Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

Author:

Beghini Francesco1ORCID,McIver Lauren J2,Blanco-Míguez Aitor1,Dubois Leonard1ORCID,Asnicar Francesco1,Maharjan Sagun23,Mailyan Ana23,Manghi Paolo1,Scholz Matthias4ORCID,Thomas Andrew Maltez1,Valles-Colomer Mireia1,Weingart George23,Zhang Yancong23ORCID,Zolfo Moreno1ORCID,Huttenhower Curtis23ORCID,Franzosa Eric A23ORCID,Segata Nicola15ORCID

Affiliation:

1. Department CIBIO, University of Trento, Trento, Italy

2. Harvard T.H. Chan School of Public Health, Boston, United States

3. The Broad Institute of MIT and Harvard, Cambridge, United States

4. Department of Food Quality and Nutrition, Research and Innovation Center, Edmund Mach Foundation, San Michele all’Adige, Italy

5. IEO, European Institute of Oncology IRCCS, Milan, Italy

Abstract

Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and IBD (1635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbe Ruminococcus bromii, previously described by only 15 isolate genomes. With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies.

Funder

H2020 European Research Council

Ministero dell’Istruzione, dell’Università e della Ricerca

H2020 Health

H2020 Food

National Institutes of Health

National Institute of Diabetes and Digestive and Kidney Diseases

Cancer Research UK

Juvenile Diabetes Research Foundation United States of America

National Human Genome Research Institute

Publisher

eLife Sciences Publications, Ltd

Subject

General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

Reference141 articles.

1. A new genomic blueprint of the human gut Microbiota;Almeida;Nature,2019

2. A unified catalog of 204,938 reference genomes from the human gut microbiome;Almeida;Nature Biotechnology,2021

3. Basic local alignment search tool;Altschul;Journal of Molecular Biology,1990

4. Andrews S O. 2010. FastQC: A Quality Control Tool for High Throughput Sequence Data.

5. Gene ontology: tool for the unification of biology the gene ontology consortium;Ashburner;Nature Genetics,2000

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3