TABLE 1.

Microbiome-dependent ontogenetic timing (MiDOT) examples from host-microbe associations across terrestrial and aquatic organisms^a

Host (reference)	Transition	Microbe	Transmission or mode of acquisition	Absolute or modulating effectb	Effectc
Mosquitoes (1, 4, 5)	Past 1st instar	Nonspecific	Aquatic environment	Absolute	NEI. Without microbiome, larvae do not develop past 1st instar and die.
Hydrothermal vent tubeworms (55)	Adult	Different gamma- proteobacterial species	Aquatic environment	Absolute	SMS. Larvae hatch without symbionts but acquire symbionts during settlement, losing digestive tract, surviving solely through mutualism with symbiotic bacteria.
C. elegans (52, 56)	Adult/ reproduction	Enterobacteriaceae species, Comamonas	Diet	Modulate	SMS. Different bacterial isolates can accelerate development compared to Escherichia coli.
Drosophila melanogaster (2, 47, 57, 58)	Pupation	Acetobacter and Lactobacillus species	Diet	Modulate	MOS. Sterile flies were slower to pupate than flies harboring bacteria. Acetobacter often accelerates, but Lactobacillus slows development.
Dung beetles Onthophagus gazella (59)	Pupation	Community	Brood ball	Modulate	NEI. Removal of maternally provisioned bacteria in the brood ball slows time to pupation and adult size. Soil microbes not associated with beetles do not rescue development.
Daphnia magna (60, 61)	Reproduction	Community	Aquatic environment	Modulate	MOS. Without microbiome, time to first egg bearing is longer compared to conventionally reared Daphnia. An increase in Acidovorax (or microbiomes enriched for) bacteria above conventionally reared Daphnia increases the percentage of adults bearing eggs over time.
Arabidopsis thaliana + Brassica rapa (48)	Flowering time	Community	Soil	Modulate	NEI. Experimentally evolved soil microbes for slow and fast flowering time determined flowering time in unevolved host plants.
Brassica rapa (8)	Flowering time	Community	Soil	Modulate	NEI. Drought-adapted accelerated flowering time compared to wet-adapted microbiomes in unevolved host plants, independent of drought conditions.
Boechera stricta (3)	Flowering time	Community	Soil	Modulate	NEI. Different bacterial communities determined flowering time in controlled genetic background of host plants.
Cuban tree frog Osteopilus septentrionalis (62)	Metamorphosis time	Community	Aquatic environment and other unknown sources	Modulate	NEI. Tadpoles raised in autoclaved water and long-term antibiotic treatment took twice as long to metamorphose and had lowered survival.
Turquoise killifish Nothobranchius furzeri (63)	Aging onset	Community	Aquatic environment	Modulate	NEI. Community transplant of microbiome of young fish into older fish increased life span and onset of aging.

^aIn these examples, experiments controlling host and microbiome variation indicate that the microbiome is a key driver in ontogenetic timing for these associations between host and environmentally acquired microbes.

^bEffects can be absolute (where transition fails to occur in the absence) or modulating (where microbes speed or slow transition).

^cWe also indicate whether the effect can be attributed to a single microbe species (SMS), more than one species (MOS) (both of which imply construction and testing of synthetic microbiomes) or whether this was not explicitly investigated (NEI).