Shifting Climates, Foods, and Diseases: The Human Microbiome through Evolution

Abstract

Human evolution has been punctuated by climate anomalies, structuring environments, deadly infections, and altering landscapes. How well humans adapted to these new circumstances had direct effects on fitness and survival. Here, how the gut microbiome could have contributed to human evolutionary success through contributions to host nutritional buffering and infectious disease resistance is reviewed. How changes in human genetics, diet, disease exposure, and social environments almost certainly altered microbial community composition is also explored. Emerging research points to the microbiome as a key player in host responses to environmental change. Therefore, the reciprocal interactions between humans and their microbes are likely to have shaped human patterns of local adaptation throughout our shared evolutionary history. Recent alterations in human lifestyle, however, are altering human microbiomes in unprecedented ways. The consequences of interrupted host–microbe relationships for human adaptive potential in the future are unknown.

Locally adapted gut microbiomes mediate host stress tolerance

“…This pattern where most D. magna genotypes had a higher fitness, in terms of survival and fecundity, when they received a local (sympatric) than a foreign (allopatric) microbiome, is in agreement with what we expected. It has earlier been shown that in stressful environments, hosts may benefit from locally adapted microbes, as hosts may use specific microbial communities with large phenotypic effects to specialize and persist in novel niches [ 37 – 41 ]. However, because of the reciprocal transplant procedure, our study is unique by providing a causal link between fitness effects and local microbiomes.…”

“…The composition of gut microbiomes differs spatially in function of the regional environmental conditions [30][31][32][33][34], and there is some evidence that different host genotypes differ in their gut microbiome [35,36]. It is therefore likely that when hosts show local genetic adaptation, this may be misleading as their gut microbiome may, at least partly, be contributing to this pattern [37]. There is recent evidence that the gut microbiome plays a role in local adaptation to environments differing in, for example, pollution [38], aridity [39] and salinity [40,41].…”

The Internal, External and Extended Microbiomes of Hominins

“…It was also likely exposed to novel disease landscapes. A plastic microbiome that could shift rapidly both within and across individuals and populations could have facilitated dietary diversity by contributing key metabolic pathways to maximize nutritional output from a range of foods and may have also increased the ability of H. erectus to endure new diseases (Amato et al, 2019a). While we cannot assess H. erectus microbiomes directly, modern human microbiomes exhibit more inter-individual variation compared to closely related non-human primates (Schnorr et al, 2016;Amato et al, 2019b).…”

Microbial control of host gene regulation and the evolution of host–microbiome interactions in primates

“…Under increasingly variable environmental conditions, microbial plasticity may become more advantageous. Indeed, microbial flexibility in early humans is proposed to have played a key role in adapting to climate-induced environmental changes [108], and Stumpf et al [109] suggest monitoring microbiomes as part of wild primate conservation.…”