Quantifying multi-species microbial interactions in the larval zebrafish gut

Abstract

These authors contributed equally to this work. AbstractThe microbial communities resident in animal intestines are composed of multiple species that together play important roles in host development, health and disease. Due to the complexity of these communities and the difficulty of characterizing them in situ, the determinants of microbial composition remain largely unknown. Further, it is unclear for many multi-species consortia whether their species-level makeup can be predicted based on an understanding of pairwise species interactions, or whether higher-order interactions are needed to explain emergent compositions. To address this, we examine commensal intestinal microbes in larval zebrafish, initially raised germ-free to allow introduction of controlled combinations of bacterial species. Using a dissection and plating assay, we demonstrate the construction of communities of one to five bacterial species and show that the outcomes from the two-species competitions fail to predict species abundances in more complex communities. With multiple species present, inter-bacterial interactions become weaker and more cooperative, suggesting that higher-order interactions in the vertebrate gut may stabilize complex communities. 5 immune regulation [5-10] and a wide range of diseases [11][12][13][14][15][16][17][18][19][20]. 6 Despite the importance of intestinal communities, the determinants of their 7 composition remain largely unknown. A growing number of studies map the effects of 8 external perturbations, such as antibiotic drugs [21, 22] and dietary fiber [23] and 9 fat [24, 25] on the relative abundance of gut microbial species. Intrinsic inter-microbial 10interactions, however, are especially challenging to measure and are important not only 11 for shaping community composition in the absence of perturbations but also for 12 propagating species-specific perturbations to the rest of the intestinal ecosystem. 13The considerable majority of studies of the gut microbiota have been performed on 14 naturally assembled microbiomes by sequencing DNA extracted from fecal samples, an 15May 28, 2020 1/23approach that provides information about the microbial species and genes present in the 16 gut, but that imposes several limitations on the inference of inter-species interactions. 17The high diversity of natural intestinal communities, and therefore the low abundance 18 of any given species among the multitude of its fellow residents, implies that stochastic 19 fluctuations in each species' abundance will be large, easily masking true biological 20 interactions. The accuracy of inference is considerably worse if only relative, rather than 21 absolute, abundance data is available [26-29], as is typically the case in 22 sequencing-based studies. Finally, we note that fecal sampling assesses only the 23 microbes that have exited the host, which may not be representative of the intestinal 24 community [30]. 25 An alternative approach to using DNA sequencing and naturally assembled 26 host-microbiota systems is to build suc...

Monoassociation with bacterial isolates reveals the role of colonization, community complexity and abundance on locomotor behavior in larval zebrafish

“…Competition experiments between A. veronii and V. cholerae have shown intestinal motility can selectively reduce the abundance of A. veronii [33]. However, with mixtures of four or five species, higher-order interactions weaken competition and facilitate diversity [34]. While it may be informative to examine longer-term outcomes in the larvae associated with single isolates or mixtures, these data indicate that species that grow rapidly in isolation outcompeted less robust taxa present in the defined mixtures.…”

Engineering complex communities by directed evolution

“…Despite these and other success stories, the bottom-up engineering of synthetic consortia remains challenging. The function of a consortium is generally affected by species interactions, which are difficult to predict from first principles and grow rapidly with species richness [10][11][12][13][14][15][16] . Perhaps more importantly, microbial communities are rapidly evolving ecological systems, and their engineered functions can be disrupted by environmental fluctuations, invasive species, species extinctions, or the fixation of mutant genotypes [17][18][19][20] .…”

Predicting bacterial interaction outcomes from monoculture growth and supernatant assays

“…However, much less is known about the microbial interactions occurring in these communities. This is why bottom-up approaches have become popular, where a set of defined bacterial species and strains are mixed, and their interactions are studied under experimental conditions (3)(4)(5)(6)(7)(8)(9). The power of simple communities is that they are tractable and allow for experimental manipulation so that the effect of specific factors on community properties can be examined.…”