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Inactivation of CRISPR-Cas Systems by Anti-CRISPR Proteins in Diverse Bacterial Species April Pawluk1, Raymond H.J
LETTERS PUBLISHED: 13 JUNE 2016 | ARTICLE NUMBER: 16085 | DOI: 10.1038/NMICROBIOL.2016.85 Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species April Pawluk1, Raymond H.J. Staals2, Corinda Taylor2, Bridget N.J. Watson2, Senjuti Saha3, Peter C. Fineran2, Karen L. Maxwell4* and Alan R. Davidson1,3* CRISPR-Cas systems provide sequence-specific adaptive immu- MGE-encoded mechanisms that inhibit CRISPR-Cas systems. In nity against foreign nucleic acids1,2. They are present in approxi- support of this hypothesis, phages infecting Pseudomonas aeruginosa mately half of all sequenced prokaryotes3 and are expected to were found to encode diverse families of proteins that inhibit constitute a major barrier to horizontal gene transfer. We pre- the CRISPR-Cas systems of their host through several distinct viously described nine distinct families of proteins encoded in mechanisms4,5,17,18. However, homologues of these anti-CRISPR Pseudomonas phage genomes that inhibit CRISPR-Cas function4,5. proteins were found only within the Pseudomonas genus. Here, We have developed a bioinformatic approach that enabled us to we describe a bioinformatic approach that allowed us to identify discover additional anti-CRISPR proteins encoded in phages five novel families of functional anti-CRISPR proteins encoded in and other mobile genetic elements of diverse bacterial phages and other putative MGEs in species spanning the diversity species. We show that five previously undiscovered families of Proteobacteria. of anti-CRISPRs inhibit the type I-F CRISPR-Cas systems of The nine previously characterized anti-CRISPR protein families both Pseudomonas aeruginosa and Pectobacterium atrosepticum, possess no common sequence motifs, so we used genomic context to and a dual specificity anti-CRISPR inactivates both type I-F search for novel anti-CRISPR genes. -
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Int. J. Environ. Res., 8(3):813-818,Summer 2014 ISSN: 1735-6865 Persian Gulf is a Bioresource of Potent L-Asparaginase Producing Bacteria: Isolation & Molecular Differentiating Izadpanah Qeshmi, F.1,2 , Javadpour, S. 2, Malekzadeh, K. 2 * ,Tamadoni Jahromi, S.3 and Rahimzadeh, M.2 1Department of Miocrobiology; Jahrom Branch; Islamic Azad University; Jahrom; Iran 2Molecular Medicine Research Center (MMRC); Hormozgan University of Medical Science (HUMS); Bandar Abbas; Iran 3Persian Gulf and Oman Sea Ecological Research Institute; Bandar Abbas; Iran Received 3 Nov. 2013; Revised 24 Dec. 2013; Accepted 5 Jan. 2014 ABSTRACT: L-asparaginase is a candidate enzyme for anti-neoplastic agent againstacute lymphoblastic leukemia and also extensively use in the food industry for prevention of acrylamide formation. L-asparaginase is widely distributed among microorganisms. In this study, marine bacteria were isolated from Persian Gulf and screened for L-asparaginase activity. Production of L-asparaginase was carried out by using M9 medium. Among L-asparaginase producing strains, 12 potent strains were differentiated based on nucleotide sequences of 16S rDNA. 12 potent strains included 2 strains of Pseudomonas spp., 8 strains of Bacillus spp, one strain of Zobellella spp. and one strain of Oceanimonas spp. identified and consequently the sequences published in the NCBI databases under the specific accession numbers. This is the first report on L-asparaginase activity of Zobellella spp. from this region. The highest (1.6 IU/ mL) and also the lowest (0.20 IU/ mL) productivity of L-asparaginase enzyme were recorded for Pseudomonas sp. PG_01 and Bacillus sp. PG_13 respectively. This study revealed marine bacteria are potential source of L-asparaginase enzyme .Pseudomonas sp.PG_01 with high productivity can be used for production of L-asparaginase. -
An Update on the Genus Aeromonas: Taxonomy, Epidemiology, and Pathogenicity
microorganisms Review An Update on the Genus Aeromonas: Taxonomy, Epidemiology, and Pathogenicity Ana Fernández-Bravo and Maria José Figueras * Unit of Microbiology, Department of Basic Health Sciences, Faculty of Medicine and Health Sciences, IISPV, University Rovira i Virgili, 43201 Reus, Spain; [email protected] * Correspondence: mariajose.fi[email protected]; Tel.: +34-97-775-9321; Fax: +34-97-775-9322 Received: 31 October 2019; Accepted: 14 January 2020; Published: 17 January 2020 Abstract: The genus Aeromonas belongs to the Aeromonadaceae family and comprises a group of Gram-negative bacteria widely distributed in aquatic environments, with some species able to cause disease in humans, fish, and other aquatic animals. However, bacteria of this genus are isolated from many other habitats, environments, and food products. The taxonomy of this genus is complex when phenotypic identification methods are used because such methods might not correctly identify all the species. On the other hand, molecular methods have proven very reliable, such as using the sequences of concatenated housekeeping genes like gyrB and rpoD or comparing the genomes with the type strains using a genomic index, such as the average nucleotide identity (ANI) or in silico DNA–DNA hybridization (isDDH). So far, 36 species have been described in the genus Aeromonas of which at least 19 are considered emerging pathogens to humans, causing a broad spectrum of infections. Having said that, when classifying 1852 strains that have been reported in various recent clinical cases, 95.4% were identified as only four species: Aeromonas caviae (37.26%), Aeromonas dhakensis (23.49%), Aeromonas veronii (21.54%), and Aeromonas hydrophila (13.07%). -
A Noval Investigation of Microbiome from Vermicomposting Liquid Produced by Thai Earthworm, Perionyx Sp
International Journal of Agricultural Technology 2021Vol. 17(4):1363-1372 Available online http://www.ijat-aatsea.com ISSN 2630-0192 (Online) A novel investigation of microbiome from vermicomposting liquid produced by Thai earthworm, Perionyx sp. 1 Kraisittipanit, R.1,2, Tancho, A.2,3, Aumtong, S.3 and Charerntantanakul, W.1* 1Program of Biotechnology, Faculty of Science, Maejo University, Chiang Mai, Thailand; 2Natural Farming Research and Development Center, Maejo University, Chiang Mai, Thailand; 3Faculty of Agricultural Production, Maejo University, Thailand. Kraisittipanit, R., Tancho, A., Aumtong, S. and Charerntantanakul, W. (2021). A noval investigation of microbiome from vermicomposting liquid produced by Thai earthworm, Perionyx sp. 1. International Journal of Agricultural Technology 17(4):1363-1372. Abstract The whole microbiota structure in vermicomposting liquid derived from Thai earthworm, Perionyx sp. 1 was estimated. It showed high richness microbial species and belongs to 127 species, separated in 3 fungal phyla (Ascomycota, Basidiomycota, Mucoromycota), 1 Actinomycetes and 16 bacterial phyla (Acidobacteria, Armatimonadetes, Bacteroidetes, Balneolaeota, Candidatus, Chloroflexi, Deinococcus, Fibrobacteres, Firmicutes, Gemmatimonadates, Ignavibacteriae, Nitrospirae, Planctomycetes, Proteobacteria, Tenericutes and Verrucomicrobia). The OTUs data analysis revealed the highest taxonomic abundant ratio in bacteria and fungi belong to Proteobacteria (70.20 %) and Ascomycota (5.96 %). The result confirmed that Perionyx sp. 1 -
Towards a Functional Hypothesis Relating Anti-Islet Cell Autoimmunity
Endesfelder et al. Microbiome (2016) 4:17 DOI 10.1186/s40168-016-0163-4 RESEARCH Open Access Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production David Endesfelder1, Marion Engel1, Austin G. Davis-Richardson2, Alexandria N. Ardissone2, Peter Achenbach3, Sandra Hummel3, Christiane Winkler3, Mark Atkinson4, Desmond Schatz4, Eric Triplett2, Anette-Gabriele Ziegler3 and Wolfgang zu Castell1,5* Abstract Background: The development of anti-islet cell autoimmunity precedes clinical type 1 diabetes and occurs very early in life. During this early period, dietary factors strongly impact on the composition of the gut microbiome. At the same time, the gut microbiome plays a central role in the development of the infant immune system. A functional model of the association between diet, microbial communities, and the development of anti-islet cell autoimmunity can provide important new insights regarding the role of the gut microbiome in the pathogenesis of type 1 diabetes. Results: A novel approach was developed to enable the analysis of the microbiome on an aggregation level between a single microbial taxon and classical ecological measures analyzing the whole microbial population. Microbial co-occurrence networks were estimated at age 6 months to identify candidates for functional microbial communities prior to islet autoantibody development. Stratification of children based on these communities revealed functional associations between diet, gut microbiome, and islet autoantibody development. Two communities were strongly associated with breast-feeding and solid food introduction, respectively. The third community revealed a subgroup of children that was dominated by Bacteroides abundances compared to two subgroups with low Bacteroides and increased Akkermansia abundances. -
Taxonomic Hierarchy of the Phylum Proteobacteria and Korean Indigenous Novel Proteobacteria Species
Journal of Species Research 8(2):197-214, 2019 Taxonomic hierarchy of the phylum Proteobacteria and Korean indigenous novel Proteobacteria species Chi Nam Seong1,*, Mi Sun Kim1, Joo Won Kang1 and Hee-Moon Park2 1Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea 2Department of Microbiology & Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea *Correspondent: [email protected] The taxonomic hierarchy of the phylum Proteobacteria was assessed, after which the isolation and classification state of Proteobacteria species with valid names for Korean indigenous isolates were studied. The hierarchical taxonomic system of the phylum Proteobacteria began in 1809 when the genus Polyangium was first reported and has been generally adopted from 2001 based on the road map of Bergey’s Manual of Systematic Bacteriology. Until February 2018, the phylum Proteobacteria consisted of eight classes, 44 orders, 120 families, and more than 1,000 genera. Proteobacteria species isolated from various environments in Korea have been reported since 1999, and 644 species have been approved as of February 2018. In this study, all novel Proteobacteria species from Korean environments were affiliated with four classes, 25 orders, 65 families, and 261 genera. A total of 304 species belonged to the class Alphaproteobacteria, 257 species to the class Gammaproteobacteria, 82 species to the class Betaproteobacteria, and one species to the class Epsilonproteobacteria. The predominant orders were Rhodobacterales, Sphingomonadales, Burkholderiales, Lysobacterales and Alteromonadales. The most diverse and greatest number of novel Proteobacteria species were isolated from marine environments. Proteobacteria species were isolated from the whole territory of Korea, with especially large numbers from the regions of Chungnam/Daejeon, Gyeonggi/Seoul/Incheon, and Jeonnam/Gwangju. -
Denitrification Likely Catalyzed by Endobionts in an Allogromiid Foraminifer
The ISME Journal (2012) 6, 951–960 & 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12 www.nature.com/ismej ORIGINAL ARTICLE Denitrification likely catalyzed by endobionts in an allogromiid foraminifer Joan M Bernhard1, Virginia P Edgcomb1, Karen L Casciotti2,4, Matthew R McIlvin2 and David J Beaudoin3 1Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA; 2Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA and 3Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA Nitrogen can be a limiting macronutrient for carbon uptake by the marine biosphere. The process of denitrification (conversion of nitrate to gaseous compounds, including N2 (nitrogen gas)) removes bioavailable nitrogen, particularly in marine sediments, making it a key factor in the marine nitrogen budget. Benthic foraminifera reportedly perform complete denitrification, a process previously considered nearly exclusively performed by bacteria and archaea. If the ability to denitrify is widespread among these diverse and abundant protists, a paradigm shift is required for biogeochemistry and marine microbial ecology. However, to date, the mechanisms of foraminiferal denitrification are unclear, and it is possible that the ability to perform complete denitrification is because of the symbiont metabolism in some foraminiferal species. Using sequence analysis and GeneFISH, we show that for a symbiont-bearing foraminifer, the potential for denitrification resides in the endobionts. Results also identify the endobionts as denitrifying pseudomonads and show that the allogromiid accumulates nitrate intracellularly, presumably for use in denitrification. Endobionts have been observed within many foraminiferal species, and in the case of associations with denitrifying bacteria, may provide fitness for survival in anoxic conditions. -
Diversity of Culturable Epiphytic Bacteria Isolated from Seagrass (Halodule Uninervis) in Thailand and Their Preliminary Antibacterial Activity
BIODIVERSITAS ISSN: 1412-033X Volume 21, Number 7, July 2020 E-ISSN: 2085-4722 Pages: 2907-2913 DOI: 10.13057/biodiv/d210706 Short Communication: Diversity of culturable epiphytic bacteria isolated from seagrass (Halodule uninervis) in Thailand and their preliminary antibacterial activity PARIMA BOONTANOM, AIYA CHANTARASIRI♥ Faculty of Science, Energy and Environment, King Mongkut's University of Technology North Bangkok. Rayong Campus, Rayong 21120, Thailand. Tel./fax.: +66-38-627000 ext. 5400, email: [email protected] Manuscript received: 1 April 2020. Revision accepted: 6 June 2020. Abstract. Boontanom P, Chantarasiri A. 2020. Short Communication: Diversity of culturable epiphytic bacteria isolated from seagrass (Halodule uninervis) in Thailand and their preliminary antibacterial activity. Biodiversitas 21: 2907-2913. Epiphytic bacteria are symbiotic bacteria that live on the surface of seagrasses. This study presents the diversity of culturable epiphytic bacteria associated with the Kuicheai seagrass (H. uninervis) collected from Rayong Province in Eastern Thailand. Nine epiphytic isolates were identified into four phylogenetical genera based on their 16S rRNA nucleotide sequence analyses. They are considered firmicutes in the genera of Planomicrobium, Paenibacillus and Bacillus, and proteobacteria in the genus of Oceanimonas. Three species of epiphytic bacteria preliminarily exhibited antibacterial activity against the human pathogenic Staphylococcus aureus using the perpendicular streak method. The knowledge obtained from this study increases understanding of the diversity of seagrass-associated bacteria in Thailand and suggests the utilization of these bacteria for further pharmaceutical applications. Keywords: Diversity, epiphytic bacteria, Halodule uninervis, perpendicular streak, seagrass INTRODUCTION of plants, while endophytic bacteria live inside the plants but have no visibly harmful effects (Tarquinio et al. -
Diversity and DMS(P)-Related Genes in Culturable Bacterial Communities in Malaysian Coastal Waters
Sains Malaysiana 45(6)(2016): 915–931 Diversity and DMS(P)-related Genes in Culturable Bacterial Communities in Malaysian Coastal Waters (Kepelbagaian dan Gen berkaitan-DMS(P) dalam Komuniti Kultur Bakteria di Perairan Pantai Malaysia) FELICITY W.I. KUEK*, AAZANI MUJAHID, PO-TEEN LIM, CHUI-PIN LEAW & MORITZ MÜLLER ABSTRACT Little is known about the diversity and roles of microbial communities in the South China Sea, especially the eastern region. This study aimed to expand our knowledge on the diversity of these communities in Malaysian waters, as well as their potential involvement in the breakdown or osmoregulation of dimethylsulphoniopropionate (DMSP). Water samples were collected during local cruises (Kuching, Kota Kinabalu, and Semporna) from the SHIVA expedition and the diversity of bacterial communities were analysed through the isolation and identification of 176 strains of cultured bacteria. The bacteria were further screened for the existence of two key genes (dmdA, dddP) which were involved in competing, enzymatically-mediated DMSP degradation pathways. The composition of bacterial communities in the three areas varied and changes were mirrored in physico-chemical parameters. Riverine input was highest in Kuching, which was mirrored by dominance of potentially pathogenic Vibrio sp., whereas the Kota Kinabalu community was more indicative of an open ocean environment. Isolates obtained from Kota Kinabalu and Semporna showed that the communities in these areas have potential roles in bioremediation, nitrogen fixing and sulphate reduction. Bacteria isolated from Kuching displayed the highest abundance (44%) of both DMSP-degrading genes, while the bacterial community in Kota Kinabalu had the highest percentage (28%) of dmdA gene occurrence and the dddP gene responsible for DMS production was most abundant (33%) within the community in Semporna. -
A Bacteria-Plant Model System to Study Nitrogen Fixation in Mangrove Ecosystems
A Bacteria-Plant Model System to Study Nitrogen Fixation in Mangrove Ecosystems by Gabriela Alfaro-Espinoza A Thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Marine Microbiology Approved Dissertation Committee Prof. Dr. Matthias Ullrich Jacobs University Bremen Prof. Dr. Frank Oliver Glöckner Jacobs University Bremen Prof. Dr. Jens Harder Max Planck Institute for Marine Microbiology PD Dr. Tim Jennerjahn Leibniz Center for Tropical Marine Ecology Date of Defense: November 25, 2014 Abstract Abstract Mangrove ecosystems are highly productive and rich in organic matter. However, they are considered low-nutrient environments, being nitrogen one of the main nutrients limiting mangrove growth. Nitrogen-fixing bacteria are one of the main inputs of nitrogen to these forests. High nitrogen fixation rates have been detected in mangrove sediments and roots. Moreover, studies indicated that the relationship between diazotrophs and mangroves might be mutualistic. Several diazotrophs from mangrove roots and the associated rhizosphere have been isolated or identify by phylogenetic studies of the nitrogenase-coding nifH gene. However, our knowledge about the molecular signals and cellular mechanisms that govern diazotroph-mangrove interactions is scarce. Thus, in this thesis a diazotroph-mangrove model system was established to better understand the importance of this interaction for the ecosystem and how environmental changes could impact this organismal interplay. For this, nitrogen-fixing bacteria were isolated from mangrove roots. Moreover, root colonization pattern of the selected nitrogen fixer and the impact of some of the environmental factors that could affect its nitrogen fixation were investigated. The first result showed that the diazotroph M. -
Comparative Genome Analysis of Oceanimonas Sp. GK1, a Halotolerant Bacterium with Considerable Xenobiotics Degradation Potentials
Ann Microbiol (2016) 66:703–716 DOI 10.1007/s13213-015-1156-4 ORIGINAL ARTICLE Comparative genome analysis of Oceanimonas sp. GK1, a halotolerant bacterium with considerable xenobiotics degradation potentials Reza Azarbaijani1 & Laleh Parsa Yeganeh1 & Jochen Blom2 & Habibollah Younesi3 & Seyyed Abolhassan Shahzadeh Fazeli1,4 & Meisam Tabatabaei1,5,6 & Ghasem Hosseini Salekdeh1,5,7 Received: 10 January 2015 /Accepted: 14 September 2015 /Published online: 2 October 2015 # Springer-Verlag Berlin Heidelberg and the University of Milan 2015 Abstract The growing pollution by xenobiotic compounds utilizes phenol via the ortho-cleavage pathway as a carbon generated through both natural and anthropogenic activities source in the citrate cycle. This was further confirmed by the has endangered the environment. The advent of the next gen- significant shortage of carbohydrate active enzymes in eration sequencing has provided fast and cost-effective tools Oceanimonas sp. GK1 genome, which has forced this bacte- to explore genomes to discover novel xenobiotic-degrading rium during the course of evolution to change its metabolism genes. A Gram-negative marine halotolerant Oceanimonas and physiology to benefit unusual carbon and energy sources sp. GK1 was analyzed for main physiological and genetically to survive under harsh conditions. important characteristics at the genome scale while being compared with six other phylogenetically-close sequenced ge- Keywords Xenobiotic pollution . Next generation nomes. This exploration revealed high potential of sequencing . Genome annotation . Comparative study . Oceanimonas sp. GK1 for biodegradation of xenobiotics Halotolerant compounds such as phenol. More specifically, the isolate Reza Azarbaijani and Laleh Parsa Yeganeh contributed equally to this Introduction work. * Ghasem Hosseini Salekdeh The increasing level of environmental pollution is among the [email protected] most catastrophic tragedies of the modern era which in turn has negatively impacted life quality in major parts of the world (Sekoai and Daramola 2015). -
Review Article Emerging Aeromonas Species Infections and Their Significance in Public Health
The Scientific World Journal Volume 2012, Article ID 625023, 13 pages The cientificWorldJOURNAL doi:10.1100/2012/625023 Review Article Emerging Aeromonas Species Infections and Their Significance in Public Health Isoken H. Igbinosa,1 Ehimario U. Igumbor,2 Farhad Aghdasi,3 Mvuyo Tom,1 and Anthony I. Okoh1 1 Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa 2 School of Public Health, University of the Western Cape, Bellville 7535, Cape Town, South Africa 3 Risk and Vulnerability Assessment Centre, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa Correspondence should be addressed to Anthony I. Okoh, [email protected] Received 29 February 2012; Accepted 20 March 2012 Academic Editors: P. Cos, M. Fernandez, and K. Hong Copyright © 2012 Isoken H. Igbinosa et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Aeromonas species are ubiquitous bacteria in terrestrial and aquatic milieus. They are becoming renowned as enteric pathogens of serious public health concern as they acquire a number of virulence determinants that are linked with human diseases, such as gastroenteritis, soft-tissue, muscle infections, septicemia, and skin diseases. Proper sanitary procedures are essential in the prevention of the spread of Aeromonas infections. Oral fluid electrolyte substitution is employed in the prevention of dehydration, and broad-spectrum antibiotics are used in severe Aeromonas outbreaks. This review presents an overview of emerging Aeromonas infections and proposes the need for actions necessary for establishing adequate prevention measures against the infections.