Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance in a model gut microbiota

Abstract

20Despite decades of investigation into how antibiotics affect isolated bacteria, it 21 remains highly challenging to predict consequences for communities in complex 22 55 or (iii) tolerance, whereby the entire population enters an altered physiological 56 state that is not susceptible to the antibiotic 5 . Members of multispecies 57 communities, such as biofilms and models of urinary tract infections, can display 58 altered sensitivity to antibiotics 6-9 . A few studies have delved into the molecular 59 mechanisms behind cross-species antibiotic protection and sensitization. For 60 5 example, the exoproducts of Pseudomonas aeruginosa affect the survival of 61 Staphylococcus aureus through changes in antibiotic uptake, cell-wall integrity, 62 and intracellular ATP pools 10 . In synthetic communities, intracellular antibiotic 63 degradation affords cross-species protection against chloramphenicol 11 . 64 Additionally, metabolic dependencies within synthetic communities can lower 65 the viability of bacteria when antibiotics eliminate providers of essential 66 metabolites, leading to an apparent change in the minimum inhibitory 67 concentration (MIC) of the dependent species 9 . However, we still lack 68 understanding of how contextual metabolic interactions between bacteria affect 69 the physiological processes targeted by antibiotics and the resulting balance 70 between growth inhibition (bacteriostatic activity) and death (bactericidal 71 activity). 72 73 Characterizing the impact of metabolic interactions on antibiotic susceptibility 74 requires functional understanding of how bacterial species interact during 75 normal growth. Interspecies interactions can occur through specific mechanisms 76 within members of a community (e.g. cross-feeding or competition for specific 77 resources), or through global environmental variables modified by bacterial 78 activity. An example of the latter is pH, which has recently been shown to drive 79 6 community dynamics in a highly defined laboratory system of decomposition 80 bacteria 12 . 81 82 While synthetic communities afford the opportunity to design and to tune 83 bacterial interactions, it is unclear whether findings are relevant to natural 84 communities. The stably associated gut microbiota of Drosophila melanogaster fruit 85 flies constitutes a naturally simple model community for determining how 86 metabolic interactions between species affect growth, physiology, and the action 87 of antibiotics 13 . This community consists of ~5 species predominantly from the 88Lactobacillus and Acetobacter genera 14 (Fig. 1a). Lactobacilli produce lactic acid 15 , 89 while acetobacters are acetic acid bacteria that are distinguished by their ability 90 to oxidize lactate to carbon dioxide and water 16 . Short chain fatty acids, such as 91 lactate, decrease the pH of natural fermentations and may constitute a 92 mechanism through which pH plays a prominent role in community dynamics. 93 The naturally low number of species in Drosophila gut microbiota and its 94 comp...