Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities

Abstract

The long-term success of introduced populations depends on both their initial size and ability to compete against existing residents, but it remains unclear how these factors collectively shape colonization dynamics. Here, we investigate how initial population (propagule) size shapes the outcome of community coalescence by systematically mixing eight pairs of in vitro microbial communities at ratios that vary over six orders of magnitude, and we compare our results to neutral ecological theory. Although the composition of the resulting cocultures deviated substantially from neutral expectations, each coculture contained species whose relative abundance depended on propagule size even after ~40 generations of growth. Using a consumer-resource model, we show that this dose-dependent colonization can arise when resident and introduced species have high niche overlap and consume shared resources at similar rates. Strain isolates displayed longer-lasting dose dependence when introduced into diverse communities than in pairwise cocultures, consistent with our model's prediction that propagule size should have larger, more persistent effects in diverse communities. Our model also successfully predicted that species with similar resource-utilization profiles, as inferred from growth in spent media and untargeted metabolomics, would show stronger dose dependence in pairwise coculture. This work demonstrates that transient, dose-dependent colonization dynamics can emerge from resource competition and exert long-term effects on the outcomes of community coalescence.

Keywords: competition; consumer–resource model; neutral ecological model; niche overlap; propagule size.

Fig. 1.

Diversity and composition of community cocultures vary by mixture ratio and deviate from neutral predictions. (A) In vitro communities were inoculated in triplicate from stool samples collected from eight healthy human subjects and passaged at a 1:200 dilution every 48 h 15 times to reach stability. (B) The diversity of each community over time, quantified as the effective number of species ($e^{H^{\prime }}$) calculated from the Shannon diversity index ($H^{\prime }$), initially decreased and then plateaued by passage 3. (C) Experimental design: eight pairs of in vitro communities were mixed in triplicate at seven mixture ratios ranging from 1,000:1 to 1:1,000. The resulting cocultures were passaged alongside the parent communities (represented by the 1:0 and 0:1 mixture ratios) five times, corresponding to ~40 generations (Materials and Methods). (D) The diversity of coculture communities was similar to or lower than the diversity of parent communities across mixture ratios. For this example mixture, gray lines represent two theoretical mixtures generated under neutral ecological expectations based on the composition of two replicate parent communities after five passages (1:0 and 0:1, shown in green), and orange lines represent three replicates of experimental community cocultures after five passages. Diversity was quantified as the effective number of species ($e^{H^{\prime }}$) calculated from the Shannon diversity index ($H^{\prime }$). (E) Variation of community composition across example mixtures and mixture ratios. Each plot shows the JSD of all coculture and theoretical communities relative to both parent communities (brown and gold) for a single mixture. Gray points along the dotted line represent theoretical mixtures generated under neutral ecological expectations, and colored points represent data from experimental coculture communities after five passages. Points show averages and error bars show the full range of values across inoculation replicates.

Fig. 2.

ASVs display a wide range of dose dependence during community coalescence. (A) Strong and weak colonizers reach the same relative abundance regardless of initial mixture ratio. Each panel shows a single representative ASV from one mixture. Gray lines represent both replicates of predicted neutral relative abundances for each ASV, and orange lines represent three replicates of experimental relative abundances after five passages. (B) Dose-dependent colonizers exhibit large changes in relative abundance across initial mixture ratios. Lines are colored as in (A) for a representative ASV from one mixture. (C) Dose-dependent ASVs are present in every mixture. Bars show the number of ASVs that displayed strong, weak, or dose-dependent colonization in each set of mixtures. ASVs were counted as present if they were detected in the 1:1 mixture at the fifth passage. (D) Total relative abundance of each type of colonizer in each set of mixtures after five passages. Only the 1:1 mixture is shown. Black lines indicate distinct ASVs. Relative abundances were averaged across the three inoculation replicates. (E) Resident ASVs are present at similar relative abundances in both parent communities. Lines are colored as in (A) for a representative ASV from one mixture. (F) Noisy ASVs show large, nonmonotonic fluctuations in relative abundance between adjacent mixture ratios. Lines are colored as in (A) for a representative ASV from one mixture. (G) Colonization behavior is not associated with ASV phylogeny for dose-dependent, strong, or weak colonizers. The heatmap shows the number of times each ASV exhibited dose-dependent (DD), strong (S), or weak (W) colonization at passage 5 in any mixture.

Fig. 3.

A consumer–resource model predicts transient dose dependence. (A) ASVs from the Enterococcus and Lactococcus genera showed dose dependence during community coalescence. Enterococcus faecalis, Enterococcus casseliflavus, and Lactococcus garvieae were isolated from the D1 community, and Lactococcus lactis was isolated from the D2 community. Gray lines represent both replicates of predicted neutral relative abundances for each ASV after five passages, and colored lines represent three replicates of experimental relative abundances after five passages. (B) Schematic of a simple consumer–resource model in which two species compete neutrally (equal consumption rates $R_{1,ab}=R_{2,ab}=1$) for resource $\mathit{ab}$, and resources $a$ and $b$ are unique to species 1 and 2, respectively (Materials and Methods). (C) The dose dependence of both species in the consumer–resource model increases as the niche overlap of species 1 with species 2 (${\gamma }_{1,2}$) increases. Dose dependence also decreases from passage 3 (dotted line) to passage 5 (solid line). Colored points highlight three values of ${\gamma }_{1,2}$ for which the relative abundances over mixture ratios of each species are shown at Right. The dose dependence of each species is defined as the magnitude of the ratio of its relative abundances, after passaging, from the starting mixture ratios of 1,000:1 and 1:1,000. (D) The species that is the weaker competitor for the shared resource shows stronger dose dependence. Lines show species relative abundances in the consumer–resource model after three (dotted line) and five (solid line) passages at three ratios of the consumption rates of the shared resource $\mathit{ab}$ by the two species ($R_{2,ab}/R_{1,ab}$), with fixed ${\gamma }_{1,2}=0.975$. The dose dependence of both species decreases with increasing $R_{2,ab}/R_{1,ab}$, but the dose dependence of species 1, the weaker competitor for the shared resource, decreases more slowly than that of species 2 and therefore remains higher at all three values. Dose dependence is defined as in (C). (E) The dose dependence of both species declines over passages in the two-species consumer–resource model, even when niche overlap (${\gamma }_{1,2})$ is high. The two species consume the shared resource at equal consumption rates ($R_{1,ab}=R_{2,ab}=1$). Dose dependence is defined as in (C).

Fig. 4.

Partial and transient dose dependence in pairwise strain mixtures. (A) Growth rates of Lactobacillales and Bacteroidales strains isolated from communities D1 and D2 formed two distinct clusters that corresponded to taxonomic order. Curves (Bottom Left) represent the average of nine replicates of blank-subtracted growth curves in monoculture after smoothing over a 30-min window, with shaded regions around each line representing one standard error (SE) above and below the average. Average instantaneous growth rates (Bottom Right) were calculated from blank-subtracted growth curves (Materials and Methods). (B) Experimental design of pairwise strain mixtures: strains were mixed in triplicate at ratios ranging from 1,000:1 to 1:1,000. The resulting cocultures were passaged five times, corresponding to ~40 generations. (C) No dose dependence was observed in a pairwise coculture of strains from distinct taxonomic orders. Strain relative abundances in cocultures of B. fragilis and L. lactis. Lines are colored as in Fig. 3A. Data from passages 1, 3, and 5 are shown. Neither strain was classified as dose dependent at any passage using the methods described in SI Appendix, Fig. S6. (D) Strains from the same taxonomic order showed transient dose dependence in pairwise coculture. Strain relative abundances in cocultures of B. fragilis and P. goldsteinii. Lines are colored as in Fig. 3A. Data from passages 1, 3, and 5 are shown. B. fragilis was classified as dose dependent at passage 1, but not at passages 3 or 5, using the methods described in SI Appendix, Fig. S6, while P. goldsteinii exhibited dose dependence at all passages. (E) Strain relative abundances in cocultures of E. casseliflavus and L. lactis. Lines are colored as in Fig. 3A. Data from passages 3 and 5 are shown. Both strains were classified as dose dependent at passage 3, but not at passage 5, using the methods described in SI Appendix, Fig. S6. (F) Strain relative abundances in cocultures of L. garvieae and L. lactis. Lines are colored as in Fig. 3A. Data from passages 3 and 5 are shown. Both strains were classified as dose dependent at passage 3, but not at passage 5, using the methods described in SI Appendix, Fig. S6. (G) Strain relative abundances in co-cultures of E. faecalis and L. lactis. Lines are colored as in Fig. 3A. Data from passage 3 and 5 are shown. E. faecalis was not classified as dose dependent at either passage using the methods described in SI Appendix, Fig. S6, while L. lactis exhibited dose dependence at passage 3 but not at passage 5.

Fig. 5.

Dose dependence increases in mixtures with more diverse communities. (A) Modification to the consumer–resource model in Fig. 3B in which a third species competes with species 1 for a fraction of the coarse-grained nutrients within $a$, dividing this grouping into resource $a^{\prime }$, the nutrients that remain exclusive to species 1, and resource $\mathit{ac}$, nutrients shared between species 1 and 3. Species 3 consumes resource $\mathit{ac}$ with relative consumption rate $r=\frac{R_{3,ac}}{R_{1,ac}}$ compared to species 1, imposing a niche overlap $\beta =\frac{y_{\mathit{ac}}}{y_{\mathit{ac}}+y_{a^{\prime }}}$ between species 1 and 3. (B) The dose dependence of species 1 after five passages increases with increasing niche overlap between species 1 and 3 ($\beta$) at constant $r=10$, while the dose dependence of species 2 is largely unaffected. Dose dependence is defined as in Fig. 3C. (C) L. lactis shows stronger dose dependence at passage 3 when cocultured with both E. faecalis and E. casseliflavus than when cocultured with either strain alone. Strain relative abundances in cocultures of E. faecalis, E. casseliflavus, and L. lactis. Data from passages 3 and 5 are shown. L. lactis was classified as dose dependent at passage 3, but not at passage 5, using the methods described in SI Appendix, Fig. S6, while neither E. faecalis nor E. casseliflavus exhibited dose dependence at either passage. (D) Dose dependence is stronger in strain-community cocultures than in pairwise cocultures. Strain relative abundances after five passages in cocultures of the D1 community and L. lactis. E. casseliflavus and L. lactis were classified as dose dependent using the methods described in SI Appendix, Fig. S6. (E) Strain relative abundances after five passages in cocultures of L. garvieae and the D2 community. L. garvieae and L. lactis were classified as dose dependent using the methods described in SI Appendix, Fig. S6. (F) Strain relative abundances after five passages in cocultures of E. casseliflavus and the D2 community. E. casseliflavus was classified as dose dependent using the methods described in SI Appendix, Fig. S6. (G) Strain relative abundances after five passages in cocultures of E. faecalis and the D2 community. No strains were classified as dose dependent using the methods described in SI Appendix, Fig. S6. Lines in (C–G) are colored as in Fig. 3A. Strain relative abundances in the cocultures shown in (D–G) after three passages are shown in SI Appendix, Fig. S16, and relative abundances in the cocultures in (E–G) after eight passages are shown in SI Appendix, Fig. S17.

Fig. 6.

Resource-utilization profiles predict dose dependence in strain and community mixtures. (A) Niche overlap was elevated among pairs of strains from the same taxonomic order. Left: niche overlap is quantified as one minus the ratio of the maximum OD₆₀₀ of the focal strain growing in the spent medium of the comparison strain or community after 24 h compared with fresh mBHI (Materials and Methods). Right: Colors show niche overlap between pairs of strain isolates/communities based on growth in spent media. Pairs of strains shown in Fig. 4 are highlighted. (B) Resource consumption rates predict relative dose dependence in pairwise cocultures. Colors show consumption rates of unique and shared resources for pairs of strains shown in Fig. 4. Metabolomic features were classified as unique or shared resources if they were depleted by ≥10,000-fold after 48 h in one or both strains, respectively (Materials and Methods). Coarse-grained nutrients were labeled using our model notation, in which a and b are consumed exclusively by species 1 and species 2, respectively, and ab is consumed by both strains. Consumption rates were quantified by calculating the median metabolomic feature fold change after 4 h for relevant features. (C) Strains that are weaker competitors for shared resources show stronger dose dependence in pairwise coculture. Colors show the dose dependence of strain pairs shown in Fig. 4 after three passages. For each species in a pair, dose dependence was calculated as the magnitude of the ratio of the strain’s relative abundance at the 1,000:1 vs. 1:1,000 mixture ratios, as in Fig. 3C.