Literature DB >> 23764387

Condensing the omics fog of microbial communities.

Emilie E L Muller1, Enrico Glaab, Patrick May, Nikos Vlassis, Paul Wilmes.   

Abstract

Natural microbial communities are ubiquitous, complex, heterogeneous, and dynamic. Here, we argue that the future standard for their study will require systematic omic measurements of spatially and temporally resolved unique samples in line with a discovery-driven planning approach. Resulting datasets will allow the generation of solid hypotheses about causal relationships and, thereby, will facilitate the discovery of previously unknown traits of specific microbial community members. However, to achieve this, solid wet lab, bioinformatic and statistical methodologies are required to have the promises of the emerging field of Eco-Systems Biology come to fruition.
Copyright © 2013 Elsevier Ltd. All rights reserved.

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Year:  2013        PMID: 23764387     DOI: 10.1016/j.tim.2013.04.009

Source DB:  PubMed          Journal:  Trends Microbiol        ISSN: 0966-842X            Impact factor:   17.079


  21 in total

1.  Relating the metatranscriptome and metagenome of the human gut.

Authors:  Eric A Franzosa; Xochitl C Morgan; Nicola Segata; Levi Waldron; Joshua Reyes; Ashlee M Earl; Georgia Giannoukos; Matthew R Boylan; Dawn Ciulla; Dirk Gevers; Jacques Izard; Wendy S Garrett; Andrew T Chan; Curtis Huttenhower
Journal:  Proc Natl Acad Sci U S A       Date:  2014-05-19       Impact factor: 11.205

Review 2.  Multifarious Responses of Forest Soil Microbial Community Toward Climate Change.

Authors:  Mukesh Meena; Garima Yadav; Priyankaraj Sonigra; Adhishree Nagda; Tushar Mehta; Prashant Swapnil; Avinash Marwal; Sumit Kumar
Journal:  Microb Ecol       Date:  2022-06-03       Impact factor: 4.552

Review 3.  Ecosystem-specific microbiota and microbiome databases in the era of big data.

Authors:  Victor Lobanov; Angélique Gobet; Alyssa Joyce
Journal:  Environ Microbiome       Date:  2022-07-16

4.  Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities.

Authors:  Shaman Narayanasamy; Emilie E L Muller; Abdul R Sheik; Paul Wilmes
Journal:  Microb Biotechnol       Date:  2015-02-12       Impact factor: 5.813

5.  Alignment-free visualization of metagenomic data by nonlinear dimension reduction.

Authors:  Cedric C Laczny; Nicolás Pinel; Nikos Vlassis; Paul Wilmes
Journal:  Sci Rep       Date:  2014-03-31       Impact factor: 4.379

6.  A hundred years of activated sludge: time for a rethink.

Authors:  Abdul R Sheik; Emilie E L Muller; Paul Wilmes
Journal:  Front Microbiol       Date:  2014-03-03       Impact factor: 5.640

7.  RNA preservation agents and nucleic acid extraction method bias perceived bacterial community composition.

Authors:  Ann McCarthy; Edna Chiang; Marian L Schmidt; Vincent J Denef
Journal:  PLoS One       Date:  2015-03-23       Impact factor: 3.240

Review 8.  Molecular Microbial Community Analysis as an Analysis Tool for Optimal Biogas Production.

Authors:  Seyedbehnam Hashemi; Sayed Ebrahim Hashemi; Kristian M Lien; Jacob J Lamb
Journal:  Microorganisms       Date:  2021-05-28

9.  Mantis: flexible and consensus-driven genome annotation.

Authors:  Pedro Queirós; Francesco Delogu; Oskar Hickl; Patrick May; Paul Wilmes
Journal:  Gigascience       Date:  2021-06-02       Impact factor: 6.524

Review 10.  Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions.

Authors:  Padhmanand Sudhakar; Kathleen Machiels; Bram Verstockt; Tamas Korcsmaros; Séverine Vermeire
Journal:  Front Microbiol       Date:  2021-05-11       Impact factor: 5.640

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