On the Origins and Control of Community Types in the Human Microbiome

Microbiome-based stratification of healthy individuals into compositional categories, referred to as "community types", holds promise for drastically improving personalized medicine. Despite this potential, the existence of community types and the degree of their distinctness have been highly debated. Here we adopted a dynamic systems approach and found that heterogeneity in the interspecific interactions or the presence of strongly interacting species is sufficient to explain community types, independent of the topology of the underlying ecological network. By controlling the presence or absence of these strongly interacting species we can steer the microbial ecosystem to any desired community type. This open-loop control strategy still holds even when the community types are not distinct but appear as dense regions within a continuous gradient. This finding can be used to develop viable therapeutic strategies for shifting the microbial composition to a healthy configurationComment: Main Text, Figures, Methods, Supplementary Figures, and Supplementary Tex

Stochastic colonization of hosts with a finite lifespan can drive individual host microbes out of equilibrium

Author summary Microbial communities are prevalent not only in the environment but also in hosts. Although the drivers of environmental microbiomes have been studied extensively, less is known about the drivers distinguishing a host environment. Recent experimental observations have highlighted the influence of ecological drift in hosts with short lifespan, including model organisms like C. elegans, D. melanogaster and D. rerio. We have developed a theoretical model to study the effect of a finite host lifespan on relevant observables of the microbiome, including the microbial load, probability of colonization of a microbial taxon, and distribution of microbiome composition in a host population. Although we focus on a case free of any selection, our results indicate the possible coexistence of hosts with alternative microbiome composition, and to a larger extent the coexistence of colonized and microbe-free hosts. A quantitative description is provided

FOUNDATION EFFECT FROM PIONEER SPECIES AFTER PHYSICAL DISRUPTION OF THE FISH SKIN MICROBIOME OF GAMBUSIA AFFINIS

Multicellular organisms provide an important ecosystem for bacteria to live and thrive upon, and in return, they support the host in many aspects, like protection from pathogens and enhancing digestion. The microbiome has been found to have profound effects on host health. A complex problem to tackle is understanding how the microbial community fails to recover after a disruption, such as antibiotic-associated enterocolitis in patients. Temporary domination of the community after disruption by one pioneer species is commonly observed, but the impact of this is unclear. Application of ecological theories may lead to more accurate prediction of such negative side effects. In this study, the fish skin microbiome of Gambusia affinis was physically disrupted and three different pioneer species were seeded. A pioneer is the first organism dominant in abundance after a community disturbance during community succession. Community biochemical profiles were measured by 25 different tests and community composition was observed by 16S rRNA gene sequencing. At 240 hours in recovery, community composition was different for all three treatments, suggesting a foundation effect for each of the pioneers. These results suggest pioneer species may act as foundation species by modulating the ecosystem, and thus affect the final recovery community structure. This suggests application of selected probiotics after disruption allow prevention of negative side effects by changing climax community composition