Microbiota, renal disease and renal transplantation

Table 1 Distribution of normal gut flora in different parts of intestine

Intestine sections	Function	Normal flora
Stomach	Acid production, pepsin, amylase, CFU < 103/mL	Lactobacillus; Streptococcus; Helycobacter pylori
Small intestine: duodenum, jejunum	Pancreatic enzymes, bicarbonate ions, bile salts, CFU: 103-104/mL	Lactobacilli; Enterococci; Streptococci; Actinobacteria
Small intestine: ileum	CFU: 103-109/mL	Enterococcus; Bacteroidetes; Lactobacillus; Clostridium; Corynebacteria
Large intestine: caecum, colon	Mucus and bicarbonate, CFU:1010-1012/mL	Bacteroidetes; Clostridium; Eubacterium; Ruminococcus; Streptococcus; Enterococcus; Lactobacillus; Fusobacteria

CFU: Colony forming units.

Table 2 Functional activities of normal gut flora

Protective function	Metabolic function	Structural function
Nutrient competition; Barrier fortification; Innate and adaptive immunity activation; Antimicrobial compounds secretion	Vitamin and amino acid biosynthesis; Bile acid biotransformation; Dietary fiber fermentation; Short chain fatty acids production	Mucus layer properties; Crypt and villi development; Villi microvascularization; Tight junction regulation

Seven division of bacteria (Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Verrucomicrobia, Actinobacteria, Cynobacteria), 300-1000 species.

Table 3 Alterations in the gut microbiota following kidney transplantation according phylum and order

Phylum	Pre Tx cohort	Post Tx cohort
Firmicutes	91.8%	87.7%
Actinobacteria	2.0%	7.6%
Proteobacteria	0.9%	4.1%
Bacteroidetes	2.8%	0.6%
Order
Clostridiales	64.8%	64.3%
Lactobacillales	19.1%	12.0%
Erysipelotrichales	5.6%	10.2%
Bifidobacteriales	1.6%	6.6%
Enterobacteriales	0.4%	3.9%
Bacteroidales	2.8%	0.6%

Table 4 Microbial composition of fecal specimens from patients with or without acute rejection, by Philum and Order

Phylum	No AR cohort	AR cohort	P value
Firmicutes	91.4%	76.6%	0.40
Actinobacteria	3.7%	8.2%	0.60
Proteobacteria	1.3%	15.2%	0.33
Bacteroidetes	3.1%	0.02%	0.03
Order
Clostridiales	63.1%	16.9%	0.01
Lactobacillales	12.7%	49.9%	0.04
Erysipelotrichales	13.3%	9.2%	0.32
Bifidobacteriales	3.1%	7.9%	0.44
Enterobacteriales	1.0%	14.7%	0.17
Bacteroidales	3.1%	0.02%	0.03

AR: Acute rejection.

Table 5 Potential transplant associated factors that may lead to changes in the gastrointestinal microbiota and cause infections

Risk factors	Microbiota changes	Consequences	Interventions
Dietary patterns	Increase in bacteria translocation	Gastrointestinal upset e.g., diarrhea	Diet
Changes to colonic and bowel transit time	Increase in metabolic endotoxemia	Urinary tract infections	Prebiotics
Immunosuppression	Increase in gut-derived microbial toxin formation	Other infections not yet explored	Probiotics
Antibiotics			Synbiotics
Lifestyle (sedentary, smoking, alcohol)

Table 6 Most significant genus level composition in the fecal specimens from the diarrhea group and the no diarrhea group

Bacterial Taxonomy Genus	Median relative abundance in the diarrhea group	Median relative abundance in the no diarrhea group	P value
Eubacterium	0.002	0.017	1.5E-09
Anaerostipes	0.000	0.005	2.7E-08
Coprococcus	0.000	0.004	3.0E-08
Romboutsia	0.000	0.014	4.2E-06
Ruminococcus	0.007	0.025	8.3E-06
Dorea	0.000	0.007	3.4E-05
Enterococcus	0.002	0.000	1.3E-04
Faecalibacterium	0.000	0.019	1.4E-04
Fusicatenibacter	0.000	0.006	0.001
Oscillibacter	0.001	0.008	0.001
Ruminiclostridium	0.005	0.021	0.002

Table 7 Actions of short-chain fatty acids on a model of ischemia reperfusion syndrome

Actions
SCFAs improve renal function
SCFAs decrease apoptosis and increase tubular proliferating cells
SCFAs decrease activation of bone marrow derived dendritic cells and inhibit their function as antigen presenting cells
SCFAs inhibit NFkB activation and nitric oxide production
SFCAs inhibit ROS production

SCAF: Short chain fatty acid; ROS: Reactive oxygen species; NFkB: Nuclear factor kappa-light-chain-enhancer of activated B cells.