MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies.
Dongwan D. Kang,Feng Li,Edward Kirton,Ashleigh Thomas,Rob Egan,Hong An,Zhong Wang,Zhong Wang,Zhong Wang +8 more
TLDR
Comparing MetaBAT 2 to alternative software tools on over 100 real world metagenome assemblies shows superior accuracy and computing speed, and recommends the community adopts Meta BAT 2 for their meetagenome binning experiments.Abstract:
We previously reported on MetaBAT, an automated metagenome binning software tool to reconstruct single genomes from microbial communities for subsequent analyses of uncultivated microbial species. MetaBAT has become one of the most popular binning tools largely due to its computational efficiency and ease of use, especially in binning experiments with a large number of samples and a large assembly. MetaBAT requires users to choose parameters to fine-tune its sensitivity and specificity. If those parameters are not chosen properly, binning accuracy can suffer, especially on assemblies of poor quality. Here, we developed MetaBAT 2 to overcome this problem. MetaBAT 2 uses a new adaptive binning algorithm to eliminate manual parameter tuning. We also performed extensive software engineering optimization to increase both computational and memory efficiency. Comparing MetaBAT 2 to alternative software tools on over 100 real world metagenome assemblies shows superior accuracy and computing speed. Binning a typical metagenome assembly takes only a few minutes on a single commodity workstation. We therefore recommend the community adopts MetaBAT 2 for their metagenome binning experiments. MetaBAT 2 is open source software and available at https://bitbucket.org/berkeleylab/metabat.read more
Citations
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A unified catalog of 204,938 reference genomes from the human gut microbiome.
Alexandre Almeida,Alexandre Almeida,Stephen Nayfach,Stephen Nayfach,Miguel Boland,Francesco Strozzi,Martin Beracochea,Zhou Jason Shi,Katherine S. Pollard,Ekaterina A. Sakharova,Donovan H. Parks,Philip Hugenholtz,Nicola Segata,Nikos C. Kyrpides,Nikos C. Kyrpides,Robert D. Finn +15 more
TL;DR: The Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant genomes from 4,644 gut prokaryotes, is presented, providing comprehensive resources for microbiome researchers.
Journal ArticleDOI
Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals.
Francesco Asnicar,Sarah Berry,Ana M. Valdes,Ana M. Valdes,Long H. Nguyen,Gianmarco Piccinno,David A. Drew,Emily R Leeming,Rachel J. Gibson,Caroline I. Le Roy,Haya Al Khatib,Lucy Francis,Mohsen Mazidi,Olatz Mompeo,Mireia Valles-Colomer,Adrian Tett,Francesco Beghini,Leonard Dubois,Davide Bazzani,Andrew Maltez Thomas,Chloe Mirzayi,Asya Khleborodova,Sehyun Oh,Rachel Hine,Christopher Bonnett,Joan Capdevila,Serge Danzanvilliers,Francesca Giordano,Ludwig Geistlinger,Levi Waldron,Richard Davies,George Hadjigeorgiou,Jonathan Wolf,Jose M. Ordovas,Jose M. Ordovas,Christopher D. Gardner,Paul W. Franks,Paul W. Franks,Andrew T. Chan,Andrew T. Chan,Curtis Huttenhower,Curtis Huttenhower,Tim D. Spector,Nicola Segata,Nicola Segata +44 more
TL;DR: This paper performed deep metagenomic sequencing of 1,203 gut microbiomes from 1,098 individuals enrolled in the Personalised Responses to Dietary Composition Trial (PREDICT 1) study, whose detailed longterm diet information, as well as hundreds of fasting and same-meal post-prandial cardiometabolic blood marker measurements were available.
Journal ArticleDOI
DRAM for distilling microbial metabolism to automate the curation of microbiome function
Michael Shaffer,Mikayla A. Borton,Bridget B. McGivern,Ahmed A. Zayed,Sabina Leanti La Rosa,Lindsey M. Solden,Pengfei Liu,Adrienne B. Narrowe,Josué Rodríguez-Ramos,Benjamin Bolduc,M. Consuelo Gazitúa,Rebecca A. Daly,Garrett J. Smith,Dean R. Vik,Phillip B. Pope,Matthew B. Sullivan,Simon Roux,Kelly C. Wrighton +17 more
TL;DR: DRAM (Distilled and Refined Annotation of Metabolism) is presented, a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits and provides critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.
Journal ArticleDOI
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome
Guillem Salazar,Lucas Paoli,Adriana Alberti,Jaime Huerta-Cepas,Hans-Joachim Ruscheweyh,Miguelangel Cuenca,Christopher M. Field,Luis Pedro Coelho,Corinne Cruaud,Stefan Engelen,Ann C. Gregory,Karine Labadie,Claudie Marec,Claudie Marec,Eric Pelletier,Marta Royo-Llonch,Simon Roux,Pablo Sánchez,Hideya Uehara,Ahmed A. Zayed,Georg Zeller,Margaux Carmichael,Céline Dimier,Céline Dimier,Joannie Ferland,Stefanie Kandels,Marc Picheral,Sergey Pisarev,Julie Poulain,Silvia G. Acinas,Marcel Babin,Peer Bork,Emmanuel Boss,Chris Bowler,Guy Cochrane,Colomban de Vargas,Michael J. Follows,Gabriel Gorsky,Nigel Grimsley,Lionel Guidi,Pascal Hingamp,Daniele Iudicone,Olivier Jaillon,Stefanie Kandels-Lewis,Lee Karp-Boss,Eric Karsenti,Fabrice Not,Hiroyuki Ogata,Stephane Pesant,Nicole J. Poulton,Jeroen Raes,Christian Sardet,Sabrina Speich,Lars Stemmann,Matthew B. Sullivan,Shinichi Sunagawa,Patrick Wincker +56 more
TL;DR: The relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and it is hypothesized that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms.
Journal ArticleDOI
Giant virus diversity and host interactions through global metagenomics
Frederik Schulz,Simon Roux,David Paez-Espino,Sean P. Jungbluth,David A. Walsh,Vincent J. Denef,Katherine D. McMahon,Konstantinos T. Konstantinidis,Emiley A. Eloe-Fadrosh,Nikos C. Kyrpides,Tanja Woyke +10 more
TL;DR: It is anticipated that the global diversity of NCLDVs that are described here will establish giant viruses—which are associated with most major eukaryotic lineages—as important players in ecosystems across Earth’s biomes.
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