Species-Level Characterization of the Microbiome in Breast Tissues with Different Malignancy and Hormone-Receptor Statuses Using Nanopore Sequencing

Abstract

Unambiguous evidence indicates that microbes are closely linked to various human diseases, including cancer. Most prior work investigating the microbiome of breast tissue describes an association between compositional differences of microbial species in benign and malignant tissues, but few studies have examined the relative abundance of microbial communities within human breast tissue at the species level. In this work, a total of 44 breast tissue samples including benign and malignant tissues with adjacent normal breast tissue pairs were collected, and Oxford Nanopore long-read sequencing was employed to assess breast tissue microbial signatures. Nearly 900 bacterial species were detected from the four dominant phyla: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. The bacteria with the highest abundance in all breast tissues was Ralstonia pickettii, and its relative abundance increased with decreasing malignancy. We further examined the breast-tissue microbiome composition with different hormone-receptor statuses, and the relative abundance of the genus Pseudomonas increased most significantly in breast tissues. Our study provides a rationale for exploring microbiomes associated with breast carcinogenesis and cancer development. Further large-cohort investigation of the breast microbiome is necessary to characterize a microbial risk signature and develop potential microbial-based prevention therapies.

Microbial Communities in Gynecological Cancers and Their Association with Tumor Somatic Variation

“…Some of the genera most informative for HGSC in the lasso multivariate analysis and in the correlation with significant genomic SNVs, Escherichia/Shigella , Pantoea , and Ralstonia , have been associated with other types of cancer, including bladder, pancreatic, cholangiocarcinoma, colorectal, breast, and oral malignancies [ 42 , 43 , 44 , 45 , 46 ]. Likewise, variants of the dynein axonemal heavy chain ( DNAH ) family have been previously associated with breast and ovarian cancer [ 47 ].…”

“…However, the overarching goal of this study was not to detect HGSC and EEC SNVs but to determine the association between this genomic variation and changes in microbial communities in neoplastic tissues. Some of the genera most informative for HGSC in the lasso multivariate analysis and in the correlation with significant genomic SNVs, Escherichia/Shigella, Pantoea, and Ralstonia, have been associated with other types of cancer, including bladder, pancreatic, cholangiocarcinoma, colorectal, breast, and oral malignancies [42][43][44][45][46]. Likewise, variants of the dynein axonemal heavy chain (DNAH) family have been previously associated with breast and ovarian cancer [47].…”