Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139T)

Bacteroides coprosuis Whitehead et al. 2005 belongs to the genus Bacteroides, which is a member of the family Bacteroidaceae. Members of the genus Bacteroides in general are known as beneficial protectors of animal guts against pathogenic microorganisms, and as contributors to the degradation of complex molecules such as polysaccharides. B. coprosuis itself was isolated from a manure storage pit of a swine facility, but has not yet been found in an animal host. The species is of interest solely because of its isolated phylogenetic location. The genome of B. coprosuis is already the 5th sequenced type strain genome from the genus Bacteroides. The 2,991,798 bp long genome with its 2,461 protein-coding and 78 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.


Introduction
Strain PC139 T (= DSM 18011 = NRRL B-41113 = JCM 13475) is the type strain of Bacteroides coprosuis which belongs to the large genus Bacteroides, which currently contains 39 members [1,2]. The species epithet is derived from the Greek noun 'kopros' meaning 'feces' and the genitive of the Latin noun 'suis' meaning 'of a pig'. B. coprosuis strain PC139 T was isolated from a manure storage pit of a swine facility. One other strain belonging to the same species has been isolated from the same source [2]. Many Bacteroides species are common inhabitants of the intestine where they help to degrade complex molecules such as polysaccharides or transform steroids [3,4]. They also play a role as beneficial protectors of the gut against pathogenic microorganisms [5]. However, so far B. coprosuis has not been isolated from an animal itself, therefore the exact habitat and the role the bacterium plays remains unknown. Here we present a summary classification and a set of features for B. coprosuis PC139 T , together with the description of the complete genomic sequencing and annotation.

Classification and features
A representative genomic 16S rRNA sequence of strain PC139 T was compared using NCBI BLAST under default settings (e.g., considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database [6] and the relative frequencies, of taxa and keywords (reduced to their stem [7]) were determined, weighted by BLAST scores. The most frequently occurring genus was Bacteroides (100.0%) (20 hits in total). Regarding the single hit to sequences from members of the species, the identity within HSPs was 99.9%, whereas the coverage by HSPs was 98.0%. Regarding the twelve hits to sequences from other members of the genus, the average identity within HSPs was 92.9%, whereas the average coverage by HSPs was 62.1%. Among all other species, the one yielding the highest score was B. propionicifaciens, which corresponded to an identity of 94.6% and an HSP coverage of 84.5%. The highest-scoring environmental sequence was AF445205 ('Swine fecal isolate str. FPC111'), which showed an identity of 99.8% and an HSP coverage of 100.0%. The most frequently occurring keywords within the labels of environmental samples which yielded hits were 'human' (6.3%), 'fecal' (5.5%), 'effect' (4.4%), 'antibiot, deep, gut, microbiota, pervas, sequenc' (4.3%) and 'feedlot' (4.2%) (230 hits in total). Environmental samples which yielded hits of a higher score than the highest scoring species were not found. Figure 1 shows the phylogenetic neighborhood of B. coprosuis in a 16S rRNA based tree. The sequences of the three 16S rRNA gene copies in the genome differ from each other by up to seven nucleotides, and differ by up to six nucleotides from the previously published 16S rRNA sequence (AF319778). Phylogenetic tree highlighting the position of B. coprosuis relative to the other type strains within the genus Bacteroides. The tree was inferred from 1,412 aligned characters [8,9] of the 16S rRNA gene sequence under the maximum likelihood criterion [10] and rooted in accordance with the current taxonomy. The branches are scaled in terms of the expected number of substitutions per site. Numbers to the right of bifurcations are support values from 1,000 bootstrap replicates [11] if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [12] and unpublished are marked with one asterisk, those listed as published (as well as the target genome) with two asterisks [13][14][15][16][17], and CP002122/3 for Prevotella melaninogenica.

Genome sequencing and annotation Genome project history
This organism was selected for sequencing on the basis of its phylogenetic position [31], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [32]. The genome project is deposited in the Genomes On Line Database [12] and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2.

Genome sequencing and assembly
The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website [35]. Pyrosequencing reads were assembled using the Newbler assembler version 2.3-PreRelease-09-14-2009 (Roche). The initial Newbler assembly consisting of 100 contigs in two scaffolds was converted into a phrap assembly

Genome annotation
Genes were identified using Prodigal [40] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [41]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, Uni-Prot, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and In-terPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes -Expert Review (IMG-ER) platform [42].

Genome properties
The genome consists of a 2,991,798 bp long circular chromosome (in one contig with one remaining unclosed sequencing gap), with a G+C content of 35.0% (Table 3). Of the 2,539 genes predicted, 2,461 were protein-coding genes, and 78 RNAs; 68 pseudogenes were also identified. The majority of the protein-coding genes (66.4%) were assigned with a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4. The Genome-to-Genome Distance Calculator, GGDC [43,44] was used for the estimation of the overall similarity between the three Bacteroides genomes. The system calculates the distances by comparing the genomes to obtain HSPs (highscoring segment pairs) and interfering distances from the set of formulas (1 HSP length / total length; 2 identities / HSP length; 3 identities / total length). The comparison of B. coprosuis with B. helcogenes and B. salanitronis revealed that only 6.1% and 3.3%, respectively, of the average of the genome lengths are covered with HSPs. The identity within the HSPs was 82.3% and 82.1%, respectively, whereas the identity over the whole genome was 5.0% and 2.7%, respectively. The comparison of B. salanitronis with B. helcogenes revealed that 11.4% of the genome is covered with HSPs, with an identity within in the HSPs of 81.4% and an identity over the whole genome of 9.2%. According to these calculations the similarity between B. salanitronis and B. helcogenes is higher than the similarity between B. coprosuis and B. salanitronis as well as the similarity between B. coprosuis and B. helcogenes.    coprosuis. This fraction of genes includes genes coding for glycoside hydrolases, which are responsible for the degradation of polysaccharides. Only 12 glycoside hydrolases were identified in the genome of B. coprosuis, whereas the number of glycoside hydrolases identified in B. helcogenes and B. salanitronis, is much higher, 38 and 45, respectively. Whereas only two transposase genes were identified in the genome of B. helcogenes, the genomes of B. coprosuis and B. salanitronis encode a high number of transposases, 34 and 29, respectively. As a consequence, genome rearrangements can occur, which result in a quite dynamic genome structure (Figure 4). Only a small number of the genes (588 genes) found in B. coprosuis are not present in B. helcogenes and/or B. salanitronis.