Microbial abundance, activity and population genomic profiling with mOTUs2
Alessio Milanese,Daniel R. Mende,Lucas Paoli,Guillem Salazar,Hans-Joachim Ruscheweyh,Miguelangel Cuenca,Pascal Hingamp,Renato J. Alves,Paul I. Costea,Luis Pedro Coelho,Thomas Schmidt,Alexandre Almeida,Alex L. Mitchell,Robert D. Finn,Jaime Huerta-Cepas,Peer Bork,Georg Zeller,Shinichi Sunagawa +17 more
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TLDR
mOTUs2, an updated and functionally extended profiling tool for microbial abundance, activity and population profiling, shows that mOTUs, which are based on essential housekeeping genes, are demonstrably well-suited for quantification of basal transcriptional activity of community members.Abstract:
Metagenomic sequencing has greatly improved our ability to profile the composition of environmental and host-associated microbial communities. However, the dependency of most methods on reference genomes, which are currently unavailable for a substantial fraction of microbial species, introduces estimation biases. We present an updated and functionally extended tool based on universal (i.e., reference-independent), phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) enabling the profiling of >7700 microbial species. As more than 30% of them could not previously be quantified at this taxonomic resolution, relative abundance estimates based on mOTUs are more accurate compared to other methods. As a new feature, we show that mOTUs, which are based on essential housekeeping genes, are demonstrably well-suited for quantification of basal transcriptional activity of community members. Furthermore, single nucleotide variation profiles estimated using mOTUs reflect those from whole genomes, which allows for comparing microbial strain populations (e.g., across different human body sites).read more
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Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
Jakob Wirbel,Paul Theodor Pyl,Paul Theodor Pyl,Ece Kartal,Konrad Zych,Alireza Kashani,Alessio Milanese,Jonas S. Fleck,Anita Y. Voigt,Albert Pallejà,Ruby Ponnudurai,Shinichi Sunagawa,Luis Pedro Coelho,Petra Schrotz-King,Emily Vogtmann,Nina Habermann,Emma Niméus,Andrew Maltez Thomas,Andrew Maltez Thomas,Paolo Manghi,Sara Gandini,Davide Serrano,Sayaka Mizutani,Sayaka Mizutani,Hirotsugu Shiroma,Satoshi Shiba,Tatsuhiro Shibata,Shinichi Yachida,Takuji Yamada,Takuji Yamada,Levi Waldron,Alessio Naccarati,Nicola Segata,Rashmi Sinha,Cornelia M. Ulrich,Hermann Brenner,Manimozhiyan Arumugam,Manimozhiyan Arumugam,Peer Bork,Georg Zeller +39 more
TL;DR: A meta-analysis of eight geographically and technically diverse fecal shotgun metagenomic studies of colorectal cancer identified a core set of 29 species significantly enriched in CRC metagenomes, establishing globally generalizable, predictive taxonomic and functional microbiome CRC signatures as a basis for future diagnostics.
Journal ArticleDOI
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with biobakery 3
Francesco Beghini,Lauren J. McIver,Aitor Blanco-Míguez,Leonard Dubois,Francesco Asnicar,Sagun Maharjan,Sagun Maharjan,Ana Mailyan,Ana Mailyan,Paolo Manghi,Matthias Scholz,Andrew Maltez Thomas,Mireia Valles-Colomer,George Weingart,George Weingart,Yancong Zhang,Yancong Zhang,Moreno Zolfo,Curtis Huttenhower,Curtis Huttenhower,Eric A. Franzosa,Eric A. Franzosa,Nicola Segata,Nicola Segata +23 more
TL;DR: BioBakery 3 as mentioned in this paper is 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.
Posted ContentDOI
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
Francesco Beghini,Lauren J. McIver,Aitor Blanco-Míguez,Leonard Dubois,Francesco Asnicar,Sagun Maharjan,Sagun Maharjan,Ana Mailyan,Ana Mailyan,Andrew Maltez Thomas,Paolo Manghi,Mireia Valles-Colomer,George Weingart,George Weingart,Yancong Zhang,Yancong Zhang,Moreno Zolfo,Curtis Huttenhower,Curtis Huttenhower,Eric A. Franzosa,Eric A. Franzosa,Nicola Segata,Nicola Segata +22 more
TL;DR: 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.
Journal ArticleDOI
MGnify: the microbiome analysis resource in 2020
Alex L. Mitchell,Alexandre Almeida,Alexandre Almeida,Martin Beracochea,Miguel Boland,Josephine Burgin,Guy Cochrane,Michael R. Crusoe,Varsha Kale,Simon C. Potter,Lorna Richardson,Ekaterina A. Sakharova,Maxim Scheremetjew,Anton Korobeynikov,Alexander Shlemov,Olga Kunyavskaya,Alla Lapidus,Robert D. Finn +17 more
TL;DR: An updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility.
Journal ArticleDOI
Benchmarking Metagenomics Tools for Taxonomic Classification.
TL;DR: The key metrics used to assess performance are described, a framework for the comparison of additional classifiers is offered, and the future of metagenomic data analysis is discussed.
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