Complete genome sequence of Brachyspira intermedia reveals unique genomic features in Brachyspira species and phage-mediated horizontal gene transfer
© Håfström et al; licensee BioMed Central Ltd. 2011
Received: 20 April 2011
Accepted: 4 August 2011
Published: 4 August 2011
Brachyspira spp. colonize the intestines of some mammalian and avian species and show different degrees of enteropathogenicity. Brachyspira intermedia can cause production losses in chickens and strain PWS/AT now becomes the fourth genome to be completed in the genus Brachyspira.
15 classes of unique and shared genes were analyzed in B. intermedia, B. murdochii, B. hyodysenteriae and B. pilosicoli. The largest number of unique genes was found in B. intermedia and B. murdochii. This indicates the presence of larger pan-genomes. In general, hypothetical protein annotations are overrepresented among the unique genes. A 3.2 kb plasmid was found in B. intermedia strain PWS/AT. The plasmid was also present in the B. murdochii strain but not in nine other Brachyspira isolates. Within the Brachyspira genomes, genes had been translocated and also frequently switched between leading and lagging strands, a process that can be followed by different AT-skews in the third positions of synonymous codons. We also found evidence that bacteriophages were being remodeled and genes incorporated into them.
The accessory gene pool shapes species-specific traits. It is also influenced by reductive genome evolution and horizontal gene transfer. Gene-transfer events can cross both species and genus boundaries and bacteriophages appear to play an important role in this process. A mechanism for horizontal gene transfer appears to be gene translocations leading to remodeling of bacteriophages in combination with broad tropism.
The genus Brachyspira currently comprises seven validly published species: B. aalborgi, B. alvinipulli, B. hyodysenteriae, B. innocens, B. intermedia, B. murdochii and B. pilosicoli. Collectively these form a distinct evolutionary line within the phylum Spirochaetes. Brachyspira spp. are oxygen-tolerant anaerobes that colonize the intestines of some mammalian and avian species but they differ in enteropathogenicity from important pathogens of livestock to presumed commensals. B. hyodysenteriae and B. pilosicoli are important porcine pathogens, causing swine dysentery and porcine intestinal spirochetosis respectively. Two species, B. pilosicoli and B. aalborgi, can colonize humans and are suspected causes of colitis. For a review, see Tsinganou and Gebbers .
B. intermedia commonly colonize the large intestine of commercially farmed pigs and chickens and has also been isolated from rodents  and ducks (Jansson, D. unpublished data). The species was originally named Serpulina intermedia and described as possessing characteristics related to both the pathogen B. hyodysenteriae and the commensal B. innocens. Later the species was transferred to the genus Brachyspira. Data from field studies have suggested that B. intermedia may be a mild enteropathogen of pigs [6–8], but experimental challenge in porcine isolates has failed to produce clinical disease [9–11]. In contrast, an experimental challenge in chickens with B. intermedia isolates caused diarrhea, slow growth, and reduced egg production. [12–14]. Diagnostically relevant features associated with both B. hyodysenteriae and B. intermedia include tryptophanase and β-glucosidase activity. In addition, they lack α-galactosidase activity and are unable to hydrolyze hippurate [4, 7]. The two species can be differentiated by haemolytic properties, i.e., there is strong β-haemolysis in B. hyodysenteriae and weak β-haemolysis in B. intermedia. Other recognized representatives of the genus Brachyspira lack tryptophanase activity. Identification of isolates of B. hyodysenteriae, B. intermedia and the proposed species "B. suanatina"  by 16S rRNA gene- sequence analysis is not feasible because they form a common phylogenetic cluster . Moreover, the high genetic diversity between isolates as seen from the results of pulsed-field gel electrophoresis, multi-locus sequence typing, and E-burst analysis have recently challenged the species delineation of weakly β-haemolytic and tryptophanase-producing isolates as B. intermedia.[17, 18]. It remains to be seen whether all isolates with the phenotype described as characteristic for B. intermedia will be included in this species in the future.
Complete genome data from the two important porcine pathogens B. hyodysenteriae and B. pilosicoli and the presumed commensal B. murdochii have been recently published [19–21]. The B. hyodysenteriae genome consists of a 3 Mb chromosome and a ~36 kb plasmid. Many of these genes are more related to Clostridium and Escherichia species than to non-Brachyspira spirochetes which suggests that horizontal gene-transfer events have taken place . The 36 kb plasmid is conserved among a large number of B. hyodysenteriae isolates but is not detected in any avirulent field strain, which suggests that it is important for virulence . The only recognized gene-transfer agent in Brachyspira spp. is a mitomycin-inducible defective prophage (VSH-1), which transducts 7.5 kb random genomic fragments . The B. pilosicoli genome is somewhat smaller, 2.6 Mb, and contains no plasmids. The B. pilosicoli genome has been compared to B. hyodysenteriae and a draft version of B. murdochii. In our study the genome of B. intermedia type strain PWS/AT (ATCC 51140) of porcine origin was completed and subjected to comparative genomic analysis. With this new data we can now compare four completed Brachyspira genomes and significantly increase the understanding of different and shared properties of the genomes. We also discuss horizontal movements of genes and the potential involvement of bacteriophages in this process.
Results and discussion
General genomic features and genome plasticity
General genome features
B. intermedia PWS/AT
B. intermedia PWS/ATPlasmid
B. hyodysenteriae WA1
B. hyodysenteriae WA1 Plasmid
B. murdochii 56-150T
B. pilosicoli 95/1000
Coding region (%)
G+C content (%)
A+T content (%)
Average CDS length (bp)
Number of CDS
The G+C content for the B. intermedia strain PWS/AT chromosome was 27.2% which is similar to that of the other genomes in the genus. Interestingly, the small plasmid had only 21.0% G+C content (Table 1). The G+C content in intergenic regions was 20.4%, and in the third positions of synonymous codons it was less than 10%. This indicates that Gs and Cs are shunned and the average G+C content is determined by the requirements of the G+C-containing codons. The small plasmid had a lower coding density and therefore also a lower G+C content.
GC- and AT-Skew for the chromosome of B. intermedia PWS/AT
Direction of replication (LES )
Total all positions
Total all positions
Direction of transcription (Genes)
Total all positions
Synonymous position 3
Total all positions
Synonymous position 3
Total all positions
Synonymous position 3
The 3.2 Kb plasmid in B. Intermedia PWS/AT is also present in B. murdochii 56-150T
PCR targeting the 3.2 kb plasmid of Brachyspira intermedia
B. hyodysenteriae AN1409:2/01
B. intermedia PWS/AT
B. intermedia AN2004/1/01
"B. suanatina" AN4859/03R
B. innocens B256T
B. innocens AN64/1/04
B. murdochii 56-150T
B. murdochii AN1780/3/03
B. alvinipulli AN1268/3/04
B. pilosicoli P43/6/78T
The 55.9 kb B. hyodysenteriae WA1 plasmid previously described was not present in B. intermedia PWS/AT. However, some of the B. hyodysenteriae WA1 plasmid genes were homologous to genes in the B. intermedia, B. murdochii and/or B. pilosicoli chromosomes. Several of the homologous genes showed high conservation and only 10 genes, many of which encode glycosyltransferases (Additional file 1, "plasmids" tab), were genuinely unique to the plasmid. A cluster of four genes (rfbA, rfbB, rfbC and rfbD) has been discussed previously in terms of virulence [19, 22]. They were all conserved in the B. intermedia chromosome although one gene (rfbA) contained two nonsense mutations. The rfbaA-D genes are involved in the rhamnose biosynthesis pathway and are believed to modify the O-antigen backbone of the cell wall LOS. These data suggest that rhamnose biosynthesis capacity may be present in B. intermedia strains, independent of their 32 kb plasmid. However, the inactivation of the rfbA gene in this strain suggests it may not be essential for virulence in B. intermedia PWS/AT. It will be interesting to see if the rfbA-D gene cluster is present and if it is functional in other B. intermedia strains and correlates to pathogenicity.
Conserved and shared genes between the four Brachyspira species
Distribution of Clusters of Orthologous Genes (COG) categories
COG classifications were assigned to each protein by comparison to the COG database . COG classifications have previously been made on Brachyspira genomes [19–21]. Our extended analysis showed that all four available Brachyspira genomes had a similar overall COG profile (Additional file 1, "COG1" tab). The COG assignments were also incorporated into the descriptions of the 15 conservation classes in Additional file 1, (tab 1-15) and the classes were compared in Additional file 1, "COG2" tab. The unique gene classes (I, H, M and P) were generally similar in the COGs suggesting that the main difference lies among the more poorly characterized functions. Some exceptions can be noted. The B. murdochii specific genes were 5-10 times more abundant in the COG "Amino acid transport and metabolism" and 2-5 times more abundant in "Replication, recombination and repair" compared to the other unique classes. The IHM class (genes lost by B. pilosicoli) was particularly abundant in COGs representing transport and metabolism of inorganic ions, amino acids and carbohydrates. The lower number of inorganic ion transport and metabolism genes in B. pilosicoli has previously been observed .
More specialized species usually undergo reductive evolution, thereby losing unnecessary genes . The smaller number of specific genes in the more niched pathogens B. hyodysenteriae (swine dysenteriae) and B. pilosicoli (intestinal spirochaetosis) suggests they have a higher degree of specialization. Thus, the major reason for the greater number of unique genes in B. intermedia and B. murdochii is probably related to the presence of larger pan-genomes due to higher diversity within these species.
A majority of the unique genes, in all species, were annotated as coding for hypothetical proteins. This shows that, in general, the specific traits and aspects of virulence mechanisms are poorly studied. In the high-cutoff comparison (BLASTP e-value < 1e-4), only 13 functionally annotated chromosomal genes specific for B. hyodysenteriae were found. There were three citrate lyases, two pepdidases, an acetyltransferase, a transmembrane protein, an ethanolamine utilization protein, an Appr-1-p processing enzyme, a small MutS-related domain protein, an ankyrin repeat-containing protein, an YcfA-like protein, and an OrfC protein. The B. hyodysenteriae plasmid also contained several specific glycosyltransferases and hydrolases. B. intermedia specific genes, apart from phage-related genes, included five microcompartmental proteins, a beta-galactosidase, three glucose-1-phosphate thymidylyltransferase, several restriction enzyme system-related genes and an extracellular solute-binding protein. B. pilosicoli specific genes included several transporters, a peptidase, two sialidase (neuraminidase) family-like proteins, a class D beta-lactamase and a protein possibly involved in chromosome segregation. B. murdochii specific genes included a CRISPR system, two capsular polysaccharide biosynthesis proteins, two SNARE associated Golgi -related proteins, two STAM (AMSH)-SH3 domain associated-proteins, several transcription regulators, and DNA replication proteins.
Genes shared by two species
One could expect that the two more specialized pathogens, B. hyodysenteriae and B. pilosicoli, would share some virulence-associated genes, but they had the least number of shared genes. Actually, only two hypothetical proteins were shared at the higher stringency level. This most likely reflects the fact that these two species seem to exploit distinctly different life strategies. The greatest number of shared genes for any pair of species was that for B. murdochii and B. pilosicoli. The high number was partly a result of a common phage found in one copy in B. pilosicoli and in three copies in B. murdochii. The phages are described in more detail below.
Genes shared by three species (conserved genes lost by one species)
The greatest number of shared genes between three species was in the class B. intermedia, B. hyodysenteriae and B. murdochii. One could see these genes as conserved genes lost by B. pilosicoli during reductive evolution. In particular, B. pilosicoli has lost many transport-related proteins which could reflect its adaptation to a more specialized ecological niche. The higher level of reductive evolution in B. pilosicoli suggests it is an older pathogen than B. hyodysenteriae. The pathogenicity of the younger B. hyodysenteriae could be related to its acquisition of the 32 kb plasmid. The least number of genes was found in the B. hyodysenteriae, B. murdochii and B. pilosicoli category. This corresponds to conserved genes lost by B. intermedia. This, once again, shows B. intermedia to be the species with the largest number of accessory genes.
Bacteriophages and their role in horizontal gene transfer (HGT)
A phage-like gene transfer element named VSH-1 is known to have the capacity to transduct randomly packaged genomic material between B. hyodysenteriae strains . The B. intermedia VSH-1 region had a small cluster of putative VSH-1 like genes located approximately 16 kb upstream of the main part of VSH-1, similarly as previously described in B. hyodysenteria. Here we report two new B. intermedia bacteriophages, pI1 and pI2 (Figure 3). pI1 was located almost completely adjacent to the VSH-1 phage-like element (Bint_0105- Bint_0143). It had a size of ~28 kb and contained 37 genes (Bint_0068- Bint_0103) of which 36 were unique to B. intermedia also at the high stringency level (e-value < 1e-4). Interestingly, one gene coding for a hypothetical membrane-spanning protein, Bint_0072, was conserved in B. hyodysenteriae (BHWA1_02012, e-value = 5e-18). This suggests that an HGT event has taken place and that the pI1 phage has acquired this gene from another B. intermedia or B. hyodysenteriae strain and transferred it to this strain.
The second phage, pI2, was ~16 kb and contained 24 genes (Bint_1512- Bint_1535) divided into three regions. The first region (Bint_1512-Bint_1525) and the third (Bint_1531- Bint_1535) were unique for B. intermedia also at the high stringency level. However, the second region (Bint_1526-Bint_1530) had similarities to both the VSH-1 phage-like element of the Brachyspira species and to the shared phage found in B. pilosicoli and B. murdochii. Thus, this phage seems to be a hybrid that has acquired new properties from other phages or VSH-1 phage-like elements. The genes in this region were annotated as hypothetical proteins and endolysin glycoside hydrolase.
It has been shown that Brachyspira spp. and Clostridium share an unexpected amount of significant gene similarity . When comparing the pP1 and pM1-3 phages to sequences in GenBank, we found homology to a Clostridium phage in the complete genome of the C. botulinum strain A2 Kyoto (Additional file 2). This suggests the phages may occasionally transfer between species and genera and exchange genetic material resulting in cross-species and cross-genus HGT events.
In our analysis, we have seen several indications of putative HGT events mediated by bacteriophages. However, we still have only a single genome sequence for each species and this is a major limitation when analyzing HGT events. The rapid development of sequencing technology will hopefully give us opportunity to characterize a larger set of genomic data from Brachyspira spp. in the future. This will permit a more robust HGT analysis. Also the gene classification will become more robust as the dataset will grow. The accessory gene-pool is likely to increase, but the truly unique genes for each spices will likely decrease, sorting out the essential species specific factors better.
In this study, we classified the accessory gene pool into different classes of shared and unique genes. In general, the unique genes are poorly annotated, which shows our lack of knowledge about species-specific processes. B. intermedia and B. murdochii contain more material specific to them and probably a larger pan-genome. B. hyodysenteriae and B. pilosicoli are both more specialized pathogens that have less accessory genetic material and diversity. They have specialized independently, as seen by the little genetic material shared only between them. These two genomes were also the two smallest, indicating that reductive evolution had taken place . The traces of reductive evolution involved loss of genes, especially transport proteins. This is most obvious in B. pilosicoli suggesting it has been influenced by reductive evolution for a longer time. The pathogenicity of B. hyodysenteriae could in analogy with Yersinia pestis, be a result of the acquisition of a plasmid.
The gene content of the different classes of accessory genes is under the influence of HGT. Here we outlined a mechanism for HGT between classes that involves gene rearrangements involving bacteriophages with broad tropism. Our data also suggest cross genus HGT events could have occurred via the phages. These mechanisms need further studies if we want to understand the dynamics of the complete pan-genome of the species.
Genome sequencing of more strains will probably reduce the numbers of unique and shared features even more. Although we now have a markedly more confined list of candidate genes, the large number of annotations for "hypothetical proteins" among the unique genes shows that it is of great importance to study gene functions in order to understand species-specific traits.
Bacterial culture, DNA preparation and 454 sequencing
The B intermedia type strain PWS/AT was obtained from the American type culture collection (ATCC®51140). The strain was cultured twice on fastidious anaerobe agar plates supplemented with 10% equine blood (FAA). The purity of the strain was assessed by phase-contrast microscopy. Genomic DNA was prepared using the Qiagen DNAeasy kit. Parallel sequencing was performed using the Roche 454 FLX platform. One half picotiterplate of shotgun sequences was produced and de novo assembled using the GS assembler (Newbler). In total, 193,367 reads with an average length of 245 bp were assembled into 203 contigs with sizes ranging between 100 and 138,989 bp. The average coverage was 14X. Contigs were handled by the Consed package . Gaps, uncertain regions, and misassemblies were closed and solved manually by PCR, Sanger sequencing, and local reassemblies. The estimated average sequence quality as reported by Consed, based on the Q values of the reads (-10log(Pe)) was 1.5 errors in 10,000 bp. Sequence reactions were performed with the BigDye® Terminator v.3.1 kit (Applied Biosystems) and analysed in an ABI PRISM® 3100 Genetic Analyzer at Applied Biosystems, Carlsbad, CA, USA. A total of 218 Sanger reads were incorporated into the assembly.
Sequence analysis and annotation
Genes were predicted using Glimmer 3 . Annotations were handled by the Artemis software . Conserved genes for B. intermedia, B. hyodysenteriae, B. murdochii and B. pilosicoli were automatically annotated by comparison at protein level and transfer of annotation data. Less conserved genes were queried against the proteins of all microbial genomes and NCBI nr. Manual inspections were made when similarities were weak. tRNAscan-SE  was used to identify tRNAs genes and rRNA genes were defined by their similarity to other Brachyspira sequences. Circular DNA plots of the B. intermedia genome and plasmid were drawn with DNAplotter . Genome alignments were made with Mummer  and ACT .
Complete nucleotide sequences and annotations of the B. intermedia chromosome and plasmid have been deposited in the GenBank database, accession numbers CP002874 (chromosome) and CP002875 (plasmid).
The skew analysis was made by functions in Artemis and DNAplotter and by in-house made scripts. LES and LAS genes were defined and exported in Artemis and a perl script was used to count the number of a/c/t and g's in each codon position. The whole genome was also analyzed using a perl script where LES and LAS were separated based on the positioning of oriC and the genome feature file was used to identify non-coding regions.
Unique and shared genes
All-against-all protein sequence comparisons were made and genome-specific best hits (BeTs) were calculated . A BeT was considered to represent conservation between two proteins if the e-value was lower than 1e-9. The BeTs were used to assign each gene to a class using a perl script that compared all BeTs from every protein to all proteomes in the analysis. The results were collected in Additional file 1. Genes were compared using BLASTP. Genes with a best hit e-value < 10-9 were considered to be conserved. Gene pairs with e-values between 1e-4 and 1e-9 were considered to be in a "twilight zone". Genes were classified into 15 classes (IHMP, IHM, IHP, IMP, HMP, IH, IM, IP, HM, HP, MP, I, H, M and P) on the basis of the BLASTP values. Functional classification into phage and putative virulence factors were made by manual inspection.
The plasmid was purified with a standard plasmid miniprep protocol. The PCR amplifications of plasmid genes were made with the following primer-pairs G1f 5'-CAATTTTAATGCTAAGACTTTGAA-3', G1r 5'-CGCTTTAATGTTCTATTCGG-3', G2f 5'-GTTTTACCTTTCATATCATCACAA-3', G2r 5'-TTTTCTGTCGTCATTATCTTTTC-3', G3f 5'-GACTAACGCACCGACAATAAT-3', G3r 5'-AATTCTTAATAGTTGCCTTTCAGTA-3'. The following templates were used: B. intermedia PWS/AT, B. intermedia AN2004/1/01, B. hyodysenteriae AN1409:2/01, B. "suanatina" AN4859/03R, B. innocens B256T, B. innocens AN64/1/04, B. murdochii 56-150TB. murdochii AN1780/3/03, B. alvinipulli AN1268/3/04 and B. pilosicoli P43/6/78T.
Average Similarity of the conserved Core method (ASC)  was used to measure the phylogenomic distance between the complete genomes of B. intermedia PWS/AT, B. hyodysenteriae WA1, B. murdochii 56-150T, B. pilosicoli 95/1000 and Leptospira interrogans (AE016823-24). A dendrogram was created by converting a similarity matrix to a distance matrix and calculating a tree rooted using Leptospira interrogans as outgroup species with the UPGMA method using PHYLIP 3.67 through the Mobyle platform (http://mobyle.pasteur.fr/). A phylogenetic tree was then plotted using PhyloDraw (http://www.bioinformatics.org/wiki/PhyloDraw).
Distribution of Clusters of Orthologous Genes (COG) categories
All proteins from all four Brachyspira g enomes in the analysis were compared with the COG database . BeTs were identified and COG classes were assigned to all proteins matching the COG database with an e-value below 1e-9. The COGs for each species and gene content class were summarized in a table (Additional file 1) and inspected to identify conservation patterns of specific functions.
This work was supported by the royal Swedish academy of agriculture and forestry, by local funding at National Veterinary Institute, Sweden and by the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning. We thank Märit Pringle for her involvement in the study.
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