Fate, activity, and impact of ingested bacteria within the human gut microbiota

Highlights • Ingested bacteria can temporarily complement resident bacterial communities as part of our transient microbiome. • The extent of integration is highly species- and strain-dependent and may vary depending on dietary context and baseline microbiota structure. • Ingested bacteria can cause major shifts in the composition of the microbiome of the small intestine, whereas alterations in the colon are mostly of limited extent. • Clinical data have provided evidence that ingested bacteria may stimulate production of short-chain fatty acids and inhibit some opportunistic pathogens.