Johanna Rapp

The human nasal microbiome is a low-diversity ecosystem whose assembly principles and mechanisms of colonization resistance remain poorly understood. Staphylococcus aureus is a member of the nasal microbiome of some individuals with variable abundance. We hypothesized that nutritional competition, strain-level diversity, and nutrient availability shape community stability and the ability of commensal species to inhibit S. aureus. To test this, we constructed 50 defined synthetic communities inoculated with 5 to 10 representative human nasal bacterial species differing in strain and species composition and tracked their compositional changes across serial passages, S. aureus growth, metabolic profiles, and nutritional interactions. The resulting consortia, which assembled into communities of up to 6 co-existing species converged in one of three community types. Synthetic communities dominated by specific Corynebacterium propinquum strains showed exclusion of most other community members, including S. aureus. Conversely, communities lacking C. propinquum dominance showed that exclusion of S. aureus was driven primarily by a combination of Staphylococcus epidermidis and Staphylococcus lugdunensis. Growth and coculture assays showed that C. propinquum outcompetes S. aureus in conditions that resemble the nasal environment, whereas S. aureus dominates in nutrient-rich conditions. Metabolomics analyses indicated that nutritional competition, including siderophore utilization and amino acid limitation, likely underlies this colonization resistance. These results establish a reproducible and tractable synthetic community model for the human nasal microbiome and suggest that nutrient-dependent competition and microbial metabolite production are key drivers of community structure and pathogen exclusion.

Healthy human gut microbiota is dominated by Bacteroidaceae in industrialized populations and by Prevotellaceae in those with traditional lifestyles, but diet alone is insufficient to explain this dominance of different Bacteroidota. Here we screened 94 dietary components in synthetic gut communities and find that these two bacterial families compete for overlapping nutritional niches. Segatella copri , a key member of Prevotellaceae-rich communities, outcompeted Bacteroidaceae when preferred polysaccharides such as arabinan were available, but this advantage depended on community composition, particularly the presence of Enterobacteriaceae. Metatranscriptomics and targeted metabolomics further revealed that Enterobacteriaceae synergized with dietary components to promote Segatella dominance in human and mouse gut communities. These interactions were validated by using multiple E. coli and Segatella isolates. Analyses of global metagenomes also showed a positive correlation between Segatella -rich non-industrialized microbiomes and Enterobacteriaceae abundance. Our results establish an ecosystem-level dynamic interplay between dietary components and key gut commensals that favour the dominance of Prevotellaceae.

In a healthy host, the residential microbes help regulate the growth of pathobionts, which are common members of the human gut microbiome, preventing them from causing diseases, including infections, under certain conditions. In cases of dysbiosis, this protection may be compromised. Targeted microbiome modulation offers a promising approach to restore healthy conditions in a disrupted community and consequently prevent infections using the natural colonization resistance of the microbiome. Elucidating the interaction mechanisms between microbial species within a microbiome is crucial for understanding how a microbiome can be modulated precisely and effectively to benefit the host’s well-being. Here, we investigated the interactions between the pathobiont C. perfringens and human gut commensals on physiological and molecular levels. We found that commensal strains affect C. perfringens growth by competing for substrates such as amino acids or a carbon source other than glucose. We further observed that Bacteroidaceae strains altered the levels of C. perfringens proteins, among others, the host-directed θ-toxin. Our findings reinforce the notion that modulating the composition of the gut microbiome is an effective strategy to prevent infections.

L-lysine (Lys) has been explored as a potential cyanobactericide due to its inhibitory effects on cyanobacterial growth at micromolar concentrations, comparable to many antibiotics. Here, we investigated the early metabolic and physiological responses of the model cyanobacterium Synechocystis sp. PCC 6803 to Lys exposure. Physiological analyses revealed cell enlargement, oxidative stress, and photosynthesis inhibition, leading to growth arrest. Metabolomic profiling indicated disruptions in peptidoglycan biosynthesis, evidenced by the accumulation of L-/D-alanine, meso-diaminopimelate, and D-Ala-D-Ala, suggesting interference with cell wall integrity. Furthermore, levels of energy metabolites and other amino acids, including tyrosine, tryptophan, valine, and iso-/leucine, were significantly altered, implying broader metabolic impacts of Lys toxicity. To explore potential resistance mechanisms, we used a CRISPRi-based genetic screen to identify key genes involved in relieving Lys toxicity. The Bgt permease system, responsible for basic amino acid uptake, was essential for acquiring Lys resistance, as a bgtA mutant exhibited normal growth on elevated Lys concentrations, thereby validating our CRISPRi screen. Additionally, UirR, a DNA-binding response regulator, and genes linked to c-di-AMP signaling, seemed implicated in Lys metabolism. Deletion of the c-di-AMP synthase gene increased Lys sensitivity, supporting a role for c-di-AMP in cell wall homeostasis and osmotic stress regulation. Altogether, our findings explored the early metabolic responses and physiological consequences of Lys exposure in Synechocystis, demonstrating its effects on peptidoglycan biosynthesis, amino acid metabolism, and nucleotide biosynthesis. This, as well as the identification of key genetic factors contributing to Lys resistance, provides insights into cyanobacterial physiology and the potential application of Lys in bloom-control strategies.

The human nasal microbiome is a low-diversity ecosystem whose assembly principles and mechanisms of colonization resistance remain poorly understood. In particular, Staphylococcus aureus colonization shows high heterogeneity across individuals. We hypothesized that nutritional competition, strain-level diversity, and nutrient availability shape community stability and the ability of commensal species to inhibit S. aureus. To test this, we constructed 50 defined synthetic communities composed of representative human nasal bacteria differing in strain and species composition and tracked their temporal dynamics, metabolic profiles, and nutritional interactions. The composition of synthetic communities with 5-10 species showed robust and reproducible dynamics and converged in one of three stable states. Synthetic communities dominated by a specific strain of Corynebacterium propinquum were highly stable and consistently excluded S. aureus. Growth and coculture assays showed that C. propinquum outcompetes S. aureus under poor nutritional conditions resembling the nasal environment, whereas S. aureus dominates in nutrient-rich conditions. Metabolomics analyses revealed that nutritional competition, including siderophores utilization and amino acid limitation, likely underlies this colonization resistance. These results establish a tractable synthetic community model for the human nasal microbiome and identify nutrient-dependent competition and microbial metabolite production as key drivers of community structure and pathogen exclusion.

Cyanobacteria such as Synechocystis sp. PCC 6803 are promising chassis for sustainable bioproduction. During nitrogen starvation, Synechocystis redirects fixed carbon from biomass growth toward glycogen accumulation as a carbon and energy reserve. Inhibiting glycogen synthesis results in the excretion of excess carbon as organic acids, predominantly pyruvate and 2-oxoglutarate. Efficiently rerouting this carbon toward the formation of value-added products such as the plastic alternative polyhydroxybutyrate requires a deeper understanding of carbon partitioning and overflow metabolism. To investigate this, we quantified intra- and extracellular metabolites in Synechocystis wild-type and mutant strains with altered glycogen metabolism (Δpgm, ΔglgC, ΔglgA1, ΔglgA2), nitrogen signaling (ΔglnB), and carbon allocation (ΔpirC), including the double mutant ΔglgCΔpirC. Metabolites were analyzed after two days of nitrogen-replete or -depleted growth using enzymatic glycogen quantification and liquid chromatography-mass spectrometry. Excretion was primarily triggered by inhibition of glycogen synthesis but modulated by other changes in carbon flow, such as pirC deletion. Besides pyruvate and 2-oxoglutarate, small amounts of glutamate, succinate, and malate were excreted. Our findings suggest that, rather than a passive consequence of metabolite accumulation, excretion is a selective, threshold-dependent process that limits intracellular metabolite buildup, revealing an additional layer of metabolic control relevant to cyanobacterial bioengineering.

CutA, a conserved protein across all domains of life, has been suggested to be involved in copper tolerance in bacteria, though recent studies have questioned this association, leaving its biological role unknown. To clarify its function, we studied cutA knockout mutants from two phylogenetically distant species, Synechococcus elongatus PCC 7942 and Escherichia coli , using phenotyping combined with metabolomics. To investigate the interaction of CutA with potential substrates and cofactors, we performed a series of native metabolomics experiments with CutA and cell extracts from which we identified the lumazine 2’-deoxyxanthopterin B2, a previously uncharacterized pteridine, to bind CutA in both species. Based on these results, we identified a set of other pteridines, including the essential cofactor tetrahydrobiopterin, as ligands of CutA. In the presence of pterins, we observed an increased affinity of CutA for copper ions. In addition, E. coli CutA mutants exhibited decreased copper resistance. These findings, alongside the known role of pteridines as redox shuttles, suggest a previously unrecognized role for CutA in coordinating cellular copper homeostasis and redox balance via pteridine metabolism.

Cyanobacteria such as Synechocystis sp. PCC 6803 are promising chassis for sustainable bioproduction. During nitrogen starvation, Synechocystis redirects fixed carbon from biomass growth toward glycogen accumulation as a carbon and energy reserve. Inhibiting glycogen synthesis results in the excretion of excess carbon as organic acids, predominantly pyruvate and 2-oxoglutarate. Efficiently rerouting this carbon toward the formation of value-added products such as the plastic alternative polyhydroxybutyrate requires a deeper understanding of carbon partitioning and overflow metabolism. To investigate this, we quantified intra- and extracellular metabolites in Synechocystis wild-type and mutant strains with altered glycogen metabolism (Δpgm, ΔglgC, ΔglgA1, ΔglgA2), nitrogen signaling (ΔglnB), and carbon allocation (ΔpirC), including the double mutant ΔglgCΔpirC. Metabolites were analyzed after two days of nitrogen-replete or -depleted growth using enzymatic glycogen quantification and liquid chromatography–mass spectrometry. Excretion was primarily triggered by inhibition of glycogen synthesis but modulated by other changes in carbon flow, such as pirC deletion. Besides pyruvate and 2-oxoglutarate, small amounts of glutamate, succinate, and malate were excreted. Our findings suggest that, rather than a passive consequence of metabolite accumulation, excretion is a selective, threshold-dependent process that limits intracellular metabolite buildup, revealing an additional layer of metabolic control relevant to cyanobacterial bioengineering.