Table 1.
Ref. no. | POPULATION | No. | SAMPLE | METHODOLOGY | PHYLUM | CLASS | FAMILY | GENUS | SPECIES |
---|---|---|---|---|---|---|---|---|---|
29 | HBV-C Alcohol-C HC | 24 12 24 | Stool | 16S rRNA gene 454-pyrosequencing, quantitative real-time PCR | ↓Bacteroidetes | ↓Bacteroidia | ↓Bacteroidaceae | ||
↔Firmicutes | ↑Bacilli ↔Clostridia ↔Negativicutes | ↑Streptococcaceae ↓Lachnospiriaceae ↑Veillonellaceae | ↑Enterococcocus ↑Clostridium XI | ||||||
↑Proteobacteria | ↑γ−Proteobacteria | ↑Enterobacteriaceeae ↑Pasturellaceae | |||||||
↑Fusobacteria | ↑Fusbacteriaceae | ||||||||
47 | HBV-C HBV-CH HBV carriers HC | 31 31 30 32 | Stool | Quantitative PCR | ↓Bifidobacterium ↓Clostridium XI ↓Clostridium XIVab | ||||
↑Enterobacteriaceeae | |||||||||
48 | C HC | 23 10 | Duodenal mucosa | Real-time PCR FISH | ↑Enterococaceae | ||||
32 | C HE C non-HE HC | 19 17 17 | Stool and colonic mucosa | 16S rRNA gene pyrosequencing, quantitative real-time PCR | Firmicutes | Colstridiaceae Lachnospiriaceae Ruminococcaceae Veillonellaceae Enterococcaceae | ↑Clostridium ↓Dorea ↓Subdoligranulum ↑Acidaminococcus ↑Enterococcus | ||
Proteobacteria | Burkholderiaceae Enterobacteriaceae | ↑Burkholderia, ↑Ralstonia ↑Proteus | |||||||
49 | C HE C non-HE HC | 17 8 10 | Stool | 16S rRNA gene Multitag pyrosequencing, quantitative LH- PCR | ↓Lachnospiriaceae ↓Ruminococcaceae ↑Fusobacteriacee ↑Leuconostocaceae ↑Alcaligenaceae | ↓Clostridium XIVab | |||
50 | C HC | 6 4 | Stool | Real-Time PCR PCR-DGGE | ↑Enterococaceae ↑Enterobacteriaceae | ||||
51 | Early-C Advanced-C HC | 23 24 14 | Stool | 16S rRNA gene Multitag pyrosequencing, quantitative LH- PCR | Firmicutes Bacteroidetes Proteobacteria | ↓Lachnospiriaceae ↓Ruminococcaceae ↑Veillonellaceae ↓Rikenellaceae ↑Enterobacteriaceae | ↓Blautia | ||
52 | C HC | 6 4 | Stool | 16S rDNA gene pyrosequencing | ↑Veillonellaceae ↑Streptococcaceae | S. salivarius | |||
31 | C HC | 98 83 | Stool | 16S rRNA gene high-throughput Solexa sequencing quantitative real-time PCR | ↓Bacteroidetes | ↓Bacteroides ↓Alistipes ↑Prevotella | |||
Firmicutes | ↑ Veillonella ↑ Clostridium Faecalibacterium Coprococcus ↑ Streptococcus ↓ Eubacterium | ↑ V. dispar, V. atypica, V. parvula ↑ C. perfringens ↓ F. prausnitzii ↓ C. comes ↑ S. anginosus, S. salivarus | |||||||
↑Proteobacteria | ↑ Campylobacter ↑ Haemophilus | ↑H. parainfluenzae | |||||||
↑Fusobacteria | |||||||||
53 | Alcoholic C- Non-alcoholic C HC Healthy volunteers | 13 13 14 7 | Stool | Real-Time PCR | ↑Enterobacteriaceae | ↑Bacteroides | |||
54 | C HC CD OGD | 20 20 20 20 | Stool | Culture | ↑Lactobacillus | ||||
55 | C HE C non-HE HC | 43 59 32 | Saliva Stool | 16S rRNA gene Multitag Pyrosequencing | ↑Prevotellaceaea ↑Enterococcaceaea ↑Fusobacteriaceaea ↑Enterobacteriaceaea ↓Erysipelothricaceaea ↓Clostridiales XIVb ↓Lachnospiriaceaeb ↓Ruminococcaceaeb | ||||
↑Enterococcaceaea ↓Clostridiales XIVb ↓Lachnospiriaceaeb ↓Ruminococcaceaeb ↓Erysipelothricaceaeb | |||||||||
33 | C HC | 30 28 | Duodenal mucosa | 16S rRNA gene Multitag Pyrosequencing | ↑Firmicutes | ↑ Veillonella ↑ Megasphera ↑ Dialister ↑ Atopobium ↑ Prevotella ↓ Neisseria ↓ Haemophilus ↓ SR1 genera incertae sedis | |||
56 | HBV-C HC | 120 | Stool | 16S rRNA gene high-throughput Solexa sequencing quantitative real-time PCR | ↓Bacteroidetes | ||||
↔Firmicutes | ↑Bacilli ↑Negativicutes | ↑Streptococcaceae ↑Veillonellaceae | |||||||
↑Proteobacteria | ↑γ−Proteobacteria | ↑Enterobacteriaceeae | |||||||
57 | C HE C non-HE HC | 85 62 40 | Stool | 16S rRNA gene Multitag pyrosequencing | ↓Bacteroidetesb | ↓Prevotellaceaeb ↓Bacteroidaceaeb ↑Porphyromondaceaeb ↑Reikenelleacaeb | |||
↓Firmicutesb | ↓Clostridiales XIVb ↓Lachnospiriaceaeb ↓Ruminococcaceaeb ↑Enterococcaceaeb ↑Lactobacillaceaeb | ||||||||
↑Proteobacteriab | ↑Enterobacteriaceaea* | ||||||||
34 | HCC non-HCC | 15 15 | Stool | Culture | ↑ E. coli | ||||
35 | HCC HC | 35 25 | Tongue coat | 16S rRNA gene Multitag Pyrosequencing | ↑Oribacterium ↑Fusobacterium |
C: cirrhosis; CD: Crohn's Disease; HCC: hepatocellular carcinoma; HC: healthy controls; HBV: hepatitis B virus; HE: hepatic encephalopathy; DGGE: denaturing gradient gel electrophoresis; OGD: Other Gastrointestinal Disease; PCR: polymerase chain reaction; rRNA: ribosomal RNA.
Significant differences between controls and cirrhotics, but no difference between HE and non-HE patients.
Significant differences between controls, HE, and non-HE patients.