Probiotic Properties of Alcaligenes Faecalis Isolated from Argyrosomus Regius in Experimental Peritonitis (Rat Model)
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Achromobacter Infections and Treatment Options
AAC Accepted Manuscript Posted Online 17 August 2020 Antimicrob. Agents Chemother. doi:10.1128/AAC.01025-20 Copyright © 2020 American Society for Microbiology. All Rights Reserved. 1 Achromobacter Infections and Treatment Options 2 Burcu Isler 1 2,3 3 Timothy J. Kidd Downloaded from 4 Adam G. Stewart 1,4 5 Patrick Harris 1,2 6 1,4 David L. Paterson http://aac.asm.org/ 7 1. University of Queensland, Faculty of Medicine, UQ Center for Clinical Research, 8 Brisbane, Australia 9 2. Central Microbiology, Pathology Queensland, Royal Brisbane and Women’s Hospital, 10 Brisbane, Australia on August 18, 2020 at University of Queensland 11 3. University of Queensland, Faculty of Science, School of Chemistry and Molecular 12 Biosciences, Brisbane, Australia 13 4. Infectious Diseases Unit, Royal Brisbane and Women’s Hospital, Brisbane, Australia 14 15 Editorial correspondence can be sent to: 16 Professor David Paterson 17 Director 18 UQ Center for Clinical Research 19 Faculty of Medicine 20 The University of Queensland 1 21 Level 8, Building 71/918, UQCCR, RBWH Campus 22 Herston QLD 4029 AUSTRALIA 23 T: +61 7 3346 5500 Downloaded from 24 F: +61 7 3346 5509 25 E: [email protected] 26 http://aac.asm.org/ 27 28 29 on August 18, 2020 at University of Queensland 30 31 32 33 34 35 36 37 38 39 2 40 Abstract 41 Achromobacter is a genus of non-fermenting Gram negative bacteria under order 42 Burkholderiales. Although primarily isolated from respiratory tract of people with cystic Downloaded from 43 fibrosis, Achromobacter spp. can cause a broad range of infections in hosts with other 44 underlying conditions. -
Plant-Derived Benzoxazinoids Act As Antibiotics and Shape Bacterial Communities
Supplemental Material for: Plant-derived benzoxazinoids act as antibiotics and shape bacterial communities Niklas Schandry, Katharina Jandrasits, Ruben Garrido-Oter, Claude Becker Contents Supplemental Tables 2 Supplemental Table 1. Phylogenetic signal lambda . .2 Supplemental Table 2. Syncom strains . .3 Supplemental Table 3. PERMANOVA . .6 Supplemental Table 4. PERMANOVA comparing only two treatments . .7 Supplemental Table 5. ANOVA: Observed taxa . .8 Supplemental Table 6. Observed diversity means and pairwise comparisons . .9 Supplemental Table 7. ANOVA: Shannon Diversity . 11 Supplemental Table 8. Shannon diversity means and pairwise comparisons . 12 Supplemental Table 9. Correlation between change in relative abundance and change in growth . 14 Figures 15 Supplemental Figure 1 . 15 Supplemental Figure 2 . 16 Supplemental Figure 3 . 17 Supplemental Figure 4 . 18 1 Supplemental Tables Supplemental Table 1. Phylogenetic signal lambda Class Order Family lambda p.value All - All All All All 0.763 0.0004 * * Gram Negative - Proteobacteria All All All 0.817 0.0017 * * Alpha All All 0 0.9998 Alpha Rhizobiales All 0 1.0000 Alpha Rhizobiales Phyllobacteriacae 0 1.0000 Alpha Rhizobiales Rhizobiacaea 0.275 0.8837 Beta All All 1.034 0.0036 * * Beta Burkholderiales All 0.147 0.6171 Beta Burkholderiales Comamonadaceae 0 1.0000 Gamma All All 1 0.0000 * * Gamma Xanthomonadales All 1 0.0001 * * Gram Positive - Actinobacteria Actinomycetia Actinomycetales All 0 1.0000 Actinomycetia Actinomycetales Intrasporangiaceae 0.98 0.2730 Actinomycetia Actinomycetales Microbacteriaceae 1.054 0.3751 Actinomycetia Actinomycetales Nocardioidaceae 0 1.0000 Actinomycetia All All 0 1.0000 Gram Positive - All All All All 0.421 0.0325 * Gram Positive - Firmicutes Bacilli All All 0 1.0000 2 Supplemental Table 2. -
Supplementary Fig. S2. Taxonomic Classification of Two Metagenomic Samples of the Gall-Inducing Mite Fragariocoptes Seti- Ger in Kraken2
Supplementary Fig. S2. Taxonomic classification of two metagenomic samples of the gall-inducing mite Fragariocoptes seti- ger in Kraken2. There was a total of 708,046,814 and 82,009,061 classified reads in samples 1 and 2, respectively. OTUs (genera) were filtered based on a normalized abundance threshold of ≥0.0005% in either sample, resulting in 171 OTUs represented by 670,717,361 and 72,439,919 reads (sample 1 and 2, respectively). Data are given in Supplementary Table S3. Sample1 Sample2 0.000005 0.002990 Bacteria:Proteobacteria:Inhella Read % (log2) 0.000005 0.005342 Bacteria:Actinobacteria:Microbacteriaceae:Microterricola 10.00 0.000006 0.003983 Bacteria:Actinobacteria:Microbacteriaceae:Cryobacterium 5.00 0.000012 0.006576 Eukaryota:Ascomycota:Mycosphaerellaceae:Cercospora 0.00 0.000013 0.002947 Bacteria:Actinobacteria:Bifidobacteriaceae:Gardnerella 0.000017 0.003555 Eukaryota:Ascomycota:Chaetomiaceae:Thielavia -5.00 0.000014 0.004244 Bacteria:Firmicutes:Clostridiaceae:Clostridium -10.00 0.000010 0.001699 Bacteria:Proteobacteria:Caulobacteraceae:Phenylobacterium -15.00 0.000012 0.001183 Bacteria:Actinobacteria:Microbacteriaceae:Leifsonia 0.000009 0.001144 Bacteria:Proteobacteria:Desulfovibrionaceae:Desulfovibrio -20.00 0.000016 0.000777 Bacteria:Firmicutes:Leuconostocaceae:Weissella -25.00 0.000014 0.000761 Bacteria:Cyanobacteria:Oscillatoriaceae:Oscillatoria 0.000013 0.000683 Bacteria:Proteobacteria:Methylobacteriaceae:Microvirga Read % 0.000011 0.000578 Bacteria:Fusobacteria:Leptotrichiaceae:Leptotrichia 0.000009 0.000842 Bacteria:Firmicutes:Paenibacillaceae:Paenibacillus -
Pigmentiphaga Kullae Gen. Nov., Sp. Nov., a Novel Member of the Family
International Journal of Systematic and Evolutionary Microbiology (2001), 51, 1867–1871 Printed in Great Britain Pigmentiphaga kullae gen. nov., sp. nov., a NOTE novel member of the family Alcaligenaceae with the ability to decolorize azo dyes aerobically 1 Institut fu$ r Mikrobiologie, Silke Blu$ mel,1 Barbara Mark,2 Hans-Ju$ rgen Busse,2,3 Peter Ka$ mpfer4 and Universita$ t Stuttgart, 1 Allmandring 31, D-70569 Andreas Stolz Stuttgart, Germany 2 Institut fu$ r Bakteriologie, Author for correspondence: Andreas Stolz. Tel: j49 711 6855489. Fax: j49 711 6855725. Mykologie und Hygiene, e-mail: andreas.stolz!po.uni-stuttgart.de Veterina$ rmedizinische Universita$ t Wien, Veterina$ rplatz 1, A-1210 Wien, Austria The taxonomic position of Pseudomonas strain K24, which was isolated previously after an aerobic enrichment with the azo compound 1-(4’- 3 Institut fu$ r Mikrobiologie und Genetik, Universita$ t carboxyphenylazo)-4-naphthol as the sole source of carbon and energy, was Wien, Dr Bohrgasse 9, investigated. The detection of a quinone system with ubiquinone Q-8 as the A-1030 Wien, Austria predominant compound and a polyamine pattern with putrescine and 2- 4 Institut fu$ r Angewandte hydroxyputrescine as the major polyamines present suggested that strain K24T Mikrobiologie, Justus- belongs to the β-subclass of the Proteobacteria. This was supported by Liebig-Universita$ t Giessen, Heinrich-Buff-Ring 26–32 sequencing the 16S rRNA gene, which demonstrated about 95–96% sequence (IFZ), D-35392 Giessen, similarity to different species of the genera Achromobacter, Alcaligenes and Germany Bordetella. This suggested that strain K24T is a member of the family Alcaligenaceae. -
Alteration of the Gut Microbiota Associated with Childhood Obesity by 16S Rrna Gene Sequencing
Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing Xiaowei Chen1,2, Haixiang Sun1, Fei Jiang1,2, Yan Shen1,2, Xin Li1, Xueju Hu1, Xiaobing Shen1,2 and Pingmin Wei1,2 1 Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China 2 Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China ABSTRACT Background. Obesity is a global epidemic in the industrialized and developing world, and many children suffer from obesity-related complications. Gut microbiota dysbiosis might have significant effect on the development of obesity. The microbiota continues to develop through childhood and thus childhood may be the prime time for microbiota interventions to realize health promotion or disease prevention. Therefore, it is crucial to understand the structure and function of pediatric gut microbiota. Methods. According to the inclusion criteria and exclusion criteria, twenty-three normal weight and twenty-eight obese children were recruited from Nanjing, China. Genomic DNA was extracted from fecal samples. The V4 region of the bacterial 16S rDNA was amplified by PCR, and sequencing was applied to analyze the gut microbiota diversity and composition using the Illumina HiSeq 2500 platform. Results. The number of operational taxonomic units (OTUs) showed a decrease in the diversity of gut microbiota with increasing body weight. The alpha diversity indices showed that the normal weight group had higher abundance and observed species than the obese group (Chao1: P < 0.001; observed species: P < 0.001; PD whole tree: P < 0.001; Shannon index: P D 0.008). -
A Genomic Perspective on a New Bacterial Genus and Species from the Alcaligenaceae Family, Basilea Psittacipulmonis
UC Irvine UC Irvine Previously Published Works Title A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis. Permalink https://escholarship.org/uc/item/0f60f7jm Journal BMC genomics, 15(1) ISSN 1471-2164 Authors Whiteson, Katrine L Hernandez, David Lazarevic, Vladimir et al. Publication Date 2014-03-01 DOI 10.1186/1471-2164-15-169 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Whiteson et al. BMC Genomics 2014, 15:169 http://www.biomedcentral.com/1471-2164/15/169 RESEARCH ARTICLE Open Access A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis Katrine L Whiteson1,5*, David Hernandez1, Vladimir Lazarevic1, Nadia Gaia1, Laurent Farinelli2, Patrice François1, Paola Pilo3, Joachim Frey3 and Jacques Schrenzel1,4 Abstract Background: A novel Gram-negative, non-haemolytic, non-motile, rod-shaped bacterium was discovered in the lungs of a dead parakeet (Melopsittacus undulatus) that was kept in captivity in a petshop in Basel, Switzerland. The organism is described with a chemotaxonomic profile and the nearly complete genome sequence obtained through the assembly of short sequence reads. Results: Genome sequence analysis and characterization of respiratory quinones, fatty acids, polar lipids, and biochemical phenotype is presented here. Comparison of gene sequences revealed that the most similar species is Pelistega europaea, with BLAST identities of only 93% to the 16S rDNA gene, 76% identity to the rpoB gene, and a similar GC content (~43%) as the organism isolated from the parakeet, DSM 24701 (40%). The closest full genome sequences are those of Bordetella spp. -
Supplementary Material
1 Supplementary Material 2 Changes amid constancy: flower and leaf microbiomes along land use gradients 3 and between bioregions 4 Paul Gaube*, Robert R. Junker, Alexander Keller 5 *Correspondence to Paul Gaube (email: [email protected]) 6 7 Supplementary Figures and Tables 8 Figures 9 Figure S1: Heatmap with relative abundance of Lactobacillales and Rhizobiales ASVs of each sample 10 related to tissue type. Differences in their occurrence on flowers and leaves (plant organs) were 11 statistically tested using t-test (p < 0.001***). 12 Figure S2A-D: Correlations between relative abundances of 25 most abundant bacterial genera and LUI 13 parameters. Correlations are based on linear Pearson correlation coefficients against each other and LUI 14 indices. Correlation coefficients are displayed by the scale color in the filled squares and indicate the 15 strength of the correlation (r) and whether it is positive (blue) or negative (red). P-values were adjusted 16 for multiple testing with Benjamini-Hochberg correction and only significant correlations are shown (p < 17 0.05). White boxes indicate non-significant correlations. A) Ranunculus acris flowers, B) Trifolium pratense 18 flowers, C) Ranunculus acris leaves (LRA), D) Trifolium pratense leaves (LTP). 19 20 Tables 21 Table S1: Taxonomic identification of the most abundant bacterial genera and their presence (average 22 in percent) on each tissue type. 23 Table S2: Taxonomic identification of ubiquitous bacteria found in 95 % of all samples, including their 24 average relative abundance on each tissue type. 25 Table S3: Bacterial Classes that differed significantly in relative abundance between bioregions for each 26 tissue type. -
Comparative Semen Microbiota Composition of a Stallion in a Taylorella Equigenitalis Carrier and Non-Carrier State
animals Article Comparative Semen Microbiota Composition of a Stallion in a Taylorella equigenitalis Carrier and Non-Carrier State Carlota Quiñones-Pérez 1,* , Amparo Martínez 2 , Francisco Crespo 3 and José Luis Vega-Pla 1 1 Laboratorio de Investigación Aplicada, Cría Caballar de las Fuerzas Armadas, Carretera de Madrid Km 395A, 14014 Córdoba, Spain; [email protected] 2 Genetics Department, University of Córdoba, edificio Gregor Mendel (C-5), Campus de Rabanales, 14071 Córdoba, Spain; [email protected] 3 Centro Militar de Cría Caballar de Ávila, Cría Caballar de las Fuerzas Armadas, Calle Arsenio Gutiérrez Palacios, s/n, 05005 Ávila, Spain; [email protected] * Correspondence: [email protected] Received: 2 April 2020; Accepted: 15 May 2020; Published: 17 May 2020 Simple Summary: Contagious equine metritis carriers have become a new cause of concern in horse stud farms. Their detection can result in significant financial loss and force owners to have their animals undergo antibiotic treatment. Current research has not been able to satisfactorily explain the appearance of carriers in agent-free farms. Studies made on microbial flora have given new insights into the diagnosis and treatment of different issues in animal systems. Next-generation sequencing (NGS) is a powerful tool that can draw an accurate picture of microbial flora. Therefore, the aim of this study was to compare the seminal bacterial composition of one stallion before and after being diagnosed with Taylorella equigenitalis using NGS. Our results show that the microbial seminal flora visibly changed between the samples analyzed. Corynebacteriaceae, an opportunistic bacterial family, was more common in the infected sample. -
A Genomic Perspective on a New Bacterial Genus and Species From
Whiteson et al. BMC Genomics 2014, 15:169 http://www.biomedcentral.com/1471-2164/15/169 RESEARCH ARTICLE Open Access A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis Katrine L Whiteson1,5*, David Hernandez1, Vladimir Lazarevic1, Nadia Gaia1, Laurent Farinelli2, Patrice François1, Paola Pilo3, Joachim Frey3 and Jacques Schrenzel1,4 Abstract Background: A novel Gram-negative, non-haemolytic, non-motile, rod-shaped bacterium was discovered in the lungs of a dead parakeet (Melopsittacus undulatus) that was kept in captivity in a petshop in Basel, Switzerland. The organism is described with a chemotaxonomic profile and the nearly complete genome sequence obtained through the assembly of short sequence reads. Results: Genome sequence analysis and characterization of respiratory quinones, fatty acids, polar lipids, and biochemical phenotype is presented here. Comparison of gene sequences revealed that the most similar species is Pelistega europaea, with BLAST identities of only 93% to the 16S rDNA gene, 76% identity to the rpoB gene, and a similar GC content (~43%) as the organism isolated from the parakeet, DSM 24701 (40%). The closest full genome sequences are those of Bordetella spp. and Taylorella spp. High-throughput sequencing reads from the Illumina-Solexa platform were assembled with the Edena de novo assembler to form 195 contigs comprising the ~2 Mb genome. Genome annotation with RAST, construction of phylogenetic trees with the 16S rDNA (rrs) gene sequence and the rpoB gene, and phylogenetic placement using other highly conserved marker genes with ML Tree all suggest that the bacterial species belongs to the Alcaligenaceae family. -
Burkholderiales Participating in Pentachlorophenol Biodegradation in Iron-Reducing
Electronic Supplementary Material (ESI) for Environmental Science: Processes & Impacts. This journal is © The Royal Society of Chemistry 2015 Burkholderiales participating in pentachlorophenol biodegradation in iron-reducing paddy soil as identified by stable isotope probing Hui Tong a,b,c,1, Min Hu b,1, Fangbai Li *b, Manjia Chen b, Yahui Lv b,d a Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China b Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, PR China c Graduate University of Chinese Academy of Sciences, Beijing 100049, PR China d School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, PR China * Corresponding author. Tel.: +86 20 87024721; fax: +86 20 87024123. E-mail address: [email protected] (F.B., Li). 1These authors contributed equally to this work. Number of pages: 5 Number of figures: 1 Number of tables: 2 Figure S1 The relative abundance of T-RFs in the 13C-DNA heavy fractions. The solid line is the model-fitted relative abundance using the pseudo-first-order kinetic model. Table S1. Phylogenetic affiliation of two (A and B) 16S rRNA clone in PCP degrading microcosms. A 12C-Heavy fraction of clones Phylum Class Order Family Genus 8 Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia/Shigella 7 Proteobacteria Betaproteobacteria Unclassified 4 Planctomycetes Planctomycetacia Planctomycetales Planctomycetaceae -
Detection and Characterization of Clinical Bordetella Trematum Isolates from Chronic Wounds
pathogens Article Detection and Characterization of Clinical Bordetella trematum Isolates from Chronic Wounds Christian Buechler 1,*, Claudio Neidhöfer 1 , Thorsten Hornung 2 , Marcel Neuenhoff 1 and Marijo Parˇcina 1 1 Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany; [email protected] (C.N.); [email protected] (M.N.); [email protected] (M.P.) 2 Clinic and Polyclinic for Dermatology and Allergology, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany; [email protected] * Correspondence: [email protected] Abstract: Bordetella trematum is a relatively newly discovered and potentially frequently overlooked Bordetella species, mostly isolated from chronic wounds and predominantly in those of the lower extremities. Its susceptibility profile and clinical significance is still debated, given the limited amount of available data. We contribute providing a molecular and phenotypical analysis of three unique clinical B. trematum isolates detected between August 2019 and January 2020 to aid the matter. Cryo- conserved isolates were subcultured and re-identified using various routine means of identification. Bacterial genomes were fully Illumina-sequenced and phenotypical susceptibility was determined by broth microdilution and gradient-strip tests. All isolates displayed increased susceptibility to piperacillin–tazobactam (<2/4 mg/L), imipenem (<1 mg/L), and meropenem (<0.047 mg/L), whereas they displayed decreased susceptibility to all tested cephalosporins and fluoroquinolones (according to PK-PD, EUCAST 10.0 2020). One isolate carried a beta-lactamase (EC 3.5.2.6) and a sulfonamide resistance gene (sul2) and cells displayed resistance to ampicillin, ampicillin/sulbactam, Citation: Buechler, C.; Neidhöfer, C.; Hornung, T.; Neuenhoff, M.; Parˇcina, and trimethoprim/sulfamethoxazole. -
Phenotypic and Genotypic Characterization of Bordetella Bronchiseptica Strains Isolated from Pigs in Poland
Polish Journal of Veterinary Sciences Vol. 17, No. 1 (2014), 71–77 DOI 10.2478/pjvs-2014-0009 Original article Phenotypic and genotypic characterization of Bordetella bronchiseptica strains isolated from pigs in Poland K. Stępniewska, K. Urbaniak, I. Markowska-Daniel Department of Swine Diseases, National Veterinary Research Institute Al. Partyzantów 57, 24-100 Puławy, Poland Abstract A total of 209 Bordetella bronchiseptica (Bbr) strains isolated from pigs were examined. Phenotypic study included: biochemical characterization (motility, catalase, oxidase, urease activity, nitrate reduction and growth on MacConkey agar) and antimicrobial susceptibility (disc diffusion method). Genotypic studies based on detection of three genes encoded virulence factors, such as: flagella (fla), dermonecrotoxin (dnt), and exogenous ferric siderophore receptor (bfrZ), using PCR. Most of the Bbr strains tested had a homogeneous biochemical profile. 97.6% of them provided suitable results in biochemical tests. All Bbr isolates tested showed high resistance to penicillin (100%), linco-spectin (100%) and ceftiofur (97.9%). Over 57% and 43% of Bbr strains were resistant to ampicillin and amoxicillin, respectively. All Bbr isolates showed high sensitivity to most chemother- apeutics used such as enrofloxacin (97.9%), tetracycline (97.9%), oxytetracycline (97.9%), amoxicillin with clavulonic acid (95.8%), florfenicol (90.4%), and gentamicine (77.6%). Over of 94% of Bbr strains were moderately susceptible to norfloxacine. Molecular analysis confirmed that almost all evaluated Bbr strains (94.7%) possessed the fla gene. A lower percentage of isolates had the dnt gene (72.7%) and the lowest percentage of strains (51.7%), had the bfrZ gene. Key words: swine, Bordetella bronchiseptica, phenotypic and genotypic characterization, antimic- robial susceptibility Introduction of many animal species such as: swine, dogs, cats, rab- bits, horses, rats and guinea pigs.