Table 2 Overview of the key finding in this study.

Section “The microbiome is variable during the different regeneration stages”

Figure 1

Figure S1

Developmental stage

The composition of the associated microbiome changes during the regenerative phases. During the initial phases of the regeneration process the relative abundance of Curvibacter increases, while Burkholderia s.l. decreases. The composition changes again in favor of the latter in the later phases of regeneration.

Section “Changing the food source alters planarian physiology, but not profoundly the microbial composition”

Figure 2

Figure S2

Alternative diet

An alternative diet does not significantly alter the microbiome composition of planarians. Other environmentally related factors play a more defining role, as the microbiome after 8 weeks differs from the other timepoints.

Section “External stressors influence the microbial composition”

Figure 3

Figure S3

Exposure to antibiotics

Exposure to antibiotics targeting Gram-negative and Gram-positive bacteria influences the planarian microbiome. The relative abundance of several genera is affected, some specific for the antibiotic uses, while others are affected in both conditions.

Section “External stressors influence the microbial composition”

Figure 3

Figure S3

Exposure to chemical stressors

Exposure to chemical stressors influences the planarian microbiome; i.e. the relative abundance of Firmicutes and Gammaproteobacteria decreased, with a concomitant increase in Bacteroidetes.

Section “External stressors influence the microbial composition”

Figure 4

Recurring patterns after environmental stress

After environmental stress several genera are recurrently affected, including Curvibacter, Ca. Symbiobacter, Undibacterium and Acidovorax.

Section “The microbiome of S. mediterranea is variable over time and over different laboratories”

Figure 5

Temporal variation

Temporal variation is present, both in composition as in diversity. The most abundant phylum was Proteobacteria in all conditions, although the proportion of Bacteroidetes varied.

Section “The microbiome of S. mediterranea is variable over time and over different laboratories”

Figure 6

Figure S5

Origin laboratories

At higher taxonomic level, the ratio of Proteobacteria vs. Bacteroidetes differs depending on the origin laboratory. At lower taxonomic level (i.e. genus) differences were more pronounced.

Section “The microbiomes of closely related planarian species share bacterial taxa”

Figure 7

Figure S6

Planarian species

Closely related planarian species share bacterial taxa and are also dominated by Proteobacteria and Bacteroidetes, although their specific ratios vary.

Section “The microbiome of S. mediterranea is highly variable, although a set of three genera is consistently present in adult animals”

Commonly associated bacteria

Relative abundances at higher taxonomic levels (e.g. Proteobacteria and Bacteroidetes) remain similar over multiple conditions. Within healthy individuals, three common genera were detected: Curvibacter, Staphylococcus and Sphingomonas.

Section “The planarian microbiome might be important for the metabolism of biomolecules”

Figures S7–S8

Functional prediction of associated bacteria

Based on a predictive analyses (with known limitations and no definitive conclusions) we found altered predicted genes involved in the metabolism of biomolecules after exposure to stressors.

Section “The planarian microbiome is present in the gut”

Figure S9

Location of bacteria

Bacteria were detected in the planarian gut.

Multiple

Individual variation

Variation between individuals is present.