16S, ITS and Sanger sequencing of Small Cell Lung Cancer samples
Background The tumor-associated microbiome influences cancer development and progression, yet the microbial landscape of small cell lung cancer (SCLC) remains unexplored. Given the absence of SCLC–specific microbiome studies, we conducted an exploratory analysis to describe the bacterial and fungal communities present in SCLC tissue. Results Using 16S rRNA sequencing, we profiled the bacteriome of lung specimens from SCLC and control cases and observed increased bacterial signal and reduced bacterial diversity in SCLC, accompanied by relative enrichment of Firmicutes and Bacteroidota. Actinobacteria were comparatively underrepresented, resulting in a higher Proteobacteria–to–Actinobacteria ratio, although this difference did not reach statistical significance. At the genus level, SCLC samples were dominated by Pseudomonas, Streptococcus, Haemophilus, and Granulicatella, which together accounted for approximately half of the bacterial community. As a secondary, hypothesis–generating analysis, we examined the mycobiome using ITS sequencing and detected the unexpected presence of the biotrophic plant–pathogenic genus Taphrina in a subset (25%) of SCLC samples. Given the methodological constraints and contamination risks inherent to low–biomass FFPE tissues, this fungal signal is interpreted cautiously and framed strictly as preliminary. Conclusions This study provides the first descriptive characterization of the lung bacteriome and mycobiome in SCLC using FFPE tissue. The observed alterations in microbial composition, including an unexpected fungal signal, offer hypothesis–generating insights that require validation in larger, prospectively collected cohorts incorporating more comprehensive contamination–control strategies.