Bdellovibrio reynosensis sp. nov., from a Mexico soil sample.

A novel predatory bacterium, strain LBG001T, has been isolated from Reynosa, Mexico. The 16S rRNA shares approximately 97 % sequence identity with many reported strains in the genus Bdellovibrio including the type strain Bdellovibrio bacteriovorus HD100T. Phylogenetic trees based on the 16S rRNA gene and on 30 concatenated housekeeping genes or core genes showed that LBG001T is on a separate branch from the B. bacteriovorus group. LBG0001T has a genome size of 3 582 323 bp with a G+C content of 43.1 mol %. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values with other members of the genus Bdellovibrio (<79, <72 and <17 %, respectively) qualifies the strain to represent a new species in the genus. Strain LBG001T formed visible plaques on all 10 tested Gram-negative bacterial species. The phenotypic characteristics, phylogenetic analysis and genomic taxonomic studies support the classification of the strain as representing a new species for which the name Bdellovibrio reynosensis sp. nov. is proposed. The type strain is LBG001T(=ATCC TSD-288T =CM-CNRG 0932T).

The decolorization and degradation of azo dyes by two Stenotrophomonas strains isolated from textile effluent (Tepetitla, Mexico).

Stenotrophomonas' metabolic versatility plays important roles in the remediation of contaminated environment and plant growth promotion. We investigated two Stenotrophomonas strains isolated from textile polluted sewage for their ability to decolorize and degrade azo dyes. Two Stenotrophomonas strains (TepeL and TepeS) were isolated from textile effluents (Tepetitla, Mexico) using the selective agar Stenotrophomonas vancomycin, imipenem, amphotericin B agar (SVIA). Isolates' identity was determined by the sequencing of their partial 16S rRNA fragments. Their abilities to decolorize dyes were tested in a Luria broth supplemented with varying concentrations (50 mg/L-1 g/L) of textile dyes (acidic red, methyl orange, reactive green, acidic yellow, and reactive black). Fourier-transform infrared (FTIR) spectroscopy and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) metabolite analyses were used to determine the effect of the isolates' growth on the dyes (acidic red, methyl orange). We also identified the enzymes that may be involved in the degradation process. Phylogenetic analysis based on the 16S rDNA sequences showed that the isolates belong to the genus Stenotrophomonas. Stenotrophomonas sp. TepeL and TepeS respectively decolorize all the azo dyes at the tested concentration except at 1 g/L and degraded the azo dyes. The degradation resulted in the formation of N, N-dimethyl p-phenylenediamine, and sodium 4-amino-1-naphthalenesulfonate from methyl orange and acid red. TepeL and TepeS rapidly decolorized and degraded the azo dyes tested. This result showed that the two isolates have a good potential for the decontamination of textile effluents.

Difference of MreBCD Complex Interactome in Salmonella Typhimurium ST19 and ST213 Genotypes on Pathogenesis and Stress Response Pathways.

BACKGROUND: Salmonella enterica is the etiological agent of salmonellosis, with a high infection rate worldwide in Mexico, ST213 genotype of S. enterica ser. Typhimurium is displacing the ancestral ST19 genotype. Bacterial cytoskeleton protein complex MreBCD plays an important role in S. enterica pathogenesis, but underlying mechanisms are unknown. RESULTS: In this study, 106 interactions among MreBCD and 15 proteins from S. Typhimurium Pathogenicity Islands 1 (SP-I) and 2 (SP-2) involved in both bacterial virulence and stress response were predicted in ST213 and ST19 genotypes, of which 12 interactions were confirmed in vitro. In addition, gene cluster analysis in 100 S. Typhimurium genomes was performed for these genes. RESULTS AND CONCLUSION: The in silico and in vitro results showed a novel MreBCD interactome involved in regulating pathogenesis and stress response through interactions with virulence factors located at SPI-1 and SPI-2. Furthermore, both pseudogene presence and sequence variations in four tested proteins between genotypes resulted in differential interaction patterns involved in Salmonella motility and survival in eukaryotic cells, which could explain the replacement of ST19 by ST213 in Mexico.

The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strain Stenotrophomonas sp. Pemsol isolated from Mexico.

BACKGROUND: Stenotrophomonas are ubiquitous gram-negative bacteria, which can survive in a wide range of environments. They can use many substances for their growth and are known to be intrinsically resistant to many antimicrobial agents. They have been tested for biotechnological applications, bioremediation, and production of antimicrobial agents. METHOD: Stenotrophomonas sp. Pemsol was isolated from a crude oil contaminated soil. The capability of this isolate to tolerate and degrade polycyclic aromatic hydrocarbons (PAH) such as anthraquinone, biphenyl, naphthalene, phenanthrene, phenanthridine, and xylene was evaluated in Bushnell Hass medium containing PAHs as the sole carbon sources. The metabolites formed after 30-day degradation of naphthalene by Pemsol were analyzed using Fourier Transform Infra-red Spectroscopic (FTIR), Ultra-Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) and Gas Chromatography-Mass Spectrometry (GC-MS). The genome of Pemsol was also sequenced and analyzed. RESULTS: Anthraquinone, biphenyl, naphthalene, phenanthrene, and phenanthridine except xylene can be used as sole carbon sources for Pemsol's growth in Bushnell Hass medium. The degradation of naphthalene at a concentration of 1 mg/mL within 30 days was tested. A newly formed catechol peak and the disappearance of naphthalene peak detected on the UPLC-MS, and GC-MS analyses spectra respectively confirmed the complete degradation of naphthalene. Pemsol does not produce biosurfactant and neither bio-emulsify PAHs. The whole genome was sequenced and assembled into one scaffold with a length of 4,373,402 bp. A total of 145 genes involved in the degradation of PAHs were found in its genome, some of which are Pemsol-specific as compared with other 11 Stenotrophomonas genomes. Most specific genes are located on the genomic islands. Stenotrophomonas sp. Pemsol's possession of few genes that are associated with bio-emulsification gives the genetic basis for its inability to bio-emulsify PAH. A possible degradation pathway for naphthalene in Pemsol was proposed following the analysis of Pemsol's genome. ANI and GGDH analysis indicated that Pemsol is likely a new species of Stenotrophomonas. It is the first report on a complete genome sequence analysis of a PAH-degrading Stenotrophomonas. Stenotrophomonas sp. Pemsol possesses features that make it a good bacterium for genetic engineering and will be an excellent tool for the remediation of crude oil or PAH-contaminated soil.

Complete Genome Sequence of Stenotrophomonas maltophilia Strain SVIA2, Isolated from Crude Oil-Contaminated Soil in Tabasco, Mexico.

Stenotrophomonas maltophilia strain SVIA2 was isolated from crude oil-contaminated soil from Tabasco, Mexico, and displayed a good potential for the degradation of polycyclic aromatic hydrocarbons (PAHs), using naphthalene, anthracene, phenanthridine, or biphenyl as the unique source of carbon. The SVIA2 genome contains essential genes involved in the degradation of PAHs.

Genes de virulencia en Aeromonas spp. (Aeromonadales: Aeromonadaceae) aisladas de Oreochromis spp. (Perciformes: Cichlidae) para consumo humano en México / Virulence genes in Aeromonas spp. (Aeromonadales: Aeromonadaceae) isolated from Oreochromis spp. (Perciformes: Cichlidae) destined for human consumption in Mexico

Resumen Las especies del género Aeromonas se encuentran ampliamente distribuidas en ecosistemas acuáticos, son bacilos Gram negativas, oxidasa positivas y fermentadoras de glucosa que han sido consideradas patógenas emergentes en humanos. Por otra parte, Aeromonas pertenece a la microbiota normal de los peces, no obstante, estos microorganismos poseen una diversidad de factores de virulencia responsables de una variedad de infecciones en humanos, principalmente de tipo gastrointestinal. La presencia de Aeromonas en productos destinados a consumo de alta demanda comercial como la tilapia genera preocupación sanitaria por el potencial patogénico que posee esta bacteria. En este contexto, identificar genes de virulencia presentes en cepas de Aeromonas aisladas en Oreochromis spp. para consumo humano en Reynosa, Tamaulipas, México; es de importancia ante la escasez de estudios moleculares al respecto en la zona. En el presente estudio se analizó el potencial patogénico de 15 cepas de Aeromonas previamente identificadas molecularmente mediante PCR y secuenciación, procedentes de Oreochromis spp. Mediante PCR se analizaron seis genes de virulencia (alt, ast, aerA, hlyA, gcat y stx1) y las cepas utilizadas como control fueron: Aeromonas hydrophila subsp. hydrophila ATCC 7966, Aeromonas caviae 429865 INP, Escherichia coli O157:H7 y Escherichia coli K12. El 100 % (n = 15) de las cepas presentaron al menos un gen de virulencia, el gen aerA se detectó en 86.66 % de las cepas analizadas, mientras que los genes ast y stx1 no fueron identificados. Se encontró que las cepas de Aeromonas presentaban genes asociados en una misma cepa: aerA/gcat, alt/aerA, alt/ aerA/gcat/hlyA y alt/aerA/gcat, de los cuales aerA/gcat se observó con mayor frecuencia y principalmente en A. veronii, mientras que, A. hydrophila presentó el mayor número de asociaciones de genes de virulencia. Estos hallazgos indican que las cepas de Aeromonas aisladas en Oreochromis spp. tienen el potencial de causar enfermedades en humanos. Por lo tanto, es necesario proporcionar información sobre esta bacteria emergente, para tratar y controlar eficazmente cualquier posible evento epidemiológico causado por la misma.(AU)

Abstract The genus Aeromonas are widely distributed in aquatic ecosystems are Gram-negative rods, oxidase-positive, and glucose-fermenting, considered emerging pathogens in humans. Aeromonas belongs to the fish microbiota, these microorganisms have a diversity of virulence factors responsible for a variety of infections in humans mainly gastrointestinal diseases. The presence of Aeromonas in products intended for consumption with high commercial demand such as tilapia generates sanitary concern due to the pathogenic potential of this bacteria. In this context, identification of virulence genes in strains of Aeromonas isolated in Oreochromis spp. intended for human consumption in Reynosa, Tamaulipas, Mexico is important due to the lack of molecular studies in this geographical area. In the present study the pathogenic potential of 15 strains of Aeromonas (A. veronii, A. hydrophila and A. schubertii) from Oreochromis spp. for human consumption were analyzed. Through PCR six virulence genes were analyzed (alt, ast, aerA, hlyA, gcat and stx1) and the strains used as control were: Aeromonas hydrophila subsp. hydrophila ATCC 7966, Aeromonas caviae 429865 INP, Escherichia coli O157: H7 and Escherichia coli K12. El 100 % (n = 15) of the strains harbored at least one virulence gene, aerA gene was detected in 86.66 % of the analyzed strains, while ast and stx1 genes were not identified. Moreover, Aeromonas strains had associated genes in the same strain: aerA / gcat, alt / aerA, alt / aerA / gcat / hlyA and alt / aerA / gcat, of which aerA / gcat were observed mostly in A. veronii, while A. hydrophila had the highest associations. These findings indicate that the strains of Aeromonas isolated in Oreochromis spp. have the potential to cause human diseases, and therefore, this species used as food, could be a vehicle for infections caused by Aeromonas. It also allows to provide information on this emerging microorganism to effectively treat and control any epidemiological event caused by Aeromonas spp. in the future.(AU)

Draft Genome Sequence of Aeromonas caviae Strain 429865 INP, Isolated from a Mexican Patient.

Aeromonas caviae is an emerging human pathogen. Here, we report the draft genome sequence of Aeromonas caviae strain 429865 INP which shows the presence of various putative virulence-related genes.

Large-scale genomic analysis of codon usage in dengue virus and evaluation of its phylogenetic dependence.

The increasing number of dengue virus (DENV) genome sequences available allows identifying the contributing factors to DENV evolution. In the present study, the codon usage in serotypes 1-4 (DENV1-4) has been explored for 3047 sequenced genomes using different statistics methods. The correlation analysis of total GC content (GC) with GC content at the three nucleotide positions of codons (GC1, GC2, and GC3) as well as the effective number of codons (ENC, ENCp) versus GC3 plots revealed mutational bias and purifying selection pressures as the major forces influencing the codon usage, but with distinct pressure on specific nucleotide position in the codon. The correspondence analysis (CA) and clustering analysis on relative synonymous codon usage (RSCU) within each serotype showed similar clustering patterns to the phylogenetic analysis of nucleotide sequences for DENV1-4. These clustering patterns are strongly related to the virus geographic origin. The phylogenetic dependence analysis also suggests that stabilizing selection acts on the codon usage bias. Our analysis of a large scale reveals new feature on DENV genomic evolution.

The detection of inherent homologous recombination between repeat sequences in H. pylori 26695 by the PCR-based method.

Helicobacter pylori infects more than half of the world's population, making it the most widespread infection of bacteria. It has high genetic diversity and has been considered as one of the most variable bacterial species. In the present study, a PCR-based method was used to detect the presence and the relative frequency of homologous recombination between repeat sequences (>500 bp) in H. pylori 26695. All the recombinant structures have been confirmed by sequencing. The inversion generated between inverted repeats showed distinct features from the recombination for duplication or deletion between direct repeats. Meanwhile, we gave the mathematic reasoning of a general formula for the calculation of relative recombination frequency and indicated the conditions for its application. This formula could be extensively applied to detect the frequency of homologous recombination, site-specific recombination, and other types of predictable recombination. Our results should be helpful for better understanding the genome evolution and adaptation of bacteria.

Analysis of genetic variation in ribosomal DNA internal transcribed spacer and the NADH dehydrogenase subunit 4 mitochondrial genes of the onchocerciasis vector Simulium ochraceum.

Onchocerciasis is a serious disease vectored by black flies in the genus Simulium that are infected with the filarial parasite Onchocerca volvulus. In the Americas, black flies of the Simulium ochraceum s.l. species complex are important vectors of this parasite. Cytological studies have suggested that this species complex consists of at least three cytotypes that inhabit distinct habitats. In this study, the NADH dehydrogenase subunit four (ND4) and internal transcribed spacer (ITS) of the ribosomal RNA gene cluster were used to explore the degree of genetic diversity among S. ochraceum s.l. populations found in the three O. volvulus foci in Mexico. Both sequence regions were found to exhibit intra- and interpopulation variation. Four different ND4 alleles were found among the populations examined. Similarly, variation was noted in the ITS domain sequences within and among populations. Variation within the ITS sequence was primarily confined to a complex microsatellite locus. Four ITS length variants were observed, two of which were only seen in flies collected from the onchocerciasis focus in northern Chiapas. These data suggest that the ND4 and ITS sequences may prove to be useful markers for exploring interactions within and among the S. ochraceum s.l. populations in Mexico.