Table 3.
Diet associated changes of microbiome in chronic kidney disease (CKD) patients. Average of relative abundance (%) of bacterial species differently found (p < 0.05) in feces of CKD patients after free diet (FD), Mediterranean diet (MD), and very low protein diet plus essential amino acids and ketoanalogs (ALFA-KAPPA) (VLPD + Ka).
| Phylum/Family | Specie | FD | MD | VLPD + Ka | p FD vs. MD | p FD vs. VLPD + ka | p MD vs. VLPD + ka |
|---|---|---|---|---|---|---|---|
| Actinobacteria/Bifidobacteriaceae | Bifidobacterium adolescentis | 1.22 | 0.56 | 1.72 | 0.037 | 0.227 | 0.020 |
| Bifidobacterium catenulatum | 0.16 | 0.15 | 0.00 | 0.458 | 0.113 | 0.007 | |
| Bifidobacterium pseudolongum | 0.00 | 0.00 | 0.28 | - | 0.034 | 0.034 | |
| Actinobacteria/Coriobacteriaceae | Collinsella aerofaciens | 2.92 | 1.41 | 2.02 | 0.025 | 0.040 | 0.139 |
| Actinobacteria/Eggerthellaceae | Eggerthella sinensis | 0.23 | 0.12 | 0.37 | 0.090 | 0.081 | 0.002 |
| Bacteroidetes/Bacteroidaceae | Bacteroides coprocola | 0.10 | 0.00 | 0.13 | 0.013 | 0.417 | 0.140 |
| Bacteroides eggerthii | 0.12 | 0.10 | 0.00 | 0.413 | 0.003 | 0.125 | |
| Bacteroides stercoris | 0.63 | 0.35 | 0.84 | 0.093 | 0.233 | 0.023 | |
| Bacteroides thetaiotaomicron | 0.16 | 0.04 | 0.30 | 0.006 | 0.246 | 0.093 | |
| Bacteroides uniformis | 0.71 | 0.16 | 0.39 | 0.000 | 0.076 | 0.110 | |
| Bacteroides vulgatus | 1.01 | 0.32 | 0.43 | 0.003 | 0.016 | 0.260 | |
| Bacteroidetes/Tannerellaceae | Parabacteroides merdae | 0.35 | 0.17 | 0.12 | 0.023 | 0.009 | 0.246 |
| Euryarchaeota/Methanobacteriaceae | Methanobrevibacter smithii | 0.54 | 0.30 | 0.11 | 0.155 | 0.034 | 0.015 |
| Firmicutes/Acidaminococcaceae | Phascolarctobacterium succinates | 0.23 | 0.15 | 0.07 | 0.225 | 0.033 | 0.132 |
| Firmicutes/Clostridiaceae | Clostridium cadaveris | 0.53 | 1.01 | 3.57 | 0.207 | 0.000 | 0.006 |
| Clostridium perfringens | 0.39 | 0.28 | 0.00 | 0.313 | 0.005 | 0.015 | |
| Sarcina maxima | 0.12 | 0.13 | 0.54 | 0.394 | 0.016 | 0.022 | |
| Firmicutes/Enterococcaceae | Enterococcus durans | 0.01 | 0.09 | 0.17 | 0.048 | 0.163 | 0.327 |
| Enterococcus lactis | 0.16 | 0.76 | 0.08 | 0.029 | 0.231 | 0.027 | |
| Firmicutes/Eubacteriaceae | Eubacterium cylindroides | 0.17 | 0.00 | 0.00 | 0.033 | 0.033 | - |
| Firmicutes/Lachnospiraceae | Blautia coccoides | 1.99 | 2.07 | 3.19 | 0.408 | 0.005 | 0.013 |
| Blautia hydrogenotrophica | 0.01 | 0.00 | 0.24 | 0.163 | 0.009 | 0.009 | |
| Blautia obeum | 0.84 | 0.65 | 1.43 | 0.238 | 0.069 | 0.003 | |
| Blautia wexlerae | 1.92 | 1.54 | 3.22 | 0.300 | 0.042 | 0.013 | |
| Coprococcus eutactus | 0.14 | 0.16 | 0.51 | 0.435 | 0.022 | 0.001 | |
| Dorea formicigenerans | 0.17 | 0.28 | 0.13 | 0.066 | 0.260 | 0.005 | |
| Lachnospira pectinoachiza | 0.47 | 0.48 | 0.67 | 0.469 | 0.024 | 0.041 | |
| Pseudobutyrivibrio xylanivorans | 0.05 | 0.08 | 0.30 | 0.275 | 0.008 | 0.029 | |
| Roseburia faecis | 0.63 | 0.38 | 1.91 | 0.133 | 0.011 | 0.004 | |
| Firmicutes/Lactobacillaceae | Lactobacillus delbrueckii | 0.02 | 0.14 | 0.00 | 0.182 | 0.012 | 0.139 |
| Lactobacillus equi | 0.12 | 0.33 | 0.00 | 0.052 | 0.142 | 0.020 | |
| Lactobacillus fermentum | 0.15 | 0.39 | 0.00 | 0.012 | 0.005 | 0.000 | |
| Lactobacillus gasseri | 0.86 | 0.59 | 0.05 | 0.250 | 0.019 | 0.020 | |
| Lactobacillus intermedius | 0.09 | 0.26 | 0.05 | 0.013 | 0.322 | 0.042 | |
| Lactobacillus oris | 0.18 | 0.40 | 0.00 | 0.095 | 0.063 | 0.010 | |
| Lactobacillus salivarius | 2.12 | 7.61 | 0.05 | 0.047 | 0.142 | 0.021 | |
| Lactobacillus taiwanensis | 0.32 | 0.31 | 0.02 | 0.482 | 0.020 | 0.013 | |
| Lactobacillus ultunensis | 0.04 | 0.15 | 0.00 | 0.206 | 0.014 | 0.124 | |
| Firmicutes/Proteinivoraceae | Anaerobranca zavarzinii | 0.78 | 0.18 | 0.22 | 0.036 | 0.049 | 0.323 |
| Firmicutes/Ruminococcaceae | Faecalibacterium prausnitzii | 2.53 | 2.19 | 3.75 | 0.275 | 0.008 | 0.005 |
| Ruminococcus callidus | 0.30 | 0.08 | 0.08 | 0.014 | 0.009 | 0.491 | |
| Ruminococcus gnavus | 0.70 | 1.00 | 0.52 | 0.016 | 0.088 | 0.002 | |
| Firmicutes/Streptococcaceae | Lactococcus garvieae | 0.54 | 0.13 | 0.00 | 0.114 | 0.042 | 0.139 |
| Streptococcus anginosus | 0.05 | 0.26 | 0.38 | 0.035 | 0.190 | 0.380 | |
| Streptococcus bovis | 0.22 | 0.38 | 0.03 | 0.227 | 0.001 | 0.048 | |
| Streptococcus milleri | 0.02 | 0.13 | 0.33 | 0.058 | 0.177 | 0.276 | |
| Streptococcus mutans | 0.16 | 0.36 | 0.00 | 0.118 | 0.025 | 0.022 | |
| Streptococcus parasanguinis | 0.32 | 0.35 | 0.02 | 0.390 | 0.000 | 0.001 | |
| Streptococcus sobrinus | 0.15 | 0.67 | 0.00 | 0.039 | 0.163 | 0.022 | |
| Streptococcus vestibularis | 4.80 | 5.04 | 1.46 | 0.432 | 0.021 | 0.010 | |
| Proteobacteria/Enterobacteriaceae | Escherichia albertii | 3.18 | 2.96 | 0.20 | 0.404 | 0.032 | 0.013 |
| Proteobacteria/Yersiniaceae | Serratia entomophila | 0.25 | 0.31 | 0.01 | 0.214 | 0.040 | 0.009 |
| Verrucomicrobia/Akkermansiaceae | Akkermansia muciniphila | 2.25 | 1.82 | 0.96 | 0.356 | 0.014 | 0.218 |