A. M. Deutschbauer

Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface

This study investigates how genomic and environmental factors influence the distribution of Castellaniella species in a contaminated subsurface, identifying genetic mechanisms underlying their adaptation to stress.

Geochemical constraints on bacteriophage infectivity in terrestrial environments

This study measures ion thresholds for phage infection and shows that phage impact on terrestrial microbiomes is strongest in high-ion environments with simple carbon sources.

A mutant fitness compendium in Bifidobacteria reveals molecular determinants of colonization and host-microbe interactions

The paper creates a mutant fitness compendium for Bifidobacterium breve to identify molecular factors affecting colonization and host-microbe interactions.

Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem

This study evaluates how different inoculation practices and harvesting times affect microbial community reproducibility in a fabricated ecosystem with Brachypodium distachyon.

Barcoded overexpression screens in gut Bacteroidales identify genes with new roles in carbon utilization and stress resistance

The paper identifies new gene functions in gut Bacteroidales using a barcoded overexpression screen, revealing roles in carbon utilization and stress resistance.

Dynamic genetic adaptation of Bacteroides thetaiotaomicron murine gut colonization

This study tracks genetic and metabolic changes in Bacteroides thetaiotaomicron during gut colonization, showing shifting gene usage and highlighting the importance of carbohydrate metabolism for long-term persistence.

Genome-wide identification of fitness determinants in the Xanthomonas campestris bacterial pathogen during early stages of plant infection

This study identifies key fitness determinants of Xanthomonas campestris during early plant infection using RB-TnSeq, revealing novel genes involved in adaptation and virulence.

Caulobacter requires anionic sphingolipids and deactivation of fur to lose lipid A

This study identifies that Caulobacter requires anionic sphingolipids and deactivation of Fur to survive without lipid A in its outer membrane.

Parallel multicopy-suppressor screens reveal convergent evolution of phage-encoded single gene lysis proteins

The paper identifies host suppressors of phage-encoded single gene lysis proteins, revealing convergent evolution and common mechanisms across diverse phages.

Nitrogen metabolism in Pseudomonas putida: functional analysis using random barcode transposon sequencing

This study identifies genes and proteins involved in nitrogen metabolism in Pseudomonas putida using transposon sequencing and provides an interactive visualization tool for the data.

The Genetic Basis of phage susceptibility, cross-resistance and host-range in Salmonella

This study identifies 301 host factors in Salmonella involved in phage resistance, reveals cross-resistance mechanisms between RpoS and RpoN, and shows additional constraints define phage host range.

GapMind for Carbon Sources: Automatedannotations of catabolic pathways

GapMind for carbon sources annotates catabolic pathways in bacterial and archaeal genomes using genetic data and curated information, improving coverage and confidence in pathway predictions.

Biofilm Interaction Mapping and Analysis (BIMA): A tool for deconstructing interspecific interactions in co-culture biofilms

The paper introduces BIMA, a method to analyze interspecific interactions in biofilm co-cultures by examining colony morphology, inhibition, invasion, and associated genes/metabolites.

Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance

The paper identifies 41 viral clusters in groundwater plasmidomes, links them to bacterial hosts, and detects novel phage genera and host-specific genes.

A chemically-defined growth medium to support Lactobacillus-Acetobacter community analysis

The paper develops a chemically-defined medium that supports the growth of both Lactobacillus and Acetobacter bacteria, enabling the study of their metabolic interactions.

Systematic Discovery of Pseudomonad Genetic Factors Involved in Sensitivity to Tailocins

This study identifies genetic factors in pseudomonads that influence sensitivity to tailocins using transposon libraries and genomics.

Large-scale Genetic Characterization of a Model Sulfate Reducing Bacterium

This study characterizes the genetic essentiality and conditional phenotypes of Desulfovibrio vulgaris Hildenborough using a transposon mutant library under various metabolic and stress conditions.

High-throughput mapping of the phage resistance landscape in E. coli

This study maps host genetic determinants of phage resistance in E. coli using high-throughput genetic screens, identifying both known and novel resistance factors across 14 phages.

Identification of a novel cobamide remodeling enzyme in the beneficial human gut bacterium Akkermansia muciniphila

This paper identifies a novel cobamide remodeling enzyme, CbiR, in Akkermansia muciniphila that enables the bacterium to use diverse cobamides by modifying their structure.

Genome-wide identification of tomato xylem sap fitness factors for three plant-pathogenic Ralstonia species

This paper identifies genes essential for Ralstonia spp. growth in tomato xylem sap using RB-TnSeq, revealing envelope-related factors critical for survival in this niche.

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.

Four Families of Folate-independent Methionine Synthases

The paper identifies four families of folate-independent methionine synthases and characterizes their methyl donor requirements and distribution across different organisms.

Genome-wide analysis of Escherichia coli fitness determinants in a cross-feeding mutualism with Rhodopseudomonas palustris

This study identifies E. coli genes affecting fitness in a mutualistic cross-feeding relationship with R. palustris using RB-TnSeq, revealing both expected and unexpected genetic influences.

Selective carbon sources influence the end-products of microbial nitrate respiration

The paper investigates how different carbon sources affect the end-products of nitrate respiration in microbial communities from diverse environments.

Genome-wide transposon screen of a Pseudomonas syringae mexB mutant reveals the substrates of efflux transporters

The paper identifies efflux transporter substrates in Pseudomonas syringae by screening a transposon mutant library in a mexB mutant background, revealing redundant transporters with overlapping substrate specificities.

Genome-wide identification of Pseudomonas syringae genes required for competitive fitness during colonization of the leaf surface and apoplast

This study identifies Pseudomonas syringae genes critical for leaf surface and apoplast colonization using transposon mutagenesis, revealing gene expression and fitness are not correlated.

Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolism

This paper uses RB-TnSeq to identify novel enzymes in Pseudomonas putida lysine metabolism, revealing new biochemical pathways and functions for DUF1338 proteins.

Oxidative pathways of deoxyribose and deoxyribonate catabolism

The paper identifies novel oxidative pathways for deoxyribose and deoxyribonate catabolism in bacteria using genome-wide mutant fitness assays and genetic evidence.

Defining the toxicity limits on microbial range in a metal-contaminated aquifer

The paper identifies toxic inorganic ions that inhibit sensitive microorganisms and favor Rhodanobacter in a metal-contaminated aquifer.

Dub-seq: dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits

Dub-seq enables high-throughput overexpression screens in E. coli by combining shotgun expression libraries with DNA barcode sequencing to identify genes with gain-of-function phenotypes.