Phylogenetic Diversity and Activity Screening of Cultivable Actinobacteria Isolated
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Corynebacterium Sp.|NML98-0116
1 Limnochorda_pilosa~GCF_001544015.1@NZ_AP014924=Bacteria-Firmicutes-Limnochordia-Limnochordales-Limnochordaceae-Limnochorda-Limnochorda_pilosa 0,9635 Ammonifex_degensii|KC4~GCF_000024605.1@NC_013385=Bacteria-Firmicutes-Clostridia-Thermoanaerobacterales-Thermoanaerobacteraceae-Ammonifex-Ammonifex_degensii 0,985 Symbiobacterium_thermophilum|IAM14863~GCF_000009905.1@NC_006177=Bacteria-Firmicutes-Clostridia-Clostridiales-Symbiobacteriaceae-Symbiobacterium-Symbiobacterium_thermophilum Varibaculum_timonense~GCF_900169515.1@NZ_LT827020=Bacteria-Actinobacteria-Actinobacteria-Actinomycetales-Actinomycetaceae-Varibaculum-Varibaculum_timonense 1 Rubrobacter_aplysinae~GCF_001029505.1@NZ_LEKH01000003=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_aplysinae 0,975 Rubrobacter_xylanophilus|DSM9941~GCF_000014185.1@NC_008148=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_xylanophilus 1 Rubrobacter_radiotolerans~GCF_000661895.1@NZ_CP007514=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_radiotolerans Actinobacteria_bacterium_rbg_16_64_13~GCA_001768675.1@MELN01000053=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_rbg_16_64_13 1 Actinobacteria_bacterium_13_2_20cm_68_14~GCA_001914705.1@MNDB01000040=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_13_2_20cm_68_14 1 0,9803 Thermoleophilum_album~GCF_900108055.1@NZ_FNWJ01000001=Bacteria-Actinobacteria-Thermoleophilia-Thermoleophilales-Thermoleophilaceae-Thermoleophilum-Thermoleophilum_album -
Diversity of Micromonospora Strains from the Deep Mediterranean Sea and Their Potential to Produce Bioactive Compounds
AIMS Microbiology, 2(2): 205-221. DOI: 10.3934/microbiol.2016.2.205 Received: 15 February 2016 Accepted: 06 June 2016 Published: 14 June 2016 http://www.aimspress.com/journal/microbiology Research article Diversity of Micromonospora strains from the deep Mediterranean Sea and their potential to produce bioactive compounds Andrea Gärtner 1, Jutta Wiese 1, and Johannes F. Imhoff 1,2,* 1 GEOMAR Helmholtz Center for Ocean Research Kiel, RD3 Marine Microbiology, 24105 Kiel, Germany 2 Christian-Albrechts University of Kiel, 24118 Kiel Germany * Correspondence: Email: [email protected]; Tel: +49-431-600-4450; Fax: +49-431-600-4482. Abstract: During studies on bacteria from the Eastern Mediterranean deep-sea, incubation under in situ conditions (salinity, temperature and pressure) and heat treatment were used to selectively enrich representatives of Micromonospora. From sediments of the Ierapetra Basin (4400 m depth) and the Herodotos Plain (2800 m depth), 21 isolates were identified as members of the genus Micromonospora. According to phylogenetic analysis of 16S rRNA gene sequences, the Micromonospora isolates could be assigned to 14 different phylotypes with an exclusion limit of ≥ 99.5% sequence similarity. They formed 7 phylogenetic clusters. Two of these clusters, which contain isolates obtained after enrichment under pressure incubation and phylogenetically are distinct from representative reference organism, could represent bacteria specifically adapted to the conditions in situ and to life in these deep-sea sediments. The majority of the Micromonospora isolates (90%) contained at least one gene cluster for biosynthesis of secondary metabolites for non-ribosomal polypeptides and polyketides (polyketide synthases type I and type II). The determination of biological activities of culture extracts revealed that almost half of the strains produced substances inhibitory to the growth of Gram-positive bacteria. -
Phenotypic and Microbial Influences on Dairy Heifer Fertility and Calf Gut Microbial Development
Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Animal Science, Dairy Rebecca R. Cockrum Kristy M. Daniels Alan Ealy Katharine F. Knowlton September 17, 2020 Blacksburg, VA Keywords: microbiome, fertility, inoculation Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens ABSTRACT (Academic) Pregnancy loss and calf death can cost dairy producers more than $230 million annually. While methods involving nutrition, climate, and health management to mitigate pregnancy loss and calf death have been developed, one potential influence that has not been well examined is the reproductive microbiome. I hypothesized that the microbiome of the reproductive tract would influence heifer fertility and calf gut microbial development. The objectives of this dissertation were: 1) to examine differences in phenotypes related to reproductive physiology in virgin Holstein heifers based on outcome of first insemination, 2) to characterize the uterine microbiome of virgin Holstein heifers before insemination and examine associations between uterine microbial composition and fertility related phenotypes, insemination outcome, and season of breeding, and 3) to characterize the various maternal and calf fecal microbiomes and predicted metagenomes during peri-partum and post-partum periods and examine the influence of the maternal microbiome on calf gut development during the pre-weaning phase. In the first experiment, virgin Holstein heifers (n = 52) were enrolled over 12 periods, on period per month. On -3 d before insemination, heifers were weighed and the uterus was flushed. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
Bioinformatic and Mutational Studies of Related Toxin–Antitoxin Pairs in M
Bioinformatic and mutational studies of related toxin–antitoxin pairs in M. tuberculosis predict and identify key functional residues Running title: Toxin-Antitoxin relationships in M.tuberculosis Himani Tandon1, Arun Sharma2, Saruchi Wadhwa2, Raghavan Varadarajan1, Ramandeep Singh2, Narayanaswamy Srinivasan1*, and Sankaran Sandhya1* 1Molecular Biophysics Unit, Indian Institute of Science, Bangalore- 560012, India. 2Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, PO Box # 4, Faridabad, Haryana- 121001, India. * To whom correspondence should be addressed. Sankaran Sandhya: Molecular Biophysics Unit, Indian Institute of Science, Bangalore- 560012; [email protected]; Tel: +918022932837; Fax: +918023600535. Correspondence may also be addressed to Narayanaswamy Srinivasan. Molecular Biophysics Unit, Indian Institute of Science, Bangalore- 560012; [email protected]; Tel: +918022932837; Fax: +918023600535. Keywords: Toxin-antitoxin, homology, paralogues, structure-function, Mycobacterium tuberculosis, genome analysis, bacteriostasis, VapBC, PIN domain, phylogeny, molecular modelling, protein evolution 1 S1. Trends observed in the distribution of homologues of M.tuberculosis TA systems within MTBC and conservation pattern of Rv0909-Rv0910 and Rv1546 in MTBC and other organisms. Ramage et. al, have earlier probed the spread of M.tuberculosis type II TA in 5 of the 10 genomes in the MTBC complex (1). In addition to these genomes, we have included the genomes of M.orygis, M.caprae and M.mungi that are now available since their study, for our analysis. A search of M.tuberculosis TA in MTBC revealed that not all TAs were found as a pair with the same confidence in M.mungi, M.orygis and M.canetti. -
Microbiology in Shale: Alternatives for Enhanced Gas Recovery
Graduate Theses, Dissertations, and Problem Reports 2015 Microbiology in Shale: Alternatives for Enhanced Gas Recovery Yael Tarlovsky Tucker Follow this and additional works at: https://researchrepository.wvu.edu/etd Recommended Citation Tucker, Yael Tarlovsky, "Microbiology in Shale: Alternatives for Enhanced Gas Recovery" (2015). Graduate Theses, Dissertations, and Problem Reports. 6834. https://researchrepository.wvu.edu/etd/6834 This Dissertation is protected by copyright and/or related rights. It has been brought to you by the The Research Repository @ WVU with permission from the rights-holder(s). You are free to use this Dissertation in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you must obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/ or on the work itself. This Dissertation has been accepted for inclusion in WVU Graduate Theses, Dissertations, and Problem Reports collection by an authorized administrator of The Research Repository @ WVU. For more information, please contact [email protected]. Microbiology in Shale: Alternatives for Enhanced Gas Recovery Yael Tarlovsky Tucker Dissertation submitted to the Davis College of Agriculture, Natural Resources and Design at West Virginia University in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Genetics and Developmental Biology Jianbo Yao, Ph.D., Chair James Kotcon, Ph.D. -
Accugenx-ID® Identification Report Guide Click to Learn More for Bacseq and Funits Interpretation
MICROBIAL SOLUTIONS AccuGENX-ID® Identification Report Guide Click to learn more for BacSeq and FunITS Interpretation Sample C2913343- 20190325011 has a closest match of Kytococcus sedentarius and links directly to it in the Neighbor Joining Tree. The sample and its closest match have 0.49% difference in sequence in the first 500 base-pair region of the 16S gene. The identification result is Kytococcus sedentarius, with a Species-level of confidence. Processing Lab: ® 614 Interchange Blvd Accugenix 1 Newark, DE 19711 2 www.criver.com/accugenix ® [email protected] AccuGENX-ID Report Phone +1.302.292.8888 NEW-SOP-00071 Customer: 3 Valued Customer Account: 7 110440 (ACC1) Address: 4 614 Interchange Blvd, Newark, DE, 19711, United States Accugenix® C# / Run Date: 5 C2913343-20190325011 / 2019-03-22 13:10:12 ID Request Form#: 8 100000 Customer Sample ID: 6 Sample ABC Due Date: 9 2019-03-25 10 AccuGENX-ID® Database Search Result - Bacterial Library Identification: 11 Kytococcus sedentarius Confidence Level: 12 Species Based on published literature, the above identified species has been described as a Gram-positive, cocci-shaped bacterium. Click HERE for more 13 information on this organism. Neighbor Joining Tree 15 C2913343-20180117011 14 16 Kytococcus sedentarius [0.49%] Kytococcus schroeteri [1.18%] Kytococcus aerolatus [1.58%] Sediminivirga luteola [6.90%] Serinicoccus profundi [4.95%] Serinicoccus chungangensis [5.72%] Serinicoccus marinus [6.90%] Ornithinimicrobium tianjinense [6.51%] Dermacoccus abyssi [5.33%] Dermacoccus barathri -
Phylogenetic Diversity of Gram-Positive Bacteria and Their Secondary Metabolite Genes
UC San Diego Research Theses and Dissertations Title Phylogenetic Diversity of Gram-positive Bacteria and Their Secondary Metabolite Genes Permalink https://escholarship.org/uc/item/06z0868t Author Gontang, Erin A Publication Date 2008 Peer reviewed eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Phylogenetic Diversity of Gram-positive Bacteria and Their Secondary Metabolite Genes A Dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Oceanography by Erin Ann Gontang Committee in charge: William Fenical, Chair Douglas H. Bartlett Bianca Brahamsha William Gerwick Paul R. Jensen Kit Pogliano 2008 3324374 3324374 2008 The Dissertation of Erin Ann Gontang is approved, and it is acceptable in quality and form for publication on microfilm: ____________________________________ ____________________________________ ____________________________________ ____________________________________ ____________________________________ ____________________________________ Chair University of California, San Diego 2008 iii DEDICATION To John R. Taylor, my incredible partner, my best friend and my love. ***** To my mom, Janet M. Gontang, and my dad, Austin J. Gontang. Your generous support and unconditional love has allowed me to create my future. Thank you. ***** To my sister, Allison C. Gontang, who is as proud of me as I am of her. You are a constant source of inspiration and I am so fortunate to have you in my life. iv TABLE OF CONTENTS -
Report on 31 Unrecorded Bacterial Species in Korea That Belong to the Phylum Actinobacteria
Journal of Species Research 5(1):113, 2016 Report on 31 unrecorded bacterial species in Korea that belong to the phylum Actinobacteria JungHye Choi1, JuHee Cha1, JinWoo Bae2, JangCheon Cho3, Jongsik Chun4, WanTaek Im5, Kwang Yeop Jahng6, Che Ok Jeon7, Kiseong Joh8, Seung Bum Kim9, Chi Nam Seong10, JungHoon Yoon11 and ChangJun Cha1,* 1Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Korea 2Department of Biology, Kyung Hee University, Seoul 02447, Korea 3Department of Biological Sciences, Inha University, Incheon 22212, Korea 4School of Biological Sciences, Seoul National University, Seoul 08826, Korea 5Department of Biotechnology, Hankyong National University, Anseong 17579, Korea 6Department of Life Sciences, Chonbuk National University, Jeonju-si 54896, Korea 7Department of Life Science, Chung-Ang University, Seoul 06974, Korea 8Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Korea 9Department of Microbiology, Chungnam National University, Daejeon 34134, Korea 10Department of Biology, Sunchon National University, Suncheon 57922, Korea 11Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon 16419, Korea *Correspondent: [email protected] To discover and characterize indigenous species in Korea, a total of 31 bacterial strains that belong to the phylum Actinobacteria were isolated from various niches in Korea. Each strain showed the high sequence similarity (>99.1%) with the closest bacterial species, forming a robust phylogenetic clade. These strains have not been previously recorded in Korea. According to the recently updated taxonomy of the phylum Actinobacteria based upon 16S rRNA trees, we report 25 genera of 13 families within 5 orders of the class Actinobacteria as actinobacterial species found in Korea. -
Aquatic Microbial Ecology 52:1
Vol. 52: 1–11, 2008 AQUATIC MICROBIAL ECOLOGY Published online June 19, 2008 doi: 10.3354/ame01211 Aquat Microb Ecol Comparative actinomycete diversity in marine sediments Alejandra Prieto-Davó, William Fenical, Paul R. Jensen* Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093-0204, USA ABSTRACT: The diversity of cultured actinomycete bacteria was compared between near- and off- shore marine sediments. Strains were tested for the effects of seawater on growth and analyzed for 16S rRNA gene sequence diversity. In total, 623 strains representing 6 families in the order Actino- mycetales were cultured. These strains were binned into 16 to 63 operational taxonomic units (OTUs) over a range of 97 to 100% sequence identity. The majority of the OTUs were closely related (>98% sequence identity) to strains previously reported from non-marine sources, indicating that most are not restricted to the sea. However, new OTUs averaged 96.6% sequence identity with previously cul- tured strains and ca. one-third of the OTUs were marine-specific, suggesting that sediment commu- nities include considerable actinomycete diversity that does not occur on land. Marine specificity did not increase at the off-shore sites, indicating high levels of terrestrial influence out to 125 km from shore. The requirement of seawater for growth was observed among <6% of the strains, while all members of 9 OTUs possessed this trait, revealing a high degree of marine adaptation among some lineages. Statistical analyses predicted greater OTU diversity at the off-shore sites and provided a rationale for expanded exploration of deep-sea samples. -
UNIVERSITY of CALIFORNIA, SAN DIEGO Phylogenetic and Chemical
UNIVERSITY OF CALIFORNIA, SAN DIEGO Phylogenetic and Chemical Diversity of Marine-Derived Actinomycetes from Southern California Sediments A Dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Oceanography by Alejandra Prieto-Davó Committee in charge: William Fenical, Chair Lihini Aluwihare Douglas H. Bartlett Paul R. Jensen Brian Palenik Christopher Wills 2008 The Dissertation of Alejandra Prieto-Davó is approved, and it is acceptable in quality and form for publication on microfilm: ____________________________________ ____________________________________ ____________________________________ ____________________________________ ____________________________________ ____________________________________ Chair University of California, San Diego 2008 iii DEDICATION To my father, who I have admired throughout my life and who has always been an example of strength and perseverance. ***** To my mother, who has taught me that a woman’s place is not in the kitchen and who has always supported all my crazy dreams. ***** To my husband Luis Alfonso, for showing me that love has no borders. Te amo. iv TABLE OF CONTENTS Signature Page………………………………………………………………….…..iii Dedication……………………………………………………………………….….iv Table of Contents……………………………………………………………………v List of Figures ……………………………………………………………………..vii List of Tables………………………………………………………………………..ix Acknowledgements……………………………………………………...……….….x Vita………………………………………………………………………...…....…xiv Abstract………………………………………………...…………...………….…..xv Chapter 1: Introduction: -
1 Supplementary Material a Major Clade of Prokaryotes with Ancient
Supplementary Material A major clade of prokaryotes with ancient adaptations to life on land Fabia U. Battistuzzi and S. Blair Hedges Data assembly and phylogenetic analyses Protein data set: Amino acid sequences of 25 protein-coding genes (“proteins”) were concatenated in an alignment of 18,586 amino acid sites and 283 species. These proteins included: 15 ribosomal proteins (RPL1, 2, 3, 5, 6, 11, 13, 16; RPS2, 3, 4, 5, 7, 9, 11), four genes (RNA polymerase alpha, beta, and gamma subunits, Transcription antitermination factor NusG) from the functional category of Transcription, three proteins (Elongation factor G, Elongation factor Tu, Translation initiation factor IF2) of the Translation, Ribosomal Structure and Biogenesis functional category, one protein (DNA polymerase III, beta subunit) of the DNA Replication, Recombination and repair category, one protein (Preprotein translocase SecY) of the Cell Motility and Secretion category, and one protein (O-sialoglycoprotein endopeptidase) of the Posttranslational Modification, Protein Turnover, Chaperones category, as annotated in the Cluster of Orthologous Groups (COG) (Tatusov et al. 2001). After removal of multiple strains of the same species, GBlocks 0.91b (Castresana 2000) was applied to each protein in the concatenation to delete poorly aligned sites (i.e., sites with gaps in more than 50% of the species and conserved in less than 50% of the species) with the following parameters: minimum number of sequences for a conserved position: 110, minimum number of sequences for a flank position: 110, maximum number of contiguous non-conserved positions: 32000, allowed gap positions: with half. The signal-to-noise ratio was determined by altering the “minimum length of a block” parameter.