Gut microbiota in non-alcoholic fatty liver disease: Pathophysiology, diagnosis, and therapeutics

Table 1 Gut microbiota alterations associated with non-alcoholic fatty liver disease

Number of participants	Microbiota alterations	Ref.
NASH (n = 65), HC (n = 76)	Increased Collinsella, decreased Ruminococcaceae in NASH	[61]
NAFLD (n = 87), obesity without NAFLD (n = 37)	High abundance of Prevotella copri in severe fibrosis	[62]
Obese youth with NAFLD (n = 44), without NAFLD (n = 29)	Higher Firmicutes-to-Bacteroidetes ratio and lower abundance of Bacteroidetes, Prevotella, Gemmiger, and Oscillospira in NAFLD	[63]
NAFLD (n = 43), HC (n = 83)	Reduction in Firmicutes and Clostridia, increase in Bacteroidetes and Bacteroidia, decrease in Lachnospiraceae, Ruminococcaceae, Lactobacillaceae, and Peptostreptococcaceae in NAFLD	[64]
HS (n = 56), HC (n = 49)	Fewer Lachnospiraceae and Ruminococcaceae, enrichment of Acidaminococcus, Escherichia spp., Bacteroides spp.	[66]
Stage 0-2 NAFLD-related fibrosis (n = 72), stage 3 or 4 NAFLD-related fibrosis (n = 14)	Eubacterium rectale and Bacteroides vulgatus abundant in mild/moderate NAFLD, Bacteroides vulgatus and Escherichia coli most abundant in advanced fibrosis. Ruminococcus obeum CAG:39, Ruminococcus obeum, and Eubacterium rectale significantly lower in advanced fibrosis	[67]
NAFLD (n =25), HC (n = 22)	Escherichia_Shigella, Lachnospiraceae_Incertae_Sedis, and Blautia more abundant, Prevotella decreased in NAFLD. Higher abundance of genus Blautia and the corresponding Lachnospiraceae family in NASH. Higher abundance of Escherichia_Shigella and the corresponding Enterobacteriaceae family in fibrosis	[60]
NASH (n = 46), HC (n = 38)	Significant reduction in Akkermansia muciniphila and increase in Enterobacteriaceae in NASH	[74]
Total (n = 1148), NAFLD (n = 205)	Significant reduction in family Ruminococcaceae and the genus Faecalibacterium in NAFLD	[75]
NAFLD-cirrhosis (n = 27), non-NAFLD control (n = 54)	Enrichment in Negativicutes, reduction in Clostridia	[68]
SS (n = 11), NASH (n = 22), HC (n = 17)	Lower percentage of Bacteroidetes (Bacteroidetes to total bacteria counts) in NASH than SS and HC	[69]
Severe steatosis (n = 36), fibrosis (n = 13)	Significantly reduction in relative abundance of fecal Clostridium sensu stricto in liver fibrosis	[70]
NAFLD (n = 60), chronic viral hepatitis (n = 32), HC (n = 50)	Escherichia coli predominant bacterium in NAFLD	[79]
NAFLD (n = 29), HC (n = 25)	Expansion of Escherichia_Shigella in NAFLD	[81]
NAFLD (n = 57)	Bacteroides abundance significantly increased, Prevotella abundance decreased in NASH and F ≥ 2. Ruminococcus abundance significantly higher in F ≥ 2 patients	[84]
Total (n = 1355), steatosis (n = 472)	Coprococcus, Ruminococcus gnavus increased in steatosis	[85]
SS (n = 15), NASH (n = 24), HC (n = 28)	Less abundance of Bacteroidetes and Firmicutes, more abundance of Lactobacillus and Lactobacillaceae in NAFLD compared to HC. Lower abundance of Ruminococcus, Faecalibacterium prausnitzii and Coprococcus in both NASH and SS patients compared to HC	[86]
NAFLD (n = 13), obese no NAFLD (n = 11), HC (n = 26)	More abundance of Gammaproteobacteria and Prevotella in NAFLD	[88]
NASH (n = 16), HC (n = 8)	More abundance of Bacteroidetes (Bacteroides and Prevotella genus) in NASH	[89]
MAFLD (n = 32), HC (n = 30)	Increased abundance of Prevotella, Bacteroides, and Escherichia-Shigella in MAFLD	[90]
Obese with NAFLD (n = 36), obese without NAFLD (n = 17), HC (n = 20)	Decreased abundance of Blautia, Alkaliphilus, Flavobacterium, and Akkermansia in obese subjects, with or without NAFLD, and increased abundance of Streptococcus in NAFLD	[92]
NAFLD (n = 90), HC (n = 90)	Increase Slackia, Dorea formicigenerans Methanobrevibacter and Phascolarctobacterium in NAFLD	[93]
MAFLD (n = 81), HC (n = 25)	Enrichment of Dorea, Lactobacillus and Megasphaera in MAFLD	[94]
Mild NAFLD (n = 33), moderate NAFLD (n = 20), severe NAFLD (n = 30), HC (n = 21)	Enrichment of Faecalibacterium, Subdoligranulum, Haemophilus, and Roseburia in NAFLD	[97]
NAFL (n = 14), NASH (n = 18), HC (n = 27)	Higher abundance of Fusobacteria and Fusobacteriaceae in NASH compared to NAFL and HCs	[98]
NAFLD-related cirrhosis and HCC (n = 21), NAFLD-related cirrhosis without HCC (n = 20), HC (n = 20)	Higher abundance of Enterobacteriaceae and Streptococcus and a reduction in Akkermansia in cirrhosis. Higher abundance of Bacteroides and Ruminococcaceae, reduction in Bifidobacterium in HCC	[8]
NAFLD (n = 98), first-degree relatives (n = 105)	Enrichment of Streptococcus and Megasphaera in NAFLD-cirrhosis	[99]
NAFLD-HCC (n = 32), NAFLD-cirrhosis (n = 28), non-NAFLD control (n = 30)	Significant enrichment of Bacteroides xylanisolvens, Ruminococcus gnavus, and Clostridium bolteae in NAFLD-HCC and NAFLD-cirrhosis	[100]

NASH: Non-alcoholic steatohepatitis; HC: Healthy controls; NAFLD: Non-alcoholic fatty liver disease; HS: Hepatic steatosis; SS: Simple steatosis; HCC: Hepatocellular carcinoma; MAFLD: Metabolic dysfunction-associated fatty liver disease; NAFL: Non-alcoholic fatty liver.

Table 2 Clinical trials on dietary interventions in non-alcoholic fatty liver disease

Number of participants	Dietary intervention	Outcome	Ref.
n = 74	Melatonin	Significant decrease in levels of pro-inflammatory cytokines, inflammation in liver and improvement in parameters of fat metabolism	[193]
n = 45	Melatonin	Significant improvement in the grade of fatty liver, ALT, AST, weight, waist and abdominal circumference and systolic and diastolic blood pressure	[194]
n = 18	MD	Significant reduction in mean body weight, waist circumference, ALT and AST	[220]
n = 49	MD or LFD	Reduction in hepatic steatosis and liver enzymes with MD and LFD. Improvements in total cholesterol, serum triglyceride, and glycated hemoglobin with MD	[221]
n = 56	MD or ML	Weight reduction with MD and ML. Significant improvement in ALT levels and liver stiffness with ML and liver stiffness with MD	[222]
n = 44	MD or LFD	Significant decrease in hepatic steatosis, serum transaminase levels, and insulin resistance with MD and LFD	[227]
n = 27	KD or LFD	Significantly reduction in liver fat with both KD and LFD	[233]
n = 37	High animal or plant protein diet	Reduction in liver fat within 6 weeks, no change in body weight	[251]
n = 40	Low free sugar diet	Reduction in hepatic steatosis and ALT level	[249]
n = 29	Low dietary sugar diet	Reduction in hepatic de novo lipogenesis, hepatic fat and fasting insulin	[250]

ALT: Alanine aminotransferase; AST: Aspartate aminotransferase; MD: Mediterranean diet; LFD: Low-fat diet; ML: Mediterranean lifestyle; KD: Keto diet.

Table 3 Clinical trials on microbiota-targeted interventions in non-alcoholic fatty liver disease

Number of participants	Intervention	Outcome	Ref.
n = 20	L. rhamnosus GG	Significant decrease in ALT and antipeptidoglycan-polysaccharide antibodies, no effect on BMI Z score and visceral fat	[280]
n = 44	VSL#3	Improvement in NAFLD and reduction in triglycerides and insulin resistance	[311]
n = 28	L. bulgaricus and S. thermophilus	Reduction in the levels of ALT, AST, and GGT	[315]
n = 20	Lepicol probiotic (L. plantarum, L. delbrueckii, L. acidophilus, L. rhamnosus and B. bifidum)	Reduction in intrahepatic triglyceride and serum AST, no change in waist circumference, BMI, and glucose and lipid levels	[316]
n = 72	Probiotic yogurt containing L. acidophilus La5 and B. lactis Bb12	Reduction in the levels of ALT, AST, total cholesterol, and LDL cholesterol	[317]
n = 42	Lactocare (L. casei, L. acidophilus, L. rhamnosus, L. bulgaricus, B. breve, B. longum, S. thermophilus)	Reduction in insulin, insulin resistance and inflammation markers such as TNF-α and IL-6	[318]
n = 64	Probiotic mixture (L. acidophilus ATCC B3208, B. lactis DSMZ 32269, B. bifidum ATCC SD6576, and L. rhamnosus DSMZ 21690)	Reduction in waist circumference, cholesterol, triglycerides, LDL-C, ALT and AST. No change in weight, BMI, and BMI Z score	[319]
n = 65	Probiotic mixture (L. acidophilus, L. rhamnosus, L. paracasei, Pediococcus pentosaceus, B. lactis, and B. breve)	Reduction in body weight, total body fat, and intrahepatic fat	[320]
n = 58	“Symbiter” containing 14 probiotic belonging to Bifidobacterium, Lactobacillus, Lactococcus, and Propionibacterium	Reduction in fatty liver index, liver stiffness, serum AST, GGT, TNF-α and IL-6	[321]
n = 39	Multi-strain probiotics containing six different Lactobacillus and Bifidobacterium spp.	Stabilization of the mucosal immune function. No effect on hepatic steatosis and fibrosis levels	[322]
n = 40	Akkermansia muciniphila	Improvement in insulin sensitivity, reduction in insulinemia, plasma total cholesterol, levels of the markers for liver dysfunction and inflammation	[334]
n = 22	Inulin-type fructans	Increased fecal Bifidobacterium. No effect on liver fat contents, liver function tests, and metabolic and inflammatory mediators	[375]
n = 197	Resistant starch	Reduction in intrahepatic triglyceride content and liver enzymes	[382]
n = 66	Synbiotic (B. longum with FOS)	Significant reduction in inflammatory markers, LDL cholesterol, steatosis, and NASH activity index	[395]
n = 52	Protexin (L. casei, L. rhamnosus, L. acidophilus, L. bulgaricus, B. breve, B. longum, S. thermophilus with prebiotic FOS)	Significant attenuation in inflammatory markers, such as ALT, AST, GGT, high-sensitivity CRP, TNF-α, and NF-κB p65	[397]
n = 50	Protexin (L. casei, L. rhamnosus, L. acidophilus, L. bulgaricus, B. breve, B. longum, S. thermophilus with prebiotic FOS)	Reduction in inflammatory mediators, hepatic steatosis and fibrosis	[398]
n = 104	Synbiotic (FOS and B. animalis subspecies lactis BB-12)	Alteration in fecal microbiota. No effect on liver fat content or markers of liver fibrosis	[406]
n = 21	Fecal microbiota transplantation	Reduction in small intestinal permeability. No improvement in insulin resistance and hepatic proton density fat fraction	[418]

L. rhamnosus: Lactobacillus rhamnosus; L. bulgaricus: Lactobacillus bulgaricus; S. thermophilus: Streptococcus thermophilus; L. acidophilus: Lactobacillus acidophilus; L. plantarum: Lactiplantibacillus plantarum; L. paracasei: Lactobacillus paracasei; L. casei: Lactobacillus casei; B. breve: Bifidobacterium breve; B. longum: Bifidobacterium longum; B. bifidum: Bifidobacterium bifidum; FOS: Fructo-oligosaccharides; B. animalis: Bifidobacterium animalis; B. lactis: Bifidobacterium lactis; ALT: Alanine aminotransferase; BMI: Body mass index; NAFLD: Non-alcoholic fatty liver disease; AST: Aspartate aminotransferase; GGT: Gamma-glutamyl transferase; LDL: Low-density lipoprotein; TNF: Tumor necrosis factor; IL: Interleukin; LDL-C: Low density lipoprotein-cholesterol; NASH: Non-alcoholic steatohepatitis; CRP: C-reactive protein; NF-κB: Nuclear factor kappa B.