High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities

The human gut microbiome is a key contributor to health, and its perturbations are linked to many diseases. Small-molecule xenobiotics such as drugs, chemical pollutants and food additives can alter the microbiota composition and are now recognized as one of the main factors underlying microbiome diversity. Mapping the effects of such compounds on the gut microbiome is challenging because of the complexity of the community, anaerobic growth requirements of individual species and the large number of interactions that need to be quantitatively assessed. High-throughput screening setups offer a promising solution for probing the direct inhibitory effects of hundreds of xenobiotics on tens of anaerobic gut bacteria. When automated, such assays enable the cost-effective investigation of a wide range of compound-microbe combinations. We have developed an experimental setup and protocol that enables testing of up to 5,000 compounds on a target gut species under strict anaerobic conditions within 5 d. In addition, with minor modifications to the protocol, drug effects can be tested on microbial communities either assembled from isolates or obtained from stool samples. Experience in working in an anaerobic chamber, especially in performing delicate work with thick chamber gloves, is required for implementing this protocol. We anticipate that this protocol will accelerate the study of interactions between small molecules and the gut microbiome and provide a deeper understanding of this microbial ecosystem, which is intimately intertwined with human health.

Conformational changes in the essential E. coli septal cell wall synthesis complex suggest an activation mechanism

The bacterial divisome is a macromolecular machine composed of more than 30 proteins that controls cell wall constriction during division. Here, we present a model of the structure and dynamics of the core complex of the E. coli divisome, supported by a combination of structure prediction, molecular dynamics simulation, single-molecule imaging, and mutagenesis. We focus on the septal cell wall synthase complex formed by FtsW and FtsI, and its regulators FtsQ, FtsL, FtsB, and FtsN. The results indicate extensive interactions in four regions in the periplasmic domains of the complex. FtsQ, FtsL, and FtsB support FtsI in an extended conformation, with the FtsI transpeptidase domain lifted away from the membrane through interactions among the C-terminal domains. FtsN binds between FtsI and FtsL in a region rich in residues with superfission (activating) and dominant negative (inhibitory) mutations. Mutagenesis experiments and simulations suggest that the essential domain of FtsN links FtsI and FtsL together, potentially modulating interactions between the anchor-loop of FtsI and the putative catalytic cavity of FtsW, thus suggesting a mechanism of how FtsN activates the cell wall synthesis activities of FtsW and FtsI.

Survival of polycyclic aromatic hydrocarbon knockout fragments in the interstellar medium

Laboratory studies play a crucial role in understanding the chemical nature of the interstellar medium (ISM), but the disconnect between experimental timescales and the timescales of reactions in space can make a direct comparison between observations, laboratory, and model results difficult. Here we study the survival of reactive fragments of the polycyclic aromatic hydrocarbon (PAH) coronene, where individual C atoms have been knocked out of the molecules in hard collisions with He atoms at stellar wind and supernova shockwave velocities. Ionic fragments are stored in the DESIREE cryogenic ion-beam storage ring where we investigate their decay for up to one second. After 10 ms the initially hot stored ions have cooled enough so that spontaneous dissociation no longer takes place at a measurable rate; a majority of the fragments remain intact and will continue to do so indefinitely in isolation. Our findings show that defective PAHs formed in energetic collisions with heavy particles may survive at thermal equilibrium in the interstellar medium indefinitely, and could play an important role in the chemistry in there, due to their increased reactivity compared to intact or photo-fragmented PAHs.