Genomic Encyclopedia of Bacteria and Archaea (GEBA) VI: learning from type strains

Type strains of species are one of the most valuable resources in microbiology. During the last decade, the Genomic Encyclopedia of Bacteria and Archaea (GEBA) projects at the US Department of Energy Joint Genome Institute (JGI) and their collaborators have worked towards sequencing the genome of all the type strains of prokaryotic species. A new project GEBA VI extends these efforts to functional genomics, including pangenome and transcriptome sequencing and exometabolite analyses. As part of this project, investigators with interests in specific groups of prokaryotes are invited to submit samples for analysis at JGI.

6. Genomics and the microbial world

Together, molecular biology and genomics have made it possible to explore the diversity and ecology of the 99 per cent of microbes that cannot be cultured in laboratories. ‘Genomics and the microbial world’ considers environmental gene sequencing; metagenomics, the isolation and analysis of large DNA fragments taken directly from the environment; and single-cell genomics and transcriptomics. It also examines the human microbiome; it is now clear that a complex array of factors contribute to the establishment and maintenance of the human microbiome over the course of a lifetime. Bioprospecting in the metagenomics era is also discussed along with the ambitious Genomic Encyclopedia of Bacteria and Archaea project.

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.

Genome sequencing and analysis of the genome of Acidithiobacillus ferrooxidans strain DLC-5, a heavy metal resistant strain from acid mine drainage in northeast China

Acidithiobacillus ferrooxidans ( A. ferrooxidans ) is a gram-negative, extremely acidophilic, mesophilic, chemolithotrophic bacterium and the most well-studied acidophilic organism which is usually found in acid environments such as acid mine drainage. The draft genome sequence of A. ferrooxidans ATCC 23270 was first reported in 2000, fourteen years ago. Here we describe the features of this organism, together with the draft genome sequence, and annotation. This is the draft genome sequence from the A. ferrooxidans, and the 3,142,890 bp long single replicon genome with its 32,719 protein-coding and 64 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Bacterial project.

Genome sequencing and analysis of the genome of Acidithiobacillus ferrooxidans strain DLC-5, a heavy metal resistant strain from acid mine drainage in northeast China

Acidithiobacillus ferrooxidans ( A. ferrooxidans ) is a gram-negative, extremely acidophilic, mesophilic, chemolithotrophic bacterium and the most well-studied acidophilic organism which is usually found in acid environments such as acid mine drainage. The draft genome sequence of A. ferrooxidans ATCC 23270 was first reported in 2000, fourteen years ago. Here we describe the features of this organism, together with the draft genome sequence, and annotation. This is the draft genome sequence from the A. ferrooxidans, and the 3,142,890 bp long single replicon genome with its 32,719 protein-coding and 64 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Bacterial project.