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Fig. 1 | BMC Microbiology

Fig. 1

From: Technical challenges regarding the use of formalin-fixed paraffin embedded (FFPE) tissue specimens for the detection of bacterial alterations in colorectal cancer

Fig. 1

Unintentional bacterial and human DNA interference in molecular analyses of formalin-fixed paraffin embedded (FFPE) tissues. a 16S rRNA amplicon sequencing pilot results showing the relative abundance of the top 20 genera in FFPE tissue samples (n = 8). A predominance of genus Ralstonia is observed in a majority of samples. b Quantitative polymerase chain reaction (qPCR) results demonstrating the amount of bacterial versus human genomic DNA in normalized template (n = 3). Statistical significance was calculated using the unpaired t-test. (c) Gel electrophoresis results following actin beta (ACTB) and 16S rRNA gene amplification, emphasizing the use of non-normalized (undiluted) template to improve bacterial DNA detection in FFPE tissue samples (n = 3). d-e Gel electrophoresis results showing bacterial and human genomic DNA presence in 41 paired FFPE tissue (T) samples and their paired empty paraffin (P) controls. Tissues consist of colorectal cancer (CRC; n = 14), normal adjacent (ADJ; n = 14) and healthy control (C; n = 13) tissues. Full length gel electrophoresis results are shown in Additional Fig. A1

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BMC Microbiology

ISSN: 1471-2180

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