Plasma butyrate and a gut microbiota signature are associated with pathological complete response to neoadjuvant therapy in HER2-positive breast cancer: a pilot study

Gut microbiota modulates systemic immunity and drug bioavailability, influencing antitumor responses. HER2-positive breast cancer, despite its biological aggressiveness, shows high sensitivity to anti-HER2 therapies. However, not all patients undergoing neoadjuvant treatment achieve pathological complete response. Since residual disease significantly worsens prognosis, understanding the biological determinants of therapeutic resistance, including microbiota-driven mechanisms, remains a critical clinical priority. Prospective cohort of HER2-positive breast cancer patients treated with neoadjuvant therapy. Patients were classified according to pathological response: pCR ( n = 10) and residual disease ( n = 9). Gut microbiota composition was assessed by 16 S rRNA sequencing of fecal samples using the QIAGEN 16S/ITS screening panel. Bioinformatics analysis was done with QIIME 2 2024.2 and RStudio. Plasma and fecal concentrations of short-chain fatty acids (SCFAs) were determined by gas chromatography (GC), and fecal polyamine profile was assessed using a fluorometric assay. pCR group exhibited higher levels of plasma butyrate ( p = 0.023), while the fecal polyamine profile showed a non-significant trend toward higher levels ( p = 0.050). Regarding the gut microbial profile, alpha (Shannon index, p = 0.45) and beta (PCoA-Bray Curtis, p = 0.416) diversity metrics showed no significant differences between groups. At the genus level, LEfSe delineated two contrasting profiles, with Bifidobacterium and Adlercreutzia enriched in pCR, and Butyribacter , Eubacterium_J , RUG115, Avispirillum , and CAG-238 enriched in residual disease. At the species level, ANCOM-BC2 identified three differentially abundant species after FDR correction (q < 0.05): Faecousia sp000434635 and CAG-127 sp900319515 , enriched in the residual disease group, and Negativibacillus massiliensis , enriched in the pCR group. Correlation analysis revealed distinct microbial–metabolite patterns according to therapeutic response: within the pCR group, plasma butyrate correlated positively with Adlercreutzia equolifaciens (rho = 0.78; p = 0.007) and Bifidobacterium bifidum (rho = 0.66; p = 0.036). Baseline plasma butyrate and specific gut microbial taxa were associated with pathological complete response in HER2-positive breast cancer patients receiving neoadjuvant therapy. Although exploratory, these findings support the gut microbiota–butyrate axis as a candidate contributor to treatment response.