Microbial single-cell omics: the crux of the matter
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MINI-REVIEW
Microbial single-cell omics: the crux of the matter Anne-Kristin Kaster 1,2
&
Morgan S. Sobol 1,2
Received: 15 April 2020 / Revised: 8 August 2020 / Accepted: 17 August 2020 # The Author(s) 2020
Abstract Single-cell genomics and transcriptomics can provide reliable context for assembled genome fragments and gene expression activity on the level of individual prokaryotic genomes. These methods are rapidly emerging as an essential complement to cultivation-based, metagenomics, metatranscriptomics, and microbial community-focused research approaches by allowing direct access to information from individual microorganisms, even from deep-branching phylogenetic groups that currently lack cultured representatives. Their integration and binning with environmental ‘omics data already provides unprecedented insights into microbial diversity and metabolic potential, enabling us to provide information on individual organisms and the structure and dynamics of natural microbial populations in complex environments. This review highlights the pitfalls and recent advances in the field of single-cell omics and its importance in microbiological and biotechnological studies. Key points • Single-cell omics expands the tree of life through the discovery of novel organisms, genes, and metabolic pathways. • Disadvantages of metagenome-assembled genomes are overcome by single-cell omics. • Functional analysis of single cells explores the heterogeneity of gene expression. • Technical challenges still limit this field, thus prompting new method developments. Keywords Targeted cell sorting . Amplification . Bioinformatics . Bacteria . Archaea
Introduction Microbial dark matter (MDM) Prokaryotic microorganisms harbor an enormous potential for biotechnological applications, such as novel natural product discovery, bioenergy production, and bioremediation of harmful anthropogenic-introduced substances (Singh et al. 2014; Katz and Baltz 2016; Kumar and Kumar 2017; Mullis et al. 2019; Stincone and Brandelli 2020). However, despite their global quantity and importance, it is estimated that over 99% of all microbial species remain uncultured or even completely
uncharacterized (Wu et al. 2009; McDonald et al. 2012; Hug et al. 2016; Lloyd et al. 2018). These microorganisms are referred to as microbial dark matter (MDM). Very often, attempts to grow microbes under laboratory conditions fail, or they grow too slowly to obtain sufficient biomass for analysis. Although new cultivation methods have been recently developed (Nichols et al. 2010; Sherpa et al. 2015; Wiegand et al. 2020), genome sequences for the vast majority of prokaryotes have been inaccessible, obscuring our knowledge of microbial diversity, metabolism, (eco)physiology, inter-organism interactions, and adaptive evolution.
Cultivation-independent approaches for exploring MDM * Anne-Kristin Kaster [email protected] 1
Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
2
Institut
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