The Effect of Semaglutide on the Intestinal Flora in Obesity
Conditions: Obesity
Sponsor: Beijing Chao Yang Hospital

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Version date: April 19, 2025.
The Impact of Semaglutide on Gut Microbiota in Obese Patients
Research Unit: Beijing Chaoyang Hospital, Capital Medical University
Principal Investigator: Jia Liu
1. Research Background and Rationale
Obesity is a chronic disease characterized by excessive fat deposition, which increases
the risk of hypertension, diabetes, non-alcoholic fatty liver disease, sleep apnea
syndrome, coronary heart disease, and other conditions. Ultimately, it affects patients'
life expectancy and raises healthcare costs, making it one of the most severe global
public health issues
[1]. Weight loss can significantly
reduce the risk
of
obesity-related complications [2]. Lifestyle interventions are the first-line treatment
for obesity management, but even with strict adherence, they typically result in only a
5–10% reduction in body weight, which is difficult to maintain long-term. There is an
urgent need for the development of highly effective and safe weight-loss drugs.
Glucagon-like peptide-1 (GLP-1) receptor agonists, represented by semaglutide, have
been approved for chronic weight management in obese patients [6–7]. Numerous
studies have shown that semaglutide treatment significantly reduces body weight in
obese patients with a good safety profile [7]. However, it is noteworthy that the
weight-loss effects of semaglutide exhibit significant individual variability [4–5]. The
STEP-5 trial found that semaglutide treatment resulted in an average weight loss of
15.2% in non-diabetic obese or overweight adults, but 23% of participants showed no
significant weight reduction [4]. The recently published SELECT trial revealed that
32.2% of obese or overweight adults experienced no significant weight changes after
using semaglutide [5].
The gut microbiota plays a crucial role in maintaining host physiology and
homeostasis [8]. Our previous research demonstrated that metformin treatment
reduces
the
abundance
of
Bacteroides
fragilis
and
increases
levels
of
glycoursodeoxycholic acid (GUDCA), thereby improving blood glucose and insulin
resistance [9]. Time-restricted feeding was found to increase the abundance
of Ruminococcus torques (R. torques), which produces 2-hydroxy-4-methylpentanoic

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acid (HMP) to inhibit the intestinal hypoxia-inducible factor-2α (HIF-2α)-ceramide
pathway, thereby ameliorating liver inflammation and fibrosis in mice [10]. Recent
studies have shown that gut microbiota also modulates host responses to treatments,
contributing to individual variability in drug efficacy [11]. J. Balaich et al. discovered
that microbial-derived acarbose kinases specifically metabolize and deactivate
acarbose, affecting its glucose-lowering effects [12]. Our team previously found that
gut microbial dipeptidyl peptidase-4 (DPP4) enters intestinal tissues under conditions
of intestinal barrier damage, degrading active host GLP-1 and inducing glucose
intolerance. Host DPP4 inhibitors like sitagliptin cannot effectively inhibit microbial
DPP4 activity, which is a major reason for the high variability in clinical responses to
sitagliptin [13].
In our preliminary study, we performed fecal metagenomic sequencing on obese
patients treated with semaglutide, matched for baseline gender, age, and body mass
index (BMI), and observed significant differences in gut microbiota composition and
abundance before and after treatment. Further experiments in a high-fat diet-induced
obese mouse model revealed that antibiotic treatment enhanced the weight-loss effects
of semaglutide. These findings suggest that gut microbiota modulates host responses
to semaglutide treatment, although the specific mechanisms remain unclear.
This study aims to elucidate the impact of semaglutide on gut microbiota in obese
patients and explore the development of targeted microbial enzyme therapies,
providing new targets for overcoming semaglutide resistance in weight loss.
2. Research Objectives
This study will employ fecal metagenomic sequencing and multi-omics technologies,
along with an in vitro bacterial strain screening platform, to investigate the effects of
semaglutide on gut microbiota in obese patients and elucidate the underlying
mechanisms. The goal is to identify novel targets for developing drugs to overcome
semaglutide resistance in weight loss.
3. Research Methods
3.1 Study Setting and Population
Obese patients visiting the Department of Endocrinology at Beijing Chaoyang

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Version date: April 19, 2025.
Hospital, Capital Medical University, from April 2025 to April 2026 will be recruited
based on the following inclusion and exclusion criteria:
Inclusion Criteria:

Age 18–60 years;

BMI ≥30 kg/m²;

At least one self-reported unsuccessful attempt at lifestyle-based weight loss;

Willingness to participate and signed informed consent.
Exclusion Criteria:

Self-reported weight change >5% in the 3 months before screening;

Use of any weight-loss medication in the 3 months before screening;

Use of glucose-lowering drugs in the 3 months before screening, HbA1c ≥6.5%,
or history of type 1 or type 2 diabetes;

Use of immunosuppressants, steroids, antidiarrheals, antibiotics, probiotics,
lipid-lowering drugs, or other gastrointestinal motility drugs in the 3 months
before screening;

History of endocrine-related overweight or obesity (e.g., Cushing’s syndrome);

Triglycerides ≥500 mg/dL (5.65 mmol/L) at screening;

Clinically significant gastric emptying abnormalities (e.g., severe diabetic
gastroparesis or gastric outlet obstruction), gastrointestinal diseases, or surgical
history;

Thyroid dysfunction;

History of mental illness;

Personal or family history of multiple endocrine neoplasia or medullary thyroid
carcinoma, or calcitonin ≥6 pg/mL;

Abnormal liver function at screening (ALT and/or AST >3× ULN);

Abnormal renal function at screening (eGFR <60 mL/min/1.73 m²);

History of cardiovascular disease;

History of malignancy;

Pregnancy or lactation;

Other conditions deemed unsuitable for participation by the investigator.

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3.2 Study Design
Recruitment:
A self-controlled cohort study design will be used to recruit obese patients from the
Department of Endocrinology at Beijing Chaoyang Hospital from April 2025 to April
2026.
Treatment and Follow-up:
Eligible participants will receive subcutaneous semaglutide injections. The treatment
follows a dose-escalation regimen to achieve steady-state plasma concentrations over
4–5 weeks: Start with 0.5 mg once weekly; Increase to 1.0 mg once weekly after 4
weeks; Further increase to 1.7 mg once weekly after another 4 weeks; Total treatment
duration: 12 weeks.
Participants will visit the clinic every 4 weeks for follow-up assessments, including
general condition, physical examinations, and laboratory tests. At the 12-week
follow-up, venous blood will be collected for semaglutide plasma concentration
analysis.
Outcome Measures:
Primary Outcome: Changes in gut microbiota composition (abundance and Shannon
diversity index) from baseline to 12 weeks.
Secondary
Outcomes:
Changes
in
weight,
BMI,
waist
circumference,
hip
circumference, and lipid profiles from baseline to 12 weeks.
3.3 Sample Size Calculation
A paired t-test will be used for pre-post comparisons. Based on prior studies, the
standard deviation of paired differences (σd) is 1.2, the clinically meaningful minimal
difference (Δ) is 1.0, α = 0.05 (two-tailed), Z₁-α/₂ = 1.96, β = 0.1 (Power = 90%),
and Z₁-β = 1.28. The calculated sample size is 16, accounting for a 20% dropout rate
and 30% redundancy in microbiome data. The final sample size is 40, with
adjustments based on recruitment feasibility.
3.4 Data Collection
1) Anthropometric Data:
Height, weight, BMI, waist/hip circumference, blood pressure, etc., measured by

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trained staff.
2) Urine and Fecal Samples:
Urine: Midstream samples collected for biochemical analysis and stored at -80°C.
Fecal: Fresh samples collected internally to avoid contamination, stored at -80°C for
metagenomic sequencing. DNA extraction, sequencing (Illumina HiSeq 4000), and
bioinformatics analysis will be performed.
3) Blood Samples:
Fasting venous blood for routine tests (glucose, insulin, HbA1c, lipids, etc.) and
semaglutide concentration (LC-MS/MS).
3.5 Follow-up Schedule
Participants will be followed every 4 weeks for 12 weeks, with assessments including
physical exams, lab tests, and safety monitoring.
3.6 Data Management and Statistical Analysis
Data Management:
Double-entry verification using Epidata, with logic checks and error correction before
database locking.
Statistical Analysis:
SPSS for analysis.
Normal distribution: Mean ± SD (paired t-test); non-normal: Median (IQR)
(Wilcoxon test).P < 0.05 considered statistically significant.
3.7 Bias Control
Strict adherence to inclusion/exclusion criteria, standardized data collection, and
multivariate regression to adjust for confounders (age, sex, baseline BMI, diet).
4. Quality Control
Fecal sample collection: Avoid urine contamination, use sterile containers, store at
-80°C.
Questionnaire integrity: Trained staff, regular audits.
Accurate measurements: Certified professionals, quality-controlled lab procedures.
5. Risk Assessment and Mitigation
Risks:

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Blood draw: Syncope/hypoglycemia.
Semaglutide: GI discomfort, allergies.
Mitigation:
Emergency protocols for adverse events.
Dose escalation and monitoring to minimize risks.
6. Expected Outcomes
Elucidate semaglutide’s impact on gut microbiota and mechanisms.
Identify targets for overcoming resistance.
Publish 2–3 high-impact papers; patent applications if biomarkers are discovered.
7. Timeline
Period
Tasks
2025.04–2025.09
Recruitment and follow-up
2025.10–2025.12
Data analysis
2026.01–2026.04
Manuscript preparation/submission
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