KF-finder: a web-based tool to identify key factors from host-microbial networks in cervical cancer


Jialu Hu, Yiqun Gao, Yan Zheng, Xuequn Shang

School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi, China

Microbiota composition

To study the microbial community in cervical cancer, we examined the 16s raw data of cancer cases and assigned taxonomy to each sequence. The definition of operational taxonomic unit (OTU) was used to classify groups of closely related microbiome based on sequence similarity. Reference data sets and id-to-OTU maps for 16s rRNA sequence was downloaded from the Greengenes reference OTU builds. All these sequences were grouped into different categories based on their family-level OTU labels.

As shown in the left figure, prevotellaceade followed by tissierellaceae appears to be the most abundant microbes, accounting for 13.7% of the microbiota community. There are four other groups accounting for more than 5% of the microbiota, which are fusobacteriaceae, porphyromonadaceae, planococcaceae and bacteroidaceae. Totally, twenty-six family-level OTU groups make up more than 87% of the whole community. To examine the diversity of cervical microbiota, the PCoA analysis was performed to analyze the microbial community in cervical carcinoma, skin, mouth and vagina. As shown in the above figure, microbiota in cervical carcinoma (red dots) is less diverse than microbiota in any other body sites.

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Citation

Jialu Hu, Yiqun Gao, Xuequn Shang, KF-finder: Identification of key factors from host-microbial networks in cervical cancer, BMC Systems Biology (2018) 12(S4):54

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