Table 3.

Studies analysing microbiota population dynamics in vivo

Bacterium	Method	Number of unique identifiers	Analysed parameters	Main finding	References
E. coli, Klebsiella michiganensis (K. michiganensis)	Fluorescent proteins	2	Intestinal colonization	K. michiganensis provides colonization resistance against E. coli	52
E. coli	Fluorescent proteins	2	Niche competition in intestinal colonization	Horizontal gene transfer promotes niche adaptation	60
Microbiota	16S sequencing, qPCR quantification	n.a.	Replication and death rate of microbiota exposed to bile salts	Diet‐evoked increased bile salt concentrations perturb microbiota composition and lead to decreased colonization resistance to S. Typhimurium	59
Several microbiota members (mouse)	qPCR (16S)	n.a.	Replication rate, interstrain interactions	Colonization dynamics in the murine intestine	58
Several microbiota members (fruitfly)	Plating	n.a.	Transition time through intestine, intra‐intestinal replication and death rate	Colonization dynamics in the intestine of Drosophila melanogaster	57

bp = base pairs, n.a. = not applicable.