Draft Genome Sequences of Five Enterococcus Species Isolated from the Gut of Patients with Suspected Clostridium difficile Infection

Indexación: Scopus.We present draft genome sequences of five Enterococcus species from patients suspected of Clostridium difficile infection. Genome completeness was confirmed by presence of bacterial orthologs (97%). Gene searches using Hidden-Markov models revealed that the isolates harbor between seven and 11 genes involved in antibiotic resistance to tetracyclines, beta-lactams, and vancomycin.http://genomea.asm.org/content/5/20/e00379-17.ful

Genomic analysis of 48 paenibacillus larvae bacteriophages

Indexación: Scopus.Funding: Research at UNLV was funded by National Institute of General Medical Sciences grant GM103440 (NV INBRE), the UNLV School of Life Sciences, and the UNLV College of Sciences. E.C.-N. was funded by CONICYT-FONDECYT de iniciación en la investigación 11160905. Research at BYU was funded by the BYU Microbiology & Molecular Biology Department, and private donations through LDS Philanthropies.The antibiotic-resistant bacterium Paenibacillus larvae is the causative agent of American foulbrood (AFB), currently the most destructive bacterial disease in honeybees. Phages that infect P. larvae were isolated as early as the 1950s, but it is only in recent years that P. larvae phage genomes have been sequenced and annotated. In this study we analyze the genomes of all 48 currently sequenced P. larvae phage genomes and classify them into four clusters and a singleton. The majority of P. larvae phage genomes are in the 38–45 kbp range and use the cohesive ends (cos) DNA-packaging strategy, while a minority have genomes in the 50–55 kbp range that use the direct terminal repeat (DTR) DNA-packaging strategy. The DTR phages form a distinct cluster, while the cos phages form three clusters and a singleton. Putative functions were identified for about half of all phage proteins. Structural and assembly proteins are located at the front of the genome and tend to be conserved within clusters, whereas regulatory and replication proteins are located in the middle and rear of the genome and are not conserved, even within clusters. All P. larvae phage genomes contain a conserved N-acetylmuramoyl-L-alanine amidase that serves as an endolysin. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.https://www.mdpi.com/1999-4915/10/7/37

Comparative Genomics Analysis of a New Exiguobacterium Strain from Salar de Huasco Reveals a Repertoire of Stress-Related Genes and Arsenic Resistance

Indexación: Web of Science; Scopus.The Atacama Desert hosts diverse ecosystems including salt flats and shallow Andean lakes. Several heavy metals are found in the Atacama Desert, and microorganisms growing in this environment show varying levels of resistance/tolerance to copper, tellurium, and arsenic, among others. Herein, we report the genome sequence and comparative genomic analysis of a new Exiguobacterium strain, sp. SH31, isolated from an altiplanic shallow athalassohaline lake. Exiguobacterium sp. SH31 belongs to the phylogenetic Group II and its closest relative is Exiguobacterium sp. S17, isolated from the Argentinian Altiplano (95% average nucleotide identity). Strain SH31 encodes a wide repertoire of proteins required for cadmium, copper, mercury, tellurium, chromium, and arsenic resistance. Of the 34 Exiguobacterium genomes that were inspected, only isolates SH31 and S17 encode the arsenic efflux pump Acr3. Strain SH31 was able to grow in up to 10 mM arsenite and 100 mM arsenate, indicating that it is arsenic resistant. Further, expression of the ars operon and acr3 was strongly induced in response to both toxics, suggesting that the arsenic efflux pump Acr3 mediates arsenic resistance in Exiguobacterium sp. SH31.http://journal.frontiersin.org/article/10.3389/fmicb.2017.00456/ful

Radiation-induced toxicity in rectal epithelial stem cell contributes to acute radiation injury in rectum

Indexación ScopusBackground: Radiation-induced rectal epithelial damage is a very common side effect of pelvic radiotherapy and often compromise the life quality and treatment outcome in patients with pelvic malignancies. Unlike small bowel and colon, effect of radiation in rectal stem cells has not been explored extensively. Here we demonstrate that Lgr5-positive rectal stem cells are radiosensitive and organoid-based transplantation of rectal stem cells mitigates radiation damage in rectum. Methods: C57Bl6 male mice (JAX) at 24 h were exposed to pelvic irradiation (PIR) to determine the radiation effect in pelvic epithelium. Effect of PIR on Lgr5-positive rectal stem cells (RSCs) was determined in Lgr5-EGFP-Cre-ERT2 mice exposed to PIR. Effect of PIR or clinically relevant fractionated PIR on regenerative response of Lgr5-positive RSCs was examined by lineage tracing assay using Lgr5-eGFP-IRES-CreERT2; Rosa26-CAG-tdTomato mice with tamoxifen administration to activate Cre recombinase and thereby marking the ISC and their respective progeny. Ex vivo three-dimensional organoid cultures were developed from Lgr5-EGFP-Cre-ERT2 mice. Organoid growth was determined by quantifying the budding crypt/total crypt ratio. Organoids from Lgr5-EGFP-ires-CreERT2-TdT mice were transplanted in C57Bl6 male mice exposed to PIR. Engraftment and repopulation of Lgr5-positive RSCs were determined after tamoxifen administration to activate Cre recombinase in recipient mice. Statistical analysis was performed using Log-rank (Mantel-Cox) test and paired two-tail t test. Result: Exposure to pelvic irradiation significantly damaged rectal epithelium with the loss of Lgr5+ve rectal stem cells. Radiosensitivity of rectal epithelium was also observed with exposure to clinically relevant fractionated pelvic irradiation. Regenerative capacity of Lgr5+ve rectal stem cells was compromised in response to fractionated pelvic irradiation. Ex vivo organoid study demonstrated that Lgr5+ve rectal stem cells are sensitive to both single and fractionated radiation. Organoid-based transplantation of Lgr5+ve rectal stem cells promotes repair and regeneration of rectal epithelium. Conclusion: Lgr5-positive rectal stem cells are radiosensitive and contribute to radiation-induced rectal epithelial toxicity. Transplantation of Lgr5-positive rectal stem cells mitigates radiation-induced rectal injury and promotes repair and regeneration process in rectum. © 2021, The Author(s).https://stemcellres.biomedcentral.com/articles/10.1186/s13287-020-02111-

Draft Genome Sequence of a Multi-Metal Resistant Bacterium Pseudomonas putida ATH-43 Isolated from Greenwich Island, Antarctica

Indexación: Web of Science; Scopus.In this report we present the first draft genome sequence of a P. putida strain isolated from the Antarctic continent. The shotgun sequencing strategy, assembly, and subsequent annotation showed that the ATH-43 strain possesses a wide spectrum of genetic determinants involved in heavy metal and antibiotic resistance, apparently to cope with extreme oxidative stress conditions. P. putida ATH-43 genome now forms part of the 65 genomes of this species registered at the NCBI database (September, 2016) and it is highly related with the endophytic strain P. putida W619, which is also resistant to several heavy metals. Further characterization of multi-metal resistant psychrotrophic bacteria such as P. putida ATH-43 will be promising to develop novel strategies for heavy metal bioremediation in low temperature environments. All genome data has been submitted to NCBI.http://journal.frontiersin.org/article/10.3389/fmicb.2016.01777/ful

Genomic Variation and Arsenic Tolerance Emerged as Niche Specific Adaptations by Different Exiguobacterium Strains Isolated From the Extreme Salar de Huasco Environment in Chilean – Altiplano

Indexación: Scopus.Polyextremophilic bacteria can thrive in environments with multiple stressors such as the Salar de Huasco (SH). Microbial communities in SH are exposed to low atmospheric pressure, high UV radiation, wide temperature ranges, salinity gradient and the presence of toxic compounds such as arsenic (As). In this work we focus on arsenic stress as one of the main adverse factors in SH and bacteria that belong to the Exiguobacterium genus due to their plasticity and ubiquity. Therefore, our aim was to shed light on the effect of niche conditions pressure (particularly arsenic), on the adaptation and divergence (at genotypic and phenotypic levels) of Exiguobacterium strains from five different SH sites. Also, to capture greater diversity in this genus, we use as outgroup five As(III) sensitive strains isolated from Easter Island (Chile) and The Great Salt Lake (United States). For this, samples were obtained from five different SH sites under an arsenic gradient (9 to 321 mg/kg: sediment) and isolated and sequenced the genomes of 14 Exiguobacterium strains, which had different arsenic tolerance levels. Then, we used comparative genomic analysis to assess the genomic divergence of these strains and their association with phenotypic differences such as arsenic tolerance levels and the ability to resist poly-stress. Phylogenetic analysis showed that SH strains share a common ancestor. Consequently, populations were separated and structured in different SH microenvironments, giving rise to multiple coexisting lineages. Hence, this genotypic variability is also evidenced by the COG (Clusters of Orthologous Groups) composition and the size of their accessory genomes. Interestingly, these observations correlate with physiological traits such as growth patterns, gene expression, and enzyme activity related to arsenic response and/or tolerance. Therefore, Exiguobacterium strains from SH are adapted to physiologically overcome the contrasting environmental conditions, like the arsenic present in their habitat. © Copyright © 2020 Castro-Severyn, Pardo-Esté, Mendez, Morales, Marquez, Molina, Remonsellez, Castro-Nallar and Saavedra.https://www.frontiersin.org/articles/10.3389/fmicb.2020.01632/ful

Geochemistry and microbial communities in Salar de Pajonales and Salar de Gorbea, Northern Chile: Influence on the gypsum microbialites formation

Pajonales y Gorbea son dos salares andinos de Chile, compuestos mayoritariamente de yeso, y poseen lagunas de un amplio rango de salinidades, índices de saturación (IS) de yeso y pH. Hay varios estudios que han abordado la geología de los salares de forma general, pero la geoquímica, petrografía y mineralogía de estos depósitos salinos han sido poco estudiado. El objetivo es comparar la información geoquímica de las aguas de las lagunas subsaturadas y sobresaturadas de yeso de ambos salares para identificar correlaciones entre la mineralogía de las comunidades microbianas y la hidroquímica que permitan desvelar el origen del yeso. En Pajonales, el yeso precipita: en lagunas subsaturadas con pH (7,4-8,1), salinidad (1,9-4,8 %) y predominancia de α-Proteobacteria (64%) en tapices microbianos. De otra manera, en Gorbea no se reconoce una relación significativa entre la precipitación de yeso, pH (1,8 a 4,5), salinidad (0,6-15 %) y predominancia de α+γ-Proteobacteria (90%). Cabe destacar que en aguas sobresaturadas se observó que los microbialitos de yeso están colonizados por fotótrofos en Pajonales (Cianobacterias) y en Gorbea (Diatomeas). Estos resultados sugieren que las comunidades de α-Proteobacteria en aguas subsaturadas y de fotótrofos en aguas sobresaturadas pueden jugar un papel en la precipitación de yeso.Pajonales and Gorbea are two Andean salt flats in Chile, composed mainly of gypsum, and have lagoons with a wide range of salinities, gypsum saturation indices (SI), and pH. There are several studies that have addressed the geology of the salt flats in a general way, but the geochemistry, petrography and mineralogy of these salt deposits have been little studied. The objective is to compare geochemical information of the waters of the undersaturated and oversaturated gypsum lagoons of both salt flats to identify correlations between the mineralogy of the microbial communities and the hydrochemistry that allows to reveal the origin of the gypsum. In Pajonales, gypsum precipitates: in subsaturated lagoons with pH (7.4-8.1), salinity (1.9-4.8%) and a predominance of α-Proteobacteria (64%) in microbial mats. Otherwise, in Gorbea a significant relationship between gypsum precipitation, pH (1.8 to 4.5), salinity (0.6-15%) and predominance of α + γ-Proteobacteria (90%) is not recognized. It should be noted that in supersaturated waters, gypsum microbialites are colonized by phototrophs in Pajonales (Cyanobacteria) and Gorbea (diatoms). These results suggested that α-Proteobacteria communities in subsaturated waters and phototrophs in supersaturated waters may play a role in gypsum precipitation.Depto. de Mineralogía y PetrologíaFac. de Ciencias GeológicasTRUEProyecto Donaciones Minera Escondida Ltda.Beca Doctorado-ANIDpu

Origin, genomic diversity and microevolution of the clostridium difficile b1/nap1/rt027/st01 strain in costa rica, chile, honduras and mexico

Indexación: Scopus.Clostridium difficile B1/NAP1/RT027/ST01 has been responsible for outbreaks of antibiotic-associated diarrhoea in clinical settings worldwide and is associated with severe disease presentations and increased mortality rates. Two fluoroquinolone-resistant (FQR) lineages of the epidemic B1/NAP1/RT027/ST01 strain emerged in the USA in the early 1990s and disseminated trans continentally (FQR1 and FQR2). However, it is unclear when and from where they entered Latin America (LA) and whether isolates from LA exhibit unique genomic features when compared to B1/NAP1/RT027/ST01 isolates from other regions of the world. To answer the first issue we compared whole-genome sequences (WGS) of 25 clinical isolates typed as NAP1, RT027 or ST01 in Costa Rica (n=16), Chile (n=5), Honduras (n=3) and Mexico (n=1) to WGS of 129 global isolates from the same genotype using Bayesian phylogenomics. The second question was addressed through a detailed analysis of the number and type of mutations of the LA isolates and their mobile resistome. All but two B1/NAP1/RT027/ST01 isolates from LA belong to the FQR2 lineage (n=23, 92 %), confirming its widespread distribution. As indicated by analysis of a dataset composed of 154 WGS, the B1/NAP1/RT027/ST01 strain was introduced into the four LA countries analysed between 1998 and 2005 from North America (twice) and Europe (at least four times). These events occurred soon after the emergence of the FQR lineages and more than one decade before the first report of the detection of the B1/NAP1/RT027/ST01 in LA. A total of 552 SNPs were identified across all genomes examined (3.8–4.3 Mb) in pairwise comparisons to the R20291 reference genome. Moreover, pairwise SNP distances were among the smallest distances determined in this species so far (0 to 55). Despite this high level of genomic conservation, 39 unique SNPs (7 %) in genes that play roles in the infection process (i.e. slpA) or antibiotic resistance (i.e. rpoB, fusA) distinguished the LA isolates. In addition, isolates from Chile, Honduras and Mexico had twice as many antibiotic resistance genes (ARGs, n=4) than related isolates from other regions. Their unique set of ARGs includes a cfr-like gene and tetM, which were found as part of putative mobile genetic elements whose sequences resemble undescribed integrative and conjugative elements. These results show multiple, independent introductions of B1/NAP1/RT027/ ST01 isolates from the FQR1 and FQR2 lineages from different geographical sources into LA and a rather rapid accumulation of distinct mutations and acquired ARG by the LA isolates.https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.00035

In-Depth Genomic and Phenotypic Characterization of the Antarctic Psychrotolerant Strain Pseudomonas sp. MPC6 Reveals Unique Metabolic Features, Plasticity, and Biotechnological Potential

We obtained the complete genome sequence of the psychrotolerant extremophile Pseudomonas sp. MPC6, a natural Polyhydroxyalkanoates (PHAs) producing bacterium able to rapidly grow at low temperatures. Genomic and phenotypic analyses allowed us to situate this isolate inside the Pseudomonas fluorescens phylogroup of pseudomonads as well as to reveal its metabolic versatility and plasticity. The isolate possesses the gene machinery for metabolizing a variety of toxic aromatic compounds such as toluene, phenol, chloroaromatics, and TNT. In addition, it can use both C6- and C5-carbon sugars like xylose and arabinose as carbon substrates, an uncommon feature for bacteria of this genus. Furthermore, Pseudomonas sp. MPC6 exhibits a high-copy number of genes encoding for enzymes involved in oxidative and cold-stress response that allows it to cope with high concentrations of heavy metals (As, Cd, Cu) and low temperatures, a finding that was further validated experimentally. We then assessed the growth performance of MPC6 on glycerol using a temperature range from 0 to 45°C, the latter temperature corresponding to the limit at which this Antarctic isolate was no longer able to propagate. On the other hand, the MPC6 genome comprised considerably less virulence and drug resistance factors as compared to pathogenic Pseudomonas strains, thus supporting its safety. Unexpectedly, we found five PHA synthases within the genome of MPC6, one of which clustered separately from the other four. This PHA synthase shared only 40% sequence identity at the amino acid level against the only PHA polymerase described for Pseudomonas (63-1 strain) able to produce copolymers of short- and medium-chain length PHAs. Batch cultures for PHA synthesis in Pseudomonas sp. MPC6 using sugars, decanoate, ethylene glycol, and organic acids as carbon substrates result in biopolymers with different monomer compositions. This indicates that the PHA synthases play a critical role in defining not only the final chemical structure of the biosynthesized PHA, but also the employed biosynthetic pathways. Based on the results obtained, we conclude that Pseudomonas sp. MPC6 can be exploited as a bioremediator and biopolymer factory, as well as a model strain to unveil molecular mechanisms behind adaptation to cold and extreme environments