Table 2 Characteristics of included studies

 Ticinesi 2018 [50]

Italy

N = 52 recurrent idiopathic calcium stones

Age: 48 ± 11yrs, 60% male; ethnicity not reported

N = 48

Age: 47 ± 13yrs, 58% male; ethnicity not reported.

Self-sampled; Delivered to clinic within 2 hours from collection and stored at -22°C; Processed ≤ 2 weeks of receipt

Excluded if taken in prior 30 days.

Not reported

SILVA (16S rRNA), whole NCBI nr (shotgun)

16S ribosomal RNA gene sequencing

(V3 region)

Illumina MiSeq &

shotgun metagenomics on sub-sample (n=10)

Illumina NextSeq

↓ α-diversity in KS group vs. controls (Chao1 index; p<0.05);

β-diversity significantly different between groups (p=0.002 with PERMANOVA and p=0.004 with Adonis test based on Bray-Curtis and weighted UniFrac metrics)

EPIC FFQ delivered by a nutritionist; Calcium intake lower in adults with KS (p<0.04). Calcium intake considered as a covariate in the analysis of gut microbiota data.

 Stern 2016 [58]

USA

N = 23; all stone types included

Age: 53.7 ± 15.4yrs, 22% male; 13% African American, 35% Hispanic, 52% Caucasian.

N = 6

Age: 53.5 ± 16.0yrs, 67% male; 50% African American and 50% Caucasian.

Self-sampled; Flash-frozen with dry ice & stored -80°C

Excluded if taken in prior 2 weeks.

Not reported

Greengenes

16S ribosomal RNA gene sequencing

(V4 region)

Illumina MiSeq

Not reported

Not reported

 Tang 2018 [53]

China

N = 13; stone types not reported.

Age: 52.25 ± 7.25yrs, 38% male; 100% Chinese.

N = 13

Age: 55.81 ±5.79yrs,

38% male; 100% Chinese.

Self-sampled; Immediately frozen & stored -80°C. (DNA samples stored at -20°C)

Control group did not have antibiotics in prior 3 months; unclear if this was the same for kidney stone group.

None of the adults with kidney stones were reported to be on any medications before sample collection.

RDP

16S ribosomal RNA amplicon sequencing

(V4 region)

Illumina Hiseq 2500 platform

α-diversity reported not significantly different (Chao1, Shannon, Simpson’s and Good’s coverage indices, p>0.05)

Overall, β-diversity was distinct but not significantly different (p=0.096 with ANOSIM and p=0.058 with MPRR based on Bray-Curtis distance metric)

Not reported

 Suryavanshi 2016 [38]

India

N = 24 recurrent calcium oxalate stones.

Age: 22-50yrs, 100% male; ethnicity not reported.

N = 15

Age: 22-52yrs, 100% male; ethnicity not reported.

Self-sampled; Stored -80°C

Excluded if taken in prior 3 months.

Not reported

Greengenes (16S rRNA) & M5NR database (frc-gene)

16S ribosomal RNA gene and frc-gene amplicon sequencing; quantitative polymerase chain reaction & PCR-DGGE

(V3 region of 16S rRNA gene)

Iron Torrent PGM system

α-diversity reported not significantly different (Chao1, observed species/OTUs, phylogenetic diversity, Shannon and Simpson’s indices)

β-diversity metrics reported to reveal compositional differences between groups (PCoA plots of weighted and unweighted UniFrac results; statistical test and p-value not reported).

Reported number of participants who follow a vegetarian diet; dietary intake results and assessment methods not reported.

 Suryavanshi 2018 [37]

India

Same as the population above

N = 24 recurrent calcium oxalate stones.

Age: 22-50yrs, 100% male; ethnicity not reported.

N = 48

(Additional n = 33 controls recruited).

Age and gender only reported for a subset of n =15 (as above); ethnicity not reported.

Not reported

Not reported

Not reported

Greengenes

Targeted sequencing (frc-, but- and buk-, 16S and 18S ribosomal RNA genes as well as fungal ITS1 region) & quantitative polymerase chain reaction

Iron Torrent PGM system

α-diversity investigated in selected sub-sample

(n = 7 KSD, n = 7 controls); authors reported significant decrease observed in KSD group (Chao1, Shannon and Simpson’s indices; p-value not reported).

β-diversity not reported.

Not reported

 Tavasoli 2019 [49]

Iran

N = 58 (majority confirmed to have calcium stones)

n = 29 recurrent stones with hyperoxaluria

Age: 44.21 ± 9.58yrs,

62.1% male.

n = 29 recurrent stones without hyperoxaluria

Age: 48.07 ± 9.20yrs, 72.4% male.

Ethnicity not reported

N = 29

Age: 41.42 ± 11.48yrs,

89.7 % male; ethnicity not reported.

Self-sampled; stored -20°C

Excluded if taken in prior 2 months.

Medications not reported; individuals excluded from the study if taking calcium, magnesium, potassium or pyridoxine supplementation.

N/A

Real-time polymerase chain reaction

N/A

Not reported

  Al-Obaide 2017 [42]

USA

N = 20 CKD* (CKD stage not reported, all were reported to have T2DM) eGFR: 16.54 ± 3.01; Age: 64.4 ± 2.3yrs.

Gender and ethnicity not reported.

*Stool samples of n=18/20 were analysed to identify the gut microbial profile

N = 20

Age:54.3±3.2yrs;

eGFR, gender and ethnicity not reported.

Self-sampled;

Processed ≤24hrs of receipt

Excluded if taken for atleast 3 consecutive days in the prior month

Participants of the T2DM-CKD group treated with insulin, OHAs, ranitidine, PPI, ACEi, ARBs, statin therapy

Curated database from Greengenes, RDPII & NCBI

16S ribosomal RNA gene sequencing

(V3-V4 region)

Illumina MiSeq

Not reported.

Dietary assessment methods not stated.

Macronutrient data presented as a percentage of total energy intake; protein intake higher in controls (p<0.05) and fat intake higher in CKD group (p<0.01)

  Barrios 2015 [61]

UK

N = 62 (CKD stage not reported).

eGFR: reported ≤60;

Age, gender and ethnicity not reported for sub-sample.

N = 793

eGFR >60;

Age, gender and ethnicity not reported for sub-sample.

Self-sampled;

Refrigerated up to 2 days prior to clinic visit; Stored at -80°C

Data on antibiotics usage was collected for the prior month; data available for only 11% of study participants.

Not reported

Greengenes

16S ribosomal RNA gene sequencing

(V4 region)

Illumina MiSeq

Not reported

Dietary scores were obtained from EPIC FFQ generated through PCA. Diet scores were considered as covariates in the linear mixed effects regression models; no significant results reported.

  De Angelis 2014 [39]

Italy

N = 32 IgAN (CKD stage not reported)

n = 16 non-progressors,

eGFR: 76 ± 15;

Age: 41 ± 10yrs, 69% males.

n=16 progressors,

eGFR: 30±18;

Age:45 ± 6 yrs, 63% male. 100% Caucasian.

N = 16

eGFR: 96 ± 7;

Age: 43 ± 8yrs, 60% male. 100% Caucasian

Self-sampled; Stored -80°C

Excluded if taken in prior 3 months.

All IgAN participants treated with ACEi. Other medications undefined; no remarkable changes reported to medications in prior month.

RDP

Bacterial tag-encoded FLX-titanium amplicon pyrosequencing bTEFTAP

(V1-V3 region)

454 FLX Sequencer

↓ α-diversity in IgAN group vs. controls (Chao1, observed species/OTUs and Shannon indices; p<0.05)

β-diversity not reported.

Reported no remarkable changes to participant’s diet in prior month. Dietary assessment method or results not reported.

  Jiang 2016 [47]

China

N = 65 (CKD stage 1-5 )

eGFR: 55.61 ± 52.55;

Age: 43.45 ± 16.90 yrs, 46% male. 100% Chinese

N = 20

eGFR: 104.99 ± 19.82; Age: 43.05 ± 9.88yrs,

30% male. 100% Chinese

Self-sampled;

Stored at -80°C

Excluded if taken in prior 4 weeks.

Not reported

N/A

Quantitative polymerase chain reaction

N/A

Not reported

  Xu 2017 [56]

China

N = 32 (CKD stages 4-5)

eGFR: reported <30; Age: 53.34 ± 14.47yrs, 50% male; 100% Chinese

N = 32

eGFR: reported ≥90; Age: 55.03 ± 10.38yrs,

50% male; 100% Chinese

Sample collection method unclear; Stored at -40°C

Excluded if taken in the prior month.

Not reported

Not reported

16S rDNA and rRNA sequencing

(V4 region)

Illumina MiSeq

↓ α-diversity in CKD group vs. controls (phylogenetic diversity and Shannon indices; p<0.001)

β-diversity significantly different between groups (ADONIS analysis based on unweighted UniFrac metric, p<0.001)

Not reported

  Wang 2012 [44]

China

N = 30 (reported ESKD)

Age: 54 (37-71) yrs, 53% male. eGFR and ethnicity not reported.

N = 10

Age: 55 (41-67yrs) yrs, 50% male. eGFR and ethnicity not reported.

Not reported

Excluded if taken in prior 3 weeks.

Medications not reported; Corticosteroids, statins, or cytotoxic drugs were not taken in the prior 3 weeks.

SILVA

16S ribosomal RNA gene pyrosequencing

(V1-V3 region)

Sequencing platform not reported

↑ α-diversity ESKD vs. controls (observed species/OTUs index; p=0.017).

β-diversity not reported.

Not reported

  Jiang 2017 [51]

China

N = 52 (CKD stage 5)

eGFR: 6.86 ± 2.87;

Age: 51.58 ± 18.33yrs, 56% male. 100% Han Chinese nationality.

N = 60

eGFR: 98.03 ± 27.32; Age:52.53 ± 13.98yrs, 42 % male. 100% Han nationally Chinese

Self-sampled; Stored at -80°C

Excluded if taken in prior 4 weeks.

ESKD participants treated with phosphate

binders, anti-hypertensives and various vitamin and/or mineral supplementation (iron, calcium and vitamin D)

Not reported

Quantitative polymerase chain reaction

&

16S ribosomal RNA gene pyrosequencing in sub-sample

(n = 27 ESKD and n = 26 controls)

(V4-V6 region)

Illumina GAII

α-diversity reported not significantly different (Chao1, observed species/OTUs, Shannon and Simpson’s indices).

No difference in β-diversity reported between groups (PCoA plot based on UniFrac metric, statistical test or p-value not reported).

Not reported

  Gradisteanu 2019 [41]

Romania

N = 9 DN (CKD stage not reported)

eGFR, age, gender and ethnicity not reported .

N = 5

eGFR, age, gender and ethnicity not reported.

Self-sampled;

Stored at -20°C

Not reported

Not reported

N/A

Real-time polymerase chain reaction

(Bacterial and fungal group-specific primers were also used)

N/A

Not reported

  Tao 2019 [40]

China

N = 14 DN (CKD stage not reported)

eGFR: 93.26 ± 17.0;

Age:52.93 ± 9.98 yrs, 64% male. 100% Chinese.

N = 28

n = 14 healthy controls

eGFR: 96.01 ± 9.29; Age: 52.86 ± 9.91yrs, 64% male.

n = 14 T2DM controls without CKD

eGFR: 93.48± 13.02; Age: 53.29yrs ± 9yrs, 64% male.

100% Chinese.

Self-sampled; stored at -80°C

Excluded if taken in the prior 30 days.

Not reported

SILVA

16S ribosomal RNA gene pyrosequencing

(V3-V4 region)

Illumina MiSeq

↑ α-diversity richness DN vs. T2DM controls (observed species/OTUs index, p= 0.023; but no difference found for other α-diversity indices)

β-diversity significantly different between groups (PERMANOVA based on Bray-Curtis metric, p = 0.02).

Excluded if following restrictive diets. Reported similar/same eating habits across some of their groups; however, no formal dietary assessment was undertaken.

  Li 2019 [52]

China

N = 50 (CKD stage not reported)

eGFR: 22.39 ± 15.56;

Age:52.4 ± 13.49yrs, 54% male. 100% Chinese.

N = 22

eGFR: 97.06 ± 12.98;

Age:50.27 ± 7.77yrs, 55% male. 100% Chinese

Self-sampled; transported on ice and stored at -80°C

Excluded taken in prior 3 months.

Medications not reported; Immunosuppressive drugs not to be taken in prior 3 months.

RDP

16S ribosomal RNA gene pyrosequencing

(V3-V4 region)

Illumina HiSeq

↓ α-diversity in CKD group vs. controls (Phylogenic diversity whole-tree index), p<0.05, and reduced but not significant for Shannon or Simpson’s indices p> 0.05).

β-diversity significantly different between groups (ANOSIM test based on unweighted UniFrac, p= 0.001)

Not reported

  Vaziri 2013 [48] & Wong 2014 [36]

USA

N = 24

eGFR not reported.

Dialysis vintage: ≥3 months, Kt/V =1.5 ± 0.3.

Age: 57 ± 14 yrs, 25% male.

38% Caucasian, 54% Hispanic, and 8% Asian.

N = 12

eGFR not reported.

Age: 51 ± 12 yrs,

33% male.

33% Caucasian, 58% Hispanic, and 8% Asian.

Not reported

Excluded if taken in prior 3 months.

HD patients were treated with phosphate binders, ESAs (Darbopoetin), vitamin & mineral supplementation. Immunosuppressive drugs not to be taken in prior 3 months.

Greengenes (Wong)

Microarray sequencing; 16S ribosomal RNA gene PhyloChip analysis

Relative richness (assessed for subfamilies at subphylum level) was reported to be similar between groups (p-value not reported).

β-diversity revealed tighter clustering in the control group than HD group (NMDS figure based on Bray-Curtis distance metric; statistical test or p-value not reported)

Strict fluid and dietary sodium, phosphorus, and potassium restrictions; Nutrition prescription, education or counselling methods and results not reported.

  Miao 2018 [45]

China

N = 21

Dialysis vintage: ≥3 months, spKt/V reported >1.2 and regularly monitored.

Age: 53.0 ± 9.0yrs, 57% male.

eGFR and ethnicity not reported.

N = 20 (Unit staff)

Age:31 ± 9.1yrs, 50% males.

eGFR and ethnicity not reported.

Self-sampled; storage not reported.

Not reported

Medications at baseline not reported; HD patients had not taken lanthanum carbonate in prior 3 months.

RDP, BLAST

16S ribosomal RNA gene pyrosequencing

(V1-V3 region)

Sequencing platform not reported

α-diversity not significantly different (Shannon index; p=0.429).

β-diversity not reported.

Diet reported being ‘controlled for’, although methods and results were not reported.

  Wang 2012 [43]

Taiwan

N = 29

eGFR: reported <15;

Dialysis vintage: 49.7 ± 35.4 months, Kt/V not reported; Age: 53.7 ± 11.7yrs, 34% male. Ethnicity not reported.

N = 41

Age: 58.2 ± 12.8yrs, 37% male.

eGFR and ethnicity not reported.

Self-sampled; Immediately put on ice; Processed ≤1hr of defecation

Excluded if taken in prior 30 days.

Not reported

N/A

Real-time polymerase chain reaction

N/A

Not reported

  Shi 2014 [55]

China

N = 52

n = 22 HD group

Dialysis vintage: 6-40 months, Kt/V not reported.

n = 30 reported ESKD not undertaking dialysis.

eGFR, age, gender and ethnicity not reported.

N = 10

eGFR, age, gender and ethnicity not reported.

Details of sample collection not reported; Samples immersed in 90% alcohol and stored at -20°C

Excluded if taken in prior 3 weeks.

Medications not reported; Corticosteroids, statins, cytotoxic drugs not taken in prior 3 weeks.

SILVA

16S ribosomal RNA gene

Pyrosequencing

(V1-V3 region)

Sequencing platform not reported

↑ α-diversity in HD group vs. controls (average OTUs/ species, p=0.044) and Chao1 index higher in three HD samples (p-value not reported).

β-diversity not reported between study groups. However, PCA plot of Unifrac data from selected samples at the genus level exhibited a large separation in the same three HD samples vs. the other selected samples (p-value or statistical test not report).

Not reported

  Stadlbauer 2017 [57]

Austria

N = 30

n = 15 PD group

GFR (ml/min): 7.9 (7.3; 14.0); Dialysis vintage: 25 (15-74) months.

Age: 62yrs (54-69), 80% male.

n = 15 HD group

GFR (ml/min): 6.0 (5.9; 9.3); Dialysis vintage: 70 (40-197) months, Kt/V not reported.

Age: 61yrs (54-71), 67% male;

Ethnicity not reported.

N = 21

GFR (ml/min): 77.6 (73.4; 86.6).

Age: 58 yrs (53-62),

43% male. Ethnicity not reported.

Self-sampled; Stored at -80°C

Not reported

Participants from HD and PD groups treated with phosphate binders, PPI, immunosuppressive drugs. Small number of controls (n=2) also treated with PPI.

SILVA

16S ribosomal RNA gene sequencing

(V1-V2 region)

Illumina MiSeq

↓ α-diversity in PD and HD group compared to controls (Chao1 index, p<0.05, similar results reported for observed species/OTUs and phylogenic diversity)

β-diversity significantly different between HD vs. controls p=0.012 and PD vs. controls p=0.003 (ANOSIM test based on Bray Curtis, weighted and unweighted UniFrac metrics)

Not reported

  Lun 2019 [60]

China

N = 49 (n =13 treated with HD)

Age: 54 ±14 yrs, 76% male; eGFRand ethnicity not reported.

N = 24

Age: 56 ± 9 yrs, 67% males; eGFR and ethnicity not reported.

Self-sampled; Stored at -80°C

Excluded taken in prior 3 months.

Not reported

Not reported

16S ribosomal RNA gene sequencing

(V3-V4 region)

Illumina HiSeq (PE250)

α-diversity not reported.

β-diversity reported being distinct between CKD vs. controls; unclear if statistically significant (PCA plot based on the Euclidean distance & NMDS based on the UniFrac distance metric; statistical test or p-value not reported)

Not reported

  Li 2019 [62]

China

N = 53

n = 29 HD group

eGFR: 5.75 (4.35–8.26);

Dialysis vintage and Kt/V not reported.

Age: 54yrs (41.5-69), 59% male.

n = 24 ESKD group (stage 5) not undertaking dialysis.

eGFR: 5.33 (4.31–7.72);

Age: 55.5 yrs (48.25-64.5), 50% male.

Ethnicity not explicitly reported.

N = 69

eGFR: 126.07 (102.80–148.65);

Age: 51yrs (39.5-64), 39 % male.

Ethnicity not explicitly reported.

Collected in sterile 2mL tube on ice, containing pure ethanol and frozen within 30 minutes; Stored at -80°C

Excluded if taken in prior 4 weeks.

HD and CKD participants were treated with phosphate binders. Medication history of the last month was collected, but results were not reported.

Greengenes

16S ribosomal RNA gene sequencing

(V1-V2 region)

Illumina HiSeq 2500 system

↓ α-diversity in CKD and HD group vs. controls (Chao1, ACE and Shannon indices p<0.001).

β-diversity reported being different between groups (PCoA plot presented data based on weighted and unweighted UniFrac metrics, ANOSIM test, p-value not reported)

Reported similar eating habits across the cohort, although methods and results were not reported.

  Guirong 2018 [46]

China

N = 100

n = 16 KT recipients (sampling reported within the first month after transplantation)

Age: 42.8±11.5yrs.

n = 84 CKD group (stage 3-4)

Age: 55.9±18.2 yrs.

eGFR, gender and ethnicity not reported.

N = 53

Age: 54.7 ± 12.8yrs; eGFR, gender and ethnicity not reported.

Collection and storage not reported.

None taken in prior 3 months.

Not reported

Not reported

16S ribosomal RNA gene sequencing

(V3 region)

Ion Personal Genome Machine system

↓ α-diversity in RT and HD vs. controls (Chao1 index p<0.001).

β-diversity reported being different between groups (PERMANOVA based on Bray-Curtis metric, p<0.01)

Not reported