Our results show that the acidic environment favors formation of nonstable SCVs, which reflect the SCVs found in clinics. They also provide evidence that treatment with alkalinizing agents, together with antibiotics, may provide a novel translational strategy for eradicating persisting intracellular reservoirs of staphylococci. This approach may also be extended to other intracellular bacteria.

Treatment failure in biofilm-associated bacterial infections is an important healthcare issue. In vitro studies and mouse models suggest that bacteria enter a slow-growing/non-growing state that results in transient tolerance to antibiotics in the absence of a specific resistance mechanism. However, little clinical confirmation of antibiotic tolerant bacteria in patients exists. In this study we investigate a Staphylococcus epidermidis pacemaker-associated endocarditis, in a patient who developed a break-through bacteremia despite taking antibiotics to which the S. epidermidis isolate is fully susceptible in vitro. Characterization of the clinical S. epidermidis isolates reveals in-host evolution over the 16-week infection period, resulting in increased antibiotic tolerance of the entire population due to a prolonged lag time until growth resumption and a reduced growth rate. Furthermore, we observe adaptation towards an increased biofilm formation capacity and genetic diversification of the S. epidermidis isolates within the patient.

In patients with inflammatory bowel diseases (IBD), dietary micronutrient intake is low and deficiencies are common. Besides the host, also the gut microbiota require micronutrients and low levels may disturb its functioning. Multi‐omics studies indeed detected shifts in micronutrient‐dependent microbial pathways in IBD. It is however not clear whether micronutrients may alleviate inflammation directly, by modulating the immune system, or also indirectly, by modulating the structure and function of the gut microbiota. The latter seems of particular interest, since the gut microbiota is one of the future therapeutic targets in IBD. A review of the most recent available literature on relevant micronutrients in context of IBD and gut microbiota was conducted. An overview per relevant micronutrient on its role on gut bacterial growth, metabolism and host–microbe interactions during gut inflammation is provided. Dietary micronutrients have potential to be part of future personalized microbiome‐targeted therapies in IBD, considering both the micronutrient status of the host and the gut microbiota. However, cohort studies together with integrated multi‐scale studies are needed to understand the mechanisms of micronutrient–microbiome–host interactions in IBD and to evaluate efficacy and safety of dietary micronutrient treatment strategies.