ArticleProceedings of the National Academy of Sciences of the United States of America2020
Metabolic and genetic basis for auxotrophies in Gram-negative species.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed, 61 citations in OpenAlex.
- Low Levels of Amino Acid Auxotrophy Among Environmental Pseudomonas Isolates.Environmental microbiology · 2026Article
- Obligate cross-feeding of metabolites is common in soil microbial communities.Nature microbiology · 2026Article
- Annotating the pangenome reveals the diversity in the genetic basis for metabolic enzymes.Science advances · 2026Article
- Systematic design of auxotrophic strains and media conditions to probe metabolic functions in E. coli.PLoS computational biology · 2026Article
- Microbial diversity of plant pathogens and insect endosymbionts in Reptalus artemisiae.BMC microbiology · 2026Article
- Bacterial mutation dynamics emerging insights into virulence evolution and drug resistance. A review study.Frontiers in medicine · 2026Review
- Predicting Strain-Specific Metabolic Capabilities in the GenusComputational and structural biotechnology journal · 2026Article
- Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2.Microbiome · 2025Article
- Unveiling the Mechanisms of Bacterial Resistance and Countermeasures.Pathogens (Basel, Switzerland) · 2025Review
- A roadmap to understanding and anticipating microbial gene transfer in soil communities.Microbiology and molecular biology reviews : MMBR · 2025Review
- Regulation of antibiotic persistence and pathogenesis in Acinetobacter baumannii by glutamate and histidine metabolic pathways.BMC microbiology · 2025Article
- The parasitic nematode Haemonchus contortus lacks molybdenum cofactor synthesis, leading to sulphite sensitivity and lethality in vitro.International journal for parasitology · 2025Article
- Comparative analysis of amino acid auxotrophies and peptidase profiles in non-dysbiotic and dysbiotic small intestinal microbiomes.Computational and structural biotechnology journal · 2025Article
- Wild-Type Domestication: Loss of Intrinsic Metabolic Traits Concealed by Culture in Rich Media.Microbial ecology · 2024Article
- Article
- The Role of the L-Arginine-Nitric Oxide Molecular Pathway in Autosomal Dominant Polycystic Kidney Disease.Journal of personalized medicine · 2024Article
- Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health.The ISME journal · 2024Article
- From microbiome composition to functional engineering, one step at a time.Microbiology and molecular biology reviews : MMBR · 2023Review
- Taxonomic and environmental distribution of bacterial amino acid auxotrophies.Nature communications · 2023Article
- Essential Amino Acid Metabolites as Chemical Mediators of Host-Microbe Interaction in the Gut.Annual review of microbiology · 2023Review
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Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
Abstract
Auxotrophies constrain the interactions of bacteria with their environment, but are often difficult to identify. Here, we develop an algorithm (AuxoFind) using genome-scale metabolic reconstruction to predict auxotrophies and apply it to a series of available genome sequences of over 1,300 Gram-negative strains. We identify 54 auxotrophs, along with the corresponding metabolic and genetic basis, using a pangenome approach, and highlight auxotrophies conferring a fitness advantage in vivo. We show that the metabolic basis of auxotrophy is species-dependent and varies with 1) pathway structure, 2) enzyme promiscuity, and 3) network redundancy. Various levels of complexity constitute the genetic basis, including 1) deleterious single-nucleotide polymorphisms (SNPs), in-frame indels, and deletions; 2) single/multigene deletion; and 3) movement of mobile genetic elements (including prophages) combined with genomic rearrangements. Fourteen out of 19 predictions agree with experimental evidence, with the remaining cases highlighting shortcomings of sequencing, assembly, annotation, and reconstruction that prevent predictions of auxotrophies. We thus develop a framework to identify the metabolic and genetic basis for auxotrophies in Gram-negatives.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.