Table A5.

Identification of the bacterial OTUs retrieved from early and late incubated eggs.

	Affiliated sequences (%)	Affiliated sequences (%)	Affiliation1
OTU identity	Early incubation	Late incubation	Phylum	Class	Closest hit23	Accession number	Similarity (%)4
0015	1.1	–	Firmicutes	Bacilli	Bacillus azotoformans	AB363732	85
0025	14.1	17.9	Proteobacteria	Gammaproteobacteria	Salmonella enterica	HF969015	99
0035	6.5	17.9	Proteobacteria	Gammaproteobacteria	Salmonella enterica	CP005995	99
004	1.1	–	Proteobacteria	Gammaproteobacteria	Psychrobacter glacinola	AJ297439	99
0055	9.8	20.0	Proteobacteria	Gammaproteobacteria	Salmonella enterica	CP005995	99
0065	2.2	1.1	Firmicutes	Bacilli	Bacillus ginsenggisoli	AB245379	68
007	1.1	–	Firmicutes	Bacilli	Trichococcus pasteurii	X87150	97
0085	7.6	–	Firmicutes	Clostridia	Clostridium sp.	AB596881	100
0095	1.1	–	Proteobacteria	Betaproteobacteria	Burkholderia nodosa	AY533861	94
0105	2.2	–	Firmicutes	Clostridia	Parvimonas micra	JN713239	66
011	1.1	–	Firmicutes	Bacilli	Enterococcus faecium	AF039901	90
012	1.1	–	Firmicutes	Bacilli	Bacillus baekryungensis	AF541965	99
013	1.1	–	Firmicutes	Clostridia	Anaerococcus prevotii	CP001708	71
0145	1.1	–	Firmicutes	Bacilli	Alloiococcus otitis	AB680896	85
015	5.4	–	Firmicutes	Bacilli	Staphylococcus pasteuri	AB009944	100
0165	1.1	–	Firmicutes	Bacilli	Lactobacillus crispatus	AB425941	88
0175	7.6	4.2	Firmicutes	Clostridia	Clostridium sp.	FJ384373	100
018	4.4	–	Firmicutes	Bacilli	Lactobacillus crispatus	AJ242969	99
019	1.1	–	Firmicutes	Bacilli	Enterococcus columbae	AJ301828	94
020	1.1	–	Firmicutes	Bacilli	Lactobacillus salivarius	AY137588	94
021	3.3	4.2	Firmicutes	Bacilli	Enterococcus columbae	AJ301828	100
022	1.1	–	Firmicutes	Bacilli	Lactobacillus sp.	AY445129	89
023	5.4	4.2	Firmicutes	Bacilli	Enterococcus faecium	AF039901	99
024	4.3	1.1	Firmicutes	Bacilli	Lactobacillus agilis	GQ231446	99
0255	1.1	–	Proteobacteria	Betaproteobacteria	Ralstonia sp.	AY509958	97
0265	1.1	–	Firmicutes	Clostridia	Clostridium sp.	JQ248565	90
0275	1.1	–	Firmicutes	Bacilli	Trichococcus pasteurii	L76599	96
0285	1.1	–	Firmicutes	Clostridia	Clostridium sp.	AB596881	94
029	1.1	–	Firmicutes	Bacilli	Lactobacillus salivarius	AY137588	83
030	1.1	–	Firmicutes	Bacilli	Lactobacillus oris	X94229	99
031	1.1	–	Proteobacteria	Gammaproteobacteria	Avibacterium sp.	EU826042	99
032	1.1	–	Firmicutes	Bacilli	Lactobacillus agilis	GQ231446	86
0335	1.1	–	Firmicutes	Clostridia	Clostridium sp.	EU869235	80
034	1.1	–	Firmicutes	Bacilli	Enterococcus columbae	AJ301828	94
0355	1.1	3.2	Firmicutes	Bacilli	Aerococcus viridans	JF496382	100
0365	1.1	–	Firmicutes	Bacilli	Bacillus sp.	FJ348039	68
037	1.1	–	Firmicutes	Bacilli	Enterococcus columbae	AJ301828	91
046	–	10.5	Firmicutes	Bacilli	Staphylococcus sp.	HM028646	100
089	–	8.4	Firmicutes	Bacilli	Enterococcus durans	AJ276354	99
0905	–	1.1	Firmicutes	Bacilli	Lactobacillus gallinarum	AB008208	85
091	–	1.1	Firmicutes	Bacilli	Enterococcus durans	AJ276354	92
0925	–	1.1	Firmicutes	Bacilli	Lactobacillus sp.	EF187258	89
0935	–	1.1	Firmicutes	Bacilli	Enterococcus asini	GQ337016	87
0945	–	1.1	Firmicutes	Bacilli	Aerococcus viridians	JF496443	86
0955	–	1.1	Proteobacteria	Gammaproteobacteria	Salmonella enterica	JQ694378	98
096	–	1.1	Firmicutes	Bacilli	Enterococcus faecalis	UK873	86

¹The taxonomic affiliation is presented at the phyla, class, and genus/species levels and was based on a single representative sequence from each operational taxonomic unit (OTU) clustered at 99% of nucleotide identity.

²The phylogenetic classification was based on a single representative sequence from each OTU clustered at 99% of nucleotide identity.

³When an uncultured bacterium was the closest hit to our sequences, it is the closest genus hit which is mentioned.

⁴The representative sequence was compared with RDP database allowing establishing similarity shared (in percentage) with a reference sequence.

⁵Uncultured bacterium was the closest hit.