| Id |
Subject |
Object |
Predicate |
Lexical cue |
| T1 |
415-425 |
http://purl.bioontology.org/ontology/NCBITAXON/1385 |
denotes |
Bacillales |
| T2 |
548-568 |
http://purl.bioontology.org/ontology/NCBITAXON/1401 |
denotes |
Paenibacillus lautus |
| T3 |
480-493 |
http://purl.bioontology.org/ontology/NCBITAXON/44249 |
denotes |
Paenibacillus |
| T4 |
921-934 |
http://purl.bioontology.org/ontology/NCBITAXON/44249 |
denotes |
Paenibacillus |
| T5 |
0-25 |
http://purl.bioontology.org/ontology/NCBITAXON/481743 |
denotes |
Paenibacillus sp.Y412MC10 |
| T6 |
784-810 |
http://purl.bioontology.org/ontology/NCBITAXON/481743 |
denotes |
Paenibacillus sp. Y412MC10 |
| T9 |
221-245 |
481743 |
denotes |
Geobacillus sp. Y412MC10 |
| T10 |
441-464 |
481743 |
denotes |
Geobacillus sp.Y412MC10 |
| T11 |
1056-1068 |
44249 |
denotes |
paenibacilli |
| T12 |
1074-1082 |
481743 |
denotes |
Y412MC10 |
| T13 |
1158-1180 |
908341 |
denotes |
Paenibacillus sp. HGF5 |
| T14 |
1359-1367 |
481743 |
denotes |
Y412MC10 |
| T25 |
1758-1771 |
http://purl.bioontology.org/ontology/NCBITAXON/1129 |
denotes |
Synechococcus |
| T26 |
3044-3057 |
http://purl.bioontology.org/ontology/NCBITAXON/44249 |
denotes |
Paenibacillus |
| T27 |
3835-3848 |
http://purl.bioontology.org/ontology/NCBITAXON/44249 |
denotes |
Paenibacillus |
| T28 |
2792-2808 |
http://purl.bioontology.org/ontology/NCBITAXON/58172 |
denotes |
Paenibacillus sp |
| T29 |
3714-3730 |
http://purl.bioontology.org/ontology/NCBITAXON/58172 |
denotes |
Paenibacillus sp |
| T30 |
2744-2770 |
http://purl.bioontology.org/ontology/NCBITAXON/481743 |
denotes |
Paenibacillus sp. Y412MC10 |
| T31 |
2933-2941 |
http://purl.bioontology.org/ontology/NCBITAXON/1386 |
denotes |
Bacillus |
| T32 |
1671-1688 |
http://purl.bioontology.org/ontology/NCBITAXON/271 |
denotes |
Thermus aquaticus |
| T33 |
3072-3094 |
http://purl.bioontology.org/ontology/NCBITAXON/1406 |
denotes |
Paenibacillus polymyxa |
| T34 |
1987-2013 |
481743 |
denotes |
bacterial isolate Y412MC10 |
| T35 |
2163-2171 |
481743 |
denotes |
Y412MC10 |
| T36 |
2308-2336 |
544556 |
denotes |
Geobacillus species Y412MC61 |
| T37 |
2355-2363 |
550542 |
denotes |
Y412MC52 |
| T38 |
2386-2426 |
634956 |
denotes |
Geobacillus thermoglucosidasius C56-YS93 |
| T39 |
1696-1714 |
http://purl.bioontology.org/ontology/NCBITAXON/56956 |
denotes |
Thermus brockianus |
| T40 |
2449-2472 |
481743 |
denotes |
Geobacillus sp.Y412MC10 |
| T41 |
2596-2607 |
129337 |
denotes |
Geobacillus |
| T42 |
2654-2662 |
481743 |
denotes |
Y412MC10 |
| T43 |
2878-2895 |
58172 |
denotes |
Paenibacillus sp. |
| T44 |
3251-3254 |
9615 |
denotes |
dog |
| T45 |
3261-3278 |
58172 |
denotes |
Paenibacillus sp. |
| T46 |
3459-3468 |
71995 |
denotes |
P. vortex |
| T47 |
3564-3581 |
130049 |
denotes |
P. dendritiformis |
| T48 |
3689-3697 |
481743 |
denotes |
Y412MC10 |
| T49 |
3116-3133 |
58172 |
denotes |
Paenibacillus sp. |
| T50 |
1720-1748 |
http://purl.bioontology.org/ontology/NCBITAXON/28049 |
denotes |
Acidothermus cellulollyticus |
| T51 |
2202-2217 |
1891658 |
denotes |
Geobacillus sp. |
| T52 |
2338-2352 |
544556 |
denotes |
GenBank 544556 |
| T53 |
2365-2379 |
550542 |
denotes |
GenBank 550542 |
| T54 |
2428-2442 |
634956 |
denotes |
GenBank 634956 |
| T55 |
4339-4352 |
http://purl.bioontology.org/ontology/NCBITAXON/44249 |
denotes |
Paenibacillus |
| T58 |
4062-4077 |
481743 |
denotes |
strain Y412MC10 |
| T59 |
4252-4260 |
481743 |
denotes |
Y412MC10 |
| T60 |
4316-4324 |
481743 |
denotes |
Y412MC10 |
| T61 |
4287-4298 |
129337 |
denotes |
Geobacillus |
| T62 |
4411-4419 |
481743 |
denotes |
Y412MC10 |
| T63 |
4662-4670 |
481743 |
denotes |
Y412MC10 |
| T64 |
4803-4836 |
1401 |
denotes |
Paenibacillus lautus NRRL NRS-666 |
| T65 |
0-6142 |
481743 |
denotes |
Paenibacillus sp.Y412MC10 was one of a number of organisms isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the National Park Service. The isolate was initially classified as a Geobacillus sp. Y412MC10 based on its isolation conditions and similarity to other organisms isolated from hot springs at Yellowstone National Park. Comparison of 16 S rRNA sequences within the Bacillales indicated that Geobacillus sp.Y412MC10 clustered with Paenibacillus species, and the organism was most closely related to Paenibacillus lautus. Lucigen Corp. prepared genomic DNA and the genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute. The genome sequence was deposited at the NCBI in October 2009 (NC_013406). The genome of Paenibacillus sp. Y412MC10 consists of one circular chromosome of 7,121,665 bp with an average G+C content of 51.2%. Comparison to other Paenibacillus species shows the organism lacks nitrogen fixation, antibiotic production and social interaction genes reported in other paenibacilli. The Y412MC10 genome shows a high level of synteny and homology to the draft sequence of Paenibacillus sp. HGF5, an organism from the Human Microbiome Project (HMP) Reference Genomes. This, combined with genomic CAZyme analysis, suggests an intestinal, rather than environmental origin for Y412MC10.
Introduction
Numerous novel microorganisms have been isolated from hot springs in Yellowstone National Park. Many of these organisms have been shown to possess enzymes with significant potential in biotechnological applications [1]. Among the organisms first isolated from Yellowstone hot springs are Thermus aquaticus [2,3], Thermus brockianus [4], Acidothermus cellulollyticus [5], and Synechococcus species [6]. As part of a project in conjunction with the Department of Energy Joint Genome Institute, Lucigen Corp. isolated, characterized, and sequenced a number of new isolates from Yellowstone hot springs. The bacterial isolate Y412MC10 was one of four microorganisms isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA and submitted for whole genome sequencing. Y412MC10 was initially classified as a Geobacillus sp. based on its isolation conditions and morphological similarity to other organisms such as Geobacillus species Y412MC61 (GenBank 544556), Y412MC52 (GenBank 550542), and Geobacillus thermoglucosidasius C56-YS93 (GenBank 634956). The Geobacillus sp.Y412MC10 draft genome sequence was deposited at the NCBI in October 2009 (NC_013406) with the lineage entry indicating that it is a Geobacillus. Following assembly of the complete genome of Y412MC10, the 16S rRNA sequence and genome properties properly assigned the organism as a Paenibacillus sp. Y412MC10 represents the first Paenibacillus sp. isolated from a hot spring to have its genome completely sequenced.
Paenibacillus sp. were originally grouped in the genus Bacillus until 1993, when Ash et al. [7] proposed that members of "group 3" should be transferred to the genus Paenibacillus, and proposed Paenibacillus polymyxa as the type species. Paenibacillus sp. have been isolated from a wide range of environments including soil [8], the Antarctic [9], and the oral cavity of a dog [10]. Paenibacillus sp. are of interest for a number of reasons, including production of antibiotics [11-13], biopolymer-degrading enzymes [14-16], and their ability to fix nitrogen [17,18]. One species, P. vortex shows highly unusual organized growth morphologies on solid surfaces [19,20]; another species, P. dendritiformis, also shows unusual growth morphologies on solid surfaces [19,21,22]. Comparison of the genetic content of Y412MC10 with genomes of Paenibacillus sp. from other environments will give insights into the evolutionary adaptations that have occurred in the Paenibacillus. The organism also may be a source of novel polysaccharide degrading enzymes for use in biomass degradation.
Classification and features
A phylogenetic tree was constructed to identify the family relationship of strain Y412MC10 (Figure 1). The tree was created using BLAST2Tree software [23]. The analysis was carried out using only type strains of validly-named organisms, and the analysis shows that Y412MC10 does not clade with known Geobacillus species. Rather, Y412MC10 clades in the Paenibacillus genus. Based on r16S analysis of validly-named organisms, Y412MC10 is most closely related to Paenibacillus lautus DSM 3055T (AB073188). The classification of the isolate was confirmed using the EzTaxon-e server [24], again on the basis of 16S rRNA sequence data. When compared to their entire r16S database, Y412MC10 was identified as being a strain of Paenibacillus lautus with 99.09% identity and 100% completeness to the r16S of the type strain, Paenibacillus lautus NRRL NRS-666 GenBank D78472.
Figure 1 Phylogenetic tree highlighting the position of Paenibacillus lautus strain Y412MC10 and relative strains within the Bacillales. Strains used for the comparison (16S rRNA accession number) were (Paenibacillus Y412MC10); Paenibacillus lautus DSM 3035T (AB073188); Paenibacillus glucanolyticus DSM 5162T (AB073189); Paenibacillus illinoisensis DSM 11733T (AB073192); Paenibacillus chibensis DSM 11731T (AB073194); Paenibacillus ginsengisoli LMG 23406 T (AB245382); Paenibacillus macquariensis subsp defensor NCIB 14397 T (AB360546); Paenibacillus kribbensis KCTC 0766BP T (AF391123); Paenibacillus daejeonensis KCCM 41557 T (AF391124); Paenibacillus borealis DSM 13188 T (AJ011322); Paenibacillus odorifer DSM 15391 T (AJ223990); Paenibacillus cookie LMG 18419 T (AJ250317); Paenibacillus jamilae DSM 13815 T (AJ271157); Paenibacillus azoreducens DSM 13822 T (AJ272249); Paenibacillus stellifer DSM 14472 T (AJ316013); Paenibacillus peoriae DSM 8320 T (AJ320494); Paenibacillus cineris LMG 18349 T (AJ575658); Paenibacillus antarcticus LMG 22078 T (AJ605292); Paenibacillus favisporus LMG 20987 T (AY208751); Paenibacillus lactis DSM 15596 T (AY257868); Paenibacillus provencensis CIP 109358T (EF212893); Paenibacillus konsidanse KCTC 13165T (EU081509). Paenibacillus sp. Y412MC10 |
| T67 |
4707-4727 |
http://purl.bioontology.org/ontology/NCBITAXON/1401 |
denotes |
Paenibacillus lautus |
| T68 |
4447-4477 |
1401 |
denotes |
Paenibacillus lautus DSM 3055T |
| T161 |
4979-4989 |
http://purl.bioontology.org/ontology/NCBITAXON/1385 |
denotes |
Bacillales |
| T162 |
4910-4946 |
481743 |
denotes |
Paenibacillus lautus strain Y412MC10 |
| T163 |
5057-5079 |
481743 |
denotes |
Paenibacillus Y412MC10 |
| T164 |
5082-5112 |
1401 |
denotes |
Paenibacillus lautus DSM 3035T |
| T165 |
5125-5163 |
59843 |
denotes |
Paenibacillus glucanolyticus DSM 5162T |
| T166 |
5176-5214 |
59845 |
denotes |
Paenibacillus illinoisensis DSM 11733T |
| T167 |
5227-5261 |
59846 |
denotes |
Paenibacillus chibensis DSM 11731T |
| T168 |
5274-5312 |
170367 |
denotes |
Paenibacillus ginsengisoli LMG 23406 T |
| T169 |
5325-5380 |
467974 |
denotes |
Paenibacillus macquariensis subsp defensor NCIB 14397 T |
| T170 |
5393-5431 |
172713 |
denotes |
Paenibacillus kribbensis KCTC 0766BP T |
| T171 |
5444-5483 |
135193 |
denotes |
Paenibacillus daejeonensis KCCM 41557 T |
| T172 |
5496-5530 |
160799 |
denotes |
Paenibacillus borealis DSM 13188 T |
| T173 |
5543-5577 |
189426 |
denotes |
Paenibacillus odorifer DSM 15391 T |
| T174 |
5590-5622 |
157839 |
denotes |
Paenibacillus cookie LMG 18419 T |
| T175 |
5635-5668 |
114136 |
denotes |
Paenibacillus jamilae DSM 13815 T |
| T176 |
5681-5718 |
116718 |
denotes |
Paenibacillus azoreducens DSM 13822 T |
| T177 |
5731-5766 |
169760 |
denotes |
Paenibacillus stellifer DSM 14472 T |
| T178 |
5779-5811 |
59893 |
denotes |
Paenibacillus peoriae DSM 8320 T |
| T179 |
5824-5857 |
237530 |
denotes |
Paenibacillus cineris LMG 18349 T |
| T180 |
5870-5907 |
253703 |
denotes |
Paenibacillus antarcticus LMG 22078 T |
| T181 |
5920-5956 |
221028 |
denotes |
Paenibacillus favisporus LMG 20987 T |
| T182 |
5969-6001 |
228574 |
denotes |
Paenibacillus lactis DSM 15596 T |
| T183 |
6014-6052 |
441151 |
denotes |
Paenibacillus provencensis CIP 109358T |
| T184 |
6065-6101 |
479474 |
denotes |
Paenibacillus konsidanse KCTC 13165T |
