Comamonas: Relationship to Aquaspirillum Aquaticum, E
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Metaproteogenomic Insights Beyond Bacterial Response to Naphthalene
ORIGINAL ARTICLE ISME Journal – Original article Metaproteogenomic insights beyond bacterial response to 5 naphthalene exposure and bio-stimulation María-Eugenia Guazzaroni, Florian-Alexander Herbst, Iván Lores, Javier Tamames, Ana Isabel Peláez, Nieves López-Cortés, María Alcaide, Mercedes V. del Pozo, José María Vieites, Martin von Bergen, José Luis R. Gallego, Rafael Bargiela, Arantxa López-López, Dietmar H. Pieper, Ramón Rosselló-Móra, Jesús Sánchez, Jana Seifert and Manuel Ferrer 10 Supporting Online Material includes Text (Supporting Materials and Methods) Tables S1 to S9 Figures S1 to S7 1 SUPPORTING TEXT Supporting Materials and Methods Soil characterisation Soil pH was measured in a suspension of soil and water (1:2.5) with a glass electrode, and 5 electrical conductivity was measured in the same extract (diluted 1:5). Primary soil characteristics were determined using standard techniques, such as dichromate oxidation (organic matter content), the Kjeldahl method (nitrogen content), the Olsen method (phosphorus content) and a Bernard calcimeter (carbonate content). The Bouyoucos Densimetry method was used to establish textural data. Exchangeable cations (Ca, Mg, K and 10 Na) extracted with 1 M NH 4Cl and exchangeable aluminium extracted with 1 M KCl were determined using atomic absorption/emission spectrophotometry with an AA200 PerkinElmer analyser. The effective cation exchange capacity (ECEC) was calculated as the sum of the values of the last two measurements (sum of the exchangeable cations and the exchangeable Al). Analyses were performed immediately after sampling. 15 Hydrocarbon analysis Extraction (5 g of sample N and Nbs) was performed with dichloromethane:acetone (1:1) using a Soxtherm extraction apparatus (Gerhardt GmbH & Co. -
Breast Milk Microbiota: a Review of the Factors That Influence Composition
Published in "Journal of Infection 81(1): 17–47, 2020" which should be cited to refer to this work. ✩ Breast milk microbiota: A review of the factors that influence composition ∗ Petra Zimmermann a,b,c,d, , Nigel Curtis b,c,d a Department of Paediatrics, Fribourg Hospital HFR and Faculty of Science and Medicine, University of Fribourg, Switzerland b Department of Paediatrics, The University of Melbourne, Parkville, Australia c Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, Australia d Infectious Diseases Unit, The Royal Children’s Hospital Melbourne, Parkville, Australia s u m m a r y Breastfeeding is associated with considerable health benefits for infants. Aside from essential nutrients, immune cells and bioactive components, breast milk also contains a diverse range of microbes, which are important for maintaining mammary and infant health. In this review, we summarise studies that have Keywords: investigated the composition of the breast milk microbiota and factors that might influence it. Microbiome We identified 44 studies investigating 3105 breast milk samples from 2655 women. Several studies Diversity reported that the bacterial diversity is higher in breast milk than infant or maternal faeces. The maxi- Delivery mum number of each bacterial taxonomic level detected per study was 58 phyla, 133 classes, 263 orders, Caesarean 596 families, 590 genera, 1300 species and 3563 operational taxonomic units. Furthermore, fungal, ar- GBS chaeal, eukaryotic and viral DNA was also detected. The most frequently found genera were Staphylococ- Antibiotics cus, Streptococcus Lactobacillus, Pseudomonas, Bifidobacterium, Corynebacterium, Enterococcus, Acinetobacter, BMI Rothia, Cutibacterium, Veillonella and Bacteroides. There was some evidence that gestational age, delivery Probiotics mode, biological sex, parity, intrapartum antibiotics, lactation stage, diet, BMI, composition of breast milk, Smoking Diet HIV infection, geographic location and collection/feeding method influence the composition of the breast milk microbiota. -
Comamonas Kerstersii Bacteremia in a Patient with Acute Perforated
® Clinical Case Report Medicine OPEN Comamonas kerstersii bacteremia in a patient with acute perforated appendicitis A rare case report ∗ Yun-heng Zhou, PhDa, Hong-xia Ma, MDb, Zhao-yang Dong, PhDc, Mei-hua Shen, PhDd, Abstract Rationale: Comamonas species are rarely associated with human infections. Recent reports found that Comamonas kerstersii was associated with severe diseases such as abdominal infection and bacteremia. However, C. kerstersii maybe be confused with Comamonas testosteroni using the automatic bacterial identification systems currently available. Patient concerns: A 31-year-old man who had onset of left upper abdominal pain developed clinical manifestations of right lower abdominal pain and classic migration of pain at the temperature of 39°C. The positive strain of aerobic and anaerobic bottles of blood cultures was identified. Diagnoses: The patient was diagnosed as acute peritonitis and perforated appendix with abdominal abscess. Interventions: The bacterium was identified by routine methods, MALDI-TOF-MS and PCR amplification of the 16S rRNA. The patient was treated with exploratory laparotomy, appendectomy, tube drainage, and prescribing antibiotic treatment. Outcomes: The patients were discharged with complete recovery. The organisms were confirmed as C. kerstersii by MALDI-TOF- MS and a combination of the other results. Lessons: Our findings suggest that C. kerstersii infection occurs most often in association with perforated appendix and bacteremia. We presume that C. kerstersii is an opportunistic pathogen or commensal with the digestive tract and appendix bacteria. Abbreviations: C. kerstersii = Comamonas kerstersii, MALDI-TOF-MS = matrix-assisted laser desorption ionization–time of flight mass spectrometry, MIC = minimum inhibitory concentration, PCR = polymerase chain reaction. -
Bacterial Sulfite-Oxidizing Enzymes
Biochimica et Biophysica Acta 1807 (2011) 1–10 Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbabio Review Bacterial sulfite-oxidizing enzymes Ulrike Kappler ⁎ Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia Qld 4072, Australia article info abstract Article history: Enzymes belonging to the Sulfite Oxidase (SO) enzyme family are found in virtually all forms of life, and are Received 12 June 2010 especially abundant in prokaryotes as shown by analysis of available genome data. Despite this fact, only a Received in revised form 5 September 2010 limited number of bacterial SO family enzymes has been characterized in detail to date, and these appear to be Accepted 14 September 2010 involved in very different metabolic processes such as energy generation from sulfur compounds, host Available online 17 September 2010 colonization, sulfite detoxification and organosulfonate degradation. The few characterized bacterial SO family enzymes also show an intriguing range of structural conformations, including monomeric, dimeric and Keywords: Sulfite oxidation heterodimeric enzymes with varying numbers and types of redox centres. Some of the bacterial enzymes even Metalloenzymes catalyze novel reactions such as dimethylsulfoxide reduction that previously had been thought not to be Sulfur oxidizing bacteria catalyzed by SO family enzymes. Classification of the SO family enzymes based on the structure of their Mo Molybdenum -
Biotransformation of Pharmaceuticals by Comamonas and Aeromonas Species
Biotransformation of Pharmaceuticals by Comamonas and Aeromonas Species Atika Sajid Shaheed Zulqar Ali Bhutto Institute of Science and Technology Saira Yahya ( [email protected] ) Shaheed Zulqar Ali Bhutto Institute of Science and Technology Research Article Keywords: Antibiotic resistance, Biotransformation, Erythromycin, Sulfamethoxazole-trimethoprim, Comamonas jiangduensis, Aeromonas hydrophila, Aeromonas caviae Posted Date: January 15th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-144884/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/22 Abstract Background: Contamination of natural niches with pharmaceutical residues has emerged out as a serious concern. Disposal of untreated euents from the pharmaceutical, hospital, and domestic settings has been identied as a signicant source of such a massive spread of antibiotics. The unnecessary persistence of pharmaceutical residues including antibiotics has been related to the increased risk of resistance selection among pathogenic and non-pathogenic microorganisms. To date, several methods have been devised to eliminate such pollutants from wastewater, but their implication on larger scales is not feasible due to complexities and high costs of the processes, especially in developing and underdeveloped countries. This study aimed to isolate and characterize bacterial strains from domestic and pharmaceutical euents having biotransformation potential towards most persistent antibiotics. Results: Antibiotic resistance screening and MIC determination experiments indicated highest resistivity of three bacterial isolates against two antibiotics Erythromycin and Sulfamethoxazole-trimethoprim, evincing extensive usage of these antibiotics in our healthcare settings. These isolates were identied as Comamonas jiangduensis, Aeromonas caviae and Aeromonas hydrophila by 16S rDNA sequencing. Growth conditions including incubation temperature, initial pH and inoculum size were optimized for these strains. -
And Pan‑Genomic Analyses of the Genus Comamonas : from Environmental Adaptation to Potential Virulence
This document is downloaded from DR‑NTU (https://dr.ntu.edu.sg) Nanyang Technological University, Singapore. The core‑ and pan‑genomic analyses of the genus Comamonas : from environmental adaptation to potential virulence Wu, Yichao; Zaiden, Norazean; Cao, Bin 2018 Wu, Y., Zaiden, N., & Cao, B. (2018). The core‑ and pan‑genomic analyses of the genus Comamonas : from environmental adaptation to potential virulence. Frontiers in Microbiology, 9, 3096‑. doi:10.3389/fmicb.2018.03096 https://hdl.handle.net/10356/103309 https://doi.org/10.3389/fmicb.2018.03096 © 2018 Wu, Zaiden and Cao. This is an open‑access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Downloaded on 27 Sep 2021 19:01:28 SGT fmicb-09-03096 December 10, 2018 Time: 13:56 # 1 ORIGINAL RESEARCH published: 12 December 2018 doi: 10.3389/fmicb.2018.03096 The Core- and Pan-Genomic Analyses of the Genus Comamonas: From Environmental Adaptation to Potential Virulence Yichao Wu1, Norazean Zaiden2 and Bin Cao2,3* 1 State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China, 2 Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore, 3 School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore Comamonas is often reported to be one of the major members of microbial communities in various natural and engineered environments. -
Phenotypic and Genetic Diversity of Pseudomonads
PHENOTYPIC AND GENETIC DIVERSITY OF PSEUDOMONADS ASSOCIATED WITH THE ROOTS OF FIELD-GROWN CANOLA A Thesis Submitted to the College of Graduate Studies and Research In Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy In the Department of Applied Microbiology and Food Science University of Saskatchewan Saskatoon By Danielle Lynn Marie Hirkala © Copyright Danielle Lynn Marie Hirkala, November 2006. All rights reserved. PERMISSION TO USE In presenting this thesis in partial fulfilment of the requirements for a Postgraduate degree from the University of Saskatchewan, I agree that the Libraries of this University may make it freely available for inspection. I further agree that permission for copying of this thesis in any manner, in whole or in part, for scholarly purposes may be granted by the professor or professors who supervised my thesis work or, in their absence, by the Head of the Department or the Dean of the College in which my thesis work was done. It is understood that any copying or publication or use of this thesis or parts thereof for financial gain shall not be allowed without my written permission. It is also understood that due recognition shall be given to me and to the University of Saskatchewan in any scholarly use which may be made of any material in my thesis. Requests for permission to copy or to make other use of material in this thesis in whole or part should be addressed to: Head of the Department of Applied Microbiology and Food Science University of Saskatchewan Saskatoon, Saskatchewan, S7N 5A8 i ABSTRACT Pseudomonads, particularly the fluorescent pseudomonads, are common rhizosphere bacteria accounting for a significant portion of the culturable rhizosphere bacteria. -
Delftia Rhizosphaerae Sp. Nov. Isolated from the Rhizosphere of Cistus Ladanifer
TAXONOMIC DESCRIPTION Carro et al., Int J Syst Evol Microbiol 2017;67:1957–1960 DOI 10.1099/ijsem.0.001892 Delftia rhizosphaerae sp. nov. isolated from the rhizosphere of Cistus ladanifer Lorena Carro,1† Rebeca Mulas,2 Raquel Pastor-Bueis,2 Daniel Blanco,3 Arsenio Terrón,4 Fernando Gonzalez-Andr es, 2 Alvaro Peix5,6 and Encarna Velazquez 1,6,* Abstract A bacterial strain, designated RA6T, was isolated from the rhizosphere of Cistus ladanifer. Phylogenetic analyses based on 16S rRNA gene sequence placed the isolate into the genus Delftia within a cluster encompassing the type strains of Delftia lacustris, Delftia tsuruhatensis, Delftia acidovorans and Delftia litopenaei, which presented greater than 97 % sequence similarity with respect to strain RA6T. DNA–DNA hybridization studies showed average relatedness ranging from of 11 to 18 % between these species of the genus Delftia and strain RA6T. Catalase and oxidase were positive. Casein was hydrolysed but gelatin and starch were not. Ubiquinone 8 was the major respiratory quinone detected in strain RA6T together with low amounts of ubiquinones 7 and 9. The major fatty acids were those from summed feature 3 (C16 : 1!7c/C16 : 1 !6c) and C16 : 0. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain RA6T should be considered as a representative of a novel species of genus Delftia, for which the name Delftia rhizosphaerae sp. nov. is proposed. The type strain is RA6T (=LMG 29737T= CECT 9171T). The genus Delftia comprises Gram-stain-negative, non- The strain was grown on nutrient agar (NA; Sigma) for 48 h sporulating, strictly aerobic rods, motile by polar or bipolar at 22 C to check for motility by phase-contrast microscopy flagella. -
Sparus Aurata) and Sea Bass (Dicentrarchus Labrax)
Gut bacterial communities in geographically distant populations of farmed sea bream (Sparus aurata) and sea bass (Dicentrarchus labrax) Eleni Nikouli1, Alexandra Meziti1, Efthimia Antonopoulou2, Eleni Mente1, Konstantinos Ar. Kormas1* 1 Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece 2 Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece * Corresponding author; Tel.: +30-242-109-3082, Fax: +30-242109-3157, E-mail: [email protected], [email protected] Supplementary material 1 Table S1. Body weight of the Sparus aurata and Dicentrarchus labrax individuals used in this study. Chania Chios Igoumenitsa Yaltra Atalanti Sample Body weight S. aurata D. labrax S. aurata D. labrax S. aurata D. labrax S. aurata D. labrax S. aurata D. labrax (g) 1 359 378 558 420 433 448 481 346 260 785 2 355 294 579 442 493 556 516 397 240 340 3 376 275 468 554 450 464 540 415 440 500 4 392 395 530 460 440 483 492 493 365 860 5 420 362 483 479 542 492 406 995 6 521 505 506 461 Mean 380.40 340.80 523.17 476.67 471.60 487.75 504.50 419.67 326.25 696.00 SEs 11.89 23.76 17.36 19.56 20.46 23.85 8.68 21.00 46.79 120.29 2 Table S2. Ingredients of the diets used at the time of sampling. Ingredient Sparus aurata Dicentrarchus labrax (6 mm; 350-450 g)** (6 mm; 450-800 g)** Crude proteins (%) 42 – 44 37 – 39 Crude lipids (%) 19 – 21 20 – 22 Nitrogen free extract (NFE) (%) 20 – 26 19 – 25 Crude cellulose (%) 1 – 3 2 – 4 Ash (%) 5.8 – 7.8 6.2 – 8.2 Total P (%) 0.7 – 0.9 0.8 – 1.0 Gross energy (MJ/Kg) 21.5 – 23.5 20.6 – 22.6 Classical digestible energy* (MJ/Kg) 19.5 18.9 Added vitamin D3 (I.U./Kg) 500 500 Added vitamin E (I.U./Kg) 180 100 Added vitamin C (I.U./Kg) 250 100 Feeding rate (%), i.e. -
Diaphorobacter Nitroreducens Gen. Nov., Sp. Nov., a Poly (3
J. Gen. Appl. Microbiol., 48, 299–308 (2002) Full Paper Diaphorobacter nitroreducens gen. nov., sp. nov., a poly(3-hydroxybutyrate)-degrading denitrifying bacterium isolated from activated sludge Shams Tabrez Khan and Akira Hiraishi* Department of Ecological Engineering, Toyohashi University of Technology, Toyohashi 441–8580, Japan (Received August 12, 2002; Accepted October 23, 2002) Three denitrifying strains of bacteria capable of degrading poly(3-hydroxybutyrate) (PHB) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) were isolated from activated sludge and characterized. All of the isolates had almost identical phenotypic characteristics. They were motile gram-negative rods with single polar flagella and grew well with simple organic com- pounds, as well as with PHB and PHBV, as carbon and energy sources under both aerobic and anaerobic denitrifying conditions. However, none of the sugars tested supported their growth. The cellular fatty acid profiles showed the presence of C16:1w7cis and C16:0 as the major com- ponents and of 3-OH-C10:0 as the sole component of hydroxy fatty acids. Ubiquinone-8 was de- tected as the major respiratory quinone. A 16S rDNA sequence-based phylogenetic analysis showed that all the isolates belonged to the family Comamonadaceae, a major group of b-Pro- teobacteria, but formed no monophyletic cluster with any previously known species of this fam- (DSM 13225؍) ily. The closest relative to our strains was an unidentified bacterium strain LW1 (99.9% similarity), reported previously as a 1-chloro-4-nitrobenzene degrading bacterium. DNA- DNA hybridization levels among the new isolates were more than 60%, whereas those between our isolates and strain DSM 13225 were less than 50%. -
Delftia Sp. LCW, a Strain Isolated from a Constructed Wetland Shows Novel Properties for Dimethylphenol Isomers Degradation Mónica A
Vásquez-Piñeros et al. BMC Microbiology (2018) 18:108 https://doi.org/10.1186/s12866-018-1255-z RESEARCHARTICLE Open Access Delftia sp. LCW, a strain isolated from a constructed wetland shows novel properties for dimethylphenol isomers degradation Mónica A. Vásquez-Piñeros1, Paula M. Martínez-Lavanchy1,2, Nico Jehmlich3, Dietmar H. Pieper4, Carlos A. Rincón1, Hauke Harms5, Howard Junca6 and Hermann J. Heipieper1* Abstract Background: Dimethylphenols (DMP) are toxic compounds with high environmental mobility in water and one of the main constituents of effluents from petro- and carbochemical industry. Over the last few decades, the use of constructed wetlands (CW) has been extended from domestic to industrial wastewater treatments, including petro-carbochemical effluents. In these systems, the main role during the transformation and mineralization of organic pollutants is played by microorganisms. Therefore, understanding the bacterial degradation processes of isolated strains from CWs is an important approach to further improvements of biodegradation processes in these treatment systems. Results: In this study, bacterial isolation from a pilot scale constructed wetland fed with phenols led to the identification of Delftia sp. LCW as a DMP degrading strain. The strain was able to use the o-xylenols 3,4-DMP and 2,3-DMP as sole carbon and energy sources. In addition, 3,4-DMP provided as a co-substrate had an effect on the transformation of other four DMP isomers. Based on the detection of the genes, proteins, and the inferred phylogenetic relationships of the detected genes with other reported functional proteins, we found that the phenol hydroxylase of Delftia sp. LCW is induced by 3,4-DMP and it is responsible for the first oxidation of the aromatic ring of 3,4-, 2,3-, 2,4-, 2,5- and 3,5-DMP. -
Unveiling Bacterial Interactions Through Multidimensional Scaling and Dynamics Modeling Received: 06 May 2015 Pedro Dorado-Morales1, Cristina Vilanova1, Carlos P
www.nature.com/scientificreports OPEN Unveiling Bacterial Interactions through Multidimensional Scaling and Dynamics Modeling Received: 06 May 2015 Pedro Dorado-Morales1, Cristina Vilanova1, Carlos P. Garay3, Jose Manuel Martí3 Accepted: 17 November 2015 & Manuel Porcar1,2 Published: 16 December 2015 We propose a new strategy to identify and visualize bacterial consortia by conducting replicated culturing of environmental samples coupled with high-throughput sequencing and multidimensional scaling analysis, followed by identification of bacteria-bacteria correlations and interactions. We conducted a proof of concept assay with pine-tree resin-based media in ten replicates, which allowed detecting and visualizing dynamical bacterial associations in the form of statistically significant and yet biologically relevant bacterial consortia. There is a growing interest on disentangling the complexity of microbial interactions in order to both optimize reactions performed by natural consortia and to pave the way towards the development of synthetic consor- tia with improved biotechnological properties1,2. Despite the enormous amount of metagenomic data on both natural and artificial microbial ecosystems, bacterial consortia are not necessarily deduced from those data. In fact, the flexibility of the bacterial interactions, the lack of replicated assays and/or biases associated with differ- ent DNA isolation technologies and taxonomic bioinformatics tools hamper the clear identification of bacterial consortia. We propose here a holistic approach aiming at identifying bacterial interactions in laboratory-selected microbial complex cultures. The method requires multi-replicated taxonomic data on independent subcultures, and high-throughput sequencing-based taxonomic data. From this data matrix, randomness of replicates can be verified, linear correlations can be visualized and interactions can emerge from statistical correlations.