J. F. Banfield

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

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 investigates virus-host dynamics in soil following rewetting, finding that a subset of viruses thrive and drive microbial lysis, contributing to CO2 efflux.

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.

The paper identifies widespread lanthanide-dependent enzymes in ocean metagenomes, showing their role in carbon metabolism and biogeochemical cycles.

The paper shows that Bifidobacterium breve can utilize 2'-fucosyllactose with help from co-existing species like Ruminococcus gnavus in infant microbiomes.

The paper predicts vitamin interdependencies in microbial communities using metagenomics-informed network analysis and validates these predictions in microcosms.

The paper examines spatial microbial heterogeneity in Brachypodium roots using EcoFABs, revealing distinct microbial communities at root tips and bases with different functional gene profiles.

The paper identifies phages capable of infecting both CPR and non-CPR bacteria, revealing their ability to use alternative genetic codes and expand host range.

The paper identifies CPR bacteria in sulfide-rich biofilms, linking them to sulfur and hydrogen metabolism through genomic and spectroscopic analyses.

This study uses qSIP with metagenomics to link microbial activity and physiology to soil moisture in Mediterranean grasslands, finding that precipitation levels influence microbial growth and phage dynamics.

The paper identifies Ca. Nealsonbacteria DGGOD1a as a biomass recycling ectosymbiont of methanogenic archaea in a benzene-degrading consortium.

This study identifies microbial gene clusters involved in lanthanide metabolism in weathered granites, highlighting their role in phosphate mineral dissolution and soil formation.

This paper identifies large plasmids in Methanoperedens archaea that are essential for their physiology and may be used to study and manipulate methane oxidation.

This study identifies contamination in metagenomics data using strain-resolved analysis, finding that contamination is more common in low-biomass samples and adjacent extraction plate positions.

The paper surveys stop codon recoding in bacteriophages, finding it widespread and suggesting it regulates gene expression and lysis timing.

The paper identifies Borgs, large extrachromosomal elements in Methanoperedens archaea, which enhance methane oxidation capacity and may influence greenhouse gas emissions.

This study identifies genetic and behavioral adaptations of C. parapsilosis in the gut microbiome of hospitalized infants using in situ genomics, transcriptomics, and proteomics.

The paper investigates microbial metabolic potential in floodplain soils along a river corridor, finding that meander-bound regions predict biogeochemical capacities at the watershed scale.

This study shows that adding a small amount of fermentable substrate to acetate-supplemented sulfate-reducing bioreactors improves performance through syntrophic H2 production.

The paper expands genomic sampling of Ca. Angelobacter, showing they are common in soil communities and enriched in biosynthetic gene clusters for specialized metabolites.

The paper identifies novel archaea in soils and sediments with divergent CuMMO enzymes, suggesting they contribute to nitrogen cycling through ammonia oxidation.

The paper shows that thiocyanate and organic carbon inputs select for specific autotrophic Afipia and Thiobacillus strains in microbiomes, with molasses removal favoring a dominant Afipia variant.

This study examines gene content and co-occurrence patterns in CPR bacteria to understand their evolutionary transitions between environmental and animal-associated habitats.

The paper investigates factors influencing gut microbiome strain persistence in infants, finding maternal origin and specific genetic functions are associated with strain survival.

The paper identifies a wide distribution of alternatively coded Lak phages in animal microbiomes, including new genomes and associations with specific animal types.

The paper determines the cryo-EM structure of a Cas6-RT-Cas1-Cas2 complex and shows bidirectional and unidirectional crosstalk between its active sites.

This study uses stable isotope-informed genome-resolved metagenomics to trace carbon flow in rhizosphere soil and identify microbial interactions with plants and phages.

This paper develops a method to edit specific bacteria within microbial communities using ET-Seq and DART systems, enabling genetic manipulation in complex environments.

The paper analyzes genomes of Elusimicrobia from various environments, finding groundwater-associated species show diverse metabolic capabilities and some encode novel nitrogenase paralogs.