Metabolomics profiling reveals changes in peptidoglycan and redox metabolism between ancient and modern Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb), the cause of tuberculosis, kills over 1 million people worldwide each year. Mtb is classified into 10 distinct lineages, each harboring unique genetic changes that influence its survival, virulence, and transmissibility. Although metabolism plays a critical role in Mtb infection and persistence, the metabolomic profiles of different Mtb lineages remain poorly characterized. Here, by using metabolomic and bioinformatic approaches, we have determined the metabolome of representative strains belonging to three main lineages, namely lineage 1, lineage 2, and lineage 4. We show that the ancient lineage 1 has considerable differences in its metabolome compared to lineages 2 and 4. Those differences are mainly related to amino acids, peptidoglycan synthesis intermediates, and ergothioneine, a sulfur-containing histidine derivative with potent antioxidant and redox properties. Taken together, these data represent the first comprehensive analysis of the metabolome of three main Mtb lineages. IMPORTANCE Metabolic regulation of Mycobacterium tuberculosis (Mtb) underlies its successful infection and persistence. Previous metabolic characterization has largely been limited to the reference strain H37Rv, but there are significant metabolic differences between ancient and modern lineages. This study illustrates the complexity of metabolic regulation in Mtb and the limitations of using a single strain to develop understanding. Investigation of lineage-specific changes in Mtb metabolism could help identify weaknesses that could be therapeutically targeted and could inform the evaluation of broad-spectrum antibiotics.