Ethics Statement
All procedures performed in this study involving human participants were in accordance with the principles of the 1964 Helsinki declaration and its later amendments or comparable ethical standards. All the participants were thoroughly informed about the study and procedures before signing consent forms. Participants were assured of anonymity and confidentiality. The Research Ethics Committee of the Pasteur Institute of Iran, Tehran, approved this study (Approval ID: IR.PII. REC.1397.029).
Patient Population
In this hospital-based case-control study, 120 obese patients presenting to the Department of Surgery in Shariati Educational Hospital (Tehran, Iran) with a clinical diagnosis of diabetes or hypothyroidism (18 with diabetes, 23 with hypothyroidism, and 79 without either diabetes or hypothyroidism as a control group) who were candidates for laparoscopic sleeve gastrectomy (LSG) enrolled from September 2018 to January 2020. The inclusion criteria were: (1) age limit from 30 to 50 years; (2) body mass index (BMI) ≥35 kg/m2; (3) without dairy allergy; (4) no infectious disease; (5) no use of antibiotic, probiotic, and medication affecting the findings over the last 6 months prior to the enrollment; (6) no gastrointestinal disease; and (7) non-pregnant/non-lactating women. Our exclusion criteria include: (1) recent illnesses (i.e. one month prior to the enrolment or less), (2) genetic or psychotic disorders, and (3) psychoactive drug misuse. Also, obese control subjects (n = 79) were selected at random among candidates for LSG, and subjects with a current or past diabetic and the hypothyroid syndrome were excluded from the control group.
Collection of Clinical Data
Each patient was provided with a standardized questionnaire regarding socio-demographic, lifestyle, anthropometric (height, weight, and BMI), medical treatments, and underlying medical history.
Hypothyroidism was diagnosed by a physician according to increased serum thyroid-stimulating hormone (TSH) level [9]. Diabetes mellitus was diagnosed according to the International Diabetes Federation (IDF) criteria [13].
Sample Collection and DNA Extraction
Stool samples were collected in a hermetically sealed sterile container and placed into the freezer immediately at −80 °C until DNA extraction. Total bacterial DNA was extracted from feces samples using the QIAamp DNA Stool Mini Kit (QIAGEN, GmbH, Hilden, Germany) following the manufacturer’s instructions. DNA purity and quantity were evaluated using a Nanodrop spectrophotometer (BioTek Instruments, Inc., Winooski, VT, USA) and stored at −20 °C until processed.
Quantitative Real-Time Polymerase Chain Reaction (qPCR)
Bacterial diversity of extracted DNA from feces samples was evaluated using quantitative real-time PCR with 16S rRNA gene-based specific primers (Metabion, Germany, Table 1). DNA amplifications were performed in a final volume of 20 μL containing 10 μL 2× QPCR Green Master Mix HRox (Biotechrabbit GmbH, Hennigsdorf, Germany), 5 μM of each primer and 2 μL of target DNA. Amplification reactions were performed in a thermal cycler (StepOne™ Real-Time PCR System, Applied Biosystems, USA) under following conditions: one cycle of initial denaturation at 95°C for 3 min, 40 cycles of 95°C for 15 s, and annealing temperature suitable for each primer pair for 30 s. Standard curves were made for each run using 10-fold serial dilutions of known concentration of bacterial genomic DNA (Phylum Proteobacteria) and then, the copy number of the 16S rRNA gene for each species calculated using the following equation:
Number of copies = (DNA concentration (ng/µl) x [6.022 x 1023]) / (length of template (bp) x [1x109] x 650). Also, qPCR products were visualized in an agarose gel electrophoresis (Figure 1).
Biochemical and Cytokine Evaluation
Biochemistry and cytokine parameters were detected in fasting peripheral venous blood obtained from patients. Fasting blood sugar (FBS), triglycerides (Tg), cholesterol (Chol), low-density lipoprotein (LDL), high-density lipoprotein (HDL), aspartate aminotransferase (SGOT), alanine aminotransferase (SGPT), blood urea nitrogen (BUN), creatinine (CRE), and alkaline phosphatase (ALP) were measured by colorimetric enzymatic assays (COBAS MIRA® Plus).
Inflammatory cytokines (IL-6, IL-1β, and TNF-α), anti-inflammatory cytokines (IL-10 and TGF–β 1), insulin, and glucagon were analyzed using ELISA kits (Abcam, Cambridge, UK). Blood insulin was used to calculate the insulin resistance, as defined by the equation homeostasis model assessment (HOMA-IR) = fasting insulin (μU/mL) x fasting glucose (mmol/L) / 22.5. Each measure was evaluated in duplicate and the median of the two measurements was reported.
Statistical Analysis
Categorical variables were compared between diabetic/hypothyroid obese patients and the control group using Fisher’s Exact Test. To check for normality Kolmogorov–Smirnov was used. To compare the association between diabetic/hypothyroid obese patients and the control group, The Kruscall Walis test was used. Colony-forming unit (CFU) of the Bacteroides fragilis group, Akkermansia muciniphilai, Clostridium cluster IV, Roseburia spp., and Prevotella spp. were analyzed in log10 scale. Binary logistic regression analysis was used to estimate the effect of each unit increase in bacterial abundance to the chance of diabetes/ hypothyroidism, either in crude and adjusted models. In the adjusted model, best-fitting model was selected using the backward method.