. 2014 Aug 19;69(1):118–134. doi: 10.1007/s00248-014-0481-7

Table 1.

Phylogenetic affinities of partial 16S rRNA coding sequences retrieved from swab samples of the Archimedes Palimpsest

Phylum	Clones (%) and selected clone	Closest identified phylogenetic relatives [EMBL accession numbers] and validated species as closest relatives [RDP accession numbers]	Similarity (%)	Acc. Nr.
Proteobacteria (Alpha-class) (6 %)	2 % AP-K3	Uncultured bacterium clones 16S ribosomal RNA gene, partial sequence [GQ009750; GQ009436] from the human skin microbiome. Caedibacter caryophilus ^a (T); 221. [X71837].	99.0 94.4	KF983492
2 % AP-K32	Uncultured bacterium clones 16S ribosomal RNA gene, partial sequence [GQ009750; GQ009436] from the human skin microbiome. Caedibacter caryophilus ^a (T); 221. [X71837].	99.0 94.2	KF983493
2 % AP-K43	Uncultured bacterium clones 16S ribosomal RNA gene, partial sequence [GQ009750; GQ009436] from the human skin microbiome. Caedibacter caryophilus ^a (T); 221. [X71837].	94.0 90.8	KF983494
Proteobacteria (Gamma-class) (90 %)	22.4 % AP-K2	Uncultured Legionellales bacterium clone Hv(lab)_1.9 16S ribosomal RNA gene, partial sequence [EF667907] microbiota in the basal metazoan Hydra. Legionella pneumophila ^a (T); Philadelphia 1 [AE017354].	98.0 96.0	KF983495
12.4 % AP-K48	Uncultured Legionellales bacterium clone Hv(lab)_1.9 16S ribosomal RNA gene, partial sequence [EF667907] microbiota in the basal metazoan Hydra. Legionella pneumophila ^a (T); Philadelphia 1 [AE017354].	98.0 96.0	KF983496
6.2 % AP-K4	Uncultured bacterium clones 16S ribosomal RNA gene, partial sequence [JF681650, JF681408] from the Gastrointestinal tract of a wood-eating fish. Legionella rowbothamii ^a (T); LLAP6 [X97359].	96.0 91.4	KF983497
28.6 % AP-K5	Uncultured gammaproteobacterium clone 61-01-00d090 small subunit ribosomal RNA gene, partial sequence [DQ316803] in uranium-contaminated subsurface sediments. Methylococcus capsulatus ^a (T); Texas = NCIMB 11853 [AJ563935].	95.0 91.2	KF983498
2 % AP-K7	Uncultured gamma proteobacterium clone 61-01-00d090 small subunit ribosomal RNA gene, partial sequence [DQ316803] in uranium-contaminated subsurface sediments. Natronocella acetinitrilica ^a (T); ANL 6–2 [EF103128].	95.0 91.2	KF983499
2 % AP-K19	Uncultured gamma proteobacterium clone 61-01-00d090 small subunit ribosomal RNA gene, partial sequence [DQ316803] in uranium-contaminated subsurface sediments. Natronocella acetinitrilica ^a (T); ANL 6–2 [EF103128].	95.0 91.2	KF983500
8.2 % AP-K10	Uncultured bacterium clone ncd266e08c1 16S ribosomal RNA gene, partial sequence [HM270496] skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Perlucidibaca piscinae ^a (T); IMCC1704. [DQ664237].	99.0 96.2	KF983501
8.2 % AP-K50	Acinetobacter spp. 16S ribosomal RNA gene, partial sequence [KJ806334, AB859733, JX490072, JX290088, and JQ618289]. Acinetobacter lwoffii ^a (T); DSM 2403 [X81665].	99.0 99.3	KF983502
Actinobacteria (2 %)	2 % AP-K44	Nocardiopsis salina strain YIM 90010 16S ribosomal RNA, partial sequence [NR_025768, AY373031] a novel halophilic actinomycete isolated from saline soil in China. Nocardiopsis salina ^a (T); YIM 90010. [AY373031].	99.0 99.8	KF983503
Nonclassified (2 %)	2 % AP-K47	Environmental 16 s rDNA sequence from Evry wastewater treatment plant anoxic basin [CU466697] microbial community composition of an anoxic basin of a municipal wastewater treatment plant. Vampirovibrio chlorellavorus ^a (T); ICPB 3707 [HM038000].	99.0 85.7	KF983504

Phylum

Clones (%) and selected clone

Closest identified phylogenetic relatives [EMBL accession numbers] and validated species as closest relatives [RDP accession numbers]

Similarity (%)

Acc. Nr.

Proteobacteria

(Alpha-class)

(6 %)

2 %

AP-K3

Uncultured bacterium clones 16S ribosomal RNA gene, partial sequence [GQ009750; GQ009436] from the human skin microbiome.

Caedibacter caryophilus ^a (T); 221. [X71837].

99.0

94.4

KF983492

2 %

AP-K32

Uncultured bacterium clones 16S ribosomal RNA gene, partial sequence [GQ009750; GQ009436] from the human skin microbiome.

Caedibacter caryophilus ^a (T); 221. [X71837].

99.0

94.2

KF983493

2 %

AP-K43

Uncultured bacterium clones 16S ribosomal RNA gene, partial sequence [GQ009750; GQ009436] from the human skin microbiome.

Caedibacter caryophilus ^a (T); 221. [X71837].

94.0

90.8

KF983494

Proteobacteria (Gamma-class)

(90 %)

22.4 %

AP-K2

Uncultured Legionellales bacterium clone Hv(lab)_1.9 16S ribosomal RNA gene, partial sequence [EF667907] microbiota in the basal metazoan Hydra.

Legionella pneumophila ^a (T); Philadelphia 1 [AE017354].

98.0

96.0

KF983495

12.4 %

AP-K48

Uncultured Legionellales bacterium clone Hv(lab)_1.9 16S ribosomal RNA gene, partial sequence [EF667907] microbiota in the basal metazoan Hydra.

Legionella pneumophila ^a (T); Philadelphia 1 [AE017354].

98.0

96.0

KF983496

6.2 %

AP-K4

Uncultured bacterium clones 16S ribosomal RNA gene, partial sequence [JF681650, JF681408] from the Gastrointestinal tract of a wood-eating fish.

Legionella rowbothamii ^a (T); LLAP6 [X97359].

96.0

91.4

KF983497

28.6 %

AP-K5

Uncultured gammaproteobacterium clone 61-01-00d090 small subunit ribosomal RNA gene, partial sequence [DQ316803] in uranium-contaminated subsurface sediments.

Methylococcus capsulatus ^a (T); Texas = NCIMB 11853 [AJ563935].

95.0

91.2

KF983498

2 %

AP-K7

Uncultured gamma proteobacterium clone 61-01-00d090 small subunit ribosomal RNA gene, partial sequence [DQ316803] in uranium-contaminated subsurface sediments.

Natronocella acetinitrilica ^a (T); ANL 6–2 [EF103128].

95.0

91.2

KF983499

2 %

AP-K19

Uncultured gamma proteobacterium clone 61-01-00d090 small subunit ribosomal RNA gene, partial sequence [DQ316803] in uranium-contaminated subsurface sediments.

Natronocella acetinitrilica ^a (T); ANL 6–2 [EF103128].

95.0

91.2

KF983500

8.2 %

AP-K10

Uncultured bacterium clone ncd266e08c1 16S ribosomal RNA gene, partial sequence [HM270496] skin microbiome associated with disease flares and treatment in children with atopic dermatitis.

Perlucidibaca piscinae ^a (T); IMCC1704. [DQ664237].

99.0

96.2

KF983501

8.2 %

AP-K50

Acinetobacter spp. 16S ribosomal RNA gene, partial sequence [KJ806334, AB859733, JX490072, JX290088, and JQ618289].

Acinetobacter lwoffii ^a (T); DSM 2403 [X81665].

99.0

99.3

KF983502

Actinobacteria

(2 %)

2 %

AP-K44

Nocardiopsis salina strain YIM 90010 16S ribosomal RNA, partial sequence [NR_025768, AY373031] a novel halophilic actinomycete isolated from saline soil in China.

Nocardiopsis salina ^a (T); YIM 90010. [AY373031].

99.0

99.8

KF983503

Nonclassified

(2 %)

2 %

AP-K47

Environmental 16 s rDNA sequence from Evry wastewater treatment plant anoxic basin [CU466697] microbial community composition of an anoxic basin of a municipal wastewater treatment plant.

Vampirovibrio chlorellavorus ^a (T); ICPB 3707 [HM038000].

99.0

85.7

KF983504

^aValidated species as closest relatives retrieved from the RDPII database