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Table 1 The relative effects of biological covariates affecting the microbiome

From: Tiny microbes, enormous impacts: what matters in gut microbiome studies?

Covariate References Findings
Large
 Host species [4144] The gut microbiome of host species separates by dietary patterns and phylogeny. Animals that have diets that diverge from those of their ancestors have microbiomes that are adapted to their new diets.
 Age [45, 46, 52] Infants have dramatically different microbiomes to adults, and undergo a rapid period of developmental maturation. After the introduction of solid food, the microbiomes of older children begin to resemble those of their parents and move toward an adult community structure.
 Lifestyle [45, 54] Western adults and adults living traditional lifestyles (e.g., agriculturists, hunter-gatherers) have large differences in their microbiomes.
Medium
 Antibiotic use [55, 56, 58, 59] Antibiotics have a sustained effect on the microbiome, leading to altered community structure and lower alpha diversity. Individualized responses to the same antibiotic vary, and different antibiotics may have different impacts.
Medium to small; difficult to rank
 Long-term dietary patterns [61, 62] A low-fiber diet leads to the loss of species, although diversity can be recovered by returning to a high-fiber diet.
 Non-antibiotic xenobiotics [6973] Drugs including actominopin, proton pump inhibitors, and metformin alter the microbiome. Microbial metabolism may contribute to side effects associated with drugs.
 Genetics [3, 66, 67] Identical twins have microbiomes that have more similarity than those of fraternal twins. Some clades are heritable, although the heritability varies. Microbes that coevolved with an ancestral group may be better symbionts.
 Exercise [6365] Extreme athletes have different microbiomes than sex-, age-, and weight-matched controls. It is, however, difficult to separate the effect of diet from the effect of exercise. Mouse models suggest that exercise alone has an impact.
 Pet ownership and cohabitation [68] Individuals living together—whether genetically related or unrelated—share more of their microbiomes than people who do not cohabitate. Pets act as vectors, although their largest effect is on the skin microbiome.
Small
 Short-term dietary intervention [61, 74] Short-term diet may change microbial communities, but they return to the previous configuration once the intervention has ended.