Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle

Abstract

Background: Human-to-human transmission of symbiotic, anaerobic bacteria is a fundamental evolutionary adaptation essential for membership of the human gut microbiota. However, despite its importance, the genomic and biological adaptations underpinning symbiont transmission remain poorly understood. The Firmicutes are a dominant phylum within the intestinal microbiota that are capable of producing resistant endospores that maintain viability within the environment and germinate within the intestine to facilitate transmission. However, the impact of host transmission on the evolutionary and adaptive processes within the intestinal microbiota remains unknown.

Results: We analyze 1358 genomes of Firmicutes bacteria derived from host and environment-associated habitats. Characterization of genomes as spore-forming based on the presence of sporulation-predictive genes reveals multiple losses of sporulation in many distinct lineages. Loss of sporulation in gut Firmicutes is associated with features of host-adaptation such as genome reduction and specialized metabolic capabilities. Consistent with these data, analysis of 9966 gut metagenomes from adults around the world demonstrates that bacteria now incapable of sporulation are more abundant within individuals but less prevalent in the human population compared to spore-forming bacteria.

Conclusions: Our results suggest host adaptation in gut Firmicutes is an evolutionary trade-off between transmission range and colonization abundance. We reveal host transmission as an underappreciated process that shapes the evolution, assembly, and functions of gut Firmicutes.

Keywords: Bacterial transmission; Genome evolution; Genome reduction; Host adaptation; Intestinal microbiota; Metabolic specialization; Metagenomics; Microbiome; Sporulation.

Fig. 1

Sporulation loss in distinct evolutionary lineages of gut Firmicutes. a Prediction of sporulation capability in human-associated Firmicutes families based on the presence of 66 sporulation-associated genes. Erysipelotrichaceae, Peptostreptococcaceae, Clostridiaceae, Ruminococcaceae, and Lachnospiraceae families have a bimodal pattern with genomes either having a high scoring (blue dots) (classified as Spore-Formers) or a low scoring sporulation signature score (red dots) (classified as Former-Spore-Formers). Lactobacillaceae, Enterococcaceae, Actinobacteria, Bacteroidetes, and Proteobacteria are all non-spore-forming (yellow dots) and contain low scoring genomes that lack spo0A which is essential for sporulation. b Presence and absence of sporulation signature genes were determined in gut-associated Spore-Formers (SF) (n=456) and Former-Spore-Formers (FSF) (n=117) bacteria. FSF have less sporulation signature genes for all sporulation stages compared to SF (all stages q< 0.0001, except for stage 0 q=0.0491, Fisher’s exact test, adjusted for multiple testing). The cartoon describes sporulation stages. c Phylogeny of the Firmicutes constructed from 40 universal protein-coding genes extracted from 1358 whole-genome sequences. Sporulation has been lost at large taxonomic scales (Lactobacillales order) and at small taxonomic scales (within host-associated Erysipelotrichales and Clostridiales orders). Major taxonomic orders are indicated by branch colors and name, black branches at the base of phylogeny represent non-Firmicutes root derived from Actinobacteria genomes

Fig. 2

Genome reduction and metabolic specialization during host-adaptation by gut Former-Spore-Formers. a A marker of host adaptation, genomes of gut FSF are smaller than SF genomes (P< 0.0001, Mann-Whitney test), with a strong correlation between genome size and gene number, Spearman rho, R= 0.96 for SF and R= 0.89 for FSF. Inset shows distribution by genome size. b Functional enrichment analysis revealed 489 enriched gut SF genes and 272 enriched FSF genes. Enriched genes were grouped by functional classes. The graph presents the comparison of enriched gene numbers in their functional class and ordered by decreasing statistical significance. Motility, amino acid and cofactor metabolism and sporulation functional classes are statistically more enriched in gut Spore-Formers (SF) compared to Former-Spore-Formers (FSF). No functional classes are more enriched in FSF. Fisher’s exact test, N.S. = not significant. c FSF encode a smaller number of total CAZymes and a smaller number of CAZyme families per genome compared to gut SF (P<0.0001 for both total number and family number, Welch’s t-test). Inset shows the distribution by CAZyme number. d Erysipelotrichaceae FSF have a more restricted carbohydrate utilization profile compared to Erysipelotrichaceae SF. The ability of FSF (n=4) and SF (n=4) to use 95 different carbon sources was tested. N-Acetyl-Beta-D-Mannosamine (P=0.006) (a precursor of sialic acid), D-Melezitose (P=0.009), turanose (P=0.011), glycerol (P=0.020) and maltotriose (P=0.029) are metabolized to a statistically significant greater degree by SF whereas urocanic acid (a derivative of histidine) was metabolized to a statistically significant greater degree by FSF (P=0.018), based on Fisher’s exact test

Fig. 3

Host adaptation is associated with reduced prevalence and higher colonization abundance levels in Former-Spore-Formers. a Former-Spore-Formers are less prevalent (P=0.0015, two-tailed Wilcoxon rank-sum test) compared to Spore-Formers within 9966 fecal metagenomes reflecting a reduced transmission range. b While less prevalent, Former-Spore-Formers are more abundant (P=0.0034, two-tailed Wilcoxon rank-sum test) compared to Spore-Formers within the same 9966 fecal metagenomes reflecting greater host adaptation and an ability to colonize to higher levels. Each dot represents an individual species. Box lengths represent the IQR of the data, and the whiskers the lowest and highest values within 1.5 times the IQR from the first and third quartiles, respectively

Fig. 4

Host adaptation is associated with an altered transmission cycle in gut Firmicutes. Former-Spore-Formers (FSF) are more host-adapted compared to Spore-Forming (SF) bacteria as measured by their reduced genome size and genomic redundancy and their more specialist metabolic capabilities. This greater level of host-adaptation corresponds to an ability to colonize to higher abundance levels which promote onward direct transmission to hosts in close proximity. By contrast, SF are less host-adapted and colonize to lower abundance levels. SF transmission cycle relies on the production of resilient spores that promote environmental persistence; thus, they are capable of colonizing a greater proportion of hosts and have a greater prevalence in human populations. Figure adapted from [7]