Protocol to study the impact of breast cancer on colonization resistance of mouse microbiota using network node manipulation

TL;DR

This paper provides a detailed protocol for studying how breast cancer affects gut microbiota interactions in mice using network analysis.

Contribution

The novelty lies in using network-based approaches to study microbiota changes in a breast cancer mouse model.

Findings

A protocol for tumor cell production and 16S rRNA data processing is described.

Steps for constructing co-occurrence networks based on microbial abundance correlations are detailed.

The study includes guidance for functional trait prediction of the mouse microbiome.

Abstract

Network analysis is a powerful tool for investigating complex interactions between different microbial taxa within a community. We present a protocol to study the gut microbial community in a mouse model of breast cancer using a network-based approach. Here, we describe the procedures for tumor cell production and inoculation and 16S rRNA data processing. We then detail steps for constructing co-occurrence networks based on correlations between microbial abundances.

For complete details on the use and execution of this protocol, please refer to Wu-Chuang et al.1

•Guidance for establishing a mouse model of breast cancer•Protocol for downstream analysis of the 16S rRNA sequencing from mouse fecal samples•Steps to study the bacterial community assembly using a network-based approach•Procedure for functional trait prediction of the mouse microbiome

Guidance for establishing a mouse model of breast cancer

Protocol for downstream analysis of the 16S rRNA sequencing from mouse fecal samples

Steps to study the bacterial community assembly using a network-based approach

Procedure for functional trait prediction of the mouse microbiome

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Network analysis is a powerful tool for investigating complex interactions between different microbial taxa within a community. We present a protocol to study the gut microbial community in a mouse model of breast cancer using a network-based approach. Here, we describe the procedures for tumor cell production and inoculation and 16S rRNA data processing. We then detail steps for constructing co-occurrence networks based on correlations between microbial abundances.

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