Table 1. Genera found in greater than 90% of larval, juvenile or adult intestines.

Genus or best (taxa level) classification	Phylum	All intestinal samples		Larval		Juvenile		Adult		Relative core genera from Roeselers et al., 2011a	Zebrafish isolated strain representatives with genome sequencesb,c
		% Presence in all intestines (n=137)d	% Total intestinal readse	% Presence in larval intestines (n=40)	% Total larval readse	% Presence in juvenile intestines (n=57)	% Total juvenile readse	% Presence in adult intestines (n=38)	% Total adult readse
Unclassified Aeromonadaceae (family)	Proteobacteria	100.00	13.92	100.00	14.22	100.00	16.92	100.00	9.84	Aeromonas	ZOR0001, ZOR0002
Shewanella	Proteobacteria	97.08	2.65	100.00	6.77	100.00	1.07	89.47	0.76	Shewanella	ZOR0012
Unclassified Enterobacteriaceae (family)	Proteobacteria	95.62	2.82	100.00	7.32	100.00	0.77	84.21	1.32	Unclassified Enterobacteriaceae	ZOR0011, ZOR0014
Other Enterobacteriaceae (family)	Proteobacteria	95.62	1.35	100.00	3.46	94.74	0.65	92.11	0.24
Unclassified Comamonadaceae (family)	Proteobacteria	95.62	11.31	97.50	6.03	100.00	21.39	89.47	2.35	Diaphorobacter	ZNC0006, ZNC0007, ZNC0008
Plesiomonas	Proteobacteria	95.62	6.81	97.50	8.95	91.23	0.96	100.00	12.35		ZOR0011
Other Gammaproteobacteria (class)	Proteobacteria	94.89	0.88	100.00	2.34	96.49	0.35	86.84	0.18
Cetobacterium	Fusobacteria	94.89	6.92	85.00	0.38	98.25	1.31	100.00	22.39	Cetobacterium	ZWU0022, ZOR0034
Unclassified Neisseriaceae (family)	Proteobacteria	94.16	3.76	95.00	0.40	100.00	8.01	89.47	1.14		ZOR0017
Pseudomonas	Proteobacteria	90.51	3.49	100.00	4.13	100.00	4.01	71.05	2.22	Pseudomonas	ZWU0006
Rhodobacter	Proteobacteria	89.78	1.10	87.50	0.20	100.00	1.51	81.58	1.47
Other Pseudomonadaceae (family)	Proteobacteria	89.05	0.62	97.50	0.80	94.74	0.60	73.68	0.48
Unclassified CK-1C4-19 (class)	Firmicutes	89.05	4.76	80.00	0.46	91.23	0.94	94.74	13.97		ZOR0006
Other Comamonadaceae (family)	Proteobacteria	86.86	1.10	95.00	0.92	98.25	1.95	65.79	0.07
Unclassified Xanthomonadaceae (family)	Proteobacteria	84.67	0.38	100.00	0.79	78.95	0.21	78.95	0.23	Stenotrophomonas
Vibrio	Proteobacteria	83.21	1.83	100.00	5.39	89.47	0.55	57.89	0.10	Vibrio	ZWU0020, ZOR0035
Unclassified Betaproteobacteria (class)	Proteobacteria	81.75	0.22	97.50	0.39	91.23	0.23	55.26	0.04
Unclassified Rhizobiales (order)	Proteobacteria	81.75	1.44	75.00	0.15	100.00	3.21	63.16	0.23		ZNC0028, ZNC0032
Pseudoalteromonas	Proteobacteria	81.02	2.01	100.00	5.48	96.49	0.89	39.47	0.13
Unclassified Legionellales (order)	Proteobacteria	80.29	0.74	87.50	0.87	98.25	0.85	50.00	0.49
Unclassified Aeromonadales (order)	Proteobacteria	78.83	0.18	97.50	0.19	71.93	0.13	73.68	0.23		ZOR0001, ZOR0002
Unclassified Hyphomicrobiaceae (family)	Proteobacteria	78.83	0.30	90.00	0.60	87.72	0.23	57.89	0.11
Other Rhizobiales (order)	Proteobacteria	78.83	3.18	85.00	1.47	100.00	6.56	42.11	0.07
Other Betaproteobacteria (class)	Proteobacteria	77.37	0.16	85.00	0.15	100.00	0.26	39.47	0.02
Unclassified Rhodospirillaceae (family)	Proteobacteria	75.91	0.22	92.50	0.36	85.96	0.18	47.37	0.12
Streptococcus	Firmicutes	72.99	0.63	100.00	1.73	77.19	0.26	42.11	0.08	Streptococcus
Delftia	Proteobacteria	72.26	0.30	92.50	0.33	66.67	0.13	63.16	0.54		ZNC0008
Unclassified Pseudomonadaceae (family)	Proteobacteria	70.80	0.41	90.00	0.37	87.72	0.69	28.95	0.07		ZWU0006
Unclassified Rhodobacteraceae (family)	Proteobacteria	70.07	0.89	40.00	0.03	98.25	1.91	63.16	0.29
Other Rhodobacteraceae (family)	Proteobacteria	68.61	1.80	20.00	0.02	100.00	3.99	73.68	0.48
Unclassified Vibrionaceae (family)	Proteobacteria	67.88	1.34	72.50	0.23	45.61	0.02	94.74	4.54	Vibrio	ZWU0020, ZOR0018, ZOR0035
Pelomonas	Proteobacteria	66.42	0.81	97.50	1.52	68.42	0.84	34.21	0.04
Marinomonas	Proteobacteria	65.69	0.25	92.50	0.64	82.46	0.14	15.79	0.01
Unclassified Rhizobiaceae (family)	Proteobacteria	64.23	1.83	47.50	0.05	96.49	4.08	34.21	0.43		ZNC0028
Corynebacterium	Actinobacteria	62.77	0.43	95.00	1.24	56.14	0.12	39.47	0.05
Mycobacterium	Actinobacteria	62.77	0.26	92.50	0.48	56.14	0.07	44.74	0.33
Zoogloea	Proteobacteria	61.31	0.48	90.00	1.40	54.39	0.13	42.11	0.08
Halomonas	Proteobacteria	60.58	1.19	95.00	3.54	70.18	0.35	13.16	0.04
Erwinia	Proteobacteria	58.39	0.14	95.00	0.38	50.88	0.06	34.21	0.02
Staphylococcus	Firmicutes	56.93	0.41	92.50	0.64	43.86	0.49	39.47	0.07		ZWU0021
Candidatus Rhabdochlamydia	Chlamydiae	50.36	0.21	92.50	0.68	42.11	0.02	21.05	0.03

^aGenera shared in all adults from Roeselers, et al. are listed with corresponding genera (or family where genus was ambiguous) from this study. No attempt is made to relate the single core operational taxonomic unit (OTU) from Roeselers, et al. with only a phylum-level assignment.

^bIsolated strains with newly sequenced genomes that belong within a listed taxonomic group. Some strains are listed more than once where they may fall within more than one taxonomic grouping that could not be confidently classified to finer levels with short Illumina reads.

^cIsolated strains which were identified as discriminatory for a given age class are highlighted in bold (larval), italics (juvenile) or underlined (adult).

^d'All intestines' includes the two parent samples as well as the larval, juvenile and adult intestines from their offspring, listed to the right.

^ePercentages are derived from samples rarefied to 4250 sequences per sample.