AbstractThere is currently an urgent need to identify factors predictive of immunogenicity in colorectal cancer (CRC). Mucinous CRC is a distinct histological subtype of CRC, associated with a poor response to chemotherapy. Recent evidence suggests the commensal facultative anaerobeFusobacteriummay be especially prevalent in mucinous CRC. The objectives of this study were to assess the association ofFusobacteriumabundance with immune cell composition and prognosis in mucinous CRC. Our study included two independent colorectal cancer patient cohorts, The Cancer Genome Atlas (TCGA) cohort, and a cohort of rectal cancers from the Beaumont RCSI Cancer Centre (BRCC). Multiplexed immunofluorescence staining of a tumour microarray (TMA) from the BRCC cohort was undertaken using Cell DIVE technology. Our cohorts included 87 cases (13.3%) of mucinous and 565 cases (86.7%) of non-mucinous CRC. Mucinous CRC in the TCGA dataset was associated with an increased proportion of CD8 + lymphocytes (p= 0.018), regulatory T-cells (p= 0.001) and M2 macrophages (p= 0.001). In the BRCC cohort, mucinous RC was associated with enhanced CD8 + lymphocyte (p= 0.022), regulatory T-cell (p= 0.047), and B-cell (p= 0.025) counts. HighFusobacteriumabundance was associated with an increased proportion of CD4 + lymphocytes (p= 0.031) and M1 macrophages (p= 0.006), whilst M2 macrophages (p= 0.043) were under-represented in this cohort. Patients with increasedFusobacteriumrelative abundance in our mucinous CRC TCGA cohort tended to have better clinical outcomes (DSS: likelihood ratiop= 0.04, logrankp= 0.052).Fusobacteriumabundance may be associated with improved outcomes in mucinous CRC, possibly due to a modulatory effect on the host immune response.Key messages• IncreasedFusobacteriumrelative abundance was not found to be associated with microsatellite instability in mucinous CRC.• IncreasedFusobacteriumrelative abundance was associated with an M2/M1 macrophage switch, which is especially significant in mucinous CRC, where M2 macrophages are overexpressed.• IncreasedFusobacteriumrelative abundance was associated with a significant improvement in disease specific survival in mucinous CRC.• Our findings were validated at a protein level within our own in house mucinous and non-mucinous rectal cancer cohorts.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00109-023-02324-5.