A. Crits-Christoph

Predicting microbial growth conditions from amino acid composition

This paper develops genome-based models to predict microbial growth conditions using amino acid composition, showing high accuracy for oxygen tolerance, temperature, salinity, and pH.

Genetic elements and defense systems drive diversification and evolution in Asgard archaea

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

Asgard archaea modulate potential methanogenesis substrates in wetland soil

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.

MicrobeMod: A computational toolkit for identifying prokaryotic methylation and restriction-modification with nanopore sequencing

MicrobeMod identifies prokaryotic methylation and restriction-modification systems using nanopore sequencing, revealing 5mC and 6mA methylation patterns in diverse bacterial and archaeal strains.

Borgs are giant extrachromosomal elements with the potential to augment methane oxidation

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

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

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.

A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters

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

Soils and sediments host novel archaea with divergent monooxygenases implicated in ammonia oxidation

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

Infant gut strain persistence is associated with maternal origin, phylogeny, and functional potential including surface adhesion and iron acquisition

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

Targeted Genome Editing of Bacteria Within Microbial Communities

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

Large Freshwater Phages with the Potential to Augment Aerobic Methane Oxidation

The paper identifies large freshwater phages encoding the pmoC gene, which may enhance bacterial methane oxidation and influence greenhouse gas emissions.

InStrain enables population genomic analysis from metagenomic data and rigorous detection of identical microbial strains

InStrain analyzes metagenomic data to detect microbial strain diversity and finds siblings share more strains than unrelated infants, but identical twins do not share more than fraternal siblings.

Bacterial secondary metabolite biosynthetic potential in soil varies with phylum, depth, and vegetation type

The paper examines bacterial secondary metabolite biosynthetic potential in soil, finding variations linked to phylum, depth, and vegetation type.

Soil bacterial populations are shaped by recombination and gene-specific selection across a meadow

The paper examines genetic variation in soil bacterial populations across a meadow, finding that recombination and gene-specific selection shape local genetic diversity.

Consistent metagenome-derived metrics verify and define bacterial species boundaries

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.

Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria that may stimulate TLR4 receptors

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