Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

Abstract

Microbial organisms inhabit virtually all environments and encompass a vast biological diversity. The pangenome concept aims to facilitate an understanding of diversity within defined phylogenetic groups. Hence, pangenomes are increasingly used to characterize the strain diversity of prokaryotic species. To understand the interdependence of pangenome features (such as the number of core and accessory genes) and to study the impact of environmental and phylogenetic constraints on the evolution of conspecific strains, we computed pangenomes for 155 phylogenetically diverse species (from ten phyla) using 7,000 high-quality genomes to each of which the respective habitats were assigned. Species habitat ubiquity was associated with several pangenome features. In particular, core-genome size was more important for ubiquity than accessory genome size. In general, environmental preferences had a stronger impact on pangenome evolution than phylogenetic inertia. Environmental preferences explained up to 49% of the variance for pangenome features, compared with 18% by phylogenetic inertia. This observation was robust when the dataset was extended to 10,100 species (59 phyla). The importance of environmental preferences was further accentuated by convergent evolution of pangenome features in a given habitat type across different phylogenetic clades. For example, the soil environment promotes expansion of pangenome size, while host-associated habitats lead to its reduction. Taken together, we explored the global principles of pangenome evolution, quantified the influence of habitat, and phylogenetic inertia on the evolution of pangenomes and identified criteria governing species ubiquity and habitat specificity.These authors contributed equally: Oleksandr M. Maistrenko, Daniel R. Mende

Quantifying the information content of lake microbiomes using a machine learning-based framework

“…Applying our framework to a microbial ecology dataset collected in a large-scale survey of European lakes, the results suggest that lower levels of microbial taxonomy share a higher level of information with lake parameters (figures 1 and 2B). This supports the hypothesis that OTUs from the same species can react to environmental change differently and might, therefore, inhabit different ecological niches [44,47,[84][85][86]. Furthermore, our results show that, for most physico-chemical parameters, higher levels of taxonomy do not contain information not already present on the OTU level (see figure 3B), which is in contrast to the findings of others [87].…”

The hidden pangenome: comparative genomics reveals pervasive diversity in symbiotic and free-living sulfur-oxidizing bacteria

“…Hence, we wanted to assess to what extent other factors, such as lifestyle and environment, contribute to the evolution of the family pangenome. This is of particular interest because recent data suggest that the environment is a strong driver of pangenome evolution, explaining more of the observed pangenome variation than phylogeny alone [69]. To tease apart the role of different environmental factors, we clustered the orthologous protein sequences of the 'species pangenomes' to determine which protein sequences are shared between species or unique to species that share a specific lifestyle or environment (Fig.…”

From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes

“…However, as these genomic steps form the basis for all subsequent analyses including the functional characterisation of organisms, it is crucial for the MAGs to be reliable and to reflect the diversity of the sampled environment. In this direction, strain-resolved metagenomics appears as a critical open challenge in the field, and given the extraordinary genomic plasticity of different strains of the same species [28] , it becomes all the more important to not only define a core genome of a species, but to capture reliably the pangenome. Therefore, specialised functionality of a strain residing within a patient can be characterised together with the metabolic pathways expected within a community, to enable personalised microbiota profiling.…”

“…Reconstructing genes and genomes of microbes is extremely important to understand ecosystems, and fine-scaled deviations that might occur in non-normal states, such as complex diseases in hosts. This is because ongoing genome sequencing projects have shown the bacterial genome to be highly dynamic [28] , with mobile genetic elements and other molecular mechanisms exchanging genes between strains of the same species, or between different species. Whether this genome fluidity is an adaptive mechanism is still under active debate [29] , [30] , but for diseases such as cystic fibrosis we know that pathogens lose virulence factors as an adaptation for long term host colonisation [31] .…”

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