Summary
A prospective medRxiv study of 121 adults found six anaerobic species enriched in anal squamous cell carcinoma compared with high-grade lesions. The microbial pattern persisted during follow-up and changed after treatment initiation.
A prospective study has identified a distinct group of anaerobic microbes associated with anal squamous cell carcinoma (ASCC), an invasive cancer that can develop from high-grade squamous intraepithelial lesions (HSIL). The findings, posted as a medRxiv preprint on September 15, 2026, come from anal-canal swabs collected from 121 adults at Montefiore Medical Center.
The cohort included 102 people with histologically confirmed HSIL and 19 with nonmetastatic, treatment-naive ASCC. The researchers used shotgun metagenomic sequencing, which analyses genetic material from the microbial community to identify organisms and their potential biological functions. Human genetic reads were removed before analysis.
The study found that the two disease groups differed in both the number of microbial species detected and the overall composition of their microbial communities. The ASCC group had lower observed richness, with an adjusted beta of -21.28 and p = 0.035, while Shannon and inverse Simpson diversity measures did not differ significantly. Community-composition differences were detected using Bray-Curtis, Jaccard and Aitchison distance measures, with reported R² values of 0.100, 0.133 and 0.172, respectively.
A six-species pattern separated the disease groups
Six species were enriched in samples from people with ASCC: Fusobacterium nucleatum, Parvimonas micra, Peptococcus niger, Porphyromonas asaccharolytica, Porphyromonas levii and Porphyromonas sp. CAG:1061.
The researchers initially identified 60 differentially abundant species using ANCOM-BC2, a method for analysing differences in microbiome data. Fifty-eight of those findings were validated using adjusted centred log-ratio regression. The statistical analyses accounted for age, sex, tobacco use, HIV status and HPV status.
The six ASCC-enriched species also remained associated with ASCC during longitudinal sampling. Five showed larger decreases from baseline to month six in the ASCC group than in the HSIL group after treatment initiation. The study therefore links the microbial pattern not only with disease category at baseline but also with changes observed during follow-up.
The researchers additionally identified 26 MetaCyc biological pathways associated with the persistent ASCC-enriched species. These pathways were also more prominent in ASCC samples and involved amino-acid metabolism, anaerobic degradation, and carbohydrate and energy metabolism. In this context, an anaerobic signature refers to microbes and microbial functions associated with environments where oxygen availability is limited.
Why the finding matters for cancer research
Persistent human papillomavirus infection is an important part of the pathway to anal cancer, but only a subset of people with HSIL develop invasive disease. The study’s results suggest that the surrounding microbial community may be associated with differences between precancerous lesions and established cancer.
The findings could provide a basis for future research into whether microbial features help identify HSIL cases at higher risk of progression, reflect tumour burden, or change with treatment response. They do not yet constitute a clinical screening or diagnostic test. The study was designed to compare microbial communities and follow their changes, rather than to prospectively evaluate a microbiome-based prediction tool.
The ASCC subgroup was small, with 19 participants, and all participants were enrolled at Montefiore Medical Center. The work is also a medRxiv preprint and has not yet undergone peer review. Most importantly, the study establishes an association between the six-species pattern and ASCC; it does not determine whether these microbes contribute to cancer development, result from the tumour environment, or reflect another disease-related factor. Further cohorts will be needed to test whether the signature predicts progression from HSIL or has clinical value.