Table 1.

Descriptive characteristics and assessment of diet, physical activity, and antidiabetic drugs in GM of T2D patients.

Nutritional/dietary interventions
Country year	Participants	Sample size	Intervention implemented	Treatment duration	Aims/Outcomes	Gut-microbiota significant differences	Clinical effects	Ref
Portugal 2021	Male and female. 40–80 years old. T2D.	9	Intervention: The Mediterranean diet.	12 weeks	Primary: This study was to evaluate the modulation role of the Mediterranean diet in gut microbiota.	The effect size induced by the Mediterranean diet on the Firmicutes to Bacteroidetes ratio was considered clinically relevant after 12 weeks (p = .846; Cohen d = −0.83). Prevotella to Bacteroides ratio tended to increase right after 4 weeks of the intervention (p = .438; 4 weeks Cohen d = 0.74 and 12 weeks Cohen d = 0.74).	Twelve weeks after the intervention, HbA1c decreased by 0.67% (7.53 ± 1.07% to 6.86 ± 0.85%, p < .05; Cohen d = −0.70) and HOMA-IR decreased from 3.79 ± 2.98 to 2.76 ± 2.05 (p < .05; Cohen d = −0.41), with no accompanying changes in lipid profile.	68
China 2020	Male and female. ≥ 18 years old. T2D.	45	Intervention: a-LCD + 84 g/day almond. Control: LFD + 56 g/day almond.	3 months	Primary: This study was to determine the effect of an a-LCD on depression and glycometabolism. Secondary: This study was to determine the effect in the gut microbiota and fasting GLP-1 in patients with T2D.	At the phylum level, Firmicutes in the a-LCD group was significantly lower than that in the LFD group by the third month. At the genus level, Roseburia and Ruminococcus in the a-LCD group were significantly higher than those in the LFD group by the third month; compared to the baseline: Eubacterium, Roseburia increased significantly and Bacteroides decreased significantly in the a-LCD group.	Compared to the baseline, HbA1c levels in both groups decreased significantly (p < .01, p < .05) during the study period. At the third month, the HbA1c level in the a-LCD group decreased more than that in the LFD group (p < .01).	69
Iran 2020	Male and Female. Prediabetes.	120	Intervention: Consume 6 g/d multispecies probiotic or inulin-based symbiotic. Control: Consume 6 g/d of either a placebo containing maltodextrin.	6 months	Primary: This study was to determine the effects of probiotics and symbiotic supplementation on intestinal microbiome modifying in adults with prediabetes.	Six months’ supplementation with probiotics resulted in a statistically significant increase in abundance of Bacteroides fragilis to E. coli ratio. In the probiotic group, the relative proportion of Firmicutes to Bacteroidetes repressive was decreased significantly.	They do not report clinical parameters.	70
Physical exercise
China 2020	Male and female. 40–46.5 years old. BMI between 27–30 Kg/m2. T2D.	14	Intervention: High-intensity exercise training.	12 weeks	Primary: This study was to determine the efficacy of high-intensity exercise in the prevention of diabetes. Secondary: This study was to determine the change in the gut microbiota through the intervention of exercise in all participants.	The relative abundances of 6 species, belonging to Firmicutes, Bacteroidetes, and Proteobacteria, respectively, were significantly altered after exercise. Species falling into the Bacteroides genus and Clostridiales order, most of which are involved in the production of SCFAs, underwent a significant strain-level genomic variation by exercise.	The responders showed a remarkable 42.70% and 49.60% decrease in fasting insulin and HOMA-IR index, respectively, as well as a striking 116.29% increase of Matsuda index (a comprehensive evaluation of both hepatic and peripheral insulin sensitivity derived from oral glucose tolerance test.	71
Finland 2020	Male and female. 45–53 years old. BMI between 27.5–33.5 Kg/m2.	49	Intervention 1: SIT (session consisted of 30-s exercise bouts). Intervention 2: MICT (40 to 60 min of moderate-intensity (60% of V˙O2peak intensity).	2 weeks	Primary: This study was to determine the effects of SIT and MICTn intestinal metabolism and microbiota in subjects with insulin resistance.	Both training modes decreased the ratio of Firmicutes/Bacteroidetes (time, P = .04), and the abundance of Blautia spp. (time P = .051) and Clostridium spp. (time P = .04). Mainly due to the increase in the relative abundance of Bacteroidetes phyla (time, P = .03). Lachnospira genus was present in higher abundance after SIT compared with baseline (P = .025) and significantly higher abundance of Veillonella genus. Interestingly, the abundance of the Faecalibacterium genus (F. prausnitzii) was increased after MICT (P = .057) while no change after SIT was found.	Improved HBA1c (P = .003). Both training modes significantly reduced systemic inflammatory marker TNF α (p = .03) and tended to reduce C-reactive protein (p = .08) and intestinal inflammatory marker lipopolysaccharide-binding protein (p = .02). Lipopolysaccharide-binding protein correlated positively with HBA1c (r = 0.54; P = .02).	73
Italy 2019	Male and female. T2D.	30	Intervention: Program of endurance, resistance, and flexibility training.	6 months	Primary: This study was to evaluate the role of chronic exercise on gut flora composition and leaky gut in T2D stable patients.	Chronic exercise modified the composition of the gut microbiota, reduced intestinal mycelial overgrowth, leaky gut, and systemic inflammation.	They do not report clinical parameters.	76
Canada 2015	Six-week-old male type 2 diabetic db/db (C57BL/KsJ-leprdb/leprdb) and db/+ (heterozygote; control) littermates.	19	Intervention: Exercise (Exercise consisted of a low-intensity treadmill running 5 days/week for 60 min /session. Control: Sedentary.	6 weeks	Primary: The purpose of this study was to determine if exercise influences the gut microbial profile in normal and diabetic mice.	This study revealed a main effect of exercise, with a greater abundance of select Firmicutes species and lower Bacteroides/Prevotella spp. in both normal and diabetic exercised mice compared to sedentary counterparts. Conversely, Bifidobacterium spp. was greater in exercised normal but not diabetic mice (exercise for diabetes interaction).	The diabetic mice had higher blood glucose (P < .001). However, there was a trend toward an interaction between diabetic state and exercise training (P = .070), such that glucose was higher in Ex-db/+ than Sed-db/+ (12.9 ± 1.9 vs. 8.1 ± 0.6 mmol/L), but similar in Ex-db/db compared to Sed-db/db (20.4 ± 2.4 vs. 21.9 ± 1.7 mmol/L).	77
Antidiabetic drugs
Biguanide (metformin)
Colombia 2017	Male and female. 18–62 years old. BMI ≥18,5 kg/m2. T2D.	98	Intervention: Metformin. Control: Subjects without T2D.	5 months	Primary: This study determines the influence of metformin on the association of T2D and gut dysbiosis in an adult population.	Compared with participants without T2D, participants with diabetes taking metformin had a higher relative abundance of Akkermansia muciniphila.	Compared with ND participants, T2D-met+ participants had higher fasting glucose, HbA1c, and insulin resistance than ND participants and lower levels of the insulin-sensitizing hormone adiponectin (P < .05).	85
Sweden 2017	Male and female. 50–58 years old. T2D.	40	Intervention: Metformin. Control: Placebo.	4 months	Primary: This study was to determine the effects of metformin in treatment-naïve adults with DM2.	Increased abundance of Akkermansia muciniphila in individuals who received metformin for 4 months. Bifidobacterium adolescentis, fecal propionate, and butyrate concentrations were significantly increased by the metformin group.	Significant decreases in % hemoglobin A1c (HbA1c) and fasting blood glucose were observed only in the group randomized to metformin treatment.	86
Korea 2017	Five-week-old male C57BL/6 mice.	18	Intervention: HFD + metformin. Control: HFD and regular diet.	16 weeks	Primary: This study was to investigate the effect of metformin on the gut microbiota in elderly mice.	The abundance of the genera Akkermansia, Bacteroides, Butyricimonas, and Parabacteroides was significantly increased by metformin in mice fed an HFD.	Metformin administration for 16 weeks to mice fed an HFD significantly decreased the serum glucose level compared to mice fed only an HFD. Metformin also significantly improved glucose tolerance.	87
China 2019	Male and female. 40–75 years old. T2D.	180	Intervention: Antidiabetic drugs (Metformin, insulin, α- glucosidase inhibitor). Control: Non-therapeutic and health subject.	3 months	Primary: This study was to explore the interaction between the gut microbiome and T2D or hypoglycemics in the Chinese population.	Metformin increased the abundance of Spirochete, Turicibacter, Fusobacterium, and Ruminococcus (butyrate-producing bacteria), Ruminococcus was related to the impaired glucose control with regard to T2D.	They do not report clinical parameters.	88
GLP-1 analogue
China 2017	Five-week-old male Sprague-Dawley.	60	Intervention: Liraglutide 0.2 g/kg and Liraglutide 0.4 g/kg. Control: Normal and diabetic conditions.	12 weeks	Primary: This study was to determine the influence of liraglutide on fecal microbiota in diabetic male rats.	SCFA-producing bacterias including Bacteroides, Lachnospiraceae, and probiotic bacteria, Bifidobacterium, were selectively enhanced in liraglutide-treated diabetic male rats. Lactobacillus was negatively correlated with fasting blood glucose.	Liraglutide significantly decreased serum insulin level, HOMA-IR, and IL-6 (P < .01).	90
China 2016	10 weeks old male ApoE -/- mice with a C57BL/6 genetic background.	60	Intervention: Hyperglycemia + liraglutide and Hyperglycemia + saxagliptin. Control: Normal glucose control, Normal glucose + liraglutide, and normal glucose + saxagliptin.	8 weeks	Primary: This study determines the structural modulation of the gut microbiota and the relationship with body weight, compared evaluation of liraglutide and saxagliptin treatment.	The enriched phylotypes were the genera Allobaculum and Turicibacter within the family Erysipelotrichaceae, the genera Anaerostipes, and Blautia within the family Lachnospiraceae, the genus Lactobacillus within the family Lactobacillaceae, genus Butyricimonas within the family Porphyromonadaceae, and the genus Desulfovibrio (phylum Proteobacteria, class Deltaproteobacteria).	The mean blood glucose level was significantly lower in liraglutide-treated mice compared with the control mice, who were fed ad libitum (6.70 ± 0.43 mmol/L vs. 7.62 ± 0.68 mmol/L, p = 9.0e-6). There were no substantial differences in the LPS concentrations.	96
Dipeptidyl peptidase-4 inhibitor (DPP-4i)
China 2016	Four-week-old male Sprague-Dawley (SD) rats (induce TD2).	15	Intervention: Sitagliptin.	4 weeks	Primary: This study was on determining the effects of sitagliptin in rats (induce T2D).	At the level of genus, SCFA-producing bacteria, Blautia, Roseburia, and Clostridium, and probiotics Lactobacillus, Bifidobacterium, and so forth were identified as significantly different (T2D vs T2D-sitagliptin conditions).	Sitagliptin resulted in a significant reduction in blood glucose (p < .05).	94
China 2017	Five-week-old male Sprague-Dawley SD rats.	30	Intervention: Vildagliptin 0.01 g/kg + HFD and Vildagliptin 0.02 g/kg + HFD. Control: Control, control + Vildagliptin 0.02 g/kg and HFD + STZ.	12	Primary: This study was to identify whether vildagliptin modifies the gut microbiota structure during T2D treatment.	At the phylum level, a higher relative abundance of Bacteroidetes, lower abundance of Firmicutes, and reduced ratio of Firmicutes/Bacteroidetes were observed in the vildagliptin-treated group. Moreover, vildagliptin treatment increased butyrate-producing bacteria, including Bacteroides and Erysipelotrichaeae, in the diabetic rats.	Both doses of vildagliptin treatment reduced the fasting blood glucose and HbA1c levels (P < .01). Vildagliptin treatment reduced the blood glucose levels before and after glucose load, and the area under the curve of blood glucose (P < .01). Serum insulin levels, HOMA-IR, and IL-6 levels in the diabetic rats were higher than that in the normal controls (P < .01), Vildagliptin reduced the serum insulin and IL-6 levels, alleviated insulin resistance, and increased serum GLP-1 in diabetic rats (P < .05).	95
Thiazolidinediones
Denmark 2021	Eight weeks-old male B6.BKS(D)-Leprdb/J (db/db) mice.	24	Intervention: Rosiglitazone. Control: Placebo.	8 weeks	Primary: This study was to characterize local gut microbiome and intestinal transcriptome responses in diabetic db/db mice following rosiglitazone treatment.	Lactobacillaceae and Lachnospiraceae were predominant in the small and large intestines, respectively. While Lactobacillus was the most relatively abundant genus (>75% of all genera) in the small intestine, the large intestine was characterized by a more diverse genus composition predominantly composed of Kineothrix, Lactobacillus, and Blautia.	Plasma insulin levels remained stable throughout the entire dosing period in vehicle controls (baseline: 6999 ± 327 pg/mL; termination: 7628 ± 1076 pg/mL, p = .570) and rosiglitazone-treated db/db mice (baseline: 5988 ± 295 pg/mL; termination: 5718 ± 841 pg/mL, p = .741). Rosiglitazone significantly improved glucose excursions in two successive OGTTs performed on treatment day 28 (p < .001) and 49 (p < .001). Rosiglitazone also improved weekly fasting blood glucose levels and terminal HbA1c levels (p < .001).	79
Sulfonylureas
Netherlands 2020	Male and female (postmenopausal). 35–75 years old. BMI scores > 25 kg/m2. T2D.	44	Intervention1: Dapagliflozin. Intervention2: Gliclazide.	12 weeks	Primary: This study was to evaluate the effects of 12-week treatment with the SGLT2 inhibitor dapagliflozin and sulfonylurea gliclazide on gut microbiome composition in T2D patients treated with metformin.	Differential abundance analysis yielded no significant shift in specific microbes.	Both dapagliflozin and gliclazide similarly improved glycemic control (p < .001), while dapagliflozin reduced gliclazide slightly increased fasting insulin (p = .011 and p = .569, respectively).	81
Antibiotics
Netherlands 2022	Male with PreT2D and BMI was 31.0 ± 0.5 kg/m2. Male C57BL/6 J mice and 6-week-old male mice.	57	Intervention: amoxicillin, vancomycin. Control: placebo.	7 days	Primary: This study was to explore the effects of the gut microbiota on the function of the exocrine pancreas and the gut endocrine system.	Gut microbiota alters host intestinal proteome. Proteolysis-related proteins, such as elastase and dipeptidase 1, were increased by the HFD, whereas proteins involved in iron homeostasis, such as ferritin heavy chain, were reduced with the HFD. Notably, serine protease inhibitors (serpin) proteins, which have been previously linked to metabolic diseases, were one of the main groups affected by diet and gut microbiota.	In the donor mice, the HFD caused a decrease in circulating GLP-1 levels, and this was reversed with vancomycin treatment. Transferring microbiota from antibiotic-treated mice to GF mice was sufficient to transfer significant changes in GLP-1 secretion.	101
Netherlands 2016	Male with overweight and obese. 35–70-year-old Caucasian.	57	Intervention: amoxicillin, vancomycin. Control: placebo.	7 days	Primary: This study was to investigate how gut microbiota manipulation by antibiotics (7-day administration of amoxicillin, vancomycin, or placebo) affects host metabolism in 57 obese, prediabetic men.	The fecal microbiota composition showed that 7-day vancomycin markedly decreased microbial diversity (p < .001), whereas this was not affected by amoxicillin (p = .42) as compared to placebo. vancomycin decreased the relative abundance of mainly Gram-positive bacteria of the Firmicutes phylum. Among the most strongly affected groups were genus-like groups that contain known butyrate-producing species from Clostridium clusters IV and XIVa, such as Coprococcus eutactus, Faecalibacterium prausnitzii, and Anaerostipes caccae, as well as species involved in BA dehydroxylation such as Clostridium leptum. Conversely, Gram-negative Proteobacteria, members of Clostridium cluster IX, and vancomycin resistant Gram-positive Bacilli such as Lactobacillus plantarum and Enterococcus, showed increased relative abundance after vancomycin treatment.	Antibiotic treatment did not significantly alter Rd as compared to PLA. Additionally, no effects were found on hepatic and adipose tissue insulin sensitivity, as determined by the insulin-mediated suppression of endogenous glucose production (EGP) and plasma-free fatty acid (FFA) concentrations. In accordance, antibiotic treatment neither altered whole-body insulin sensitivity (HOMA-IR) immediately after cessation of treatment nor at 8 weeks follow-up.	102
Bariatric surgery
France 2022	Male and female T2D with Roux-en-Y gastric bypass.	136	Intervention: Roux-en-Y gastric bypass.	5 years	Primary: This study was to decipher the participation of the GM in the long-term improvement of T2D after bariatric surgery, as well as its implication in the severity of the persisting cases of T2D.	The more severe cases of unresolved T2D were associated with a major increase in the class Bacteroidia, including 12 species comprising Phocaeicola dorei, Bacteroides fragilis, and Bacteroides caecimuris. A key observation is that patients who underwent major metabolic improvements do not harbor this enrichment in Bacteroidia, as those who presented mild cases of T2D at all times.	The prevalence of patients in the Severe cluster decreased from 55% at baseline to 30% at 5 years, confirming an overall decrease in T2D severity after RYGB.	109
Portugal 2021	Male and female, age ≥ 20 and ≤ 65 years old; BMI ≥ 30 and < 35 kg/m2; previous diagnosis of T2D.	20	Intervention: Roux-en-Y gastric bypass surgery. Control: Standard medical therapy.	12 months	Primary: This study was to evaluate gut microbiota changes after metabolic surgery versus standard medical therapy in diabetic adult patients with class 1 obesity.	Ruminococcus, unclassified_Lachnospiraceae_ family, and Faecalibacterium significantly decreased, while Klebsiella, Gammaproteobacteria, Enterobacter, unclassified_Gammaproteobacteria, unclassified_Veillonellaceae increased after 12 months of RYGB. In the medical arm, unclassified_Lachnospiraceae and Sutterella significantly decreased, while unclassified_Clostridiales and unclassified_Bacteria increased, when comparing baseline with M12.	The fasting glucose, insulinemia, C-peptide, and HOMA-IR were significantly lower in the surgical arm (p = .007, p = .020, p = .020, and p = .027, respectively), and HDL-C was higher (p = .004). The surgical arm, 5 participants (62.5%) experienced remission from their diabetes (p = .007 for comparison with the medical arm.	108

T2D: Diabetes Mellitus type 2; a-LCD: almond-based low carbohydrate diet; LFD: Low-fat diet; GLP-1: glucagon-like peptide 1; BMI: body mass index; SCFA: short-chain fatty acids; SIT: sprint Interval; MICT: moderate-intensity continuous training; HFD: high-fat diet; STZ: streptozotocin; db/db: diabetic; SGLT2: sodium-glucose co-transporter-2.