Table 2.
Evidence from human studies depicting associations of various bacterial species and metabolic signatures in patients with NAFLD.
| Human Studies | ||||
|---|---|---|---|---|
| Study, Year | Population | Lab Techniques | Microbiome | Remarks |
| Belgaumkar et al., 2016 [55] | NAFLD as described by serum cytokeratin 18, 18 patients who underwent laparoscopic sleeve gastrectomy (UK) |
Serum: Liquid chromatography tandem-mass spectometry for BA | No bacteria were further detected | Total BA did not change; ↓ primary glycine- and taurine-conjugated BA, ↓ cholic acid, and ↑ secondary BA, ↑ glycine-conjugated urodeoxycholic acid over the study period. These changes are associated with reduction in insulin resistance, pro-inflammatory cytokines, and CK-18 levels |
| Boursier et al., 2016 [56] | Biopsy-proven NAFLD among 57 patients (France, USA) |
Fecal Microbiome: 16S rRNA gene Sequencing | Patients with NASH and F2≥2: ↑ Bacteroides ↓ Prevotella. Patients with F2 ≥ 2: ↑↑ Ruminococcus |
NASH was related to ↑ Bacteroides, while significant fibrosis to ↑↑ Ruminococcus |
| Loomba et al., 2017 [57] | Biopsy-proven NAFLD among 86 patients (USA) |
Fecal Microbiome: Whole-genome shotgun sequencing of DNA from feces | Patients with NAFLD: ↑ Proteobacteria ↑ Firmicutes Patients with NAFLD and ≤F2: ↑ Eubacterium rectale ↑ Bacteroides vulgatus Patients with NAFLD and >F2: ↑ Bacteroides vulgaris ↑ Escherischia coli |
Patients with NAFLD and ≤F2: ↑ Lactate ↑ Acetate ↑ Formate Patients with NAFLD and >F2: ↑ Butyrate ↑ D-Lactate ↑ Propionate ↑ Succinate |
| Del Chierico et al., 2017 [36] | NAFLD in 61 patients and 51 non-NAFLD controls (Italy) |
Fecal Microbiome: rRNA Sequencing Serum metabolites: GC/MS |
Patients with NAFLD: ↑ Actinobacteria ↓ Bacteroidetes ↑ Ruminococcus ↑ Blautia ↑ Dorea ↓ Oscillospira ↓ Rikenellaceae |
Patients with NAFLD: ↑ 2-butanone ↑ 1-pentanol ↑ 4-methyl-2-pentanone |
| Puri et al., 2018 [58] | Biopsy-proven NAFLD among 86 patients and 24 non-NAFLD controls (USA) |
Serum metabolites: LC/MS | No bacteria were further detected | Patients with NAFLD and ≥F2: ↑ conjugated cholate ↓ ratio of total secondary to primary BAs Patients with NASH had ↑↑ total conjugated primary BAs when compared to controls |
| Hoyles et al., 2018 [59] | Biopsy-proven NAFLD among 56 patients (UK, Italy, France) |
Fecal Microbiome: Shotgun Metagenomic Sequencing Serum and urine metabolites: LC/MS |
Among patients with steatosis: ↑ Proteobacteria ↑ Actinobacteria |
Among patients with steatosis: -Serum BCAAs: ↑ leucine ↑ valine ↑ isoleucine ↑ phenylacetic acid -Urine: ↑ choline |
| Caussy et al., 2018 [60] | Discovery cohort of 156 twins Validation cohort of Biopsy-proven NAFLD among 156 patients (USA, France) |
Fecal Microbiome: Whole Shotgun Metagenomics Sequencing Liver: MRI-PDFF; MRE Serum metabolites: LC/MS; GC/MS |
Patients with NAFLD and >F2: ↑ Furmicutes ↑ Bacteroidetes ↑ Proteobacteria |
56 metabolites had a relationship with hepatic fibrosis, among which 3-(4-hydroxyphenyl) lactate, N-formylmethionine, phenyllactate, mannitol, allantoine and N-(2-furoyl) glycine were the most abundant 3-(4-hydroxyphenyl) lactate was ↑↑ in liver fibrosis and steatosis |
| Caussy et al., 2019 [61] | Cross-sectional; 203 participants including NAFLD and healthy controls (USA) |
Fecal Microbiome: 16S rRNA Sequencing Liver: MRI/MRE |
Patients with NAFLD and cirrhosis: ↑ Enterobacteriaceae ↑ Streptococcus ↑ Gallibacterium ↑ Megasphaera A trend towards Gram negative species in advanced fibrosis was reported |
No metabolites were further detected |
| Lee et al., 2020 [62] | Biopsy-proven NAFLD among 171 patients and 31 non-NAFLD controls (USA, Korea) |
Fecal Microbiome: 16S rRNA Sequencing | Patients with NAFLD and >F2, non-obese: ↑ Ruminococcaceae ↑ Veillonellaceae |
Patients with NAFLD and >F2, non-obese: ↑ BA ↑ Propionate in feces |
| Adams et al., 2020 [63] | Biopsy-proven NAFLD among 67 patients and 55 non-NAFLD controls (USA) |
Fecal Microbiome: 16S rRNA Sequencing Serum and fecal metabolites: HPLC/MS |
Patients with NAFLD and >F2: ↑ Firmicutes ↑ Proteobacteria ↑ Actinobacteria ↓ Bacteriodetes ↑ Actinomycetaceae ↓ Lachnospiraceae |
Patients with NAFLD and >F2: ↑ BA in serum and feces |
| Masarone et al., 2021 [64] | Biopsy-proven NAFLD among 144 patients (Italy) |
Serum metabolites: GC/MS | No bacteria were further detected |
Patients with NAFLD and >F2: ↑ Glycocholic acid ↑ Taurocholic acid ↑ Phenylalanine ↑ BCAAs ↓ Glutathione |
| Nimer et al., 2021 [65] | Biopsy-proven NAFLD among 102 patients and 50 non-NAFLD controls (USA) |
Plasma BA metabolites: LC/MS | No bacteria were further detected |
Patients with NAFLD and >F2: ↑↑ Plasma 7-keto-DCA levels Some glycine conjugated forms of BAs ↑↑ in more advanced stages of NAFLD |
Abbreviations: BA: Bile Acids; BCAAs: Branched-Chain Amino Acids; FMT: Fecal Microbiota Transplantation; GC/MS: Gas Chromatography/Mass Spectrometry; LC/MS: Liquid Chromatography/Mass Spectrometry; MRE: Magnetic Resonance Elastography; MRI-PDFF: Magnetic Resonance Imaging Proton Density Fat Fraction; NAFLD: Non-Alcoholic Fatty Liver Disease; NASH: Non-Alcoholic Steatohepatitis; qPCR: quantitative Polymerase Chain Reaction; WGS: Whole Genome Shotgun; ↑: increased, ↓: decreased.