Table 1.

Major features of studies overviewed in the present mini-review.

Study	Sample size	Study design	Specimen	Microbiome profiling technique	Statistical analysis	Age	Race/ethnicity	Factors potentially affecting the gut microbiota	Sexual behavior	PrEP treatment length	Adherence to PrEP	Increased gut flora	Decreased gut flora	Alpha diversity	Beta diversity	Overall diversity and composition
Dubé et al., 2018	8	Sub-study from the RCT NCT01761643 (cohort “California Collaborative Treatment Group study 595,” CCTG-595)	Self-collected rectal swab	Short-read sequencing of bacterial 16S rRNA gene V4 region and long-read sequencing of bacterial 16S–23S rRNA gene V4 region	Permutation tests and PCA clustering analysis	34.8 ± 9.1 (range 22–52) years	Half white, one Asian, one black, and two “of multiple races”	6/8 reporting rectal douching 6/8 reporting any drug use 3/8 reporting drug abuse	NA	48–72 weeks (72 weeks in 5 participants, 48 weeks in 2 subjects, and 60 weeks in 1 participant)	Very good or excellent in 100% of the participants	Erysipelotrichaceae (Catenibacterium mitsuokai, Holdemanella biformis, and Turicibacter sanguinis)	Streptococcaceae (Streptococcus agalactiae, Streptococcus oralis, and S. mitis)	No changes	β diversity between each participant’s pre and post-PrEP specimens was smaller than the β diversity of pre-PrEP specimen pairs of different individuals	No changes
Fulcher et al., 2019	74 (37 on PrEP versus 37 off PrEP)	Cross-sectional, matched case–control study, with participants selected from the ongoing cohort mSTUDY	Rectal swabs collected under direct mucosal visualization via anoscopy without preparatory enema	Sequencing of the V4 region of the 16S rRNA gene	Zero-inflated negative binomial models, multinomial LASSO as confirmatory analysis	30.1 ± 6.7 (median 29) years for the control and 29.8 ± 6.5 (median 28) years for the PrEP users’ group	56.8% black non-Hispanic, 32.4% Hispanic, 10.8% other non-Hispanic	26/37 reporting marjuana use 7/37 reporting methamphetamine use 10/37 reporting tobacco use 28/37 reporting binge alcohol use 4/37 reporting antibiotic use in the past month 35.1% obese	45.9% recent receptive anal intercourse (2.2 ± 4.5) per month)	41 weeks (IQR 14–59 weeks)	Very good or excellent in 78% of the participants	Streptococcus, Mitsuokella, and Fusobacterium	Escherichia and Shigella	No changes	NA	No changes
Perler et al., 2021	27: 14 taking PrEP	Cross-sectional, case–control study	Self-collected rectal swabs	Sequencing of the V4 region of the 16S rRNA gene	Linear regressions, linear discriminant analysis, Bray–Curtis dissimilarity analysis	36 years (on PrEP), 29 years off PrEP	NA	NA	8.43 partners per month	171 weeks (3.3 years)	NA	Catenibacterium and Prevotella 2	Pasteurellaceae, Corynebacteriaceae, Clostridiales Family XI (at the family level), and Finegoldia and Corynebacterium 1 (at the genus level)	No changes	Significant changes in the PrEP group	No changes