Daniel Amador‐Noguez

This paper investigates how engineered Pseudomonas putida reconfigures metabolic fluxes to enhance muconate production from lignin-related aromatics.

The paper designs synthetic gut microbial communities using mechanistic and machine learning models to robustly inhibit C. difficile growth in vitro and in vivo.

This study identifies PDH complex defects in L. monocytogenes as critical for intracellular survival, showing that PDH mutants fail to utilize PTS-dependent carbon sources, leading to reduced virulence.

This study shows that dietary cholesterol and saturated fat together drive fibrosing MASH via gut microbiota changes, specifically increasing Parasutterella spp. and activating hepatic stellate cells.

The paper identifies thermodynamic limitations in engineered microbial strains that prevent high-titer ethanol production by analyzing metabolite profiles and thermodynamic driving forces.

The paper identifies sulfur-containing metabolites specific to inflammatory macrophages, showing they are produced from cysteine and central metabolism intermediates and are elevated in human inflammatory lesions.

This study investigates BSH activity in human gut bacteria and finds that some strains can directly dehydrogenate conjugated bile acids to produce conjugated secondary bile acids, challenging the idea that deconjugation is a prerequisite for further modifications.

The paper quantifies enzyme burdens in glycolytic pathways of three bacteria, finding that thermodynamically favorable pathways require less enzymatic protein to sustain the same flux.

The paper examines sex differences in gut microbiota and bile acid composition in mice, finding distinct microbial diversity and portal bile acid profiles between males and females.

This study identifies a deoxyguanosine triphosphate triphosphohydrolase (Dgt) that promotes the G1 to S phase transition by regulating dNTP levels in Caulobacter crescentus.

The paper identifies pyruvate kinase's role in GTP synthesis during glycolysis in bacteria, showing it reduces guanosine toxicity and contributes to NTP production.

This study identifies allosteric regulation of pyruvate kinase in Bacillus subtilis as critical for efficient gluconeogenesis by preventing metabolic conflicts and carbon overflow.

This study identifies conditionally essential genes in Zymomonas mobilis for aerobic and anaerobic growth using CRISPRi-seq, revealing roles of DNA repair and respiratory complexes in energy coupling and isoprenoid biosynthesis.

This study shows that species richness in synthetic human gut communities determines the outcome of C. difficile invasion, with mechanisms like acidification and resource competition playing key roles.

The paper designs a synthetic human gut microbiome to explore butyrate production using a model-guided experimental framework.

This study identifies genetic loci associated with gut microbiota composition and bile acid profiles in mice using QTL analysis and validation experiments.