| 1. |
- Kyrpides, Nikos C, et al.
(författare)
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Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.
- 2014
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1545-7885. ; 12:8
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Tidskriftsartikel (refereegranskat)abstract
- Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.
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| 2. |
- Larsson, D. G. Joakim, 1969, et al.
(författare)
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Release of active pharmaceutical ingredients from Indian bulk drug manufacture – environmental fate and effects on antibiotic resistance development, microbial ecosystems and vertebrate physiology
- 2008
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Ingår i: 2008 Society of Environmental Toxicology and Chemistry, November 16-20, Tampa, USA.
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Konferensbidrag (refereegranskat)abstract
- Last year, we published a paper showing extraordinary high levels of several drugs in treated effluent from a plant receiving process water from about 90 bulk drug manufacturers from the Hyderabad region in India. Particularly, the levels of various fluoroquinolones (up to 31 mg/L) called for more information on the potential development of antibiotic resistance of exposed bacteria, as well as potential ecological effects on microbial ecosystems. In this study we will present the first characterization of 93 strains of bacteria sampled inside the treatment facility for their sensitivity/resistance to 39 different antibiotics. Furthermore, controlled exposure experiments suggest that the treated effluent affects the functional structure of natural freshwater microbial communities at a dilution of 1:1000. Short to medium-term exposure experiments with frogs and fish demonstrate sublethal effects of the treated effluent at similar dilutions, suggesting that expected environmental effects are not restricted to disturbed microorganism communities. Data on the fate of different pharmaceuticals in a gradient up and downstream from the treatment facility will be presented, as well as levels in drinking water wells in seven nearby villages, showing a transport of drugs via the groundwater. We conclude that the environmental impact of drug production in the Hyderabad region is of great environmental concern. We will also present summary data on the origin of active substances present in pharmaceutical products on the Swedish market, implying an international responsibility for improving the environmental pollution situation related to bulk drug production in India.
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| 3. |
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| 4. |
- Moore, Fiona Porteous, et al.
(författare)
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Endophytic bacterial diversity in poplar trees growing on a BTEX-contaminated site: the characterisation of isolates with potential to enhance phytoremediation.
- 2006
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Ingår i: Systematic and applied microbiology. - : Elsevier BV. - 0723-2020. ; 29:7, s. 539-56
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Tidskriftsartikel (refereegranskat)abstract
- The diversity of endophytic bacteria found in association with poplar was investigated as part of a larger study to assess the possibility and practicality of using endophytic bacteria to enhance in situ phytoremediation. Endophytic bacteria were isolated from the root, stem and leaf of two cultivars of poplar tree growing on a site contaminated with BTEX compounds. They were further characterised genotypically by comparative sequence analysis of partial 16S rRNA genes and BOX-PCR genomic DNA fingerprinting, and phenotypically by their tolerance to a range of target pollutants, heavy metals and antibiotics. One hundred and 21 stable, morphologically distinct isolates were obtained, belonging to 21 genera, although six isolates could not be identified with confidence to a genus. The endophytic bacteria exhibited marked spatial compartmentalisation within the plant, suggesting there are likely to be species-specific and non-specific associations between bacteria and plants. A number of isolates demonstrated the ability to degrade BTEX compounds or to grow in the presence of TCE. This study demonstrates that within the diverse bacterial communities found in poplar several endophytic strains are present that have the potential to enhance phytoremediation strategies.
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| 5. |
- Abraham, Wolf-Rainer, et al.
(författare)
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Woodsholea maritima gen. nov., sp. nov., a marine bacterium with a low diversity of polar lipids.
- 2004
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 54:Pt 4, s. 1227-34
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Tidskriftsartikel (refereegranskat)abstract
- Two cauliform bacteria (CM243T and CM251) isolated by J. Poindexter from the Atlantic Ocean were characterized by 16S rRNA gene sequencing, TaqI restriction fragment length polymorphism and single-strand conformation polymorphism analyses of the internally transcribed 16S-23S rDNA spacer (ITS1) region, analysis of fatty acids from cellular lipids, mass spectrometry of polar lipids and physiological properties. The two strains showed very low diversity of polar lipids with diacyl-sulfoquinovosyl glycerols as the predominant lipids. The two bacterial strains were observed to have nearly identical 16S rRNA gene sequences and could not be differentiated by their ITS1 regions. The isolates differed from species of the genus Maricaulis by their 16S rRNA gene sequences, polar lipids and fatty acid patterns. On the basis of the genotypic analyses and estimations of phylogenetic similarities, physiological and chemotaxonomic characteristics, it is proposed that the isolates represent a new genus and species, for which the name Woodsholea maritima gen. nov., sp. nov. (type strain CM243T=VKM B-1512T=LMG 21817T) is proposed.
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| 6. |
- Alves, G., et al.
(författare)
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Identification of Antibiotic Resistance Proteins via MiCId's Augmented Workflow. A Mass Spectrometry-Based Proteomics Approach
- 2022
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Ingår i: Journal of the American Society for Mass Spectrometry. - : American Chemical Society (ACS). - 1044-0305 .- 1879-1123. ; 33:6, s. 917-931
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Tidskriftsartikel (refereegranskat)abstract
- Fast and accurate identifications of pathogenic bacteria along with their associated antibiotic resistance proteins are of paramount importance for patient treatments and public health. To meet this goal from the mass spectrometry aspect, we have augmented the previously published Microorganism Classification and Identification (MiCId) workflow for this capability. To evaluate the performance of this augmented workflow, we have used MS/MS datafiles from samples of 10 antibiotic resistance bacterial strains belonging to three different species: Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The evaluation shows that MiCId's workflow has a sensitivity value around 85% (with a lower bound at about 72%) and a precision greater than 95% in identifying antibiotic resistance proteins. In addition to having high sensitivity and precision, MiCId's workflow is fast and portable, making it a valuable tool for rapid identifications of bacteria as well as detection of their antibiotic resistance proteins. It performs microorganismal identifications, protein identifications, sample biomass estimates, and antibiotic resistance protein identifications in 6-17 min per MS/MS sample using computing resources that are available in most desktop and laptop computers. We have also demonstrated other use of MiCId's workflow. Using MS/MS data sets from samples of two bacterial clonal isolates, one being antibiotic-sensitive while the other being multidrug-resistant, we applied MiCId's workflow to investigate possible mechanisms of antibiotic resistance in these pathogenic bacteria; the results showed that MiCId's conclusions agree with the published study.
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| 7. |
- An, Y., et al.
(författare)
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Therapeutic efficacy of new botulinum toxin identified in CCUG 7968 strain
- 2021
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Ingår i: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 0175-7598 .- 1432-0614. ; 105, s. 8727-8737
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Tidskriftsartikel (refereegranskat)abstract
- Botulinum neurotoxin type A (BoNT/A) induces muscle atrophy by cleaving synaptosomal-associated protein 25. Thus, BoNT/A has been actively utilized for the treatment of masseter and gastrocnemius hypertrophy. In this study, INI101 toxin was newly identified from the CCUG 7968 strain, and its therapeutic efficacy was evaluated both in vitro and in vivo. The INI101 toxin showed identical genetic sequence, amino acid sequence, and protein subunit composition to BoNT/A produced from strain Hall A. Electromyography (EMG), and immunofluorescence staining demonstrated that INI101 (at 2 - 8 U/rat) effectively blocked the neuromuscular junction with no toxicity in a rat model. The EMG results showed INI101 toxin-induced weight loss and volume reduction of the gastrocnemius, similar to the effects of Botox (R) (BTX). Histological and immunofluorescence staining was consistent with this EMG result, showing that INI101 toxin caused muscle fiber reduction in the gastrocnemius. Notably, INI101 toxin diffused less into adjacent muscle tissue than BTX, indicating that INI101 toxin may reduce potential side effects due to diffusion into normal tissues. INI101 toxin isolated from the novel strain CCUG 7968 is a newly identified meaningful biopharmaceutical comparable to the conventional BoNT/A in the medical field.
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| 8. |
- Arahal, David, et al.
(författare)
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The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes
- 2024
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Ingår i: International Journal of Systematic and Evolutionary Microbiology. - 1466-5026 .- 1466-5034. ; 74:1
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Tidskriftsartikel (refereegranskat)abstract
- The naming of prokaryotes is governed by the International Code of Nomenclature of Prokaryotes (ICNP) and partially by the International Code of Nomenclature for Algae, Fungi and Plants (ICN). Such codes must be able to determine names of taxa in a universal and unambiguous manner, thus serving as a common language across different fields and activities. This unity is undermined when a new code of nomenclature emerges that overlaps in scope with an established, time-tested code and uses the same format of names but assigns different nomenclatural status values to the names. The resulting nomenclatural confusion is not beneficial to the wider scientific community. Such ambiguity is expected to result from the establishment of the ‘Code of Nomenclature of Prokaryotes Described from DNA Sequence Data’ (‘SeqCode’), which is in general and specific conflict with the ICNP and the ICN. Shortcomings in the interpretation of the ICNP may have exacerbated the incompatibility between the codes. It is reiterated as to why proposals to accept sequences as nomenclatural types of species and subspecies with validly published names, now implemented in the SeqCode, have not been implemented by the International Committee on Systematics of Prokaryotes (ICSP), which oversees the ICNP. The absence of certain regulations from the ICNP for the naming of as yet uncultivated prokaryotes is an acceptable scientific argument, although it does not justify the establishment of a separate code. Moreover, the proposals rejected by the ICSP are unnecessary to adequately regulate the naming of uncultivated prokaryotes. To provide a better service to the wider scientific community, an alternative proposal to emend the ICNP is presented, which would result in Candidatus names being regulated analogously to validly published names. This proposal is fully consistent with previous ICSP decisions, preserves the essential unity of nomenclature and avoids the expected nomenclatural confusion.
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| 9. |
- Armengaud, J., et al.
(författare)
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The Importance Of Naturally Attenuated Sars-Cov-2 In The Fight Against Covid-19
- 2020
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 22:6, s. 1997-2000
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Tidskriftsartikel (refereegranskat)abstract
- The current SARS-CoV-2 pandemic is wreaking havoc throughout the world and has rapidly become a global health emergency. A central question concerning COVID-19 is why some individuals become sick and others not. Many have pointed already at variation in risk factors between individuals. However, the variable outcome of SARS-CoV-2 infections may, at least in part, be due also to differences between the viral subspecies with which individuals are infected. A more pertinent question is how we are to overcome the current pandemic. A vaccine against SARS-CoV-2 would offer significant relief, although vaccine developers have warned that design, testing, and production of vaccines may take a year if not longer. Vaccines are based on a handful of different designs (1), but the earliest vaccines were based on live, attenuated virus. As has been the case for other viruses during earlier pandemics, SARS-CoV-2 will mutate and may naturally attenuate over time (2). What makes the current pandemic unique is that, thanks to state-of-the-art nucleic acid sequencing technologies, we can follow in detail how SARS-CoV-2 evolves while it spreads. We argue that knowledge of naturally emerging attenuated SARS-CoV-2 variants across the globe should be of key interest in our fight against the pandemic. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
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| 10. |
- Backrud, Oscar, et al.
(författare)
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Chromobacterium sp. septicemia in Sweden. A clinical case report
- 2024
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Ingår i: ANNALS OF CLINICAL MICROBIOLOGY AND ANTIMICROBIALS. - 1476-0711. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- Background Chromobacterium is a genus of fourteen species with validly published names, most often found in soil and waters in tropical and subtropical regions around the world. The most well-known species of the genus, C. violaceum, occasionally causes clinically relevant infections; cases of soft tissue infections with septicemia and fatal outcomes have been described. Case presentation Here, we present a clinical case report of a 79-year-old man from Sweden with a soft-tissue infection and septicemia. The pathogen was identified as a strain of Chromobacterium species, but not C. violaceum. The patient was treated with clindamycin and ciprofloxacin and recovered well. Conclusions This case report demonstrates the potential of Chromobacterium species as infectious agents in immunocompetent patients. It also indicates the existence of a novel species.
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| 11. |
- Bennasar-Figueras, Antoni, et al.
(författare)
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Complete Genome Sequence of Pseudomonas balearica DSM 6083T.
- 2016
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Ingår i: Genome Announcements. - 2169-8287. ; 4:2
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Tidskriftsartikel (refereegranskat)abstract
- The whole-genome sequence of ITALIC! Pseudomonas balearicaSP1402 (DSM 6083(T)) has been completed and annotated. It was isolated as a naphthalene degrader from water of a lagooning wastewater treatment plant. ITALIC! P.balearicastrains tolerate up to 8.5% NaCl and are considered true marine denitrifiers.
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| 12. |
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| 13. |
- Boulund, Fredrik, 1985, et al.
(författare)
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Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics
- 2017
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Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 16:6, s. 1052-1063
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Tidskriftsartikel (refereegranskat)abstract
- Methods for rapid and reliable microbial identification are essential in modern healthcare. The ability to detect and correctly identify pathogenic species and their resistance phenotype is necessary for accurate diagnosis and efficient treatment of infectious diseases. Bottom-up tandem mass spectrometry (MS) proteomics enables rapid characterization of large parts of the expressed genes of microorganisms. However, the generated data are highly fragmented, making downstream analyses complex. Here we present TCUP, a new computational method for typing and characterizing bacteria using proteomics data from bottom-up tandem MS. TCUP compares the generated protein sequence data to reference databases and automatically finds peptides suitable for characterization of taxonomic composition and identification of expressed antimicrobial resistance genes. TCUP was evaluated using several clinically relevant bacterial species (Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pneumoniae, Moraxella catarrhalis, and Haemophilus influenzae), using both simulated data generated by in silico peptide digestion and experimental proteomics data generated by liquid chromatography-tandem mass spectrometry (MS/MS). The results showed that TCUP performs correct peptide classifications at rates between 90.3 and 98.5% at the species level. The method was also able to estimate the relative abundances of individual species in mixed cultures. Furthermore, TCUP could identify expressed beta-lactamases in an extended spectrum beta-lactamase-producing (ESBL) E.coli strain, even when the strain was cultivated in the absence of antibiotics. Finally, TCUP is computationally efficient, easy to integrate in existing bioinformatics workflows, and freely available under an open source license for both Windows and Linux environments.
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| 14. |
- Busse, H. J., et al.
(författare)
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Reclassification of Arthrobacter nasiphocae (Collins et al. 2002) as Falsarthrobacter nasiphocae gen. nov., comb. nov
- 2018
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Ingår i: International Journal of Systematic and Evolutionary Microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 68:4, s. 1361-1364
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Tidskriftsartikel (refereegranskat)abstract
- The original description of Arthrobacter nasiphocae M597/99/10(T) demonstrated that it is distantly related to the type species of the genus Arthrobacter, Arthrobacter globiformis, and that this phylogenetic relationship is reflected by the distinct peptidoglycan type [Lys-Ala(2)-Gly(2-3)-Ala(Gly)] and the features of the quinone system, which is composed of menaquinones MK-9(H-2) and MK-8(H-2). Here, we report a re-evaluation of the taxonomic status of A. nasiphocae. Phylogenetically, it was observed to be only distantly related to the genus Arthrobacter and to the type species of related genera. Re-analysis confirmed the quinone system menaquinones MK-9(H-2) and MK-8(H-2) in A. nasiphocae. Analysis of cell polar lipids showed a profile consisting of the predominant lipids diphosphatidylglycerol, phosphatidylglycerol, dimannosylglyceride, an unidentified phospholipid and an unidentified aminophosphoglycolipid, and several minor unidentified lipids. This profile clearly is different from that of Arthrobacter species. The cell fatty acid profile also showed characteristics that distinguished A. nasiphocae from Arthrobacter species. The phylogenetic distance of A. nasiphocae from any type species of genera within the family Micrococcaceae and the distinct chemotaxonomic traits warrant the reclassification of A. nasiphocae within a novel genus, for which we propose the name Falsarthrobacter nasiphocae gen. nov., comb. nov. The type strain is M597/99/10(T) (=CCUG 42953(T)=CIP 107054(T)=DSM 13988(T)=JCM 11677(T)).
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| 15. |
- Carvalheira, A., et al.
(författare)
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Acinetobacter portensis sp. Nov. and acinetobacter guerrae sp. nov., isolated from raw meat
- 2020
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 70:8, s. 4544-4554
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Tidskriftsartikel (refereegranskat)abstract
- The taxonomic status of six strains of Acinetobacter obtained from meat samples, collected from supermarkets in Porto, Por-tugal, was investigated using polyphasic analysis. Partial rpoB sequence similarities lower than 95 % to other Acinetobacter species with validly published names led to the hypothesis that these strains represented novel species. This was confirmed based on comparative multilocus sequence analysis, which included the gyrB, recA and 16S rRNA genes, revealing that these strains represented two coherent lineages that were distinct from each other and from all known species. The names Acine-tobacter portensis sp. nov. (comprising four strains) and Acinetobacter guerrae sp. nov. (comprising two strains) are proposed for these novel species. The species status of these two groups was confirmed by low (below 95 %) whole-genome sequence average nucleotide identity values and low (below 70 %) digital DNA–DNA hybridization similarities between the whole-genome sequences of the proposed type strains of each novel species and the representatives of the known Acinetobacter species. Phylogenomic treeing from core genome analysis supported these results. The coherence of each new species lineage was supported by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry differentiation of the species at the protein level, by cellular fatty acid profiles, and by unique and differential combinations of metabolic and physiological properties shared by each novel species. The type strain of A. portensis sp. nov. is AC 877T (=CCUG 68672T=CCM 8789T) and the type strain of A. guerrae sp. nov. is AC 1271T (=CCUG 68674T=CCM 8791T). © 2020 The Authors.
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| 16. |
- Claverías, Fernanda, et al.
(författare)
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Corynebacterium alimapuense sp. nov., an obligate marine actinomycete isolated from sediment of Valparaíso bay, Chile.
- 2019
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5034 .- 1466-5026. ; 69:3, s. 783-790
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Tidskriftsartikel (refereegranskat)abstract
- A novel Gram-positive, non-motile, non-spore-forming and aerobic bacterium, designated strain VA37-3T, was isolated from a marine sediment sample collected at 19.2m water depth from Valparaíso bay, Chile. Strain VA37-3T exhibits 97.6% 16S rRNA gene sequence similarity to Corynebacterium marinum D7015T, 96.4% to Corynebacterium humireducens MFC-5T and 96% to Corynebacterium testudinoris M935/96/4T; and a rpoB gene sequence similarity of 85.1% to Corynebacterium pollutisoli VMS11T, both analyses suggesting that strain VA37-3T represents a novel species of Corynebacterium. Physiological testing indicated that strain VA37-3T requires artificial sea water or sodium-supplemented media for growth, representing the first obligate marine actinomycete of the genus Corynebacterium. The genome of the proposed new species, along with the type strains of its most closely related species were sequenced and characterized. In silico genome-based similarity analyses revealed an ANIb of 72.8% (C. marinum D7015T), ANIm of 85.0% (Corynebacterium mustelae DSM 45274T), tetra of 0.90 (Corynebacterium callunae DSM 20147T) and ggdc of 24.7% (Corynebacterium kutscheri DSM 20755T) when compared with the closest related strains. The genomic DNA G+Ccontent of strain VA37-3T was 57.0%. Chemotaxonomic assessment of strain VN6-2T showed the major fatty acids were C18:1ω9c and C16:0. Menaquinones predominantly consisted of MK-8(II-H2). Polar lipids consisted of diphosphatidylglycerol, glycolipids, phosphatidylglycerol, phosphoglycolipid and phosphatidylinositol. Mycolic acids also were present. Overall, the results from phylogenetic, phenotypic and genomic analyses confirmed that strain VA37-3T represents a novel species of the genus Corynebacterium, for which the name Corynebacterium alimapuense sp. nov. is proposed, with VA37-3T as the type strain (=CCUG 69366T=NCIMB 15118T).
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| 17. |
- Cohen, A., et al.
(författare)
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A multifaceted 'omics' approach for addressing the challenge of antimicrobial resistance
- 2015
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Ingår i: Future Microbiology. - : Future Medicine Ltd. - 1746-0913 .- 1746-0921. ; 10:3, s. 365-376
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Tidskriftsartikel (refereegranskat)abstract
- The inappropriate use of antibiotics has severe global health and economic consequences, including the emergence of antibiotic-resistant bacteria. A major driver of antibiotic misuse is the inability to accurately distinguish between bacterial and viral infections based on currently available diagnostic solutions. A multifaceted 'omics' approach that integrates personalized patient data such as genetic predisposition to infections (genomics), natural microbiota composition and immune response to infection (proteomics and transcriptomics) together with comprehensive pathogen profiling has the potential to help physicians improve their antimicrobial prescribing practices. In this respect, the EU has funded a multidisciplinary project (TAILORED-Treatment) that will develop novel omics-based personalized treatment schemes that have the potential to reduce antibiotic consumption, and help limiting the spread of antibiotic resistance.
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| 18. |
- Cotta, Michael A, et al.
(författare)
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Robinsoniella peoriensis gen. nov., sp. nov., isolated from a swine-manure storage pit and a human clinical source.
- 2009
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 59:1, s. 150-155
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Tidskriftsartikel (refereegranskat)abstract
- A polyphasic taxonomic study was performed on six strains of an unknown Gram-positive, non-motile, spore-forming, short oval to rod-shaped bacterium isolated from a swine-manure storage pit. In addition to these strains, an isolate deposited in the Culture Collection of the University of Göteborg (Sweden) was found to be biochemically related to the manure strains. The major end products of metabolism included acetate and succinate but not butyrate. Comparative 16S rRNA gene sequencing confirmed that all these isolates were closely related to each other and formed a hitherto unknown lineage within the clostridial rRNA XIVa cluster of organisms. On the basis of phylogenetic, biochemical and phenotypic evidence, it is proposed that the unknown bacterium represents a novel genus and species, for which the name Robinsoniella peoriensis gen. nov., sp. nov. is proposed. The type strain of Robinsoniella peoriensis is PPC31T (=CCUG 48729T =NRRL B-23985T).
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| 19. |
- Cotta, M. A., et al.
(författare)
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Two novel species Enterococcus lemanii sp nov and Enterococcus eurekensis sp nov., isolated from a swine-manure storage pit
- 2013
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Ingår i: Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology. - : Springer Science and Business Media LLC. - 0003-6072. ; 103:1, s. 89-98
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Tidskriftsartikel (refereegranskat)abstract
- A polyphasic taxonomic study using morphological, biochemical, chemotaxonomic and molecular genetic methods was performed on six strains of unknown Gram-positive, nonspore-forming, facultative anaerobic coccus-shaped bacteria isolated from a swine-manure storage pit. On the basis of the 16S rRNA, RNA polymerase alpha-subunit (rpoA) and 60 kDa chaperonin (cpn60) gene sequence analyses, it was shown that all the isolates were enterococci but formed two separate lines of descent. Pairwise 16S rRNA gene sequence comparisons demonstrated that the two novel organisms were most closely related to each other (97.9 %) and to Enterococcus aquimarinus (97.8 %). Both organisms contained major amounts of C-16:0, C-16:1 omega 7c, C-16:1 omega 7c, and C-18:1 omega 7c/12t/9t as the major cellular fatty acids. Based on biochemical, chemotaxonomic and phylogenetic evidence, the names Enterococcus lemanii sp. nov. (type strain PC32(T) = CCUG 61260(T) = NRRL B-59661(T)) and Enterococcus eurekensis sp. nov. (type strain PC4B(T) = CCUG 61259(T) = NRRL B-59662(T)) are proposed for these hitherto undescribed species.
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| 20. |
- Crespi, S., et al.
(författare)
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Legionella maioricensis sp. nov., a new species isolated from the hot water distribution systems of a hospital and a shopping center during routine sampling
- 2023
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Ingår i: International Journal of Systematic and Evolutionary Microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 73:1
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Tidskriftsartikel (refereegranskat)abstract
- Two Legionella- like strains isolated from hot water distribution systems in 2012 have been characterized phenotypically, bio-chemically and genomically in terms of DNA relatedness. Both strains, HCPI- 6T and EUR- 108, exhibited biochemical pheno-typic profiles typical of Legionella species. Cells were Gram-negative motile rods which grew on BCYE alpha agar but not on blood agar and displayed phenotypic characteristics typical of the family Legionellaceae, including a requirement for L-cysteine and testing catalase positive. Both strains were negative for oxidase, urease, nitrate reduction and hippurate negative, and non -fermentative. The major ubiquinone was Q12 (59.4 % HCPI- 6T) and the dominant fatty acids were C16:1 omega 7c (28.4 % HCPI- 6T, 216 % EUR- 108), C16: 0 iso (222.5 % and 213 %) and C15: 0 anteiso (19.5 % and 223.5 %, respectively). The percent G+C content of genomic DNA was determined to be 39.3 mol %. The 16S rRNA gene, mip sequence and comparative genome sequence -based analyses (average nucleotide identity, ANI; digital DNA-DNA hybridization, dDDH; and phylogenomic treeing) demonstrated that the strains represent a new species of the genus Legionella. The analysis based on the 16S rRNA gene sequences showed that the sequence similarities for both strains ranged from 98.8-90.1 % to other members of the genus. The core genome- based phylogenomic tree (protein-concatemer tree based on concatenation of 418 proteins present in single copy) revealed that these two strains clearly form a separate cluster within the genus Legionella. ANI and dDDH values confirmed the distinctiveness of the strains. Based on the genomic, genotypic and phenotypic findings from a polyphasic study, the isolates are considered to represent a single novel species, for which the name Legionella maioricensis sp. nov. is proposed. The type strain is HCPI- 6T (=CCUG 75071T=CECT 30569T).
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| 21. |
- Cuadrado, Virginia, et al.
(författare)
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Cupriavidus pampae sp. nov., a novel herbicide-degrading bacterium isolated from agricultural soil
- 2010
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Ingår i: International journal of systematic and evolutionary microbiology. - : Microbiology Society. - 1466-5034 .- 1466-5026. ; 60:11, s. 2606-2612
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Tidskriftsartikel (refereegranskat)abstract
- A bacterial consortium able to degrade the herbicide 4-(2,4-dichlorophenoxy) butyric acid (2,4-DB) was obtained from an agricultural soil of the Argentinean Humid Pampa region which has a history of long-term herbicide use. Four bacterial strains were isolated from the consortium and identified as members of the genera Cupriavidus, Labrys and Pseudomonas. A polyphasic systematic analysis was carried out on strain CPDB6(T), the member of the 2,4-DB-degrading consortium able to degrade 2,4-DB as a sole carbon and energy source. The Gram-negative, rod-shaped, motile, non-sporulating, non-fermenting bacterium was shown to belong to the genus Cupriavidus on the basis of 16S rRNA gene sequence analyses. Strain CPDB6(T) did not reduce nitrate, which differentiated it from the type species of the genus, Cupriavidus necator; it did not grow in 0.5-4.5% NaCl, although most species of Cupriavidus are able to grow at NaCl concentrations as high as 1.5%; and it was able to deamidate acetamide, which differentiated it from all other species of Cupriavidus. DNA-DNA hybridization data revealed low levels of genomic DNA similarity (less than 30%) between strain CPDB6(T) and the type strains of Cupriavidus species with validly published names. The major cellular fatty acids detected were cis-9-hexadecenoic (16:1ω7c) and hexadecanoic (16:0) acids. On the basis of phenotypic and genotypic characterizations, strain CPDB6(T) was recognized as a representative of a novel species within the genus Cupriavidus. The name Cupriavidus pampae sp. nov. is proposed, with strain CPDB6(T) (=CCUG 55948(T)=CCM-A-29:1289(T)) as the type strain.
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| 22. |
- Cumsille, A., et al.
(författare)
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Exploring the biosynthetic gene clusters in Brevibacterium: a comparative genomic analysis of diversity and distribution
- 2023
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Ingår i: Bmc Genomics. - 1471-2164. ; 24:1
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Tidskriftsartikel (refereegranskat)abstract
- Exploring Brevibacterium strains from various ecosystems may lead to the discovery of new antibiotic-producing strains. Brevibacterium sp. H-BE7, a strain isolated from marine sediments from Northern Patagonia, Chile, had its genome sequenced to study the biosynthetic potential to produce novel natural products within the Brevibacterium genus. The genome sequences of 98 Brevibacterium strains, including strain H-BE7, were selected for a genomic analysis. A phylogenomic cladogram was generated, which divided the Brevibacterium strains into four major clades. A total of 25 strains are potentially unique new species according to Average Nucleotide Identity (ANIb) values. These strains were isolated from various environments, emphasizing the importance of exploring diverse ecosystems to discover the full diversity of Brevibacterium. Pangenome analysis of Brevibacterium strains revealed that only 2.5% of gene clusters are included within the core genome, and most gene clusters occur either as singletons or as cloud genes present in less than ten strains. Brevibacterium strains from various phylogenomic clades exhibit diverse BGCs. Specific groups of BGCs show clade-specific distribution patterns, such as siderophore BGCs and carotenoid-related BGCs. A group of clade IV-A Brevibacterium strains possess a clade-specific Polyketide synthase (PKS) BGCs that connects with phenazine-related BGCs. Within the PKS BGC, five genes, including the biosynthetic PKS gene, participate in the mevalonate pathway and exhibit similarities with the phenazine A BGC. However, additional core biosynthetic phenazine genes were exclusively discovered in nine Brevibacterium strains, primarily isolated from cheese. Evaluating the antibacterial activity of strain H-BE7, it exhibited antimicrobial activity against Salmonella enterica and Listeria monocytogenes. Chemical dereplication identified bioactive compounds, such as 1-methoxyphenazine in the crude extracts of strain H-BE7, which could be responsible of the observed antibacterial activity. While strain H-BE7 lacks the core phenazine biosynthetic genes, it produces 1-methoxyphenazine, indicating the presence of an unknown biosynthetic pathway for this compound. This suggests the existence of alternative biosynthetic pathways or promiscuous enzymes within H-BE7's genome.
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| 23. |
- Dos Santos, V A P Martins, et al.
(författare)
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Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440.
- 2004
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Ingår i: Environmental microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 6:12, s. 1264-86
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Tidskriftsartikel (refereegranskat)abstract
- A major challenge in microbiology is the elucidation of the genetic and ecophysiological basis of habitat specificity of microbes. Pseudomonas putida is a paradigm of a ubiquitous metabolically versatile soil bacterium. Strain KT2440, a safety strain that has become a laboratory workhorse worldwide, has been recently sequenced and its genome annotated. By drawing on both published information and on original in silico analysis of its genome, we address here the question of what genomic features of KT2440 could explain or are consistent with its ubiquity, metabolic versatility and adaptability. The genome of KT2440 exhibits combinations of features characteristic of terrestrial, rhizosphere and aquatic bacteria, which thrive in either copiotrophic or oligotrophic habitats, and suggests that P. putida has evolved and acquired functions that equip it to thrive in diverse, often inhospitable environments, either free-living, or in close association with plants. The high diversity of protein families encoded by its genome, the large number and variety of small aralogous families, insertion elements, repetitive extragenic palindromic sequences, as well as the mosaic structure of the genome (with many regions of 'atypical' composition) and the multiplicity of mobile elements, reflect a high functional diversity in P. putida and are indicative of its evolutionary trajectory and adaptation to the diverse habitats in which it thrives. The unusual wealth of determinants for high affinity nutrient acquisition systems, mono- and di-oxygenases, oxido-reductases, ferredoxins and cytochromes, dehydrogenases, sulfur metabolism proteins, for efflux pumps and glutathione-S-transfereases, and for the extensive array of extracytoplasmatic function sigma factors, regulators, and stress response systems, constitute the genomic basis for the exceptional nutritional versatility and opportunism of P. putida , its ubiquity in diverse soil, rhizosphere and aquatic systems, and its renowned tolerance of natural and anthropogenic stresses. This metabolic diversity is also the basis of the impressive evolutionary potential of KT2440, and its utility for the experimental design of novel pathways for the catabolism of organic, particularly aromatic, pollutants, and its potential for bioremediation of soils contaminated with such compounds as well as for its application in the production of high-added value compounds.
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| 24. |
- Duran, R. E., et al.
(författare)
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Complete Genome Sequence of the Marine Hydrocarbon Degrader Alcaligenes aquatilis QD168, Isolated from Crude Oil-Polluted Sediment of Quintero Bay, Central Chile
- 2019
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Ingår i: Microbiology Resource Announcements. - : American Society for Microbiology. - 2576-098X. ; 8:5
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Tidskriftsartikel (refereegranskat)abstract
- Alcaligenes aquatilis strain QD168 (= CCUG 69566) is a marine hydrocarbon-degrading bacterium isolated from crude oil-polluted sediment from Quintero Bay, Central Chile. Here, we present the 4.32-Mb complete genome sequence of strain QD168, with 3,892 coding sequences, 58 tRNAs, and a 56.3% G+C content.
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| 25. |
- Duran, R. E., et al.
(författare)
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Genomic and Physiological Traits o the Marine Bacterium Alcaligenes aquatilis QD168 Isolated From Quintero Bay, Central Chile, Reveal a Robust Adaptive Response to Environmental Stressors
- 2019
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Alcaligenes aquatilis QD168 is a marine, aromatic hydrocarbon-degrading bacterium, isolated from an oil-polluted sediment of Quintero Bay, an industrial-coastal zone that has been chronically impacted by diverse pollutants. The aims of this study were to characterize the phylogenomic positions of Alcaligenes spp. and to characterize the genetic determinants and the physiological response of A. aquatilis QD168 to model environmental stressors (benzene, oxidizing agents, and salt). Phylogenomic analyses, using 35 housekeeping genes, clustered A. aquatilis QD168 with four other strains of Alcaligenes spp. (A. aquatilis BU33N, A. faecalis JQ135, A. faecalis UBA3227, and A. faecalis UBA7629). Genomic sequence analyses of A. aquatilis QD168 with 25 Alcaligenes spp., using ANIb, indicated that A. aquatilis BU33N is the closest related strain, with 96.8% ANIb similarity. Strain QD168 harbors 95 genes encoding proteins of seven central catabolic pathways, as well as sixteen peripheral catabolic pathways/reactions for aromatic compounds. A. aquatilis QD168 was able to grow on 3-hydroxybenzoate, 4-hydroxybenzoate, benzoate, benzene, 3-hydroxycinnamate, cinnamate, anthranilate, benzamide, 4-aminobenzoate, nicotinate, toluene, biphenyl and tryptophan, as sole carbon or nitrogen source. Benzene degradation was further analyzed by growth, metabolite identification and gene expression analyses. Benzene strongly induced the expression of the genes encoding phenol hydroxylase (dmpP) and catechol 1,2-dioxygenase (catA). Additionally, 30 genes encoding transcriptional regulators, scavenging enzymes, oxidative damage repair systems and isozymes involved in oxidative stress response were identified. Oxidative stress response of strain QD168 to hydrogen peroxide and paraquat was characterized, demonstrating that A. aquatilis QD168 is notably more resistant to paraquat than to H2O2. Genetic determinants (47 genes) for osmoprotective responses were identified, correlating with observed high halotolerance by strain QD168. The physiological adaptation of A. aquatilis QD168 to environmental stressors such as pollutants, oxidative stress and salinity may be exploited for bioremediation of oil-polluted saline sites.
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