R. J. Giannone

Laboratory evolution in Novosphingobium aromaticivorans enables rapid catabolism of a model lignin-derived aromatic dimer

This study uses experimental evolution to identify mutations that enhance catabolism of a lignin-derived aromatic dimer in Novosphingobium aromaticivorans, revealing a key enzyme involved in its degradation.

Fungal antibiotics control bacterial community diversity in the cheese rind microbiome

This study shows that fungal antibiotics, specifically pseurotins, regulate bacterial community diversity in cheese rind microbiomes by controlling bacterial abundance and composition.

Critical Assessment of Metaproteome Investigation (CAMPI): a Multi-Lab Comparison of Established Workflows

CAMPI evaluates metaproteomic workflows across labs, finding sample processing drives peptide variability while workflows yield similar functional profiles.

Microbiota functional activity biosensors for characterizing nutrient utilization in vivo

The paper develops MFABs to quantify gut microbiota metabolism of structurally distinct arabinans in vivo using fluorescent beads.

Understanding and eliminating the detrimental effect of endogenous thiamine auxotrophy on metabolism of the oleaginous yeast Yarrowia lipolytica

This study identifies the genetic basis of thiamine auxotrophy in Yarrowia lipolytica and engineers a thiamine-prototrophic strain with enhanced lipid production.

Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis

The paper shows that horizontal transfer of coumarate catabolism pathways into E. coli requires host mutations to function, as intermediates inhibit purine biosynthesis, and some mutations are already present in the native host.

Identification of parallel and divergent optimization solutions for homologous metabolic enzymes

The paper identifies mutations improving enzyme activity in heterologous expression of 4-hydroxybenzoate monooxygenase homologs in E. coli, showing both common and specific mutations across homologs.