Antibiotics are used for fighting pathogens, but also target our commensal bacteria as a side effect, disturbing the gut microbiota composition and causing dysbiosis and disease [1][2][3] . Despite this well-known collateral damage, the activity spectrum of the different antibiotic classes on gut bacteria remains poorly characterized. Having monitored the activities of >1,000 marketed drugs on 38 representative species of the healthy human gut microbiome 4 , we here characterize further the 144 antibiotics therein, representing all major classes. We determined >800 Minimal Inhibitory Concentrations (MICs) and extended the antibiotic profiling to 10 additional species to validate these results and link to available data on antibiotic breakpoints for gut microbes. Antibiotic classes exhibited distinct inhibition spectra, including generation-dependent effects by quinolones and phylogeny-independence by βlactams. Macrolides and tetracyclines, two prototypic classes of bacteriostatic protein synthesis inhibitors, inhibited almost all commensals tested. We established that both kill different subsets of prevalent commensal bacteria, and cause cell lysis in specific cases. This species-specific activity challenges the long-standing divide of antibiotics into bactericidal and bacteriostatic, and provides a possible explanation for the strong impact of macrolides on the gut microbiota composition in animals 5-8 and humans [9][10][11] . To mitigate the collateral damage of macrolides and tetracyclines on gut commensals, we exploited the fact that drug combinations have species-specific outcomes in bacteria 12 and sought marketed drugs, which could antagonize the activity of these antibiotics in abundant gut commensal species. By screening >1,000 drugs, we identified several such antidotes capable of protecting gut species from these antibiotics without compromising their activity against relevant pathogens. Altogether, this study broadens our understanding of antibiotic action on gut commensals, uncovers a previously unappreciated and broad bactericidal effect of prototypical bacteriostatic antibiotics on gut bacteria, and opens avenues for preventing the collateral damage caused by antibiotics on human gut commensals..

Chemical-genetic approaches are based on measuring the cellular outcome of combining genetic and chemical perturbations in large-numbers in tandem. In these approaches the contribution of every gene to the fitness of an organism is measured upon exposure to different chemicals. Current technological advances enable the application of chemical genetics to almost any organism and at an unprecedented throughput. Here we review the underlying concepts behind chemical genetics, present its different vignettes and illustrate how such approaches can propel drug discovery.

24Antibiotics are used for fighting pathogens, but also target our commensal bacteria as a side 25 effect, disturbing the gut microbiota composition and causing dysbiosis and disease 1-3 . 26Despite this well-known collateral damage, the activity spectrum of the different antibiotic 27 classes on gut bacteria remains poorly characterized. Having monitored the activities of 28 >1,000 marketed drugs on 38 representative species of the healthy human gut microbiome 4 , 29 we here characterize further the 144 antibiotics therein, representing all major classes. We 30 determined >800 Minimal Inhibitory Concentrations (MICs) and extended the antibiotic 31 profiling to 10 additional species to validate these results and link to available data on 32 antibiotic breakpoints for gut microbes. Antibiotic classes exhibited distinct inhibition spectra, 33including generation-dependent effects by quinolones and phylogeny-independence by β-34 lactams. Macrolides and tetracyclines, two prototypic classes of bacteriostatic protein 35 synthesis inhibitors, inhibited almost all commensals tested. We established that both kill 36 different subsets of prevalent commensal bacteria, and cause cell lysis in specific cases. 37This species-specific activity challenges the long-standing divide of antibiotics into 38 bactericidal and bacteriostatic, and provides a possible explanation for the strong impact of 39 macrolides on the gut microbiota composition in animals 5-8 and humans 9-11 . To mitigate the 40 collateral damage of macrolides and tetracyclines on gut commensals, we exploited the fact 41 that drug combinations have species-specific outcomes in bacteria 12 and sought marketed 42 drugs, which could antagonize the activity of these antibiotics in abundant gut commensal 43 species. By screening >1,000 drugs, we identified several such antidotes capable of 44 protecting gut species from these antibiotics without compromising their activity against 45 relevant pathogens. Altogether, this study broadens our understanding of antibiotic action on 46 gut commensals, uncovers a previously unappreciated and broad bactericidal effect of 47 prototypical bacteriostatic antibiotics on gut bacteria, and opens avenues for preventing the48 collateral damage caused by antibiotics on human gut commensals.49 3 MAIN TEXT 50 Medication is emerging as major contributor for changes in the composition of the human gut 51 microbiota 4,13-15 . Such severe and long-lasting changes are associated, and in some cases 52 causatively linked, to dysbiosis and a wide range of diseases 16 . Although several non-53 antibiotic drugs may also have a previously unappreciated impact on the gut microbiome 54 composition 4,16,17 , antibiotics, developed to have broad spectra and thereby target very 55 diverse pathogens, are long known to take a heavy toll on our gut flora, causing a variety of 56 gastrointestinal side-effects 18 , including Clostridioides (former Clostridium) difficile infections. 57Recently more attention has been given to this collateral damage of antibiot...

McQ is a SARS-CoV-2 quantification assay that couples early-stage barcoding with high-throughput sequencing to enable multiplexed processing of thousands of samples. McQ is based on homemade enzymes to enable low-cost testing of large sample pools, circumventing supply chain shortages.Implementation of cost-efficient high-throughput methods for detection of RNA viruses such as SARS-CoV-2 is a potent strategy to curb ongoing and future pandemics. Here we describe Multiplexed SARS-CoV-2 Quantification platform (McQ), an in-expensive scalable framework for SARS-CoV-2 quantification in saliva samples. McQ is based on the parallel sequencing of barcoded amplicons generated from SARS- CoV-2 genomic RNA. McQ uses indexed, target-specific reverse transcription (RT) to generate barcoded cDNA for amplifying viral- and human-specific regions. The barcoding system enables early sample pooling to reduce hands-on time and makes the ap-proach scalable to thousands of samples per sequencing run. Robust and accurate quantification of viral load is achieved by measuring the abundance of Unique Molecular Identifiers (UMIs) introduced during reverse transcription. The use of homemade reverse transcriptase and polymerase enzymes and non-proprietary buffers reduces RNA to library reagent costs to 92 cents/sample and circumvents potential supply chain short-ages. We demonstrate the ability of McQ to robustly quantify various levels of viral RNA in 838 clinical samples and accu-rately diagnose positive and negative control samples in a test-ing workflow entailing self-sampling and automated RNA ex-traction from saliva. The implementation of McQ is modular, scalable and could be extended to other pathogenic targets in future.

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Drug combinations present a powerful strategy to tackle antimicrobial resistance, but have not been systematically tested in many bacterial species. Here, we used an automated high-throughput setup to profile ~ 8000 combinations between 65 antibacterial drugs in three Gram-positive species: the model species, Bacillus subtilis and two prominent pathogens, Staphylococcus aureus and Streptococcus pneumoniae. Thereby, we recapitulate previously known drug interactions, but also identify ten times more interactions than previously reported in the pathogen S. aureus, including two synergies that were also effective in multi-drug resistant clinical S. aureus isolates in vitro and in vivo. Interactions were largely species-specific and mostly synergistic for drugs targeting the same cellular process, as observed also for Gram-negative species1. Yet, the dominating synergies are clearly distinct between Gram-negative and Gram-positive species, and are driven by different bottlenecks in drug uptake and vulnerabilities of their cell surface structures. To further explore interactions of commonly prescribed non-antibiotic drugs with antibiotics, we tested 2728 of such combinations in S. aureus, detecting a plethora of unexpected antagonisms that could compromise the efficacy of antimicrobial treatments in the age of polypharmacy. We uncovered even more synergies than antagonisms, some of which we could demonstrate as effective combinations in vivo against multi-drug resistant clinical isolates. Among them, we showed that the antiaggregant ticagrelor interferes with purine metabolism and changes the surface charge of S. aureus, leading to strong synergies with cationic antibiotics. Overall, this exemplifies the untapped potential of approved non-antibacterial drugs to be repurposed as antibiotic adjuvants. All data can be browsed through an interactive interface (https://apps.embl.de/combact/).

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