Host Immunity Alters Community Ecology and Stability of the Microbiome in a Caenorhabditis elegans Model

Abstract

A growing body of data suggests that the microbiome of a species can vary considerably from individual to individual, but the reasons for this variation-and the consequences for the ecology of these communities-remain only partially explained. In mammals, the emerging picture is that the metabolic state and immune system status of the host affect the composition of the microbiome, but quantitative ecological microbiome studies are challenging to perform in higher organisms. Here, we show that these phenomena can be quantitatively analyzed in the tractable nematode host Caenorhabditis elegans Mutants in innate immunity, in particular the DAF-2/insulin growth factor (IGF) pathway, are shown to contain a microbiome that differs from that of wild-type nematodes. We analyzed the underlying basis of these differences from the perspective of community ecology by comparing experimental observations to the predictions of a neutral sampling model and concluded that fundamental differences in microbiome ecology underlie the observed differences in microbiome composition. We tested this hypothesis by introducing a minor perturbation into the colonization conditions, allowing us to assess stability of communities in different host strains. Our results show that altering host immunity changes the importance of interspecies interactions within the microbiome, resulting in differences in community composition and stability that emerge from these differences in host-microbe ecology.IMPORTANCE Here, we used a Caenorhabditis elegans microbiome model to demonstrate how genetic differences in innate immunity alter microbiome composition, diversity, and stability by changing the ecological processes that shape these communities. These results provide insight into the role of host genetics in controlling the ecology of the host-associated microbiota, resulting in differences in community composition, successional trajectories, and response to perturbation.

Keywords: Caenorhabditis elegans; immunocompromised hosts; microbial communities; microbial ecology.

FIG 1

Eight-species microbial communities in the N2 intestine show distinct trends and variation. N2 worms were sampled from 12 independent experiments conducted over the course of ∼1 year. Each individual experiment contains data for 12 to 36 individual N2 worms taken from a single well. (A) CFU-per-worm data for the full data set of individual hosts (n = 164) after 4 days of colonization with this eight-species bacterial consortium. Each color represents a single host, and data are grouped by bacterial species to illustrate trends in abundance. (B) Average relative abundance of each bacterial species across all individual N2 worms. (C) Principal-component analysis (PCA) of community composition over time in N2 worms across a 6-day time series of colonization (24 individual worms/day, destructive sampling of individual hosts).

FIG 2

PCA of intestinal community composition in N2 wild-type (n = 164; black points) and mutant hosts colonized from a uniform metacommunity of eight bacterial species from the C. elegans native microbiome. (A to D) Subplots of the large ordination shown in its entirety in Fig. S3B; all worms except the constitutive daf-2 dauer mutant were grown to adulthood at 25°C. (A) Mild (eat-14; n = 69) and severe (phm-2; n = 78) grinder mutants; (B) p38 MAPK pathway-defective (AU37; n = 115) and derepressed (vhp-1; n = 84) mutants, with a glp-4 (n = 36) control for the AU37 strain; (C) TGF-β defective mutant (dbl-1; n = 69) and overexpression construct (ctls40; n = 48); (D) DAF-2/IGF defective (daf-16; n = 100) and derepressed (daf-2; n = 98) mutants. (E) Separate ordination, based on data from worms grown to adulthood at 16°C. When all worm hosts are grown to adulthood at 16°C, the double mutant CF1449 is indistinguishable from the daf-16 single mutant. Growth to adulthood at 16°C alters the later acquisition of microbial communities when adult worms (N2 and daf-16 strains) are colonized at 25°C. All data represent the results of single-worm digests and plating after 4 days total colonization on the uniformly distributed synthetic eight-species bacterial consortium. Ellipses for center of mass of the data associated with each host strain were generated using coord.ellipse (R package FactoMineR) with a confidence of 0.9999.

FIG 3

Successional ecology is altered by host genetic background. (A to E) Shannon diversity versus log₁₀(CFU/worm) for the data set shown in Fig. 2 and Fig. S3. (A) N2 wild-type worms (n = 164) show a generally negative diversity-population size trend [linear fit y = 1.83 − 0.24x; R²(adj) = 0.09; P = 8.748e−5]. (B) Mechanical mutants (eat-14 and phm-2 mutants) show a trend similar to that of the wild type. (C to E) The diversity-population size relationship in intestinal bacterial communities differs across host lineages. Mutants in the (C) p38 MAPK, (D) TGF-β, and (E) DAF-2/IGF pathways show trends that diverge in some cases (see Table S1) from that observed in N2 (black dots). Note that Shannon diversity in these experiments has a maximum at ln(8) = 2.08. (F to H) Time series of the diversity-population size relationship indicate that succession is altered in DAF-2/IGF mutant hosts. Intestinal communities were quantified for individual worms (n = 24 worms per time point per condition) of (F) N2, (G) daf-16, and (H) daf-2 lineages after 2, 4, and 6 days of colonization on the uniform eight-species metacommunity. CFU-per-worm data underlying panels F to H are shown in Fig. S5.

FIG 4

Spearman correlations between bacteria in host-associated intestinal communities differ from the predictions of a neutral sampling model. (A to C) Histograms of Spearman correlation coefficients calculated from data for (A) N2 (n = 164), (B) daf-16 (n = 100), and (C) daf-2 (n = 98) intestinal communities, with a bin size of 0.1. (D to I) Histograms of Spearman coefficient 20th and 80th quantiles from data simulated using host lineage-specific parameterizations of the Dirichlet-multinomial model (n = 10,000 simulated data sets per condition). Red lines indicate the corresponding quantile from the empirical data, and P values indicate the one-tailed percentage of simulated data sets with a lower 20th quantile (D to F) or higher 80th quantile (G to I) than the empirical data.

FIG 5

Intestinal bacterial communities in different host lineages react differently to a shared perturbation. In these experiments, adult worms were colonized with an even metacommunity of seven bacterial species (MYb27, -45, -53, -71, -120, -181, -238 [All-7]) or a metacommunity where each species in turn is dropped (indicated with the letter “d”) to 10% relative abundance. Worms were sampled at day 6 of colonization to allow time for communities to pass through early ecological succession. Data represent two (daf-16 mutant) or three (N2 and daf-2 mutant) independent runs, with 12 individual worms per host lineage/metacommunity combination; individual worms with <100 CFU (daf-2) or <1,000 CFU (N2 and daf-16 mutant) were removed from data to minimize errors due to low colony counts.