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1.  Pan-Genome Analysis of Human Gastric Pathogen H. pylori: Comparative Genomics and Pathogenomics Approaches to Identify Regions Associated with Pathogenicity and Prediction of Potential Core Therapeutic Targets 
BioMed Research International  2015;2015:139580.
Helicobacter pylori is a human gastric pathogen implicated as the major cause of peptic ulcer and second leading cause of gastric cancer (~70%) around the world. Conversely, an increased resistance to antibiotics and hindrances in the development of vaccines against H. pylori are observed. Pan-genome analyses of the global representative H. pylori isolates consisting of 39 complete genomes are presented in this paper. Phylogenetic analyses have revealed close relationships among geographically diverse strains of H. pylori. The conservation among these genomes was further analyzed by pan-genome approach; the predicted conserved gene families (1,193) constitute ~77% of the average H. pylori genome and 45% of the global gene repertoire of the species. Reverse vaccinology strategies have been adopted to identify and narrow down the potential core-immunogenic candidates. Total of 28 nonhost homolog proteins were characterized as universal therapeutic targets against H. pylori based on their functional annotation and protein-protein interaction. Finally, pathogenomics and genome plasticity analysis revealed 3 highly conserved and 2 highly variable putative pathogenicity islands in all of the H. pylori genomes been analyzed.
doi:10.1155/2015/139580
PMCID: PMC4325212
2.  Draft Genome Sequences of Vibrio fluvialis Strains 560 and 539, Isolated from Environmental Samples 
Genome Announcements  2015;3(1):e01344-14.
Vibrio fluvialis is a halophilic bacterium found in many environments and is mainly associated with sporadic cases and outbreaks of gastroenteritis in humans. Here, we describe the genome sequences of environmental strains of V. fluvialis 560 (Vf560) and V. fluvialis 539 (Vf539) possessing a variant of the integrative and conjugative element (ICE) SXT for the first time in Brazil and South America.
doi:10.1128/genomeA.01344-14
PMCID: PMC4290981  PMID: 25573928
3.  Omics profiles used to evaluate the gene expression of Exiguobacterium antarcticum B7 during cold adaptation 
BMC Genomics  2014;15(1):986.
Background
Exiguobacterium antarcticum strain B7 is a Gram-positive psychrotrophic bacterial species isolated in Antarctica. Although this bacteria has been poorly studied, its genome has already been sequenced. Therefore, it is an appropriate model for the study of thermal adaptation. In the present study, we analyzed the transcriptomes and proteomes of E. antarcticum B7 grown at 0°C and 37°C by SOLiD RNA-Seq, Ion Torrent RNA-Seq and two-dimensional difference gel electrophoresis tandem mass spectrometry (2D-DIGE-MS/MS).
Results
We found expression of 2,058 transcripts in all replicates from both platforms and differential expression of 564 genes (absolute log2FC ≥1, P-value <0.001) comparing the two temperatures by RNA-Seq. A total of 73 spots were differentially expressed between the two temperatures on 2D-DIGE, 25 of which were identified by MS/MS. Some proteins exhibited patterns of dispersion in the gel that are characteristic of post-translational modifications.
Conclusions
Our findings suggest that the two sequencing platforms yielded similar results and that different omic approaches may be used to improve the understanding of gene expression. To adapt to low temperatures, E. antarcticum B7 expresses four of the six cold-shock proteins present in its genome. The cold-shock proteins were the most abundant in the bacterial proteome at 0°C. Some of the differentially expressed genes are required to preserve transcription and translation, while others encode proteins that contribute to the maintenance of the intracellular environment and appropriate protein folding. The results denote the complexity intrinsic to the adaptation of psychrotrophic organisms to cold environments and are based on two omic approaches. They also unveil the lifestyle of a bacterial species isolated in Antarctica.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-986) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2164-15-986
PMCID: PMC4247613  PMID: 25407400
Exiguobacterium antarcticum; Psychrotrophic; Proteomic; RNA-Seq; Gene expression
4.  Genome Sequence of Corynebacterium pseudotuberculosis MB20 bv. equi Isolated from a Pectoral Abscess of an Oldenburg Horse in California 
Genome Announcements  2014;2(6):e00977-14.
The genome of Corynebacterium pseudotuberculosis MB20 bv. equi was sequenced using the Ion Personal Genome Machine (PGM) platform, and showed a size of 2,363,089 bp, with 2,365 coding sequences and a GC content of 52.1%. These results will serve as a basis for further studies on the pathogenicity of C. pseudotuberculosis bv. equi.
doi:10.1128/genomeA.00977-14
PMCID: PMC4241654  PMID: 25395628
5.  Draft Genome Sequence of Non-O1 and Non-O139 Vibrio cholerae Strain VCC19 
Genome Announcements  2014;2(6):e01094-14.
Vibrio cholerae O1 is the causative agent of cholera and is ubiquitous in the aquatic environment, while V. cholerae strains non-O1 and non-O139 are recognized as causative agents of sporadic and localized outbreaks of diarrhea. Here, we report the complete sequence of a non-O1 and non-O139 V. cholerae strain (VCC19), which was isolated from the environment in Brazil. The sequence includes the integrative conjugative element (ICE). This paper is the first report of the presence of such an element in a V. cholerae strain isolated in Brazil.
doi:10.1128/genomeA.01094-14
PMCID: PMC4223450  PMID: 25377699
6.  Genome Sequence of Lactococcus lactis subsp. lactis NCDO 2118, a GABA-Producing Strain 
Genome Announcements  2014;2(5):e00980-14.
Lactococcus lactis subsp. lactis NCDO 2118 is a nondairy lactic acid bacterium, a xylose fermenter, and a gamma-aminobutyric acid (GABA) producer isolated from frozen peas. Here, we report the complete genome sequence of L. lactis NCDO 2118, a strain with probiotic potential activity.
doi:10.1128/genomeA.00980-14
PMCID: PMC4183873  PMID: 25278529
7.  A Novel Cell Line Derived from Pleomorphic Adenoma Expresses MMP2, MMP9, TIMP1, TIMP2, and Shows Numeric Chromosomal Anomalies 
PLoS ONE  2014;9(8):e105231.
Pleomorphic adenoma is the most common salivary gland neoplasm, and it can be locally invasive, despite its slow growth. This study aimed to establish a novel cell line (AP-1) derived from a human pleomorphic adenoma sample to better understand local invasiveness of this tumor. AP-1 cell line was characterized by cell growth analysis, expression of epithelial and myoepithelial markers by immunofluorescence, electron microscopy, 3D cell culture assays, cytogenetic features and transcriptomic study. Expression of matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs) was also analyzed by immunofluorescence and zymography. Furthermore, epithelial and myoepithelial markers, MMPs and TIMPs were studied in the tumor that originated the cell line. AP-1 cells showed neoplastic epithelial and myoepithelial markers, such as cytokeratins, vimentin, S100 protein and smooth-muscle actin. These molecules were also found in vivo, in the tumor that originated the cell line. MMPs and TIMPs were observed in vivo and in AP-1 cells. Growth curve showed that AP-1 exhibited a doubling time of 3.342 days. AP-1 cells grown inside Matrigel recapitulated tumor architecture. Different numerical and structural chromosomal anomalies were visualized in cytogenetic analysis. Transcriptomic analysis addressed expression of 7 target genes (VIM, TIMP2, MMP2, MMP9, TIMP1, ACTA2 e PLAG1). Results were compared to transcriptomic profile of non-neoplastic salivary gland cells (HSG). Only MMP9 was not expressed in both libraries, and VIM was expressed solely in AP-1 library. The major difference regarding gene expression level between AP-1 and HSG samples occurred for MMP2. This gene was 184 times more expressed in AP-1 cells. Our findings suggest that AP-1 cell line could be a useful model for further studies on pleomorphic adenoma biology.
doi:10.1371/journal.pone.0105231
PMCID: PMC4138172  PMID: 25137137
8.  Draft Genome Sequence of Haloferax sp. Strain ATB1, Isolated from a Semi-Arid Region in the Brazilian Caatinga 
Genome Announcements  2014;2(4):e00812-14.
Organisms in the Haloferax genus are extreme halophiles that grow in environments with pH values between 4 and 12, and temperatures between 0°C and 60°C. In the present study, a draft of the first Haloferax sp. strain ATB1 genome isolated from the region of Cariri (in Paraíba State, Brazil) is presented.
doi:10.1128/genomeA.00812-14
PMCID: PMC4132625  PMID: 25125649
9.  Value of a newly sequenced bacterial genome 
Next-generation sequencing (NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft (partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the “scientific value” of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information.
doi:10.4331/wjbc.v5.i2.161
PMCID: PMC4050110  PMID: 24921006
Next-generation sequencing; Drafts; Prokaryotic genomes; Computational tools; Omics
10.  Draft Genome Sequence of Corynebacterium ulcerans FRC58, Isolated from the Bronchitic Aspiration of a Patient in France 
Genome Announcements  2014;2(1):e01132-13.
Corynebacterium ulcerans is a bacterial species with high importance because it causes infections in animals and, rarely, in humans. Its virulence mechanisms remain unclear. The current study describes the draft genome of C. ulcerans FRC58, which was isolated from the bronchitic aspiration of a patient in France.
doi:10.1128/genomeA.01132-13
PMCID: PMC3886953  PMID: 24407640
11.  Differential transcriptional profile of Corynebacterium pseudotuberculosis in response to abiotic stresses 
BMC Genomics  2014;15:14.
Background
The completion of whole-genome sequencing for Corynebacterium pseudotuberculosis strain 1002 has contributed to major advances in research aimed at understanding the biology of this microorganism. This bacterium causes significant loss to goat and sheep farmers because it is the causal agent of the infectious disease caseous lymphadenitis, which may lead to outcomes ranging from skin injury to animal death. In the current study, we simulated the conditions experienced by the bacteria during host infection. By sequencing transcripts using the SOLiDTM 3 Plus platform, we identified new targets expected to potentiate the survival and replication of the pathogen in adverse environments. These results may also identify possible candidates useful for the development of vaccines, diagnostic kits or therapies aimed at the reduction of losses in agribusiness.
Results
Under the 3 simulated conditions (acid, osmotic and thermal shock stresses), 474 differentially expressed genes exhibiting at least a 2-fold change in expression levels were identified. Important genes to the infection process were induced, such as those involved in virulence, defence against oxidative stress, adhesion and regulation, and many genes encoded hypothetical proteins, indicating that further investigation of the bacterium is necessary. The data will contribute to a better understanding of the biology of C. pseudotuberculosis and to studies investigating strategies to control the disease.
Conclusions
Despite the veterinary importance of C. pseudotuberculosis, the bacterium is poorly characterised; therefore, effective treatments for caseous lymphadenitis have been difficult to establish. Through the use of RNAseq, these results provide a better biological understanding of this bacterium, shed light on the most likely survival mechanisms used by this microorganism in adverse environments and identify candidates that may help reduce or even eradicate the problems caused by this disease.
doi:10.1186/1471-2164-15-14
PMCID: PMC3890534  PMID: 24405787
Differential gene expression; Transcripts; RNAseq; SOLID™; Stress; C. pseudotuberculosis
12.  Draft Genome Sequence of Serratia fonticola UTAD54, a Carbapenem-Resistant Strain Isolated from Drinking Water 
Genome Announcements  2013;1(6):e00970-13.
Serratia fonticola UTAD54 is an environmental isolate that is resistant to carbapenems due to the presence of a class A carbapenemase and a metallo-β-lactamase that are unique to this strain. Its draft genome sequence was obtained to clarify the molecular basis of its carbapenem resistance and identify the genomic context of its carbapenem resistance determinants.
doi:10.1128/genomeA.00970-13
PMCID: PMC3869330  PMID: 24285645
13.  Draft Genome Sequence of Serratia fonticola LMG 7882T Isolated from Freshwater 
Genome Announcements  2013;1(6):e00971-13.
Serratia fonticola is a Gram-negative bacterium with a wide distribution in aquatic environments. On some occasions, it has also been regarded as a significant human pathogen. In this work, we report the first draft genome sequence of an S. fonticola strain (LMG 7882T), which was isolated from freshwater.
doi:10.1128/genomeA.00971-13
PMCID: PMC3837180  PMID: 24265499
14.  Draft Genome Sequence of Mycobacterium abscessus subsp. bolletii INCQS 00594 
Genome Announcements  2013;1(6):e00896-13.
An epidemic of surgical-site infections by a single strain of Mycobacterium abscessus subsp. bolletii affected >1,700 patients in Brazil from 2004 to 2008. The genome of the epidemic prototype strain M. abscessus subsp. bolletii INCQS 00594, deposited in the collection of the National Institute for Health Quality Control (INCQS), was sequenced.
doi:10.1128/genomeA.00896-13
PMCID: PMC3820772  PMID: 24201191
15.  Progression of ‘OMICS’ methodologies for understanding the pathogenicity of Corynebacterium pseudotuberculosis: the Brazilian experience 
Since the first successful attempt at sequencing the Corynebacterium pseudotuberculosis genome, large amounts of genomic, transcriptomic and proteomic data have been generated. C. pseudotuberculosis is an interesting bacterium due to its great zoonotic potential and because it causes considerable economic losses worldwide. Furthermore, different strains of C. pseudotuberculosis are capable of causing various diseases in different hosts. Currently, we seek information about the phylogenetic relationships between different strains of C. pseudotuberculosis isolates from different hosts across the world and to employ these data to develop tools to diagnose and eradicate the diseases these strains cause. In this review, we present the latest findings on C. pseudotuberculosis that have been obtained with the most advanced techniques for sequencing and genomic organization. We also discuss the development of in silico tools for processing these data to prompt a better understanding of this pathogen.
doi:10.5936/csbj.201303013
PMCID: PMC3962224  PMID: 24688721
Corynebacterium pseudotuberculosis; SOLiD next generation sequencing; Ion Torrent next generation sequencing; SDS-PAGE; mass spectrometry; RNA-seq
17.  Draft Genome Sequence of the Brazilian Toxic Bloom-Forming Cyanobacterium Microcystis aeruginosa Strain SPC777 
Genome Announcements  2013;1(4):e00547-13.
Microcystis aeruginosa strain SPC777 is an important toxin-producing cyanobacterium, isolated from a water bloom of the Billings reservoir (São Paulo State, Brazil). Here, we report the draft genome sequence and initial findings from a preliminary analysis of strain SPC777, including several gene clusters involved in nonribosomal and ribosomal synthesis of secondary metabolites.
doi:10.1128/genomeA.00547-13
PMCID: PMC3731843  PMID: 23908289
18.  Draft Genome Sequence of Methylobacterium mesophilicum Strain SR1.6/6, Isolated from Citrus sinensis 
Genome Announcements  2013;1(3):e00356-13.
Methylobacterium mesophilicum strain SR1.6/6 is an endophytic bacterium isolated from a surface-sterilized Citrus sinensis branch. Ecological and biotechnological aspects of this bacterium, such as the genes involved in its association with the host plant and the primary oxidation of methanol, were annotated in the draft genome.
doi:10.1128/genomeA.00356-13
PMCID: PMC3707593  PMID: 23788544
19.  Complete Genome Sequence of Corynebacterium pseudotuberculosis Cp31, Isolated from an Egyptian Buffalo 
Journal of Bacteriology  2012;194(23):6663-6664.
Corynebacterium pseudotuberculosis is of major veterinary importance because it affects many animal species, causing economically significant livestock diseases and losses. Therefore, the genomic sequencing of various lines of this organism, isolated from different hosts, will aid in the development of diagnostic methods and new prevention and treatment strategies and improve our knowledge of the biology of this microorganism. In this study, we present the genome of C. pseudotuberculosis Cp31, isolated from a buffalo in Egypt.
doi:10.1128/JB.01782-12
PMCID: PMC3497519  PMID: 23144408
20.  Genome Sequence of Exiguobacterium antarcticum B7, Isolated from a Biofilm in Ginger Lake, King George Island, Antarctica 
Journal of Bacteriology  2012;194(23):6689-6690.
Exiguobacterium antarcticum is a psychotropic bacterium isolated for the first time from microbial mats of Lake Fryxell in Antarctica. Many organisms of the genus Exiguobacterium are extremophiles and have properties of biotechnological interest, e.g., the capacity to adapt to cold, which make this genus a target for discovering new enzymes, such as lipases and proteases, in addition to improving our understanding of the mechanisms of adaptation and survival at low temperatures. This study presents the genome of E. antarcticum B7, isolated from a biofilm sample of Ginger Lake on King George Island, Antarctic peninsula.
doi:10.1128/JB.01791-12
PMCID: PMC3497522  PMID: 23144424
21.  Genome Sequence of the Corynebacterium pseudotuberculosis Cp316 Strain, Isolated from the Abscess of a Californian Horse 
Journal of Bacteriology  2012;194(23):6620-6621.
The bacterium Corynebacterium pseudotuberculosis is of major veterinary importance because it affects livestock, particularly sheep, goats, and horses, in several countries, including Australia, Brazil, the United States, and Canada, resulting in significant economic losses. In the present study, we describe the complete genome of the Corynebacterium pseudotuberculosis Cp316 strain, biovar equi, isolated from the abscess of a North American horse.
doi:10.1128/JB.01616-12
PMCID: PMC3497548  PMID: 23144380
22.  Complete genome sequence of Streptococcus agalactiae strain SA20-06, a fish pathogen associated to meningoencephalitis outbreaks 
Standards in Genomic Sciences  2013;8(2):188-197.
Streptococcus agalactiae (Lancefield group B; GBS) is the causative agent of meningoencephalitis in fish, mastitis in cows, and neonatal sepsis in humans. Meningoencephalitis is a major health problem for tilapia farming and is responsible for high economic losses worldwide. Despite its importance, the genomic characteristics and the main molecular mechanisms involved in virulence of S. agalactiae isolated from fish are still poorly understood. Here, we present the genomic features of the 1,820,886 bp long complete genome sequence of S. agalactiae SA20-06 isolated from a meningoencephalitis outbreak in Nile tilapia (Oreochromis niloticus) from Brazil, and its annotation, consisting of 1,710 protein-coding genes (excluding pseudogenes), 7 rRNA operons, 79 tRNA genes and 62 pseudogenes.
doi:10.4056/sigs.3687314
PMCID: PMC3746423  PMID: 23991251
Streptococcus agalactiae; fish pathogen; genome sequencing
23.  Complete Genome of a Methanosarcina mazei Strain Isolated from Sediment Samples from an Amazonian Flooded Area 
Genome Announcements  2013;1(3):e00271-13.
Methanosarcina mazei is a strictly anaerobic methanogen from the Methanosarcinales order, which is known for its broad catabolic range among methanogens and is widespread throughout diverse environments. The draft genome of the strain presented here was cultivated from sediment samples collected from the Tucuruí hydroelectric power station reservoir.
doi:10.1128/genomeA.00271-13
PMCID: PMC3662825  PMID: 23704185
24.  The Detection and Sequencing of a Broad-Host-Range Conjugative IncP-1β Plasmid in an Epidemic Strain of Mycobacterium abscessus subsp. bolletii 
PLoS ONE  2013;8(4):e60746.
Background
An extended outbreak of mycobacterial surgical infections occurred in Brazil during 2004–2008. Most infections were caused by a single strain of Mycobacterium abscessus subsp. bolletii, which was characterized by a specific rpoB sequevar and two highly similar pulsed-field gel electrophoresis (PFGE) patterns differentiated by the presence of a ∼50 kb band. The nature of this band was investigated.
Methodology/Principal Findings
Genomic sequencing of the prototype outbreak isolate INCQS 00594 using the SOLiD platform demonstrated the presence of a 56,264-bp circular plasmid, designated pMAB01. Identity matrices, genetic distances and phylogeny analyses indicated that pMAB01 belongs to the broad-host-range plasmid subgroup IncP-1β and is highly related to BRA100, pJP4, pAKD33 and pB10. The presence of pMAB01-derived sequences in 41 M. abscessus subsp. bolletii isolates was evaluated using PCR, PFGE and Southern blot hybridization. Sixteen of the 41 isolates showed the presence of the plasmid. The plasmid was visualized as a ∼50-kb band using PFGE and Southern blot hybridization in 12 isolates. The remaining 25 isolates did not exhibit any evidence of this plasmid. The plasmid was successfully transferred to Escherichia coli by conjugation and transformation. Lateral transfer of pMAB01 to the high efficient plasmid transformation strain Mycobacterium smegmatis mc2155 could not be demonstrated.
Conclusions/Significance
The occurrence of a broad-host-range IncP-1β plasmid in mycobacteria is reported for the first time. Thus, genetic exchange could result in the emergence of specific strains that might be better adapted to cause human disease.
doi:10.1371/journal.pone.0060746
PMCID: PMC3614916  PMID: 23565273
25.  Whole-Genome Sequence of Corynebacterium pseudotuberculosis Strain Cp162, Isolated from Camel 
Journal of Bacteriology  2012;194(20):5718-5719.
Corynebacterium pseudotuberculosis is a pathogen of great veterinary and economic importance, since it affects livestock, mainly sheep and goats, worldwide, together with reports of its presence in camels in several Arabic, Asiatic, and East and West African countries, as well as Australia. In this article, we report the genome sequence of Corynebacterium pseudotuberculosis strain Cp162, collected from the external neck abscess of a camel in the United Kingdom.
doi:10.1128/JB.01373-12
PMCID: PMC3458653  PMID: 23012291

Results 1-25 (44)