{"id":8468,"date":"2023-07-04T08:58:03","date_gmt":"2023-07-04T07:58:03","guid":{"rendered":"https:\/\/mbioworks.com\/?p=8468"},"modified":"2023-08-04T14:30:40","modified_gmt":"2023-08-04T13:30:40","slug":"multi-coverage-metagenome-binning-greatly-outperforms-single-coverage-binning","status":"publish","type":"post","link":"https:\/\/mbioworks.com\/?p=8468","title":{"rendered":"Multi-Coverage Metagenome Binning Greatly Outperforms Single-Coverage Binning"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"8468\" class=\"elementor elementor-8468\">\n\t\t\t\t\t\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-27db53e elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"27db53e\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-5e8675f\" data-id=\"5e8675f\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-5364571 elementor-widget elementor-widget-text-editor\" data-id=\"5364571\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<style>\/*! elementor - v3.11.5 - 14-03-2023 *\/\n.elementor-widget-text-editor.elementor-drop-cap-view-stacked .elementor-drop-cap{background-color:#818a91;color:#fff}.elementor-widget-text-editor.elementor-drop-cap-view-framed .elementor-drop-cap{color:#818a91;border:3px solid;background-color:transparent}.elementor-widget-text-editor:not(.elementor-drop-cap-view-default) .elementor-drop-cap{margin-top:8px}.elementor-widget-text-editor:not(.elementor-drop-cap-view-default) .elementor-drop-cap-letter{width:1em;height:1em}.elementor-widget-text-editor .elementor-drop-cap{float:left;text-align:center;line-height:1;font-size:50px}.elementor-widget-text-editor .elementor-drop-cap-letter{display:inline-block}<\/style>\t\t\t\t<h5><b>Key Takeaways<\/b><\/h5>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-5657fce elementor-widget elementor-widget-text-editor\" data-id=\"5657fce\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ul><li><p>42 rumen microbiome samples were assembled and binned. Single-coverage bins show an increased level of contamination (22.5%) vs multi-coverage bins (3.5%).<\/p><\/li><li><p>One phylum, 2 classes, 3 orders, 9 families, 35 genera, and 96 species were found only in multi-coverage bins.<\/p><\/li><li><p>Single-coverage bins contain a large number of hidden contaminants, whereas multi-coverage bins perform much better.<\/p><\/li><li>Metagenomic binning should be performed using multi-coverage data whenever possible, and significant effort must be always put into quality control and filtering.<\/li><\/ul>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-14bc6b9 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"14bc6b9\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-d34964f\" data-id=\"d34964f\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-de0ffe3 elementor-widget elementor-widget-text-editor\" data-id=\"de0ffe3\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h5><b>Title and Copyright Information<\/b><\/h5>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-37c5276 elementor-widget elementor-widget-image\" data-id=\"37c5276\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<style>\/*! elementor - v3.11.5 - 14-03-2023 *\/\n.elementor-widget-image{text-align:center}.elementor-widget-image a{display:inline-block}.elementor-widget-image a img[src$=\".svg\"]{width:48px}.elementor-widget-image img{vertical-align:middle;display:inline-block}<\/style>\t\t\t\t\t\t\t\t\t\t\t\t\t<a href=\"https:\/\/doi.org\/10.1038\/s41592-023-01934-8\">\n\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"2547\" height=\"1647\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/07\/MAGpaper.png\" class=\"attachment-full size-full wp-image-8478\" alt=\"\" srcset=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/07\/MAGpaper.png 2547w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/07\/MAGpaper-300x194.png 300w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/07\/MAGpaper-1024x662.png 1024w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/07\/MAGpaper-768x497.png 768w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/07\/MAGpaper-1536x993.png 1536w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/07\/MAGpaper-2048x1324.png 2048w\" sizes=\"auto, (max-width: 2547px) 100vw, 2547px\" \/>\t\t\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-14f212c elementor-widget elementor-widget-text-editor\" data-id=\"14f212c\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p><b><u>Attention<\/u><\/b>: all answers provided below are solely based on this research paper and thus please be mindful of any potential biases.<\/p><p>Mattock, J., Watson, M. A comparison of single-coverage and multi-coverage metagenomic binning reveals extensive hidden contamination. Nat Methods (2023). <a href=\"https:\/\/doi.org\/10.1038\/s41592-023-01934-8\">https:\/\/doi.org\/10.1038\/s41592-023-01934-8<\/a><\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-e63edd0 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"e63edd0\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-bd2ab7d\" data-id=\"bd2ab7d\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-20c012f elementor-widget elementor-widget-text-editor\" data-id=\"20c012f\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h5><b>What is Metagenome Binning?<\/b><\/h5>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-1aeb0f0 elementor-widget elementor-widget-image\" data-id=\"1aeb0f0\" data-element_type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img loading=\"lazy\" decoding=\"async\" width=\"1125\" height=\"1125\" src=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/07\/MAGmm.png\" class=\"attachment-full size-full wp-image-8471\" alt=\"\" srcset=\"https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/07\/MAGmm.png 1125w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/07\/MAGmm-300x300.png 300w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/07\/MAGmm-1024x1024.png 1024w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/07\/MAGmm-150x150.png 150w, https:\/\/mbioworks.com\/wp-content\/uploads\/2023\/07\/MAGmm-768x768.png 768w\" sizes=\"auto, (max-width: 1125px) 100vw, 1125px\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-4475eaf elementor-widget elementor-widget-text-editor\" data-id=\"4475eaf\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>A <strong>metagenome<\/strong> is a collection of all DNA from all organisms in a sample. <strong>Metagenome binning<\/strong> is a process of grouping DNA reads or contigs from a metagenomic sample into individual microbial genomes. This is done by comparing the sequences of the reads or contigs to known genomes and using statistical methods to identify groups of reads that are likely to come from the same organism.<\/p><p>Metagenome binning is extremely useful for probing the function of uncultured microbes in a sample. As sequencing technology continues to improve, metagenome binning is likely to become an even more important tool for understanding the ecology of microbes and their role in human and planetary health.<\/p><p>But <strong>challenges<\/strong> exist in applying metagenome binning:<\/p><ul><li>Sequencing errors can make it difficult to identify the correct sequences for each organism.<\/li><li>Organisms that are present in low abundance in a sample may not be represented in the metagenome reads or contigs.<\/li><li>Metagenomic samples often contain a wide variety of organisms, which can make it difficult to identify the correct bins.<\/li><\/ul>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-eee49a9 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"eee49a9\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-bbafaef\" data-id=\"bbafaef\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-10213c8 elementor-widget elementor-widget-text-editor\" data-id=\"10213c8\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h5><b>Q&amp;A<\/b><\/h5>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-fa6fb5d elementor-widget elementor-widget-text-editor\" data-id=\"fa6fb5d\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h6><b>Q1: What is the hypothesis of this study?<\/b><\/h6>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-3d9f690 elementor-widget elementor-widget-text-editor\" data-id=\"3d9f690\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>Metagenomic binning has become an essential tool for exploring the composition and function of microorganisms. In this study, the authors propose a hypothesis: when using single-coverage binning, certain contigs may be incorrectly grouped together, because they only appear in a single sample. They believe these errors are due to undetectable contamination and can be identified using multi-coverage data.\u00a0<\/p><p>Single-sample assembly provides coverage information that is insufficient to differentiate between conspecific microorganisms. On the other hand, multi-sample co-assembly (multi-coverage) improves binning accuracy. However, utilizing abundance information from multi-sample co-assembly requires more computational resources, resulting in higher time and monetary costs.<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-d1e4182 elementor-widget elementor-widget-text-editor\" data-id=\"d1e4182\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h6><b>Q2: How much can multi-coverage binning reduce the contamination and increase the number of bins compared to single-coverage binning?<\/b><\/h6>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-a673112 elementor-widget elementor-widget-text-editor\" data-id=\"a673112\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>In their study, the authors conducted assembly and binning of 42 rumen microbiome samples using two different strategies: single-coverage and multiple-coverage binning. They kept all other parameters constant for both approaches. The analysis revealed that there was no significant difference in the distributions of completeness scores between the single-coverage and multi-coverage bins.<\/p><p>However, important findings emerged from the results: the single-coverage bins showed a higher level of contamination. Specifically, 22.5% (1,273 out of 5,658) of the single-coverage bins had a contamination score of 5 or higher, while only 3.5% (293 out of 8,420) of the multi-coverage bins exhibited the same level of contamination. The single-coverage approach generated 931 filtered bins, while the multi-coverage approach generated 1,660, a 78% increase.\u00a0<\/p><p>This observation suggests that the multi-coverage binning method appears to be more effective in reducing the number of contaminated bins and increasing the total number of high-quality bins, potentially leading to more accurate and reliable results in the analysis of rumen microbiome samples.<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-f676a86 elementor-widget elementor-widget-text-editor\" data-id=\"f676a86\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h6><b>Q3: What taxa are missing in single-coverage binning?<\/b><\/h6>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-a817abd elementor-widget elementor-widget-text-editor\" data-id=\"a817abd\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>In multi-coverage binning, the proportion of Archaea (4.3%) was higher than in single-coverage binning (3.1%).\u00a0<span style=\"font-family: var( --e-global-typography-text-font-family ), Sans-serif;font-size: var( --e-global-typography-text-font-size );font-weight: var( --e-global-typography-text-font-weight );color: var( --e-global-color-text );background-color: var( --e-global-color-f898f31 )\">Notably, the multi-coverage bins revealed one phylum (Patescibacteria), two classes (Endomicrobia and Saccharimonadia), three orders, nine families, 35 genera, and 96 species that were not found in single-coverage bins.\u00a0<\/span><span style=\"background-color: var( --e-global-color-f898f31 );color: var( --e-global-color-text );font-family: var( --e-global-typography-text-font-family ), Sans-serif;font-size: var( --e-global-typography-text-font-size );font-weight: var( --e-global-typography-text-font-weight )\">In contrast, only two genera and 11 species were unique to single-coverage bins.\u00a0<\/span><\/p><p>After the dereplication of the bins at the species and strain level, single-coverage bins identified 460 species and 573 strains, while multi-coverage bins found 682 species and 943 strains. Dereplicating all bins together resulted in 700 species, of which 240 were exclusively in multi-coverage bins and 18 solely in single-coverage bins. At the strain level, a total of 969 strains were detected, with 398 found exclusively by multi-coverage and 23 only by single-coverage. This highlights that leveraging coverage data from multiple samples aids in recovering missed species and strains.<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-094d3de elementor-widget elementor-widget-text-editor\" data-id=\"094d3de\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<h6><b>Q4: Any challenges in applying multi-coverage binning?<\/b><\/h6>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-b7ed827 elementor-widget elementor-widget-text-editor\" data-id=\"b7ed827\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p>There were some challenges in the implementation of the method, such as computational burden, selection of appropriate cutoff values, and possible loss of mobile genetic elements. However, the results of this study clearly suggest that metagenomic binning should be performed using multi-coverage data whenever possible; and in all cases, significant effort must be put into quality control and filtering beyond existing methods (e.g., CheckM and GUNC), as neither single-copy core genes nor taxonomic methods are able to detect hidden contaminants that are undetectable by statistical methods.<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>A recent research paper  demonstrates that multi-coverage binning methods can produce more bins of higher quality than single-coverage binning methods, with a greater proportion of archaea and increased diversity of taxa. <\/p>\n","protected":false},"author":4,"featured_media":8471,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[15],"tags":[70,71,68,69],"class_list":["post-8468","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-literature-digest","tag-binning","tag-contamination","tag-mag","tag-metagenome"],"_links":{"self":[{"href":"https:\/\/mbioworks.com\/index.php?rest_route=\/wp\/v2\/posts\/8468","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/mbioworks.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/mbioworks.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/mbioworks.com\/index.php?rest_route=\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/mbioworks.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=8468"}],"version-history":[{"count":33,"href":"https:\/\/mbioworks.com\/index.php?rest_route=\/wp\/v2\/posts\/8468\/revisions"}],"predecessor-version":[{"id":8506,"href":"https:\/\/mbioworks.com\/index.php?rest_route=\/wp\/v2\/posts\/8468\/revisions\/8506"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/mbioworks.com\/index.php?rest_route=\/wp\/v2\/media\/8471"}],"wp:attachment":[{"href":"https:\/\/mbioworks.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=8468"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/mbioworks.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=8468"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/mbioworks.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=8468"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}