Human gut microbiota directly influences health and provides an extra means of adaptive potential to different lifestyles. To explore variation in gut microbiota and to understand how these bacteria may have co-evolved with humans, here we investigate the phylogenetic diversity and metabolite production of the gut microbiota from a community of human hunter-gatherers, the Hadza of Tanzania. We show that the Hadza have higher levels of microbial richness and biodiversity than Italian urban controls. Further comparisons with two rural farming African groups illustrate other features unique to Hadza that can be linked to a foraging lifestyle. These include absence of Bifidobacterium and differences in microbial composition between the sexes that probably reflect sexual division of labour. Furthermore, enrichment in Prevotella, Treponema and unclassified Bacteroidetes, as well as a peculiar arrangement of Clostridiales taxa, may enhance the Hadza’s ability to digest and extract valuable nutrition from fibrous plant foods.

Summary We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing ~2/3 of the ancestry of Malawi hunter-gatherers ~8100–2500 years ago, and ~1/3 of Tanzanian hunter-gatherers ~1400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ~3100 year-old pastoralist from Tanzania contributed ancestry to people from northeast to southern Africa, including a ~1200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving long-distance gene flow, or a lineage more deeply diverging than that of the San contributing more to some western Africans than others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations.

Significance Lévy walks are a random walk search strategy used by a wide variety of organisms when searching for heterogeneously distributed food. This type of search involves mostly short move steps (defined as the distance traveled before pausing or changing direction) combined with rarer longer move steps. Here, we show that the Hadza, hunter–gatherers from northern Tanzania, perform Lévy walks when foraging for a wide variety of food items, suggesting that Lévy walks are an important movement pattern for the most cognitively complex foragers on Earth. Our results suggest that scale-invariant, superdiffusive movement profiles are a fundamental feature of human landscape use, regardless of the physical or cultural environment, and may have played an important role in the evolution of human mobility.

Western lifestyles differ markedly from those of our hunter-gatherer ancestors, and these differences in diet and activity level are often implicated in the global obesity pandemic. However, few physiological data for hunter-gatherer populations are available to test these models of obesity. In this study, we used the doubly-labeled water method to measure total daily energy expenditure (kCal/day) in Hadza hunter-gatherers to test whether foragers expend more energy each day than their Western counterparts. As expected, physical activity level, PAL, was greater among Hadza foragers than among Westerners. Nonetheless, average daily energy expenditure of traditional Hadza foragers was no different than that of Westerners after controlling for body size. The metabolic cost of walking (kcal kg−1 m−1) and resting (kcal kg−1 s−1) were also similar among Hadza and Western groups. The similarity in metabolic rates across a broad range of cultures challenges current models of obesity suggesting that Western lifestyles lead to decreased energy expenditure. We hypothesize that human daily energy expenditure may be an evolved physiological trait largely independent of cultural differences.

Highlights d Thousands of gut bacterial genomes from worldwide human populations were sequenced d HGT occurs at high frequency in the gut microbiome of individual persons d HGT occurs more frequently in the microbiome of industrialized and urban populations d Transferred gene functions in the microbiome reflect the lifestyle of the host