J. F. Banfield

The paper evaluates metagenome-derived metrics to define bacterial species boundaries and finds ribosomal proteins are more effective than 16S rRNA genes for species discrimination.

This paper identifies microorganisms involved in mercury cycling in geothermal springs using metagenomics and geochemical analysis, revealing new insights into microbial mercury speciation and biogeochemical processes.

The paper investigates how increased replication of DNRA bacteria in anammox bioreactors reduces nitrogen removal capacity by out-competing anammox bacteria.

This study reconstructs RNA viruses in soil metatranscriptomes, revealing their diversity, activity, and role in carbon cycling through host cell death.

The paper improves metagenome-assembled genomes (MAGs) by curating them to achieve complete, circularized genomes (CMAGs) using cumulative GC skew and other metrics.

The paper identifies and characterizes phages infecting Fonsibacter, showing their global distribution and ecological impact on freshwater microbial communities.

The paper identifies a host-symbiont relationship between two uncultivated archaea in a deep aquifer, showing co-occurrence and metabolic interdependence.

This study identifies four microbial guilds in the rhizosphere and detritusphere of Avena fatua, showing niche differentiation drives carbohydrate depolymerization and soil carbon cycling.

The paper reports the first closed genome of a Gracilibacteria from an oil-degrading community, revealing unusual metabolism and a hypervariable repeat region with potential functional significance.

The paper identifies major clades of large phage genomes across diverse ecosystems and highlights their expanded genetic repertoires and potential functional roles.

The paper identifies microbial features predictive of necrotizing enterocolitis (NEC) in premature infants using metagenomic analysis and machine learning.

The paper analyzes lipid composition in CO2-rich subsurface aquifers to infer microbial carbon cycling and lipid sources, finding CPR bacteria may rely on lysolipids from other community members.

The paper identifies novel CRISPR-Cas systems in Roizmanbacteria from hot springs, including CasY and type I-B/III-A systems, and reports phage genomes associated with these systems.

The paper examines microbial community structure and function across a hillslope-riparian transect, finding that proximity to the stream, groundwater, and weathered bedrock significantly influences microbial composition and metabolic potential.

This study uses metagenomic analysis with strain-level resolution to examine the human pregnancy microbiome, revealing gestational age and health complications influence microbial community composition and function.

The paper identifies a new RuBisCO type in CPR bacteria and DPANN archaea, showing its lateral transfer and role in carbon metabolism.

The paper identifies large phage (Lak phage) in gut microbiomes that infect Prevotella and are widespread, especially in developing-world individuals.

This paper predicts the metabolisms of Margulisbacteria and Saganbacteria using genomic data and compares them to their phylogenetic neighbors, supporting the hypothesis that their ancestor used hydrogen metabolism and fermentation.

The paper analyzes metagenomic data from premature infants and NICUs to identify fungal strains and their genetic diversity, revealing high similarity between infant and hospital-associated fungi.

The paper investigates how the gut microbiome of premature infants shapes the microbial composition of NICU rooms over time.

This study examines microbial colonization in premature infants, finding distinct proteomic profiles among related bacterial strains and correlations with NEC development.

The paper reconstructs a complete genome from a deep subsurface archaeon, revealing that homologous recombination and transposon propagation shape its population structure.

The paper identifies a Saccharibacteria genome in rhizosphere soil that relies on externally-derived nucleotides and utilizes plant-derived carbon through fermentation and potential aerobic respiration.

The paper uses machine learning on genome-resolved metagenomics data to identify antibiotic resistance genes in the infant gut microbiome that influence bacterial survival and response to antibiotics.

This study identifies sulfate reduction capacity in twelve bacterial and archaeal phyla, doubling the known diversity of microbes involved in the sulfur cycle.

This paper introduces DAS Tool, a metagenomic binning method that improves genome recovery accuracy and completeness across diverse samples.