Abstract
To manipulate nasal microbiota for respiratory health, we need to better understand how this microbial community is assembled and maintained. Previous work has demonstrated that the pH in the nasal passage experiences temporal fluctuations. Yet, the impact of such pH fluctuations on nasal microbiota is not fully understood. Here, we examine how temporal fluctuations in pH might affect the coexistence of nasal bacteria in in silico communities. We take advantage of the cultivability of nasal bacteria to experimentally assess their responses to pH and the presence of other species. Based on experimentally observed responses, we formulate a mathematical model to numerically investigate the impact of temporal pH fluctuations on species coexistence. We assemble in silico nasal communities using up to 20 strains that resemble the isolates that we have experimentally characterized. We then subject these in silico communities to pH fluctuations and assess how the community composition and coexistence is impacted. Using this model, we then simulate pH fluctuations—varying in amplitude or frequency—to identify conditions that best support species coexistence. We find that the composition of nasal communities is generally robust against pH fluctuations within the expected range of amplitudes and frequencies. Our results also show that cooperative communities and communities with lower niche overlap have significantly lower composition deviations when exposed to temporal pH fluctuations. Overall, our data suggest that nasal microbiota could be robust against environmental fluctuations.
Highlights
Resident microbes in the human nasal passage protect us from respiratory pathogens (Brugger et al, 2016; Man et al, 2017)
These bacterial strains were chosen from a set of isolates based on three major considerations: (1) they reliably grow pH Fluctuations and Bacterial Coexistence in our cultivation media under an aerobic environment; (2) they include commonly observed Staphylococcus and Corynebacterium species; and (3) they span the phylogenetic landscape of both closely and distantly related bacteria found in the nasal environment (Escapa et al, 2018)
Using empirically measured species properties, we assembled stable in silico communities that show coexistence of nasal bacteria
Summary
Resident microbes in the human nasal passage protect us from respiratory pathogens (Brugger et al, 2016; Man et al, 2017). Previous research shows the role of resident commensals in suppressing pathogens, such as Staphylococcus aureus (Uehara et al, 2000; Iwase et al, 2010; Bomar et al, 2016) Investigating how this microbial community is formed and maintained can pH Fluctuations and Bacterial Coexistence provide powerful insights into microbiota-based therapies to prevent or treat infections. Both the species and the nasal environment can be sampled relatively (Yan et al, 2013; Proctor and Relman, 2017) The combination of these factors makes the nasal microbiota a suitable choice for mechanistic studies of human microbiota and a gateway for more detailed studies of humanassociated microbiota. Other reports have characterized and investigated the interactions among nasal microbes (Iwase et al, 2010; Bomar et al, 2016), but often with a focus on the interaction itself, and have only rarely involved the ecological consequences for the community (see Margolis et al, 2010; Yan et al, 2013; Krismer et al, 2017, for example)
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