Table 1 Selected publications since 2015 investigating microbial dysbiosis and associations with PCa

Salachan et al., 2022; in press

Comparison of microbiome between benign (AN) and malignant tumor tissue samples from 94 RP patients

Fresh frozen tissue

83 malignant and 23 adjacent benign (n=106)

Metatranscriptomic analysis of total RNA sequencing data

Significantly increased abundances of Shewanella and decreased abundances of Bacteroides fragilis, Saimiriine betaherpesvirus, Staphylococcus saprophyticus, Vibrio parahaemolyticus in malignant as compared to benign tissue samples.

Wald test within DESeq2,

P < 0.01, LFC > |0.58|

Lack of true normal comparison.

Ma et al., 2020 [50]

Comparison of microbiome between benign (AN) and malignant tumor tissue samples from RP patients

Fresh frozen tissue

242 malignant and 52 adjacent benign (n=294)

Whole-transcriptome RNA sequencing

Listeria monocytogenes, Methylobacterium radiotolerans JCM 2831, Xanthomonas Listeria monocytogenes, Methylobacterium radiotolerans JCM 2831, Xanthomonas albilineans GPE PC73, and Bradyrhizobium japonicum are overrepresented in the tumor tissue as compared to the benign tissue samples.

Kruskal-Wallis test,

P < 0.05

Lack of true normal comparison.

Feng, Ramnarine et al., 2019 [53]

Comparison of microbiome between benign (AN) and malignant tumor tissue samples from 65 RP patients

Fresh frozen tissue

65 malignant and 65 adjacent benign (n=130)

Metagenomic and metatranscriptomic analyses

Escherichia, Propionibacterium, Acinetobacter, and Pseudomonas were most abundant in the prostate. No species found to be differentially abundant, and no difference in alpha or beta diversity could be found.

Wilcoxon signed rank test,

P < 0.05, FC > 2

Lack of negative control. Propionibacterium is a known sequencing contaminant.

Banerjee et al., 2019 [56]

Comparison of microbiome between prostate adenocarcinoma and BPH tissue samples from 50 RP and 15 TURP (BPH) patients

Formalin-fixed paraffin-embedded

50 malignant and 15 BPH (n=65)

Array-based metagenomic and capture sequencing

Malignant samples were significantly associated with the bacterial phyla such as Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, fungal phyla such as Ascomycota, and Zygomycota, parasitic phyla such as Nematoda, and Sarcomastogophora, and group I and group IV viruses.

t-test, P < 0.05, LFC > 1

Lack of true normal comparison.

Feng, Jaratlerdsiri et al., 2019 [54]

Comparison of prostate tissue microbiome between African and Australian samples from PCa patients

Fresh frozen tissue

6 African and 16 Australian malignant samples (n=22)

Metagenomic analysis

Most abundant genera in prostate belong to Escherichia, Propionibacterium, and Pseudomonas. African samples had significantly increased bacterial richness as compared to Australian samples.

t-test, P < 0.01

Small sample size. Propionibacterium is a known sequencing contaminant.

Miyake et al., 2019 [76]

Comparison of specific microbial taxa between prostate adenocarcinoma and BPH tissue samples from 45 RP and 33 TURP (BPH) patients

Formalin-fixed paraffin-embedded

45 malignant and 33 BPH (n=78)

PCR screening

Increased rates of Mycoplasma genitalium was associated with Pca.

Mann-Whitney U test,

P < 0.05

Limited number of species tested.

Cavarretta et al., 2017 [77]

Comparison of microbiome between tumoral, peri-tumoral, and non-tumoral tissue samples from 16 RP patients

Formalin-fixed paraffin-embedded

16 tumoral, 16 peri-tumoral and 16 non-tumoral (n=48)

Ultradeep pyrosequencing

Actinobacteria, Firmicutes and Proteobacteria are the most abundant taxa in the prostate. Significantly increased abundances of Staphylococcus and decreased abundances of Streptococcus in tumoral + peri-tumoral tissue as compared to non-tumoral tissue samples.

Wilcoxon rank-sum test,

P < 0.05

Lack of negative control.

Yow et al., 2017 [65]

Comparison of microbiome between benign (AN) and malignant tumor tissue samples from 10 RP patients

Fresh frozen tissue

10 malignant and 10 benign (n=20)

16s rRNA amplicon sequencing and total RNA sequencing

Enterobacteriaceae, Escherichia and Propionibacterium acnes identified as most common in both malignant and benign samples. Endogenous retroviruses could be detected in both malignant and benign samples.

n/a

Propionibacterium is a known sequencing contaminant.

Chen and Wei, 2015 [64]

Comparison of 7 viral and 1 bacterial species between tumoral and benign samples from 20 Western RP and 14 Chinese patients

n/a

20 malignant and 10 matched AN from Western patients, 14 malignant and 14 matched AN tissue from Chinese patients

RNA sequencing

Propionibacterim acnes genes detected in both tumor and benign tissue. No virus detected in Western patients but few viruses detected in Chinese samples.

n/a

Limited number of species tested. No information whether fresh-frozen or FFPE tissue used.

Matsushita et al., 2021 [78]

Comparison of microbiome between high and low risk PCa group

Frozen fecal samples from a rectal swab

96 patients with PCa and 56 patients without PCa (n=152)

16s rRNA amplicon sequencing

Increased relative abundance of Rikenellaceae, Alistipes, and Lachnospira in high compared to low risk group.

Mann-Whitney U test or chi-squared test, P < 0.05

No sequencing controls.

Li et al., 2021 [79]

Comparison of microbiome between patients who underwent RP and those undergoing ADT

Frozen fecal samples

56 patients on ADT and 30 patients who underwent RP (n= 86)

16s rRNA amplicon sequencing

Increased relative abundance of Ruminococcus gnavus and Bacteroides spp. and decreased abundance of Lachnospira and Roseburia in patient undergoing ADT.

Kruskal-Wallis test, Wilcoxon rank-sum test or LDA within LEfSe, P < 0.05

Lack of independent validation.

Daisley et al., 2020 [62]

Comparison of microbiome between patients not receiving any active treatment, those receiving ADT alone and those receiving both ADT and orally administered AA

Frozen fecal samples

33, 21, and 14 samples from patients not receiving any active treatment, those receiving ADT alone and those receiving both ADT and orally administered AA, respectively (n=68)

16s rRNA amplicon sequencing

Decreased relative abundance in Corynebacterium and increased relative abundance of Akkermansia muciniphila in patients undergoing ADT+AA compared to controls.

Wilcoxon rank-sum test,

P < 0.05

Only bacterial species profiled.

Liu and Jiang, 2020 [63]

Comparison of microbiome between paired samples collected before ADT (HSPC) and after ADT on progression to CRPC

Frozen fecal samples

21 samples before ADT (HSPC) and 21 samples after ADT at CRPC (n=42)

16s rRNA amplicon sequencing

Increased abundance of Phascolarctobacterium and Ruminococcus in samples collected after ADT from patients who progressed to CRPC as compared to the samples before ADT.

LDA within LEfSe, log₁₀ LDA score > 2

Small sample size.

Alanee et al., 2019 [60]

Comparison of microbiome between patients with benign and malignant disease identified through trans-rectal biopsy of the prostate

Frozen fecal samples

16 patients with benign and 14 patients with PCa (n=30)

16s rRNA amplicon sequencing

No clustering of samples based on benign and malignant biopsy. Higher abundance of Bacteroides in patients with PCa compared to controls.

Kruskal-Wallis test,

P < 0.05

Small sample size. Negative controls not sequenced.

Sfanos et al., 2018 [61]

Comparison of microbiome from control, benign, localized PCa, biochemically recurrent PCa, and metastatic PCa patients

Frozen fecal samples

6 control, 3 benign, 7 localized PCa, 7 biochemically recurrent PCa, and 7 metastatic PCa patients (n=30)

16s rDNA amplicon sequencing

Increased abundance of Akkermansia muciniphila and Ruminococcaceae spp. in men taking ATT compared to those who did not.

Negative binomial test within DESeq, P < 0.05

Small sample size.

Liss et al., 2018 [47]

Comparison of microbiome between patients with and without PCa identified through trans-rectal biopsy of the prostate

Rectal swab kept frozen in PBS

64 samples from patients with PCa and 41 samples from patients without PCa (n=105)

16s rRNA amplicon sequencing

Bacteroides and Streptococcus species were enriched in samples from patients with PCa compared to patients without.

t-test,

P < 0.05

Use of rectal swabs instead of stool collection limits DNA yield.

Golombos et al., 2018 [59]

Comparison of microbiome between patients with benign prostatic conditions (controls) and clinically localized prostate cancer

Frozen fecal samples

8 men with benign and 12 men with PCa (n=20)

Metagenomics analysis

Higher relative abundance of Bacteriodes massiliensis observed in men with PCa compared to controls. Higher relative abundance of Faecalibacterium prausnitzii and Eubacterium rectalie among controls.

Kruskal-Wallis test, Wilcoxon rank-sum test or LDA within LEfSe, P < 0.05, log₁₀ LDA score > 2

Small sample size.

Shreshtha et al., 2018 [46]

Comparison of microbiome between patients with positive vs. negative biopsies for Pca

Urine processed within 4 hours of collection

61 samples from men with PCa, 63 from men without PCa, and 5 from men who had negative first and positive second biopsy (n=129)

16s rDNA sequencing

Propionibacterium lymphophilum identified to have significantly higher abundance in cancer vs. benign samples.

Fisher exact test, P < 0.05

Lack of true normal urine samples.

Alanee et al., 2019 [60]

Comparison of microbiome between patients with benign and malignant disease identified through trans-rectal biopsy of the prostate

Frozen first voided urine samples after prostatic massage

16 patients with benign and 14 patients with PCa (n=30)

16s rRNA amplicon sequencing

Higher abundance of clostridium XVIII & IV, lachnospira, acetanaerobacterium, and faecalibacterium in the patients with PCa compared to controls.

Kruskal-Wallis test,

P < 0.05

Small sample size. Negative controls not sequenced.

Yu et al., 2015 [49]

Comparison of microbiome between patients with BPH and PCa

Frozen urine

21 samples from patients with BPH and 13 samples from patients with PCa (n=34)

16s rDNA and PCR-DGGE and qPCR

E. coli and Enterococcus are present in significantly lower number in the urine of men with PCa compared to BPH.

ANOVA or t-test,

P < 0.05

Small sample size.

Ma et al., 2019 [48]

Comparison of microbiome between patients with PCa and those without

Fresh frozen prostatic fluid

32 samples from PCa and 27 samples from non-PCa men (n=59)

16s rRNA amplicon sequencing

Reduced microbial diversity in PCa samples. Increased proportions of Lactococcus, Carnobacterium, Streptococcus, Geobacillus, and Enterobacter, and decreased proportions of Cronobacter, Alkaliphilus, and Paenibacillus in samples from patients with PCa compared to those without.

Friedman’s test or Wilcoxon rank-sum test,

P < 0.05

Difficult to control bacterial contamination from urinary tract.

Chen and Wei, 2015 [64]

Comparison of 7 viral and 1 bacterial species between biopsy proven and biopsy negative samples from 12 individuals

Non-sperm fraction of seminal fluid freshly collected

1 pooled sample each from 6 biopsy proven and 6 biopsy negative men

Small RNA sequencing

Propionibacterium acnes genes detected in biopsy proven but not in biopsy negative pooled sample.

n/a

Limited number of species tested.

Yu et al., 2015 [49]

Comparison of microbiome between patients with BPH and PCa

Frozen expressed prostatic secretions and seminal fluid

Pooled sample from patients with BPH (n=21) or PCa (n=13)

16s rDNA and PCR-DGGE and qPCR

EPS of PCa patients were rich in Bacteroidetes bacteria, Alphaproteobacteria, Firmicutes bacteria, Lachnospiraceae, Propionicimonas, Sphingomonas, and Ochrobactrum. E. coli was present in significantly large number in the EPS and seminal fluid, whereas Enterococcus was present in significantly higher number in the seminal fluid of men with PCa compared to BPH.

ANOVA or t-test,

P < 0.05

Small sample size.