Age-related differences in the cloacal microbiota of a wild bird species

van Dongen, Wouter FD; White, Joël; Brandl, Hanja B; Moodley, Yoshan; Merkling, Thomas; Leclaire, Sarah; Blanchard, Pierrick; Danchin, Étienne; Hatch, Scott A; Wagner, Richard H

doi:10.1186/1472-6785-13-11

Table 1 Identity of OTUs isolated from cloacae of black-legged kittiwakes

OTU	ARISA peak	Clone	Difference	BLAST match	BLAST score	Most derived phylogenetic position	Phylum	Found in
1	304	308	+4	Peptoniphilus asaccharolyticus	152	Genus: Peptoniphilus	Firmicutes	Ad
1	305	309	+4	Peptoniphilus asaccharolyticus	152	Genus: Peptoniphilus	Firmicutes	Ad
1	396	399	+3	Peptoniphilus asaccharolyticus	152	Genus: Peptoniphilus	Firmicutes	Ad
1	397	400	+3	Peptoniphilus asaccharolyticus	152	Genus: Peptoniphilus	Firmicutes	Ad
1	398	401	+3	Peptoniphilus asaccharolyticus	152	Genus: Peptoniphilus	Firmicutes	Ad
2	313	315	+2	Enterococcus pseudoavium	228	Genus: Enterococcus	Firmicutes	Ch
3	331	331	0	Enterococcus faecalis	211	Order: Lactobacillales	Firmicutes	Ad, Ch
3	432	433	+1	Enterococcus faecalis	211	Order: Lactobacillales	Firmicutes	Ad, Ch
4	340	341	+1	Enterococcus malodoratus	239	Genus: Enterococcus	Firmicutes	Ch
4	341	342	+1	Enterococcus malodoratus	239	Genus: Enterococcus	Firmicutes	Ch
4	433	434	+1	Enterococcus malodoratus	239	Genus: Enterococcus	Firmicutes	Ch
5	345	342	−3	Corynebacterium propinquum	239	Genus: Corynebacterium	Actinobacteria	Ad
5	346	343	−3	Corynebacterium propinquum	239	Genus: Corynebacterium	Actinobacteria	Ad
5	347	344	−3	Corynebacterium propinquum	239	Genus: Corynebacterium	Actinobacteria	Ad
5	348	345	−3	Corynebacterium propinquum	239	Genus: Corynebacterium	Actinobacteria	Ad
6		342		Enterococcus malodoratus	206	Order: Lactobacillales	Firmicutes	Ch
7	348	349	+1	Arthromitus sp.	233	Genus: Arthromitus	Firmicutes	Ad, Ch
7	418	419	+1	Arthromitus sp.	233	Genus: Arthromitus	Firmicutes	Ad, Ch
8		349		Lactobacillus salivarius	206	Genus: Lactobacillus	Firmicutes	Ch
9	349	350	+1	Lactobacillus animalis	213	Genus: Lactobacillus	Firmicutes	Ad, Ch
9	440	443	+3	Lactobacillus animalis	213	Genus: Lactobacillus	Firmicutes	Ad, Ch
9	441	444	+3	Lactobacillus animalis	213	Genus: Lactobacillus	Firmicutes	Ad, Ch
9	519	520	+1	Lactobacillus animalis	213	Genus: Lactobacillus	Firmicutes	Ad, Ch
9	520	521	+1	Lactobacillus animalis	213	Genus: Lactobacillus	Firmicutes	Ad, Ch
10	352	353	+1	Aerococcus urinae	222	Order: Lactobacillales	Firmicutes	Ad
11	357	354	−3	Corynebacterium aurimucosum	196	Genus: Corynebacterium	Actinobacteria	Ad
12		357		Atopobium parvulum	204	Order: Clostridiales	Firmicutes	Ad
13		357		Carnobacterium mobile	237	Genus: Carnobacterium	Firmicutes	Ch
13		463		Carnobacterium mobile	237	Genus: Carnobacterium	Firmicutes	Ch
14		357		Lactobacillus crispatus	237	Genus: Lactobacillus	Firmicutes	Ad
14	603	607	+4	Lactobacillus crispatus	237	Genus: Lactobacillus	Firmicutes	Ad
15		361		Bacillus megaterium	215	Genus: Bacillus	Firmicutes	Ch
16	365	361	−4	Mycobacterium sp.	161	Suborder: Corynebacterineae	Actinobacteria	Ad
16	366	362	−4	Mycobacterium sp.	161	Suborder: Corynebacterineae	Actinobacteria	Ad
16	367	363	−4	Mycobacterium sp.	161	Suborder: Corynebacterineae	Actinobacteria	Ad
16	368	364	−4	Mycobacterium sp.	161	Suborder: Corynebacterineae	Actinobacteria	Ad
16	369	365	−4	Mycobacterium sp.	161	Suborder: Corynebacterineae	Actinobacteria	Ad
16	371	367	−4	Mycobacterium sp.	161	Suborder: Corynebacterineae	Actinobacteria	Ad
17		363		Oceanobacillus iheyensis	187	Class: Bacilli	Firmicutes	Ch
18	380	375	−5	Arcanobacterium abortisuis	174	Family: Actinomycetaceae	Actinobacteria	Ad
19		377		Clostridium difficile	217	Genus: Clostridium	Firmicutes	Ch
20	376	378	+2	Enterococcus faecalis	239	Genus: Enterococcus	Firmicutes	Ch
20	478	480	+2	Enterococcus faecalis	239	Genus: Enterococcus	Firmicutes	Ch
21	392	388	−4	Corynebacterium aurimucosum	182	Genus: Corynebacterium	Actinobacteria	Ad
22	388	390	+2	Pediococcus inopinatus	174	Order: Lactobacillales	Firmicutes	Ch
23	392	395	+3	Clostridium piliforme	219	Genus: Clostridium	Firmicutes	Ch
23	393	396	+3	Clostridium piliforme	219	Genus: Clostridium	Firmicutes	Ch
24		398		Acidimicrobineae sp.	180	Phylum: Actinobacteria	Actinobacteria	Ad
25		400		Clostridium piliforme	209	Genus: Clostridium	Firmicutes	Ad
25	753	756	+3	Clostridium piliforme	209	Genus: Clostridium	Firmicutes	Ad
26	398	401	+3	Staphylococcus vitulinus	243	Genus: Staphylococcus	Firmicutes	Ch
26	399	402	+3	Staphylococcus vitulinus	243	Genus: Staphylococcus	Firmicutes	Ch
26	406	407	+1	Staphylococcus vitulinus	243	Genus: Staphylococcus	Firmicutes	Ch
26	430	431	+1	Staphylococcus vitulinus	243	Genus: Staphylococcus	Firmicutes	Ch
26	431	432	+1	Staphylococcus vitulinus	243	Genus: Staphylococcus	Firmicutes	Ch
26	489	492	+2	Staphylococcus vitulinus	243	Genus: Staphylococcus	Firmicutes	Ch
26	520	520	0	Staphylococcus vitulinus	243	Genus: Staphylococcus	Firmicutes	Ch
26	521	521	0	Staphylococcus vitulinus	243	Genus: Staphylococcus	Firmicutes	Ch
26		621		Staphylococcus vitulinus	243	Genus: Staphylococcus	Firmicutes	Ch
27	421	422	+1	Bacillus sp.	213	Genus: Bacillus	Firmicutes	Ch
27	422	423	+1	Bacillus sp.	213	Genus: Bacillus	Firmicutes	Ch
27	570	568	+2	Bacillus sp.	213	Genus: Bacillus	Firmicutes	Ch
27	589	590	+1	Bacillus sp.	213	Genus: Bacillus	Firmicutes	Ch
28		434		Streptococcus parauberis	231	Genus: Streptococcus	Firmicutes	Ch
29		438		Acidimicrobiaceae sp.	189	Phylum: Actinobacteria	Actinobacteria	Ch
30	437	439	+2	Staphylococcus saprophyticus	239	Genus: Staphylococcus	Firmicutes	Ch
30	438	440	+2	Staphylococcus saprophyticus	239	Genus: Staphylococcus	Firmicutes	Ch
31	446	441	−5	Corynebacterium propinquum	182	Genus: Corynebacterium	Actinobacteria	Ad
32	443	445	+3	Bacillus globisporus	206	Genus: Bacillus	Firmicutes	Ch
33		446		Bacillus cereus	213	Genus: Bacillus	Firmicutes	Ch
34	452	448	−4	Corynebacterium propinquum	172	Genus: Corynebacterium	Actinobacteria	Ad
34	458	454	−4	Corynebacterium propinquum	172	Genus: Corynebacterium	Actinobacteria	Ad
34	459	455	−4	Corynebacterium propinquum	172	Genus: Corynebacterium	Actinobacteria	Ad
34	460	456	−4	Corynebacterium propinquum	172	Genus: Corynebacterium	Actinobacteria	Ad
34	461	457	−4	Corynebacterium propinquum	172	Genus: Corynebacterium	Actinobacteria	Ad
35	453	454	+1	Corynebacterium amycolatum	200	Genus: Corynebacterium	Actinobacteria	Ad
35	454	455	+1	Corynebacterium amycolatum	200	Genus: Corynebacterium	Actinobacteria	Ad
36	480	479	−1	Rhodococcus erythropolis	207	Genus: Rhodococcus	Actinobacteria	Ad
36	490	490	0	Rhodococcus erythropolis	207	Genus: Rhodococcus	Actinobacteria	Ad
36	493	492	−1	Rhodococcus erythropolis	207	Genus: Rhodococcus	Actinobacteria	Ad
37	502	505	+3	Escherichia coli	213	Genus: Escherichia	Proteobacteria	Ad, Ch
37	504	507	+3	Escherichia coli	213	Genus: Escherichia	Proteobacteria	Ad, Ch
37	506	509	+3	Escherichia coli	213	Genus: Escherichia	Proteobacteria	Ad, Ch
37	596	599	+3	Escherichia coli	213	Genus: Escherichia	Proteobacteria	Ad, Ch
37	598	601	+3	Escherichia coli	213	Genus: Escherichia	Proteobacteria	Ad, Ch
38		508		Bacillus globisporus	198	Genus: Bacillus	Firmicutes	Ch
39		509		Nocardia seriolae	174	Order: Actinomycetales	Actinobacteria	Ch
39		514		Nocardia seriolae	174	Order: Actinomycetales	Actinobacteria	Ch
40	520	522	+2	Corynebacterineae sp.	207	Order: Actinomycetales	Actinobacteria	Ad
41	527	526	−1	Microbacterium testaceum	198	Genus: Microbacterium	Actinobacteria	Ch
42	542	536	−2	Rothia mucilaginosa	174	Genus: Rothia	Actinobacteria	Ad, Ch
42	544	538	−2	Rothia mucilaginosa	174	Genus: Rothia	Actinobacteria	Ad, Ch
43	544	545	+1	Staphylococcus aureus	207	Genus: Staphylococcus	Firmicutes	Ad
44		546		Nocardia seriolae	130	Order: Actinomycetales	Actinobacteria	Ch
45		554		Lactobacillus mucosae	209	Genus: Lactobacillus	Firmicutes	Ad
46	572	577	+5	Clostridium tyrobutyricum	90	Order: Clostridiales	Firmicutes	Ad
47		580		Streptococcus pyogenes	198	Genus: Streptococcus	Firmicutes	Ad, Ch
47	707	712	+5	Streptococcus pyogenes	198	Genus: Streptococcus	Firmicutes	Ad, Ch
47	713	718	+5	Streptococcus pyogenes	198	Genus: Streptococcus	Firmicutes	Ad, Ch
47	716	721	+5	Streptococcus pyogenes	198	Genus: Streptococcus	Firmicutes	Ad, Ch
47	785	788	+3	Streptococcus pyogenes	198	Genus: Streptococcus	Firmicutes	Ad, Ch
48	592	591	−1	Micrococcus luteus	213	Genus: Micrococcus	Actinobacteria	Ch
49	611	609	−2	Corynebacterium efficiens	169	Genus: Corynebacterium	Actinobacteria	Ch
50	611	614	+3	Streptococcus dysgalactiae	213	Genus: Streptococcus	Firmicutes	Ad
51		615		Jonesia denitrificans	182	Suborder: Micrococcineae	Actinobacteria	Ch
51		620		Jonesia denitrificans	182	Suborder: Micrococcineae	Actinobacteria	Ch
51		621		Jonesia denitrificans	182	Suborder: Micrococcineae	Actinobacteria	Ch
51		622		Jonesia denitrificans	182	Suborder: Micrococcineae	Actinobacteria	Ch
52	622	625	+3	Sinobacteraceae sp.	211	Order: Xanthomonadales	Proteobacteria	Ad
53		626		Agrococcus sp.	207	Family: Microbacteriaceae	Actinobacteria	Ch
54		634		Clavibacter michiganensis	185	Family: Microbacteriaceae	Actinobacteria	Ch
55		670		Yersinia enterocolitica	215	Genus: Yersinia	Proteobacteria	Ad
56		671		Herbaspirillum sp.	217	Genus: Herbaspirillum	Proteobacteria	Ad
57		674		Arthrobacter arilaitensis	198	Family: Micrococcaceae	Actinobacteria	Ch
58		692		Azoarcus sp.	195	Family: Rhodocyclaceae	Proteobacteria	Ch
59		713		Agromyces sp.	185	Family: Microbacteriaceae	Actinobacteria	Ch
60		723		Micrococcus luteus	176	Family: Micrococcaceae	Actinobacteria	Ch
61		740		Arthrobacter arilaitensis	182	Family: Micrococcaceae	Actinobacteria	Ch
62	794	796	+2	Phenylobacterium zucineum	165	Family: Caulobacteraceae	Proteobacteria	Ad
63	973	974	+1	Bradyrhizobium elkanii	209	Genus: Bradyrhizobium	Proteobacteria	Ad, Ch
63		1047		Bradyrhizobium elkanii	209	Genus: Bradyrhizobium	Proteobacteria	Ad, Ch
63		1048		Bradyrhizobium elkanii	209	Genus: Bradyrhizobium	Proteobacteria	Ad, Ch
64		1090		Bradyrhizobiaceae sp.	198	Genus: Bradyrhizobium	Proteobacteria	Ch

For each OTU, the following variables are displayed: OTU identification number, ARISA peak size, clone fragment length, the difference between the latter two variables (i.e. clone length minus ARISA peak size), the species identity of the most similar sequence in GenBank as determined by the BLAST algorithm, the maximum BLAST score, the most derived phylogenetic position of the OTU and the phylum to which the OTU belongs. In some cases, we could not determine which ARISA peak represented a particular clone (indicated by a blank space in the “ARISA peak” column).

Back to article page

ISSN: 1472-6785

Contact us

General enquiries: ORSupport@springernature.com

BMC Ecology

Contact us