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Community structure and metabolism through reconstruction of microbial genomes from the environment
Reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II and analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.
Microbial communities in acid mine drainage.
A new view of the tree of life
New genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, are used to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included.
Unusual biology across a group comprising more than 15% of domain Bacteria
This work reconstructed 8 complete and 789 draft genomes from bacteria representing >35 phyla and documented features that consistently distinguish these organisms from other bacteria, infer that this group, which may comprise >15% of the bacterial domain, has shared evolutionary history, and describe it as the candidate phyla radiation (CPR).
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
- Christopher S. Miller, B. Baker, Brian C. Thomas, S. Singer, J. Banfield
- BiologyGenome Biology
- 19 May 2011
A novel iterative method is proposed, based on the expectation maximization algorithm, that reconstructs full-length small subunit gene sequences and provides estimates of relative taxon abundances in microbial communities.
Asgard archaea illuminate the origin of eukaryotic cellular complexity
The results expand the known repertoire of ‘eukaryote-specific’ proteins in Archaea, indicating that the archaeal host cell already contained many key components that govern eukaryotic cellular complexity.
Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences are presented, including the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum information about a Metagenome-Assembled Genomes (MIMAG), including estimates of genome completeness and contamination.
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
A tool that enables a flexible set of existing binning algorithms to be combined, resulting in improved binning accuracy and the recovery of more near-complete genomes from metagenomes compared to standalone methods is presented.
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
- Karthik Anantharaman, C. Brown, J. Banfield
- Environmental ScienceNature communications
- 24 October 2016
Terabase-scale cultivation-independent metagenomics is applied to aquifer sediments and groundwater and 2,540 draft-quality, near-complete and complete strain-resolved genomes are reconstructed, finding that few organisms within the community can conduct multiple sequential redox transformations.