the GM composition and function. There is also limited information on the GM in Arab populations.
AIM
To investigate the distinct microbial profiles and functional alterations associated with hemodialysis (HD) and peritoneal dialysis (PD) in a Saudi Arabian cohort.
METHODS
We performed whole-genome metagenomic sequencing on fecal samples from 189 participants (controls and CKD, HD, and PD patients).
RESULTS
We detected distinct microbial profiles across all patient groups compared with that of the controls. Microbial risk scores derived from differentially abundant taxa accurately distinguished CKD, PD, and HD patients from controls, with area under the curves exceeding 0.9. Compared with HD patients, PD patients exhibited reduced species richness, an increased abundance of opportunistic pathogens (particularly Proteobacteria), and increased virulence. Functional analysis revealed suppressed energy metabolism and activated proinflammatory pathways in PD patients. Cooccurrence network analysis demonstrated decreased microbial community resilience in PD patients, with increased Proteobacteria interactions. Conversely, the HD group showed partial recovery of microbial balance and beneficial metabolic functions, including increased short-chain fatty acid metabolism and reduced lipopolysaccharide biosynthesis.
CONCLUSION
The findings of this study highlight the potential of the microbial profile as a robust biomarker for CKD classification and underscore the differential impacts of different dialysis modalities.
Core Tip: In a Saudi cohort, the gut microbiota clearly differed between controls, chronic kidney disease patients, and patients on hemodialysis (HD) or peritoneal dialysis (PD). Simple microbial risk scores (area under the curve > 0.9) accurately distinguished chronic kidney disease patients, HD patients, and PD patients from controls, suggesting its potential as a noninvasive biomarker. The PD microbiota was characterized by reduced diversity, increased abundance of Proteobacteria and virulence factors, weaker microbial networks, and a proinflammatory profile. In contrast, partial restoration of a healthier microbiome was observed in HD patients, with increased short-chain fatty acid production and reduced lipopolysaccharide biosynthesis, indicating dialysis modality-specific effects on the gut microbiome and potential targets for microbiome-based interventions.
