In human microbiota, the prevention or promotion of invasions can be crucial to human health. Invasion outcomes, in turn, are impacted by the composition of resident communities and interactions of resident members with the invader. Here we study how interactions influence invasion outcomes in microbial communities, when interactions are primarily mediated by chemicals that are released into or consumed from the environment. We use a previously developed dynamic model which explicitly includes species abundances and the concentrations of chemicals that mediate species interaction. Using this model, we assessed how species interactions impact invasion by simulating a new species being introduced into an existing resident community. We classified invasion outcomes as resistance, augmentation, displacement, or disruption depending on whether the richness of the resident community was maintained or decreased and whether the invader was maintained in the community or went extinct. We found that as the number of invaders introduced into the resident community increased, disruption rather than augmentation became more prevalent. With more facilitation of the invader by the resident community, resistance outcomes were replaced by displacement and augmentation. By contrast, with more facilitation among residents, displacement outcomes shifted to resistance. When facilitation of the resident community by the invader was eliminated, the majority of augmentation outcomes turned into displacement, while when inhibition of residents by invaders was eliminated, invasion outcomes were largely unaffected. Our results suggest that a better understanding of interactions within resident communities and between residents and invaders is crucial to predicting the success of invasions into microbial communities.

7In human microbiota, the prevention or promotion of invasions can be crucial to human health. 8 Invasion outcomes, in turn, are impacted by the composition of resident communities and 9 interactions among resident microbes. Microbial communities differ from communities composed 10 of other types of organisms in that many microbial interactions are mediated by chemicals that are 11 released into or consumed from the environment. We ask what determines invasion outcomes in 12 such microbial communities. Here, we use a model based on chemical-mediated interactions 13 among microbial species to assess the impact of positive and negative interactions on invasion 14 outcomes. We classified invasion outcomes as resistance, augmentation, displacement, or 15 disruption depending on whether the richness of the resident community was maintained or 16 dropped and whether the invader was maintained in the community or went extinct. We found that 17 as the number of invaders increased relative to size of the resident community, resident 18 communities were increasingly disrupted. As facilitation of the invader by the resident community 19 increased, resistance outcomes were replaced by displacement and augmentation. By contrast, as 20 facilitation increased among residents, displacement outcomes shifted to resistance. When 21 facilitation of the resident community by the invader was eliminated, augmentation outcomes were 22 replaced by displacement outcomes, while when inhibition of residents by invaders was 23 eliminated, there was little change in the frequency of invasion outcomes. These results suggest 24 that a better understanding of the chemical-mediated interactions within resident communities and 25 between residents and invaders is crucial to predicting the success of invasions into microbial 26 communities. 27 28 31 occupying available niches, or interacting with them directly or indirectly via predation, 32 competition, facilitation, or other mechanisms. The relative importance of these factors in 33 determining invasion outcomes varies between communities and ecosystems. Functional 34 composition of resident communities, for example, is an important determinant of invasion success 35 in many grasslands (1), while release from consumer or competitive pressure is an especially 36 important factor in marine invasions (2). Among microbes, interactions often occur via chemical 37 mediators released into the environment (3,4). These mediated interactions are believed to be 38 influential in many microbial communities, but their importance to invasion outcomes remains 39 unexplored. 40In human microbiota, where preventing invasion is a first step in preventing many diseases, this 41 phenomenon is sometimes referred to as colonization resistance. The potential for resident 42 microbes to protect us from pathogens has been observed as early as 1917, by the discovery of 43 Escherichia coli Nissle 1917 that antagonized and blocked enteric pathogens (5). More examples 44 across different microbiota sites abound: nasal mic...

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.

No 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. We take advantage of the cultivability of nasal bacteria to experimentally assess their responses to pH. Based on experimentally observed responses, we formulate a mathematical model to numerically investigate the impact of temporal pH fluctuations on species coexistence. Through extensive numerical simulations, we find that the composition of nasal communities is robust against pH fluctuations. Our results suggest that nasal microbiota could be more robust than expected against environmental fluctuations.