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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. -
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. -
Hydrocarbon Pollutants Shape Bacterial Community Assembly of Harbor Sediments
Hydrocarbon pollutants shape bacterial community assembly of harbor sediments Item Type Article Authors Barbato, Marta; Mapelli, Francesca; Magagnini, Mirko; Chouaia, Bessem; Armeni, Monica; Marasco, Ramona; Crotti, Elena; Daffonchio, Daniele; Borin, Sara Citation Hydrocarbon pollutants shape bacterial community assembly of harbor sediments 2016 Marine Pollution Bulletin Eprint version Post-print DOI 10.1016/j.marpolbul.2016.01.029 Publisher Elsevier BV Journal Marine Pollution Bulletin Rights NOTICE: this is the author’s version of a work that was accepted for publication in Marine Pollution Bulletin. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Marine Pollution Bulletin, 2 February 2016. DOI: 10.1016/ j.marpolbul.2016.01.029 Download date 25/09/2021 06:13:34 Link to Item http://hdl.handle.net/10754/597022 Hydrocarbon pollutants shape bacterial community assembly of harbor sediments Marta Barbato1§, Francesca Mapelli1§, Mirko Magagnini2, Bessem Chouaia1,a, Monica Armeni2, Ramona Marasco3, Elena Crotti1, Daniele Daffonchio1,3, Sara Borin1* 1Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy 2 EcoTechSystems Ltd., Ancona, Italy. 3 Biological and Environmental Sciences and Engineering Division (BESE). King Abdullah -
Supplementary Materials
Supplementary Materials Supporting methods Sequence comparison to DNA isolation kit blank and drilling fluid (For Costa Rica sediment samples) Because DNA concentrations were very low in many of the sediment samples, and PCR tests indicated that in a few of the samples, if present at all, DNA may not be in high enough amounts to overcome the “background” DNA from the DNA extraction kits, a representative DNA extraction kit blank was sequenced along with all other samples. To remove any signal from the extraction kit in all samples, as well as to remove any samples whose genuine DNA was not in high enough abundance to overcome the extraction kit background, sequence results from the SILVA pipeline were processed initially as follows: 1. Classification of reads was examined at the “fully expanded” taxonomic depth from the SILVA pipeline output, and all lineages present in the extraction blank in any amount were flagged. 2. To account for sequencing error in classification, further lineages were added to the flagged ones by going up in taxonomic level to “order” and flagging every sequence identified as being from the same order as any sequence present in the extraction blank. There were a few cases where the taxonomy of sequences in the extraction blank did not go down as far as the level of "order", and for those, the most specific level identified above order was used to assess any further matches. For example, if the sequence was classified down to "class," then any remaining sequences in that class would also be removed. Those cases -
Science Manuscript Template
bioRxiv preprint doi: https://doi.org/10.1101/2021.08.28.458008; this version posted August 29, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Title: Dual avatars of E. coli grxB encoded Glutaredoxin 2 perform ascorbate recycling and ion 2 channel activities 3 4 Authors 5 Sreeshma Nellootil Sreekumar1,2†, Bhaba Krishna Das1†, Rahul Raina1†, Neethu 6 Puthumadathil3, Sonakshi Udinia4, Amit Kumar1, Sibasis Sahoo1, Pooja Ravichandran1, 7 Suman Kumar5, Pratima Ray2, Dhiraj Kumar4, Anmol Chandele5, Kozhinjampara R. 8 Mahendran3, Arulandu Arockiasamy1* 9 10 11 Affiliations 12 1 Membrane Protein Biology Group, International Centre for Genetic Engineering and 13 Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067. India. 14 15 2 Department of Biotechnology, Jamia Hamdard University, New Delhi 110062. India. 16 17 3Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre 18 for Biotechnology, Thiruvananthapuram 695014, India. 19 20 4 Cellular Immunology Group, International Centre for Genetic Engineering and 21 Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067. India. 22 5 23 ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and 24 Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067. India. 25 26 †these authors contributed equally to this work 27 *Correspondence should be addressed to [email protected] 28 29 Correspondence: 30 Arockiasamy Arulandu 31 Membrane Protein Biology Group, 32 International Centre for Genetic Engineering and Biotechnology, 33 Aruna Asaf Ali Marg, 34 New Delhi-110067. -
Analysis of Zobellella Denitrificans ZD1 Draft Genome
RESEARCH ARTICLE Analysis of Zobellella denitrificans ZD1 draft genome: Genes and gene clusters responsible for high polyhydroxybutyrate (PHB) production from glycerol under saline conditions and its CRISPR-Cas system 1,2 3 3 3 Yu-Wei WuID *, Shih-Hung Yang , Myung Hwangbo , Kung-Hui Chu * 1 Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical a1111111111 University, Taipei, Taiwan, 2 Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, a1111111111 Taiwan, 3 Zachry Department of Civil and Environmental Engineering, Texas A&M University, College a1111111111 Station, TX, United States of America a1111111111 a1111111111 * [email protected] (YWW); [email protected] (KHC) Abstract OPEN ACCESS Polyhydroxybutyrate (PHB) is biodegradable and renewable and thus considered as a Citation: Wu Y-W, Yang S-H, Hwangbo M, Chu K- promising alternative to petroleum-based plastics. However, PHB production is costly due H (2019) Analysis of Zobellella denitrificans ZD1 to expensive carbon sources for culturing PHB-accumulating microorganisms under sterile draft genome: Genes and gene clusters responsible conditions. We discovered a hyper PHB-accumulating denitrifying bacterium, Zobellella for high polyhydroxybutyrate (PHB) production denitrificans ZD1 (referred as strain ZD1 hereafter) capable of using non-sterile crude glyc- from glycerol under saline conditions and its CRISPR-Cas system. PLoS ONE 14(9): e0222143. erol (a waste from biodiesel production) and nitrate to produce high PHB yield under saline https://doi.org/10.1371/journal.pone.0222143 conditions. Nevertheless, the underlying genetic mechanisms of PHB production in strain Editor: Chih-Horng Kuo, Academia Sinica, TAIWAN ZD1 have not been elucidated. -
Downloaded from Genbank in May 2018
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.13.249359; this version posted August 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Evolution of Chi motifs in Proteobacteria 2 3 Angélique Buton & Louis-Marie Bobay* 4 5 Department of Biology, University of North Carolina Greensboro, 321 McIver Street, PO Box 6 26170, Greensboro, NC 27402, USA 7 8 * To whom correspondence should be addressed 9 10 11 Contact information 12 Louis-Marie Bobay 13 321 McIver Street 14 Greensboro, NC 27402, USA 15 Email address: [email protected] 16 Phone: 336-256-2590 17 18 Keywords: homologous recombination, bacteria, genome evolution, DNA motifs. 19 20 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.13.249359; this version posted August 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 21 Abstract 22 Homologous recombination is a key pathway found in nearly all bacterial taxa. The 23 recombination complex allows bacteria to repair DNA double strand breaks but also promotes 24 adaption through the exchange of DNA between cells. In Proteobacteria, this process is 25 mediated by the RecBCD complex, which relies on the recognition of a DNA motif named Chi 26 to initiate recombination. -
Structural and Serological Studies of the O6-Related Antigen of Aeromonas Veronii Bv. Sobria Strain K557 Isolated from Cyprinus
Article Structural and Serological Studies of the O6-Related Antigen of Aeromonas veronii bv. sobria Strain K557 Isolated from Cyprinus carpio on a Polish Fish Farm, which Contains L-perosamine (4-amino-4,6-dideoxy-L-mannose), a Unique Sugar Characteristic for Aeromonas Serogroup O6 Katarzyna Dworaczek 1, Dominika Drzewiecka 2, Agnieszka Pękala-Safińska 3 and Anna Turska-Szewczuk 1,* 1 Department of Genetics and Microbiology, Maria Curie-Skłodowska University in Lublin, Akademicka 19, 20-033 Lublin, Poland 2 Laboratory of General Microbiology, Department of Biology of Bacteria, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland 3 Department of Fish Diseases, National Veterinary Research Institute, Partyzantów 57, 24-100 Puławy, Poland * Correspondence: [email protected]; Tel.: +48-81-537-50-18; Fax: +48-81-537-59-59 Received: 10 June 2019; Accepted: 3 July 2019; Published: 5 July 2019 Abstract: Amongst Aeromonas spp. strains that are pathogenic to fish in Polish aquacultures, serogroup O6 was one of the five most commonly identified immunotypes especially among carp isolates. Here, we report immunochemical studies of the lipopolysaccharide (LPS) including the O- specific polysaccharide (O-antigen) of A. veronii bv. sobria strain K557, serogroup O6, isolated from a common carp during an outbreak of motile aeromonad septicemia (MAS) on a Polish fish farm. The O-polysaccharide was obtained by mild acid degradation of the LPS and studied by chemical analyses, mass spectrometry, and 1H and 13C NMR spectroscopy. It was revealed that the O-antigen was composed of two O-polysaccharides, both containing a unique sugar 4-amino-4,6-dideoxy-L- mannose (N-acetyl-L-perosamine, L-Rhap4NAc). -
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Microbial Structure and Function of Engineered Biological Nitrogen Transformation Processes: Impacts of Aeration and Organic Carbon on Process Performance and Emissions of Nitrogenous Greenhouse Gas Ariane Coelho Brotto Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2016 © 2016 Ariane Coelho Brotto All rights reserved ABSTRACT Microbial Structure and Function of Engineered Biological Nitrogen Transformation Processes: Impacts of Aeration and Organic Carbon on Process Performance and Emissions of Nitrogenous Greenhouse Gas Ariane Coelho Brotto This doctoral research provides an advanced molecular approach for the investigation of microbial structure and function in response to operational conditions of biological nitrogen removal (BNR) processes, including those leading to direct production of a major greenhouse gas, nitrous oxide (N2O). The wastewater treatment sector is estimated to account with 3% of total anthropogenic N2O emissions [1]. Nevertheless, the contribution from wastewater treatment plants (WWTPs) is considered underestimated due to several limitations on the estimation methodology approach suggested by the Intergovernmental Panel on Climate Change (IPCC)[2]. Although for the past years efforts have been made to characterize the production of N2O from these systems, there are still several limitations on fundamental knowledge and operational applications. Those include lack of information of N2O production pathways associated with control of aeration, supplemental organic carbon sources and adaptation of the microbial community to the repeated operational conditions, among others. The components of this thesis, lab-scale investigations and full-scale monitoring of N2O production pathways and emissions in conjunction with meta-omics approach, have a combined role in addressing such limitations. -
Archive of SID
Archive of SID 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.