Abstract
A Brief History of Microbial Genomics
Technical Aspects for Accessing Genomes From Uncultivated Microorganisms
From Individual Cells to Ecosystems
Future Outlook
References

A Brief History of Microbial Genomics

In 1995, the first complete genome of a free-living microorganism, that of the bacterium Haemophilus influenzae, was sequenced by J. C. Venter and colleagues. This achievement proved the utility of shotgun genome sequencing and the discipline of microbial genomics was born. The years that followed were marked by sequencing genomes of bacterial and archaeal cultured isolates, and nearly 25 years later, well over 90,000 bacterial and nearly 900 archaeal isolate genome sequences are available in the public domain (Fig. 1). Due to our inability to cultivate the majority of microorganisms, cultivation-independent approaches to microbial genome discovery and identification, namely metagenomic sequencing, came to light in 2004 (Tyson et al., 2004; Venter et al., 2004) and have since been incredibly popular. Initially, cultivation-independent approaches were necessarily restricted to gene-centric analyses unless the microbial diversity of the sampled environment was very low; however, in recent years, genomeresolved metagenomics has become feasible through advances in sequencing technologies, metagenome assembly, and, importantly, computational binning algorithms (Wrighton et al., 2012; Albertsen et al., 2013). Genome-resolved metagenomics provides clear links between phylogeny and function, and offers population-level information on genome variability. Complementary to genome-resolved metagenomics is microbial single-cell genomics, the sequencing of the genome from an individual cell directly isolated from the environment (for a review, see (Woyke et al., 2017)). Single-cell genomics emerged in 2005 when A. Raghunathan and colleagues demonstrated that sequence data from a single Escherichia coli cell could be obtained. Two years later the first genomes were recovered from the candidate phylum Saccharibacteria (formerly TM7) using single-cell sequencing. Since then, single-cell genomics methods have been widely adopted to complement metagenomics. To date, more than 5,000 bacterial and archaeal single amplified genomes (SAGs) and nearly 13,000 metagenome-assembled genomes (MAGs) from bacteria and archaea are in the public domain (Fig. 1). These genomes provide a rich resource for the phylogenetic and functional interrogation of the uncultivated majority within the tree of life.