Table 1.

Overview of the final selected articles and the characteristics and reported findings. HV = healthy volunteers; CS = coronal sulcus; BP = balanoposthitis; HIV = human immunodeficiency virus; MGLSc = male genital lichen sclerosus; BS = balanopreputial sac; BV = Bacterial vaginosis; ↓ = decrease; ↑ = increase.

Author	Study Design	Field of Study	Participants	Age (Years)	Ethnicity, Country	Anatomical Site	Sample Type	Microbial Analysis	Key Findings	Limitations	Quality Score
Iniesta et al. [16]	Control intervention	Supplementation with a probiotic	17 couples under artificial reproductive treatment	Couples: 22–40 Male (mean 36) Female (mean 35)	Caucasian, Spain	Glans	Glans, semen, and blood	16S rRNA amplification of the V3–V4 region	Treatment with Lactobacillus salivarius PS11610 modified the microbiota composition improving the urogenital tract microbiome, solving the dysbiosis in 88.9% of the couples. Male samples showed higher bacterial diversity at genus level than female samples. Most prevalent genera in glans: Initial: Peptoniphilus, Staphylococcus, Fineglodia, and Corynebacterium; 3 and 6 months: Peptonophilus, Finegoldia, Corynebacterium (↓ Staphylococcus)	Small sample size. No control group treated with placebo.	Fair
Li et al. [17]	Case control	Balanoposthitis (BP)	26 BP uncircumcised 29 HV uncircumcised	18–65	Unknown, China	Glans, penis, and prepuce	Swabs	16S rRNA amplification of the V4 region	Microbiome BP ∼ HV, but ≠ HV with redundant prepuce. Most prevalent species BP: Staphylococcus warneri (with condom use) and Prevotella bivia (without sexual activity). Most prevalent HV: Ezakiella (redundant prepuce), Porphyromonas somerae (normal prepuce).	Small sample size. No ethnicity records. V4 region is considered a relatively low informative region for taxonomic assignment.	Fair
Liu et al. [18]	Randomized controlled trial	Circumcision	77 HV uncircumcised 79 HIV-negative pre- and post-circumcision	15–49	Unknown, USA	Coronal sulcus (CS)	Swabs	16S rRNA amplification of the V3-V6 region	Male circumcision reduced the prevalence and the absolute abundance of CS bacteria and the diversity of microbiota. Day 0: Prevalent but low abundance: Prevotella sp., Clostridiales and Corynebacterium sp. At 5%: Peptoniphilus sp., Anaerococcus sp., Fenigoldia sp., Murdochiella sp., Porphyromonas sp., and Lactobacillus sp. Year 1: Reduction in bacterial load on post-circumcision: Porphymonas sp., Prevotella sp., Negativicoccus sp., Dialister sp., Mobiluncus sp., and 6 genera from Clostridiales family XI. No reduction: Atopolium sp., Sneathia sp., and Megasphaera. More prevalent: Kocuria sp. and Facklamia sp.	No ethnicity records.	Good
Liu et al. [19]	Case control	Circumcision and Human immunodeficiency virus (HIV)	46 HIV-positive uncircumcised 136 HIV-negative uncircumcised	15–49	Unknown, Uganda	Coronal sulcus	Swabs	16S rRNA amplification of the V3–V4 region	HIV-positive uncircumcised: ↑ penile anaerobes. Most prevalent genera HIV-positive uncircumcised: Prevotella, Dialister, Mobiluncus, Murdochiella, and Peptostreptococcus.	No ethnicity records.	Good
Nelson et al. [20]	Observational cohort	Circumcision	18 HV (6 uncircumcised and 12 circumcised)	14–17	Mixed Black, Caucasian, and Latin, USA	Coronal sulcus	Swabs and first catch urine	16S rRNA amplification of the V1–V3, V3–V5, and V6–V9 regions	Microbiome CS ≠ urine. Most prevalent genera CS: Corynebacteria, Staphylococcus, Anaerococcus, Peptoniphilus, Prevotella, Finegoldia, Porphyromonas, Propionibacterium, and Delftia. Uncircumcised: ↑ Prevotella and Porphyromonas. Most prevalent genera urine: Streptococcus, Lactobacillus, Gardnerella, and Veillonella.	Small sample size.	Fair
Plummer et al. [21]	Randomized controlled trial	Bacterial vaginosis under antibiotic treatment	27 couples	>18	Unknown, Australia	Penis	Swab and first catch urine	16S rRNA amplification of the V3–V4 region	Day 0: Male specimens were heterogeneous in composition. Most abundant in penile swab: Corynebacterium, Staphylococcus, Peptoniphilus, and Prevotella. Day 8: Decreased on penile swab taxa—Anaerococcus, Finegoldia, Peptoniphilus, Prevotela spp., and Dialister. (↑ Staphyloccocus)	Small sample size. Self-collected swab.	Fair
Price et al. [22]	Randomized controlled trial	Circumcision	12 HIV-negative pre- and post-circumcision	15–49	Unknown, Uganda	Coronal sulcus	Swabs	16S rRNA amplification of the V4 region	Microbiome post-circumcision: ↓ penile anaerobes. Most prevalent genera pre-circumcision: Anaerococcus, Peptoniphilus, Finegoldia, and Prevotella. Most prevalent genera post-circumcision: Staphylococcus and Corynebacterium.	Small sample size. No ethnicity records.	Poor
Storm et al. [23]	Observational cohort	Healthy	48 HV males 18 HV females	0–18	Unknown, USA	Males: urethra, perineum, and foreskin Females: urethra, perineum, and vagina	Swabs	16S rRNA amplification of the V4 region	Perineal microbiomes differed significantly by age; urethral and foreskin microbiomes did not. Most common genera foreskin: Prevotella, Staphylococcus, Corynebacterium, Peptoniphilus, Mobiluncus, and Winkia.	Small sample size. No record of the pubertal status of the older cohort. No ethnicity records. V4 region is considered a relatively low informative region for taxonomic assignment.	Fair
Watchorn et al. [24]	Case control	Male genital lichen sclerosus (MGLSc)	20 MGLSc uncircumcised 20 HV uncircumcised	MGLSs:26–73 HV:19–63	Unknown, UK	Balanopreputial sac (BS) (Glans + inner prepuce)	Swabs and first catch urine	16S rRNA amplification of the V3–V4 region	Microbiome BS (MGLSc) ∼ urine (MGLSc). Microbiome BS (MGLSc) ≠ balanopreputial sac (HV). Most prevalent genera BS (MGLSc): Enterobacteriaceae, Prevotella, Fusobacterium, and Finegoldia. Most prevalent genera BS (HV): ↑ Finegoldia, Staphyloccocus, Corynebacterium.	Small sample size. No ethnicity records.	Poor
Zozaya et al. [25]	Cross-sectional	Bacterial vaginosis (BV)	65 HV-males (23 circumcised) 65 BV-males (35 circumcised)	Mean 30.7	African American, USA	Glans, coronal sulcus, penis	Swab	16S rRNA amplification of the V4-V6 region	More penile skin diversity of BV-males than normal-males, but urethral diversity did not differ between groups. BV-associated bacteria were more abundant in penile and urethral specimens on BV-males. Most abundant on penile skin of BV-males: Peptoniphilus, Anaerococcus, Pv. 123-f-82, Pv. 123-b-46, Lactobacillus iners, and Pv.123-f-110. Most abundant on penile skin of HV: Peptoniphilus, Anaerococcus, Pv 123-f-82, L. iners, Porphyromonas, and Prevotela disiens.	No records of recruitment duration.	Good