Jillian F. Banfield

The paper models cyanobacterial consortia to identify a consistent core microbiome across different hosts and inoculation sources.

The paper investigates how microbial activity in grassland soils varies with depth and water availability, identifying active predatory bacteria and episymbionts in different soil layers.

The paper characterizes microbiomes in underground research labs, finding genomic conservation and similar functional profiles despite environmental differences.

The paper confirms a new archaeal genetic code (Code 34) where TAG codons encode pyrrolysine, showing sporadic distribution and lateral gene transfer.

The paper reconstructs genomes of soil-associated Asgard archaea and uses metatranscriptomics to show their role in carbon compound metabolism relevant to methane production in wetlands.

The paper identifies conserved genetic repertoires in Borg extrachromosomal elements of methane-oxidizing archaea and shows their higher expression than host genes.

The paper identifies and characterizes diverse extrachromosomal elements in Methanoperedens archaea, including mini-Borgs and viruses, and shows their genetic exchange and potential impact on archaeal activity.

This study identifies mobile genetic elements and defense systems in Asgard archaea, revealing their role in shaping genetic diversity and evolution.

The paper investigates how corrinoid structure affects soil microbial community composition and stability through experimental and genomic analysis.

The paper investigates phage succession in infants over three years, finding that 9% of early phage colonizers persist, with maternal transmission and stop codon reassignment playing key roles.

The paper identifies giant genes in predatory bacteria, showing they are associated with prey adhesion and cell wall degradation.

The paper traces the evolutionary origin of eukaryotic RNA-guided endonucleases, showing they evolved from a specific clade of bacterial IS607 TnpB enzymes.

COBRA enhances viral genome assembly from metagenomes, producing high-quality genomes and revealing new phage species and circular genomes.

The paper expands the global RNA virome by five-fold, identifying new clades of RNA bacteriophages and revealing novel virus-host interactions.

The paper develops a cloud computing infrastructure for petabase-scale sequence alignment, identifying over 105 novel RNA viruses and expanding known species by an order of magnitude.

The paper confirms that phages in the human gut microbiome use an alternative genetic code where TAG stop codon is read as glutamine.

The paper uses transporter gene frequencies to predict metabolite characteristics and identifies siderophore-like BGCs in gut microbiomes.

The paper investigates microbial community structure and metabolic potential along a hillslope to riparian zone transect using genome-resolved metagenomics and stable isotopes, finding distinct communities and functions across depth and landscape position.

The paper analyzes gene expression in acidophilic microorganisms, showing how environmental conditions shape transcriptional profiles and highlighting the role of non-coding RNAs in gene regulation.

This study investigates how gestational age affects the functional potential and species richness of the gut microbiome in premature infants using genome-resolved metagenomics.

The paper identifies shifts in microbial transcription patterns in preterm infants prior to NEC onset, suggesting hypoxic conditions in the gut.

The paper links genomically novel soil microbes to depth-stratified carbon and nitrogen cycling by analyzing metagenomic and proteomic data from grassland soils.

The paper analyzes microbial diversity and metabolic potential in cyanotoxin-producing cyanobacterial mats across a river network using metagenomic sequencing.

The paper introduces EukRep, a method to recover eukaryotic genomes from metagenomic samples, demonstrating its utility in analyzing microbial community responses to environmental changes.

dRep groups genomes with fast Mash distances, then accurate ANI, de-replicating 1,125 infant gut genomes in 92 CPU hours versus 2,784 for naive gANI.