Table 1.
Summary of literature on urinary microbiome dysbiosis in CKD, DM, HT, and UTI. CKD chronic kidney disease, DM diabetes mellitus, UTI urinary tract infection, HT hypertension
| Disease and reference group/s (if relevant) (n) | Age (years mean ± standard deviation) | Method of sample collection | Study techniques | Main findings | Reference |
|---|---|---|---|---|---|
| Stage 3–5 non-dialysis dependent CKDa: males (36), females (41) | 71.5 ± 7.9 | CCb | 16S rRNA sequencing (V4 region, Illumina), diversity measures: inverse Simpson, Chao, and Shannon indices | Most abundant bacterial genera or family: Corynebacterium, Staphylococcus, Streptococcus, Lactobacillus, Gardnerella, Prevotella, Escherichia Shigella, and Enterobacteriaceae | [37] |
|
Females with type 2 DMc (25), DM + HTd (24), DM + HLe (7), DM + HT + HL (11) |
DM only: 56.28 ± 13.91 DM + HT: 70.42 ± 9.00 DM + HL: 54.43 ± 10.66 DM + HT + HLP: 69.81 ± 9.64 |
Modified midstream urine collection | 16S rRNA sequencing (V3–V4 regions, Illumina), diversity measures: number of reads, OTUsf, Chao1, ACE, Shannon and Simpson indices | Number of bacterial genera and most abundant genera: DM: 320, Lactobacillus, Prevotella, Acinetobacter. DM + HT: 303, Prevotella, Streptococcus, Bacteroides. DM + HL: 236, Lactobacillus, Prevotella, Halomonas. DM + HT + HL: 225, Prevotella, Lactobacillus, Bacillus | [40] |
| Females with type 2 DM (70) and female controls (70) | all: 26–35, 36–45, 46–55, 56–65, 66–75, 76 and above | Modified midstream urine collection | 16S rRNA sequencing (V3–V4 regions, Illumina), diversity measures: number of reads, OTUs, Chao1, ACE, Shannon and Simpson indices |
Bacterial genera with different relative abundances between the type 2 DM cohort and controls: Prevotella*, Lactobacillus*, Shuttleworthia*, Acinetobacter, Bacteroides, Halmonas, Blautia, Faecalibacterium, Corynebacterium, Klebsiella, Pseudomonas |
[67] |
| Females with type 2 DM with detectable and undetectable urine IL-8 g (70) and female controls (70) | all: 26–85 | Modified midstream urine collection | 16S rRNA sequencing (V3–V4 regions, Illumina), ELISAh, diversity measures: OTUs, Chao1, Shannon, and Simpson indices |
11 bacterial genera were more abundant in the type 2 DM with detectable IL-8 cohort than the type 2 DM with undetectable IL-8 cohort: Shuttleworthia, Mobiluncus, Peptoniphilus, Corynebacterium, Thermus, Gemella, Enterococcus, Acinetobacter, Akkermansia, Aquaspirillum, and Geobacillus |
[66] |
| Females with type 2 DM (32) and female controls (26) |
DM: 56.97 ± 8.01 controls: 57.62 ± 9.24 |
CC | Standard culture, 16S rRNA sequencing (V3–V4 regions, Illumina), diversity measures: Observed Species, Chao1, ACE, Shannon and Simpson indices | Bacterial genera that were over-represented in the type 2 DM cohort: Escherichia-shigella, Klebsiella, Aerococcus, Delftia, Enterococcus, Alistipes, Stenotrophomonas, Micrococcus, Deinococcus, Rubellimicrobium | [61] |
| Kidney stone disease with normotension, prehypertension and HT (50) and controls (12) |
Kidney stone + normotension: 47.33 ± 14.95, prehypertension: 54.09 ± 13.03, HT: 54.74 ± 12.36, controls: 58.91 ± 18.97 |
BUA with a cystoscopei and TUCj | Expanded quantitative urine culture, 16S rRNA sequencing (V3–V4 regions, Illumina), diversity measures: Observed Species, Chao1, Shannon, Simpson indices |
Bacterial genera that were significantly different between the kidney stone cohorts and controls: Comamonas, Enterococcus, Bifidobacterium, Lactobacillus |
[39] |
| Females with DOSk (pelvic floor surgery) positive urine culture (13), postoperative UTIl (4) and DOS negative urine culture with postoperative no-UTI/ negative (37) |
DOS positive urine culture: 67, postoperative UTI: 60, negative: 56 |
TUC | Urine culture, 16S rRNA sequencing (Life Technologies, RDP classifier), ELISA, protease assay |
Lactobacillus was abundant in all three cohorts Most abundant bacterial genera in postoperative UTI cohort versus postoperative no-UTI (negative) cohort: Dyella, Fulvimonas, Klebsiella, and Lactobacillus |
[77] |
| Catheter-associated UTI: males (8), females (2) | 70.9 | TUC | Urine culture, 16S rRNA sequencing (V4 region, Illumina), diversity measures: observed OTUs, and Shannon index | Study subjects that developed catheter-associated UTI had a low diverse urinary microbiome | [75] |
| Females with UTI-like symptoms (75) and females without UTI-like symptoms (75) | all: 62.3 ± 14.9 | TUC | Standard culture, modified standard culture, expanded quantitative urine culture, diversity measure: species accumulation curves and Shannon index | Bacterial species that had substantially higher average CFU/ml in the UTI-cohort than no-UTI cohort: Escherichia coli, Klebsiella pneumoniae, Streptococcus agalactiae, Aerococcus urinae, Enterococcus faecalis, Staphylococcus aureus, Streptococcus anginosus | [14] |
| Females with urogynaecology surgery (pelvic organ prolapse and/or urinary incontinence) (104) | 57 | TUC | 16S rRNA sequencing (V4 region, Illumina), diversity measures: Chao 1, ACE, Shannon, and Simpson indices |
Postoperative UTI risk was associated with an abundance of diverse pathogens in the preoperative bladder microbiome: Enterobacteriaceae, Pseudomonas, Staphylococcus, the species Lactobacillus delbrueckii, Actinotignum schaalii, Anaerococcus obesiensis, Corynebacterium tuberculostearicum, Streptococcus anginosus, Aerococcus christensenii and Anaerococcus murdochii Increased Lactobacillus iners was protective against postoperative UTI risk |
[76] |
| UTI: males (149), females (234) | 56 | CC | Urinalysis, urine culture, 16S rRNA sequencing (broad range archaeal primers, mcrA gene, Technelysium) | The archaeal methanogen Methanobrevibacter smithii was present in 54% of the patients diagnosed with UTI | [64] |
| Cystitis: males (12), females (16) | 66 | CC, TUC | Standard culture, 16S rRNA sequencing (V3–V4 regions, Illumina), diversity measures: observed OTUs |
15 distinct phyla were detected in all cystitis patients. The most abundant phyla: Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria |
[57] |
aChronic kidney disease
bMidstream clean-catch method
cDiabetes mellitus
dHypertension
eHyperlipidemia
fOperational taxonomic units
gInterleukin-8
hEnzyme-linked immunosorbent assay
iBladder urine aspirate
jTransurethral catheter
kDay of Surgery
lUrinary tract infection
*most abundant genera in type 2 DM