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<h2>Replication Study: Intestinal inflammation targets cancer-inducing activity of the microbiota</h2> <p><br> <strong>Abstract:</strong></p> <p>In 2015, as part of the <a href="https://osf.io/e81xl/wiki/home/" rel="nofollow">Reproducibility Project: Cancer Biology</a>, we published a Registered Report (<a href="https://elifesciences.org/articles/04186" rel="nofollow">Eaton et al., 2015</a>), that described how we intended to replicate selected experiments from the paper “Intestinal inflammation targets cancer-inducing activity of the microbiota" (<a href="http://science.sciencemag.org/content/338/6103/120" rel="nofollow">Arthur et al., 2012</a>). Here we report the results. We observed no impact on bacterial growth or colonization capacity when the polyketide synthase (pks) genotoxic island was deleted from E. coli NC101, similar to the original study (Supplemental Figure 7; <a href="http://science.sciencemag.org/content/338/6103/120" rel="nofollow">Arthur et al., 2012</a>). However, for the experiment that compared inflammation, invasion, and neoplasia in azoxymethane (AOM)-treated interleukin-10-deficient mice mono-associated with NC101 or NC101<em>Δpks</em> the experimental timing of the replication attempt was longer than that of the original study. This difference was because in the original study the methodology was not clearly stated and likely led to the increased mortality and severity of inflammation observed in this replication attempt. Additionally, early death occurred during AOM treatment with higher mortality observed in NC101<em>Δpks</em> mono-associated mice compared to NC101, which was in the same direction, but more severe than the original study (Supplemental Figure 10; <a href="http://science.sciencemag.org/content/338/6103/120" rel="nofollow">Arthur et al., 2012</a>). A meta-analysis suggests that mice mono-associated with NC101<em>Δpks</em> have higher mortality compared to NC101. While these data were unable to address whether, under the conditions of the original study, NC101 and NC101<em>Δpks</em> differ in inflammation, invasion, and neoplasia this replication attempt demonstrates that clear description of experimental methods is essential to ensure accurate reproduction of experimental studies.</p> <hr> <h3>Contents</h3> <p><strong>Reports:</strong> Read the Replication Study <a href="https://elifesciences.org/articles/34364" rel="nofollow">Here</a>, or view the Preprint Verisons <a href="https://osf.io/jyq3m/" rel="nofollow">here</a>.</p> <p>To reproduce the Replication Study manuscript text run this in <a href="https://www.rstudio.com" rel="nofollow">R Studio</a> (note: downloads [R Markdown Here] directly from <a href="http://osf.io" rel="nofollow">osf.io</a>):</p> <pre class="highlight"><code>library(httr) library(pander) library(rmarkdown) GET(&quot;<a href="https://osf.io/ektn3/?action=download" rel="nofollow">https://osf.io/ektn3/?action=download</a>&quot;,write_disk(&quot;Replication_Study_41.Rmd&quot;, overwrite = T)) render(&quot;Replication_Study_41.Rmd&quot;, output_format =&quot;word_document&quot;)</code></pre> <p>Also, explore the <a href="https://elifesciences.org/articles/04186" rel="nofollow">Registered Report</a> and materials related to the Registered Report [here].</p> <p><br> <strong>Data and Material Availability:</strong></p> <p>The Whole Genome sequencing data generated during this study has been deposited at NCBI SRA under the Bioproject accession <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA481682/" rel="nofollow">PRJNA481682</a>. The genome assemblies have been deposited at Genbank under the accession <a href="https://www.ncbi.nlm.nih.gov/nuccore/QVAD00000000" rel="nofollow">QVAD00000000</a> and <a href="https://www.ncbi.nlm.nih.gov/nuccore/QVAE00000000" rel="nofollow">QVAE00000000</a>.</p> <p>All other associated data, protocols, analysis scripts, and other digital materials are available within this OSF project.</p> <p><br> <strong>Experiments replicated:</strong> Reproduce and explore the figures, analyses, data, and methods generated in this replication attempt.</p> <ul> <li><a href="https://osf.io/54rgt/wiki/home/" rel="nofollow">Protocol 1: comparing the growth curves of E. coli NC101 and E. coli NC101Δpks</a></li> <li> <p>Replication of Supplemental figure 7. in Arthur et al., 2012.</p> </li> <li> <p><a href="https://osf.io/ye9gh/wiki/home/" rel="nofollow">Protocol 2: PCR amplification and sequencing of polyketide synthase (pks) genotoxic island in E. coli NC101 and NC101∆pks</a></p> </li> <li> <p>This is a quality control step to confirm the absence of the pks island in the E. coli NC101Δpks strain.</p> </li> <li> <p><a href="https://osf.io/pm5xa/wiki/home/" rel="nofollow">Protocol 3: mono-associate mice with E. coli NC101 or NC101∆pks and analyze intestinal tumorigenesis and inflammation</a></p> </li> <li>Replication of Figure 4. in Arthur et al., 2012.</li> </ul> <p><br> <strong>Meta-analyses:</strong> As a measure of evaluating reproducibility a meta-analysis of each effect was performed. The forest plots, analyses, and data are available <a href="https://osf.io/2raud/" rel="nofollow">here</a>.</p> <p>Questions about the project can be directed to <a href="mailto:contact+rpcb@cos.io">contact+rpcb@cos.io</a>.</p>
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