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揭示与微生物基因组表型特征相关的代谢途径。

Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes.

作者信息

Kastenmüller Gabi, Schenk Maria Elisabeth, Gasteiger Johann, Mewes Hans-Werner

机构信息

Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse, Neuherberg, Germany.

出版信息

Genome Biol. 2009;10(3):R28. doi: 10.1186/gb-2009-10-3-r28. Epub 2009 Mar 10.

DOI:10.1186/gb-2009-10-3-r28
PMID:19284550
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2690999/
Abstract

Identifying the biochemical basis of microbial phenotypes is a main objective of comparative genomics. Here we present a novel method using multivariate machine learning techniques for comparing automatically derived metabolic reconstructions of sequenced genomes on a large scale. Applying our method to 266 genomes directly led to testable hypotheses such as the link between the potential of microorganisms to cause periodontal disease and their ability to degrade histidine, a link also supported by clinical studies.

摘要

确定微生物表型的生化基础是比较基因组学的主要目标。在此，我们提出了一种新方法，该方法使用多变量机器学习技术大规模自动比较测序基因组的代谢重建。将我们的方法应用于266个基因组，直接得出了可检验的假设，例如微生物导致牙周病的潜力与其降解组氨酸能力之间的联系，这一联系也得到了临床研究的支持。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/7753a87ed3ab/gb-2009-10-3-r28-9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/3332c1664e87/gb-2009-10-3-r28-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/f72520369f57/gb-2009-10-3-r28-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/7cac99c6d61d/gb-2009-10-3-r28-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/b393352e7c08/gb-2009-10-3-r28-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/360f9504eebc/gb-2009-10-3-r28-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/7d856a19adbb/gb-2009-10-3-r28-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/863d58dcf35d/gb-2009-10-3-r28-7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/1a66cf6b9a90/gb-2009-10-3-r28-8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/7753a87ed3ab/gb-2009-10-3-r28-9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/3332c1664e87/gb-2009-10-3-r28-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/f72520369f57/gb-2009-10-3-r28-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/7cac99c6d61d/gb-2009-10-3-r28-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/b393352e7c08/gb-2009-10-3-r28-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/360f9504eebc/gb-2009-10-3-r28-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/7d856a19adbb/gb-2009-10-3-r28-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/863d58dcf35d/gb-2009-10-3-r28-7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/1a66cf6b9a90/gb-2009-10-3-r28-8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3c0d/2690999/7753a87ed3ab/gb-2009-10-3-r28-9.jpg

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