Changes in anorectal and oropharyngeal microbiota following infection of Neisseria gonorrhoeae in men who have sex with men: a prospective cohort study

Men who have sex with men (MSM) are at high risk of Neisseria gonorrhoeae (NG) infection. While microbiota is known to influence Neisseria gonorrhoeae colonisation and transmission, anatomical site-specific microbiota dynamics in MSM remain unclear. This study aimed to investigate microbiota changes following NG infection in an MSM cohort. Samples were collected from a cohort study of 312 MSM in China. 16 S rRNA gene sequencing was used to characterize microbiota composition before and after NG infection in a self-controlled design. The linear discriminant analysis effect size (LEfSe) analysis was performed to identify differential microbiota before and after NG infection. Microbiota networks and functional metabolic pathways were also analyzed. 94 anorectal and 76 oropharyngeal samples were included in the microbiota analysis. No significant changes in alpha or beta diversity were observed following NG infection at either the anorectal or oropharyngeal site (all P > 0.05). However, LEfSe analysis revealed genus-level changes following NG infection: Dorea, Lachnoclostridium, Ruminococcus_gnavus_group, Lachnospiraceae_ND3007_group, and Family_XIII_AD3011_group were significantly enriched following anorectal infection, whereas Rothia was significantly enriched following oropharyngeal infection (Linear Discriminant Analysis [LDA] > 2, all P < 0.05). The complexity of microbiota networks was reduced following both anorectal and oropharyngeal NG infection. Functional prediction revealed enrichment in teichoic acid and pyrimidine biosynthesis pathways following anorectal infection (P < 0.05), positively correlated with Dorea and Lachnoclostridium. NG infection was significantly associated with alterations in specific genera and decreased microbiota network complexity at both the anorectal and oropharyngeal sites. These findings highlight microbiota dynamics during NG colonization and may inform novel strategies for gonorrhoea prevention.