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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).
Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
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.
Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations
- Cindy J. Castelle, C. Brown, Karthik Anantharaman, Alexander J. Probst, Raven H. Huang, J. Banfield
- BiologyNature Reviews Microbiology
- 4 September 2018
The metabolic potential of CPR and DPANN radiation is explored, focusing in particular on metabolic gaps and unexpected biological features that are unusual outside of these groups.
dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
The number of microbial genomes sequenced each year is expanding rapidly, in part due to genome-resolved metagenomic studies that routinely recover hundreds of draft-quality genomes. Rapid algorithms…
Measurement of bacterial replication rates in microbial communities
An algorithm is developed that uses draft-quality genome sequences and single time-point metagenome sequencing to infer microbial population replication rates and calculates an index of replication (iRep), based on the sequencing coverage trend that results from bi-directional genome replication from a single origin of replication.
Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages.
Subsampling assembly methods are developed to re-construct high-quality draft genomes from complex samples to evaluate the interlinked roles of the most abundant organisms in biogeochemical cycling in the aquifer sediment, and dominant members of the microbial community are interconnected through exchange of geochemical resources.
Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations
- Alexander J. Probst, Cindy J. Castelle, J. Banfield
- BiologyEnvironmental microbiology
- 1 February 2017
As in many deep underground environments, the microbial communities in subsurface high-CO2 ecosystems remain relatively unexplored. Recent investigations based on single-gene assays revealed a…
Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems
This work investigates thousands of viral and microbial genomes recovered using a cultivation-independent approach to study the frequency, variety and taxonomic distribution of viral defence mechanisms and correlates absence of CRISPR-Cas with lack of nucleotide biosynthesis capacity and a symbiotic lifestyle.