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Algoriphagus sp. strain PAP.12 (EXT111900) and Roseivirga sp. strain PAP.19 (EXT111901) were isolated from marine samples. Here, we report their draft genome sequences, 5.032 Mbp and 4.583 Mbp in size, respectively, and rate their specialized metabolite production capacity. Taxonomic ranks established by genome-based analysis indicate that Algoriphagus sp. strain PAP.12 represents a candidate new species.

Sinomicrobium sp. strain PAP.21 (EXT111902) was isolated from the coast of Cenderawasih Bay National Park in West Papua, Indonesia. Its genome was assembled into 151 contigs with a total size of 5.439 Mbp, enabling the prediction of its specialized metabolite production capacity.

Prokaryotes represent an ancestral lineage in the tree of life and constitute optimal resources for investigating the evolution of genomes in unicellular organisms. Many bacterial species possess multipartite genomes offering opportunities to study functional variations among replicons, how and where new genes integrate into a genome, and how genetic information within a lineage becomes encoded and evolves. To analyze these issues, we focused on the model soil bacterium Sinorhizobium meliloti, which harbors a chromosome, a chromid (pSymB), a megaplasmid (pSymA), and, in many strains, one or more accessory plasmids. The analysis of several genomes, together with 1.4 Mb of accessory plasmid DNA that we purified and sequenced, revealed clearly different functional profiles associated with each genomic entity. pSymA, in particular, exhibited remarkable interstrain variation and a high density of singletons (unique, exclusive genes) featuring functionalities and modal codon usages that were very similar to those of the plasmidome. All this evidence reinforces the idea of a close relationship between pSymA and the plasmidome. Correspondence analyses revealed that adaptation of codon usages to the translational machinery increased from plasmidome to pSymA to pSymB to chromosome, corresponding as such to the ancestry of each replicon in the lineage. We demonstrated that chromosomal core genes gradually adapted to the translational machinery, reminiscent of observations in several bacterial taxa for genes with high expression levels. Such findings indicate a previously undiscovered codon usage adaptation associated with the chromosomal core information that likely operates to improve bacterial fitness. We present a comprehensive model illustrating the central findings described here, discussed in the context of the changes occurring during the evolution of a multipartite prokaryote genome. Importance: Bacterial genomes usually include many thousands of genes which are expressed with diverse spatial-temporal patterns and intensities. A well-known evidence is that highly expressed genes, such as the ribosomal and other translation-related proteins (RTRPs), have accommodated their codon usage to optimize translation efficiency and accuracy. Using a bioinformatic approach, we identify core-genes sets with different ancestries, and demonstrate that selection processes that optimize codon usage are not restricted to RTRPs but extended at a genomewide scale. Such findings highlight, for the first time, a previously undiscovered adaptation strategy associated with the chromosomal-core information. Contrasted with the translationally more adapted genes, singletons (i.e., exclusive genes, including those of the plasmidome) appear as the gene pool with the less-ameliorated codon usage in the lineage. A comprehensive summary describing the inter- and intra-replicon heterogeneity of codon usages in a complex prokaryote genome is presented., Facultad de Ciencias Exactas, Instituto de Biotecnologia y Biologia Molecular

The formation of spore-filled fruiting bodies in response to starvation represents a hallmark of many members of the order Myxococcales . Here, we present the complete 9.9-Mb genome of the fruiting type strain Melittangium boletus DSM 14713, the first member of this genus to have its genome sequenced.

Among myxobacteria, the genus Cystobacter is known not only for fruiting body formation but also for formation of secondary metabolites, such as cystobactamids and cystothiazols. Here, we present the complete genome sequence of the Cystobacter fuscus strain DSM 52655, which comprises 12,349,744 bp and 9,836 putative protein-coding sequences.

In response to starvation, members of the order Myxococcales form morphologically very different fruiting bodies. To determine whether fruiting myxobacteria share a common genetic program that leads to fruiting body formation, we sequenced and assembled the genome of Nannocystis exedens DSM 71 as two contigs with a total GC content of 72%.

Members of the Myxococcales order initiate a developmental program in response to starvation that culminates in formation of spore-filled fruiting bodies. To investigate the genetic basis for fruiting body formation, we present the complete 8.9-Mb genome sequence of Myxococcus macrosporus strain DSM 14697, generated using the PacBio sequencing platform.

Several gene clusters that are responsible for toxin synthesis in bloom-forming cyanobacteria have been found to be associated with transposable elements (TEs). In particular, insertion sequence (IS) elements were shown to play a role in the inactivation or recombination of the genes responsible for cyanotoxin synthesis. Plasmids have been considered important vectors of IS element distribution to the host. In this study, we aimed to elucidate the IS elements propagated on the plasmids and the chromosome of the toxic cyanobacterium Planktothrix agardhii NIVA-CYA126/8 by means of high-throughput sequencing. In total, five plasmids (pPA5.5, pPA14, pPA50, pPA79, and pPA115, of 5, 6, 50, 79, and 120 kbp, respectively) were elucidated, and two plasmids (pPA5.5, pPA115) were found to propagate full IS element copies. Large stretches of shared DNA information between plasmids were constituted of TEs. Two plasmids (pPA5.5, pPA14) were used as candidates to engineer shuttle vectors (named pPA5.5SV and pPA14SV, respectively) in vitro by PCR amplification and the subsequent transposition of the Tn 5 cat transposon containing the R6Kγ origin of replication of Escherichia coli . While pPA5.5SV was found to be fully segregated, pPA14SV consistently co-occurred with its wild-type plasmid even under the highest selective pressure. Interestingly, the Tn 5 cat transposon became transferred by homologous recombination into another plasmid, pPA50. The availability of shuttle vectors is considered to be of relevance in investigating genome plasticity as a consequence of homologous recombination events. Combining the potential of high-throughput sequencing and in vitro production of shuttle vectors makes it simple to produce species-specific shuttle vectors for many cultivable prokaryotes.

We report here the draft genome sequence of the biocontrol strain Pantoea agglomerans P10c, composed of a draft chromosome and two plasmids: the 559-kb large Pantoea plasmid 1 (pPag3) and a 182-kb plasmid (pPag1). A genomic island containing pantocin A biosynthesis genes was identified.

González, José M. ... et al.-- 12 pages, 8 figures, 1 table, supplemental material http://aem.asm.org/content/77/24/8676/suppl/DC1, Proteorhodopsin phototrophy is expected to have considerable impact on the ecology and biogeochemical roles of marine bacteria. However, the genetic features contributing to the success of proteorhodopsin-containing bacteria remain largely unknown. We investigated the genome of Dokdonia sp. strain MED134 (Bacteroidetes) for features potentially explaining its ability to grow better in light than darkness. MED134 has a relatively high number of peptidases, suggesting that amino acids are the main carbon and nitrogen sources. In addition, MED134 shares with other environmental genomes a reduction in gene copies at the expense of important ones, like membrane transporters, which might be compensated by the presence of the proteorhodopsin gene. The genome analyses suggest Dokdonia sp. MED134 is able to respond to light at least partly due to the presence of a strong flavobacterial consensus promoter sequence for the proteorhodopsin gene. Moreover, Dokdonia sp. MED134 has a complete set of anaplerotic enzymes likely to play a role in the adaptation of the carbon anabolism to the different sources of energy it can use, including light or various organic matter compounds. In addition to promoting growth, proteorhodopsin phototrophy could provide energy for the degradation of complex or recalcitrant organic matter, survival during periods of low nutrients, or uptake of amino acids and peptides at low concentrations. Our analysis suggests that the ability to harness light potentially makes MED134 less dependent on the amount and quality of organic matter or other nutrients. The genomic features reported here may well be among the keys to a successful photoheterotrophic lifestyle, J.M.G. and C.P.-A. were supported by grant CTM2010-11060-E from the Spanish Ministry of Science and Innovation, J.P. was supported by the Swedish Research Council and FORMAS, and P.P. was supported by the intramural funds of the U.S. Department of Health and Human Services (National Library of Medicine, National Institutes of Health)

Neisseria meningitidis serogroup B strains are responsible for most meningococcal cases in the industrialized countries, and strains belonging to the clonal complex ST-41/44 are among the most prevalent serogroup B strains in carriage and disease. Here, we report the first genome and transcriptome comparison of a serogroup B carriage strain from the clonal complex ST-41/44 to the serogroup B disease strain MC58 from the clonal complex ST-32. Both genomes are highly colinear, with only three major genome rearrangements that are associated with the integration of mobile genetic elements. They further differ in about 10% of their gene content, with the highest variability in gene presence as well as gene sequence found for proteins involved in host cell interactions, including Opc, NadA, TonB-dependent receptors, RTX toxin, and two-partner secretion system proteins. Whereas housekeeping genes coding for metabolic functions were highly conserved, there were considerable differences in their expression pattern upon adhesion to human nasopharyngeal cells between both strains, including differences in energy metabolism and stress response. In line with these genomic and transcriptomic differences, both strains also showed marked differences in their in vitro infectivity and in serum resistance. Taken together, these data support the concept of a polygenic nature of meningococcal virulence comprising differences in the repertoire of adhesins as well as in the regulation of metabolic genes and suggest a prominent role for immune selection and genetic drift in shaping the meningococcal genome.

Bacterioplankton of the marine Roseobacter clade have genomes that reflect a dynamic environment and diverse interactions with marine plankton. Comparative genome sequence analysis of three cultured representatives suggests that cellular requirements for nitrogen are largely provided by regenerated ammonium and organic compounds (polyamines, allophanate, and urea), while typical sources of carbon include amino acids, glyoxylate, and aromatic metabolites. An unexpectedly large number of genes are predicted to encode proteins involved in the production, degradation, and efflux of toxins and metabolites. A mechanism likely involved in cell-to-cell DNA or protein transfer was also discovered: vir -related genes encoding a type IV secretion system typical of bacterial pathogens. These suggest a potential for interacting with neighboring cells and impacting the routing of organic matter into the microbial loop. Genes shared among the three roseobacters and also common in nine draft Roseobacter genomes include those for carbon monoxide oxidation, dimethylsulfoniopropionate demethylation, and aromatic compound degradation. Genes shared with other cultured marine bacteria include those for utilizing sodium gradients, transport and metabolism of sulfate, and osmoregulation.

Pseudomonas aeruginosa is known to cause complicated urinary tract infections (UTI). The improved 7.0-Mb draft genome sequence of P. aeruginosa RN21, isolated from a patient with an acute UTI, was determined. It carries three (pro)phage genomes, genes for two restriction/modification systems, and a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system.

The complete genome of probiotic Escherichia coli strain G3/10 is presented here. In addition, the probiotic E. coli strains G1/2, G4/9, G5, G6/7, and G8 are presented in draft form. These six strains together comprise the probiotic product Symbioflor 2 (DSM 17252).

Pseudomonas aeruginosa is a frequent agent of complicated catheter-associated urinary tract infections (CAUTIs). Here, we present the improved 7.1-Mb draft genome sequence of P. aeruginosa MH19, which was isolated from a patient with an acute hospital-acquired CAUTI. It includes unique genes not represented in other P. aeruginosa genomes.

Here we present an extensive genomic and genetic analysis of Escherichia coli strains of serotype O78 that represent the major cause of avian colisepticemia, an invasive infection caused by avian pathogenic Escherichia coli (APEC) strains. It is associated with high mortality and morbidity, resulting in significant economic consequences for the poultry industry. To understand the genetic basis of the virulence of avian septicemic E. coli, we sequenced the entire genome of a clinical isolate of serotype O78—O78:H19 ST88 isolate 789 (O78-9)—and compared it with three publicly available APEC O78 sequences and one complete genome of APEC serotype O1 strain. Although there was a large variability in genome content between the APEC strains, several genes were conserved, which are potentially critical for colisepticemia. Some of these genes are present in multiple copies per genome or code for gene products with overlapping function, signifying their importance. A systematic deletion of each of these virulence-related genes identified three systems that are conserved in all septicemic strains examined and are critical for serum survival, a prerequisite for septicemia. These are the plasmid-encoded protein, the defective ETT2 (E. coli type 3 secretion system 2) type 3 secretion system ETT2sepsis, and iron uptake systems. Strain O78-9 is the only APEC O78 strain that also carried the regulon coding for yersiniabactin, the iron binding system of the Yersinia high-pathogenicity island. Interestingly, this system is the only one that cannot be complemented by other iron uptake systems under iron limitation and in serum., IMPORTANCE Avian colisepticemia is a severe systemic disease of birds causing high morbidity and mortality and resulting in severe economic losses. The bacteria associated with avian colisepticemia are highly antibiotic resistant, making antibiotic treatment ineffective, and there is no effective vaccine due to the multitude of serotypes involved. To understand the disease and work out strategies to combat it, we performed an extensive genomic and genetic analysis of Escherichia coli strains of serotype O78, the major cause of the disease. We identified several potential virulence factors, conserved in all the colisepticemic strains examined, and determined their contribution to growth in serum, an absolute requirement for septicemia. These findings raise the possibility that specific vaccines or drugs can be developed against these critical virulence factors to help combat this economically important disease.

Pseudomonas aeruginosa is an opportunistic pathogen that typically infects patients with a compromised immune defense. Here, we present the improved 6.5-Mb draft genome of strain WS136, an ExoS-positive and ExoU-negative highly cytotoxic chronic wound isolate recovered from pyoderma gangrenosum of a patient who received bone marrow transplantation.

Pseudomonas aeruginosa is a frequent human pathogen that increasingly causes chronic infections of nonhealing wounds. Here we present the 6.8 Mb draft genome of strain WS394, a multidrug-resistant chronic ulcer isolate that exhibited outstanding high cell cytotoxicity despite defective secretion of exotoxin U, suggesting a habitat-dependent adaptation process.

Pseudomonas aeruginosa is a major nosocomial bacterial pathogen causing complicated catheter-associated urinary tract infections (CAUTIs). Here, we present the 6.9-Mb draft genome sequence of P. aeruginosa MH38 isolated from an acute nosocomial CAUTI. It exhibits resistance to several antibiotics but revealed low-level production of virulence factors.

Pseudomonas aeruginosa is a notable nosocomial pathogen causing severe chronic infections. Here we present the draft genome sequence of P. aeruginosa MH27, isolated from a patient with a chronic hospital-acquired catheter-associated urinary tract infection. The 7.1-Mb genome sequence organized in 24 scaffolds contributes to the understanding of biofilm formation and antibiotic resistance.

We report draft genome sequences of three Mexican Erwinia amylovora strains. A novel plasmid, pEA78, was identified. Comparative genomics revealed an rpsL chromosomal mutation conferring high-level streptomycin resistance in two strains. In the effector gene avrRpt2 , a single nucleotide polymorphism was detected that overcomes fire blight disease resistance in Malus × robusta 5.

The complete and annotated genome sequence of Enterococcus faecalis D32, a commensal strain isolated from a Danish pig, suggests putative adaptation to the porcine host and absence of distinct virulence-associated traits.

Fibrella aestuarina BUZ 2 T is the type strain of the recently characterized genus Fibrella . Here we report the draft genome sequence of this strain, which consists of a single scaffold representing the chromosome (with 11 gaps) and a 161-kb circular plasmid.

Fibrisoma limi strain BUZ 3 T , a Gram-negative bacterium, was isolated from coastal mud from the North Sea (Fedderwardersiel, Germany) and characterized using a polyphasic approach in 2011. The genome consists of a chromosome of about 7.5 Mb and three plasmids.

We report the complete and annotated genome sequence of the nonpathogenicListeria seeligeriSLCC3954 serovar 1/2b type strain harboring the smallest completely sequenced genome of the genusListeria.

The production of Shiga toxin (Stx) (verocytotoxin) is a major virulence factor of Escherichia coli O157:H7 strains (Shiga toxin-producing E. coli [STEC] O157). Two types of Shiga toxins, designated Stx1 and Stx2, are produced in STEC O157. Variants of the Stx2 type (Stx2, Stx2c) are associated with high virulences of these strains for humans. A bacteriophage designated 2851 from a human STEC O157 encoding the Stx2c variant was described previously. Nucleotide sequence analysis of the phage 2851 genome revealed 75 predicted coding sequences and indicated a mosaic structure typical for lambdoid phages. Analyses of free phages and K-12 phage 2851 lysogens revealed that upon excision from the bacterial chromosome, the loss of a phage-encoded IS 629 element leads to fusion of phage antA and antB genes, with the generation of a recombined antAB gene encoding a strong antirepressor. In wild-type E. coli O157 as well as in K-12 strains, phage 2851 was found to be integrated in the sbcB locus. Additionally, phage 2851 carries an open reading frame which encodes an OspB-like type III effector similar to that found in Shigella spp. Investigation of 39 stx 2c E. coli O157 strains revealed that all except 1 were positive for most phage 2851-specific genes and possessed a prophage with the same border sequences integrated into the sbcB locus. Phage 2851-specific sequences were absent from most stx 2c -negative E. coli O157 strains, and we suggest that phage 2851-like phages contributed significantly to the dissemination of the Stx2c variant toxin within this group of E. coli .

We present the complete genome sequence ofListeria welshimeri, a nonpathogenic member of the genusListeria. Listeria welshimeriharbors a circular chromosome of 2,814,130 bp with 2,780 open reading frames. Comparative genomic analysis of chromosomal regions betweenL. welshimeri,Listeria innocua, andListeria monocytogenesshows strong overall conservation of synteny, with the exception of the translocation of an FoF1ATP synthase. The smaller size of theL. welshimerigenome is the result of deletions in all of the genes involved in virulence and of “fitness” genes required for intracellular survival, transcription factors, and LPXTG- and LRR-containing proteins as well as 55 genes involved in carbohydrate transport and metabolism. In total, 482 genes are absent fromL. welshimerirelative toL. monocytogenes. Of these, 249 deletions are commonly absent in bothL. welshimeriandL. innocua, suggesting similar genome evolutionary paths from an ancestor. We also identified 311 genes specific toL. welshimerithat are absent in the other two species, indicating gene expansion inL. welshimeri, including horizontal gene transfer. The speciesL. welshimeriappears to have been derived from early evolutionary events and an ancestor more compact thanL. monocytogenesthat led to the emergence of nonpathogenicListeriaspp.

Corynebacterium jeikeium is a “lipophilic” and multidrug-resistant bacterial species of the human skin flora that has been recognized with increasing frequency as a serious nosocomial pathogen. Here we report the genome sequence of the clinical isolate C. jeikeium K411, which was initially recovered from the axilla of a bone marrow transplant patient. The genome of C. jeikeium K411 consists of a circular chromosome of 2,462,499 bp and the 14,323-bp bacteriocin-producing plasmid pKW4. The chromosome of C. jeikeium K411 contains 2,104 predicted coding sequences, 52% of which were considered to be orthologous with genes in the Corynebacterium glutamicum , Corynebacterium efficiens , and Corynebacterium diphtheriae genomes. These genes apparently represent the chromosomal backbone that is conserved between the four corynebacteria. Among the genes that lack an ortholog in the known corynebacterial genomes, many are located close to transposable elements or revealed an atypical G+C content, indicating that horizontal gene transfer played an important role in the acquisition of genes involved in iron and manganese homeostasis, in multidrug resistance, in bacterium-host interaction, and in virulence. Metabolic analyses of the genome sequence indicated that the “lipophilic” phenotype of C. jeikeium most likely originates from the absence of fatty acid synthase and thus represents a fatty acid auxotrophy. Accordingly, both the complete gene repertoire and the deduced lifestyle of C. jeikeium K411 largely reflect the strict dependence of growth on the presence of exogenous fatty acids. The predicted virulence factors of C. jeikeium K411 are apparently involved in ensuring the availability of exogenous fatty acids by damaging the host tissue.

Wickerhamomyces ciferrii is a microorganism characterized by the production and secretion of large amounts of acetylated sphingoid bases, in particular tetraacetyl phytosphingosine. Here, we present the 15.90-Mbp draft genome sequence of W. ciferrii NRRL Y-1031 F-60-10 generated by pyrosequencing and de novo assembly. The draft genome sequence comprising 364 contigs in 150 scaffolds was annotated and covered 6,702 protein-coding sequences. This information will contribute to the metabolic engineering of this yeast to improve the yield and spectrum of acetylated sphingoid bases in biotechnological production.

Neisseria meningitidisis a commensal and accidental pathogen exclusively of humans. Although the production of polysaccharide capsules is considered to be essential for meningococcal virulence, there have been reports of constitutively unencapsulated strains causing invasive meningococcal disease (IMD). Here we report the genome sequence of a capsule null locus (cnl) strain of sequence type 198 (ST-198), which is found in half of the reported cases of IMD caused bycnlmeningococcal strains.

The genome of Salmonella enterica subsp. enterica serovar Weltevreden strain 2007-60-3289-1 was sequenced. The genome sequence of this fresh-vegetable isolate from Scandinavia will be useful for the elucidation of plant host factors in comparison to other serovars of S. enterica subsp. enterica.