Diet rapidly and reproducibly alters the human gut microbiome

Abstract

Long-term diet influences the structure and activity of the trillions of microorganisms residing in the human gut1–5, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here, we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila, and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale, and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals2, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi, and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids, and the outgrowth of microorganisms capable of triggering inflammatory bowel disease6. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.

Subspecies in the global human gut microbiome

“…For example, for Eubacterium rectale , one subspecies ( E. rectale MGSS3) was almost exclusive to Chinese samples (see also Truong et al , 2017), while the other two were found in all other countries, including neighboring Kazakhstan (Fig EV2). Strong geographic segregation might explain why associations between E. rectale and host physiology have often proven to be unstable when testing in different cohorts, as these subspecies could not be profiled previously (David et al , 2014). When comparing geographic ranges across bacterial taxa, members of the Firmicutes phylum showed significantly more geographic restrictions compared to all other phyla (Wilcoxon test P ‐value = 0.002).…”

Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux's sifakas (Propithecus verreauxi)

“…While the presence of approximately 60% of bacterial species, and even specific strains, can be remarkably stable (in humans; Faith et al., 2013), short‐term changes in diet can promptly affect relative bacterial abundances (Amato et al., 2015; David et al., 2014; Williams et al., 2013). For example, switching from a high‐fat/low‐fiber to a low‐fat/high‐fiber diet affects the relative abundances of several microbial taxa in humans, for example, Bacteroides and Ruminococcus , within 24 hrs (David et al., 2014; Wu et al., 2011). These diet‐related changes may increase energy extraction from food and consequently alter host metabolic pathways (Sommer & Bäckhed, 2013; Turnbaugh et al., 2006).…”

Biome engineering‐2020

“…The seminal paper for the first approach was published by David et al . (2014). These authors offered 10 US adults a plant‐based or an animal‐based diet for 4 days.…”

“…(2014), no consistent microbiota pattern emerged from studies with long‐term differences in diet. Omnivorous compared with vegetarian young Indian women displayed a weakly increased proportion of E. rectale (Kabeerdoss et al ., 2012).…”

“…One reason could be that the effect of the diet changes on the microbiota did not overcome the inter‐subject variations in the intestinal microbiota (Walker et al ., 2011; Wu et al ., 2011). Notably, only studies using a cross‐over design where both diets were given to the same subjects showed clear effects (David et al ., 2014). Another reason could be that the orally ingested food represents only part of the food source for the gut microbiota.…”