Raphael Eisenhofer, Antton Alberdi, Ben J Woodcroft
{"title":"Quantifying microbial DNA in metagenomes improves microbial trait estimation.","authors":"Raphael Eisenhofer, Antton Alberdi, Ben J Woodcroft","doi":"10.1093/ismeco/ycae111","DOIUrl":null,"url":null,"abstract":"<p><p>Shotgun metagenomics is a powerful tool for studying the genomic traits of microbial community members, such as genome size, gene content, etc. While such traits can be used to better understand the ecology and evolution of microbial communities, the accuracy of their estimations can be critically influenced by both known and unknown factors. One factor that can bias trait estimations is the proportion of eukaryotic and viral DNA in a metagenome, as some bioinformatic tools assume that all DNA reads in a metagenome are bacterial or archaeal. Here, we add to a recent debate about the influence of eukaryotic DNA in the estimation of average genome size from a global soil sample dataset using a new bioinformatic tool. Contrary to what was assumed, our reanalysis of this dataset revealed that soil samples can contain a substantial proportion of non-microbial DNA, which severely inflated the original estimates of average genome size. Correcting for this bias significantly improves the statistical support for the negative relationship between average bacterial genome size and soil pH. These results highlight that metagenomes can contain large quantities of non-microbial DNA and that new methods that correct for this can improve microbial trait estimation.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae111"},"PeriodicalIF":5.1000,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11439404/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"ISME communications","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/ismeco/ycae111","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/1/1 0:00:00","PubModel":"eCollection","JCR":"Q1","JCRName":"ECOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Shotgun metagenomics is a powerful tool for studying the genomic traits of microbial community members, such as genome size, gene content, etc. While such traits can be used to better understand the ecology and evolution of microbial communities, the accuracy of their estimations can be critically influenced by both known and unknown factors. One factor that can bias trait estimations is the proportion of eukaryotic and viral DNA in a metagenome, as some bioinformatic tools assume that all DNA reads in a metagenome are bacterial or archaeal. Here, we add to a recent debate about the influence of eukaryotic DNA in the estimation of average genome size from a global soil sample dataset using a new bioinformatic tool. Contrary to what was assumed, our reanalysis of this dataset revealed that soil samples can contain a substantial proportion of non-microbial DNA, which severely inflated the original estimates of average genome size. Correcting for this bias significantly improves the statistical support for the negative relationship between average bacterial genome size and soil pH. These results highlight that metagenomes can contain large quantities of non-microbial DNA and that new methods that correct for this can improve microbial trait estimation.
散弹枪元基因组学是研究微生物群落成员基因组特征(如基因组大小、基因含量等)的强大工具。虽然这些性状可用于更好地了解微生物群落的生态和进化,但其估计的准确性会受到已知和未知因素的严重影响。真核生物和病毒 DNA 在元基因组中的比例是影响性状估计的一个因素,因为一些生物信息学工具假定元基因组中的所有 DNA 读数都是细菌或古细菌。在这里,我们利用一种新的生物信息学工具,对最近关于真核 DNA 在估算全球土壤样本数据集平均基因组大小中的影响的争论进行了补充。与假设相反,我们对该数据集的重新分析表明,土壤样本中可能含有相当比例的非微生物 DNA,这严重夸大了原来估计的平均基因组大小。对这一偏差进行校正后,细菌基因组平均大小与土壤 pH 值之间负相关关系的统计支持率明显提高。这些结果突出表明,元基因组可能含有大量的非微生物 DNA,而纠正这种偏差的新方法可以改善微生物性状的估计。