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Updated: Nov 7, 2025
Murine Ileocolic Bowel Resection with Primary Anastomosis
Published on: October 29, 2014
Impact of preoperative antibiotics and other variables on integrated microbiome-host transcriptomic data generated
Sarah A Malik1, Chencan Zhu2, Jinyu Li3
1Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, United States.
Background:
Integrative multi-omic approaches have been increasingly applied to discovery and functional studies of complex human diseases. Short-term preoperative antibiotics have been adopted to reduce site infections in colorectal cancer (CRC) resections. We hypothesize that the antibiotics will impact analysis of multi-omic datasets generated from resection samples to investigate biological CRC risk factors.
Aim:
To assess the impact of preoperative antibiotics and other variables on integrated microbiome and human transcriptomic data generated from archived CRC resection samples.
Methods:
Genomic DNA (gDNA) and RNA were extracted from prospectively collected 51 pairs of frozen sporadic CRC tumor and adjacent non-tumor mucosal samples from 50 CRC patients archived at a single medical center from 2010-2020. The 16S rRNA gene sequencing (V3V4 region, paired end, 300 bp) and confirmatory quantitative polymerase chain reaction (qPCR) assays were conducted on gDNA. RNA sequencing (IPE, 125 bp) was performed on parallel tumor and non-tumor RNA samples with RNA Integrity Numbers scores ≥ 6.
Results:
PERMANOVA detected significant effects of tumor vs nontumor histology (P = 0.002) and antibiotics (P = 0.001) on microbial β-diversity, but CRC tumor location (left vs right), diabetes mellitus vs not diabetic and Black/African Ancestry (AA) vs not Black/AA, did not reach significance. Linear mixed models detected significant tumor vs nontumor histology*antibiotics interaction terms for 14 genus level taxa. QPCR confirmed increased Fusobacterium abundance in tumor vs nontumor groups, and detected significantly reduced bacterial load in the (+)antibiotics group. Principal coordinate analysis of the transcriptomic data showed a clear separation between tumor and nontumor samples. Differentially expressed genes obtained from separate analyses of tumor and nontumor samples, are presented for the antibiotics, CRC location, diabetes and Black/AA race groups.
Conclusion:
Recent adoption of additional preoperative antibiotics as standard of care, has a measurable impact on -omics analysis of resected specimens. This study still confirmed increased Fusobacterium nucleatum in tumor.
Insights
Preoperative antibiotics significantly alter microbiome and human transcriptomic data in colorectal cancer (CRC) samples. This finding impacts multi-omic analyses for CRC risk factors, despite confirming increased Fusobacterium nucleatum in tumors.
Area of Science:
- Microbiology
- Genomics
- Cancer Research
Background:
- Integrative multi-omic approaches are crucial for understanding complex human diseases like colorectal cancer (CRC).
- Short-term preoperative antibiotics are standard for reducing surgical site infections in CRC resections.
- The impact of these antibiotics on multi-omic data from CRC resection samples requires investigation.
Purpose of the Study:
- To evaluate how preoperative antibiotics and other factors influence integrated microbiome and human transcriptomic data from archived CRC resection samples.
- To assess the effect of antibiotics on microbial beta-diversity and bacterial load.
- To analyze transcriptomic alterations in CRC tumors versus adjacent non-tumor tissues.
Main Methods:
- Extraction of genomic DNA (gDNA) and RNA from 51 pairs of CRC tumor and adjacent non-tumor mucosal samples.
- 16S rRNA gene sequencing and quantitative polymerase chain reaction (qPCR) for microbiome analysis.
- RNA sequencing (IPE) of paired tumor and non-tumor samples with RNA Integrity Numbers ≥ 6.
Main Results:
- Preoperative antibiotics and tumor histology significantly affected microbial beta-diversity (P < 0.01).
- Significant interactions between histology and antibiotics were observed for 14 bacterial genera.
- qPCR confirmed increased Fusobacterium abundance in tumors and reduced overall bacterial load in antibiotic-treated patients.
Conclusions:
- The routine use of preoperative antibiotics measurably impacts multi-omic analyses of resected colorectal cancer specimens.
- This study reaffirms the elevated presence of Fusobacterium nucleatum in colorectal tumors.
- Findings highlight the need to consider antibiotic treatment when interpreting multi-omic data in CRC research.
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