TABLE 1.

Select experimental findings on microbial responses to dietary interventions showing that dietary elements beyond fiber often contribute to microbial variation

Resource(s)	Finding(s)	Host	Reference
Fat	Consumption of high-saturated-fat diet increased relative abundance of Bilophila wadsworthia and promoted inflammation in genetically susceptible mice via bile acid alterations	Mouse	83
Fat	High-fat diets altered the gut microbial community, but these responses were idiosyncratic based on fat source	Mouse	112
Fat	High-fat-diet-associated small intestinal microbial community altered lipid digestion even when mice were fed a low-fat diet	Mouse	109
Fat	Switch to Westernized diet produced relative increases in Firmicutes and decreases in Bacteroidetes, a decrease in microbial diversity, and a greater increase in body fat than in controls	Mouse	110
Fat, fiber	Bacterial communities in mice fed low-fat/high-fiber diets or high-fat/high-sugar diets differed in composition but were mostly resilient to diet changes; in contrast, viral communities responded rapidly to switch between diets	Mouse	111
Fat, fiber	Microbial responses to introduction of high-fat/low-fiber or low-fat/high-fiber diets were documented within 24 h but were insufficient to overcome interindividual variability	Human	13
Fat, sugar	High-fat/high-sugar and low-fat/high-fiber diets shaped the gut microbiota consistently across mice with different genotypes and metabolic/immune phenotypes; blending the diets led to proportional changes in the gut microbiota	Mouse	12
Iron	Infant iron supplementation increased enterobacterial and Clostridium abundances, including many pathogens	Human	38
Iron	Child iron supplementation altered the gut microbiota, with a relative increase in enterobacteria and decrease in lactobacilli, even without changing human iron status	Human	146
Protein	Higher dietary casein levels increased total microbial DNA; some taxa, including members of the Clostridia and the sulfate reducer Desulfovibrio, decreased	Mouse	120
Protein	Gut microbial community was responsive to dietary fat content but not protein/sucrose ratio; host adiposity and survival were shaped by protein/sucrose ratio	Mouse	121
Protein	Increasing protein levels led to higher total microbial loads and changes in composition, including Bacteroidaceae absolute abundance	Mouse	24
Protein	High-protein diets changed fecal short-chain-fatty-acid concentrations, most notably reducing butyrate levels while also reducing the proportion of some Firmicutes and members of the Bacteroides	Human	122
Protein	Changes in dietary protein or fiber amt did not alter the microbial community at the phylum level, but high-protein diets were associated with an increase in Oscillibacter and a decrease in Collinsella aerofaciens	Human	123
Protein, fiber	Microbial relative-abundance and diversity responses to altered protein and fiber levels were more significant than responses to changes in fat or energy density across a range of diets	Mouse	23
Protein, fat	Short-term human diet interventions involving high-protein/high-fat diets resulted in rapid changes in the microbiota, including increases in bile-tolerant bacteria like Bilophila wadsworthia and members of the Bacteroides, with concurrent reductions in some Firmicutes	Human	21
Protein, fiber, fat, sugars	Microbiota changes and associated inflammation were consistently recorded in response to various levels of multiple fiber and protein sources but not digestible carbohydrates or most fats	Mouse	189