Genome-Based Taxonomic Classification of Bacteroidetes
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Table S1. Bacterial Otus from 16S Rrna
Table S1. Bacterial OTUs from 16S rRNA sequencing analysis including only taxa which were identified to genus level (those OTUs identified as Ambiguous taxa, uncultured bacteria or without genus-level identifications were omitted). OTUs with only a single representative across all samples were also omitted. Taxa are listed from most to least abundant. Pitcher Plant Sample Class Order Family Genus CB1p1 CB1p2 CB1p3 CB1p4 CB5p234 Sp3p2 Sp3p4 Sp3p5 Sp5p23 Sp9p234 sum Gammaproteobacteria Legionellales Coxiellaceae Rickettsiella 1 2 0 1 2 3 60194 497 1038 2 61740 Alphaproteobacteria Rhodospirillales Rhodospirillaceae Azospirillum 686 527 10513 485 11 3 2 7 16494 8201 36929 Sphingobacteriia Sphingobacteriales Sphingobacteriaceae Pedobacter 455 302 873 103 16 19242 279 55 760 1077 23162 Betaproteobacteria Burkholderiales Oxalobacteraceae Duganella 9060 5734 2660 40 1357 280 117 29 129 35 19441 Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas 3336 1991 3475 1309 2819 233 1335 1666 3046 218 19428 Betaproteobacteria Burkholderiales Burkholderiaceae Paraburkholderia 0 1 0 1 16051 98 41 140 23 17 16372 Sphingobacteriia Sphingobacteriales Sphingobacteriaceae Mucilaginibacter 77 39 3123 20 2006 324 982 5764 408 21 12764 Gammaproteobacteria Pseudomonadales Moraxellaceae Alkanindiges 9 10 14 7 9632 6 79 518 1183 65 11523 Betaproteobacteria Neisseriales Neisseriaceae Aquitalea 0 0 0 0 1 1577 5715 1471 2141 177 11082 Flavobacteriia Flavobacteriales Flavobacteriaceae Flavobacterium 324 219 8432 533 24 123 7 15 111 324 10112 Alphaproteobacteria -
Xiexin Tang Improves the Symptom of Type 2 Diabetic Rats by Modulation of the Gut Microbiota
www.nature.com/scientificreports OPEN Xiexin Tang improves the symptom of type 2 diabetic rats by modulation of the gut microbiota Received: 30 August 2017 Xiaoyan Wei, Jinhua Tao , Suwei Xiao, Shu Jiang, Erxin Shang, Zhenhua Zhu, Dawei Qian Accepted: 13 February 2018 & Jinao Duan Published: xx xx xxxx Type 2 diabetes mellitus (T2DM), a chronic metabolic disease which severely impairs peoples’ quality of life, currently attracted worldwide concerns. There are growing evidences that gut microbiota can exert a great impact on the development of T2DM. Xiexin Tang (XXT), a traditional Chinese medicine prescription, has been clinically used to treat diabetes for thousands of years. However, few researches are investigated on the modulation of gut microbiota community by XXT which will be very helpful to unravel how it works. In this study, bacterial communities were analyzed based on high-throughput 16S rRNA gene sequencing. Results indicated that XXT could notably shape the gut microbiota. T2DM rats treated with XXT exhibited obvious changes in the composition of the gut microbiota, especially for some short chain fatty acids producing and anti-infammatory bacteria such as Adlercreutzia, Alloprevotella, Barnesiella, [Eubacterium] Ventriosum group, Blautia, Lachnospiraceae UCG-001, Papillibacter and Prevotellaceae NK3B31 group. Additionally, XXT could also signifcantly ameliorate hyperglycemia, lipid metabolism dysfunction and infammation in T2DM rats. Moreover, the correlation analysis illustrated that the key microbiota had a close relationship with the T2DM related indexes. The results probably provided useful information for further investigation on its active mechanism and clinical application. T2DM, a chronic metabolic disease characterized by hyperglycemia as a result of insufcient insulin secretion, insulin action or both1, is estimated that its numbers in the adults will increase by 55% by 20352. -
Acetobacteroides Hydrogenigenes Gen. Nov., Sp. Nov., an Anaerobic Hydrogen-Producing Bacterium in the Family Rikenellaceae Isolated from a Reed Swamp
%paper no. ije063917 charlesworth ref: ije063917& New Taxa - Bacteroidetes International Journal of Systematic and Evolutionary Microbiology (2014), 64, 000–000 DOI 10.1099/ijs.0.063917-0 Acetobacteroides hydrogenigenes gen. nov., sp. nov., an anaerobic hydrogen-producing bacterium in the family Rikenellaceae isolated from a reed swamp Xiao-Li Su,1,2 Qi Tian,1,3 Jie Zhang,1,2 Xian-Zheng Yuan,1 Xiao-Shuang Shi,1 Rong-Bo Guo1 and Yan-Ling Qiu1 Correspondence 1Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Yan-Ling Qiu Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China [email protected] 2University of Chinese Academy of Sciences, Beijing 100049, PR China 3Ocean University of China, Qingdao, 266101, PR China A strictly anaerobic, mesophilic, carbohydrate-fermenting, hydrogen-producing bacterium, designated strain RL-CT, was isolated from a reed swamp in China. Cells were Gram-stain- negative, catalase-negative, non-spore-forming, non-motile rods measuring 0.7–1.0 mm in width and 3.0–8.0 mm in length. The optimum temperature for growth of strain RL-CT was 37 6C (range 25–40 6C) and pH 7.0–7.5 (range pH 5.7–8.0). The strain could grow fermentatively on yeast extract, tryptone, arabinose, glucose, galactose, mannose, maltose, lactose, glycogen, pectin and starch. The main end products of glucose fermentation were acetate, H2 and CO2. Organic acids, alcohols and amino acids were not utilized for growth. Yeast extract was not required for growth; however, it stimulated growth slightly. Nitrate, sulfate, sulfite, thiosulfate, elemental sulfur and Fe(III) nitrilotriacetate were not reduced as terminal electron acceptors. -
WO 2018/064165 A2 (.Pdf)
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/064165 A2 05 April 2018 (05.04.2018) W !P O PCT (51) International Patent Classification: Published: A61K 35/74 (20 15.0 1) C12N 1/21 (2006 .01) — without international search report and to be republished (21) International Application Number: upon receipt of that report (Rule 48.2(g)) PCT/US2017/053717 — with sequence listing part of description (Rule 5.2(a)) (22) International Filing Date: 27 September 2017 (27.09.2017) (25) Filing Language: English (26) Publication Langi English (30) Priority Data: 62/400,372 27 September 2016 (27.09.2016) US 62/508,885 19 May 2017 (19.05.2017) US 62/557,566 12 September 2017 (12.09.2017) US (71) Applicant: BOARD OF REGENTS, THE UNIVERSI¬ TY OF TEXAS SYSTEM [US/US]; 210 West 7th St., Austin, TX 78701 (US). (72) Inventors: WARGO, Jennifer; 1814 Bissonnet St., Hous ton, TX 77005 (US). GOPALAKRISHNAN, Vanch- eswaran; 7900 Cambridge, Apt. 10-lb, Houston, TX 77054 (US). (74) Agent: BYRD, Marshall, P.; Parker Highlander PLLC, 1120 S. Capital Of Texas Highway, Bldg. One, Suite 200, Austin, TX 78746 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. -
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 -
Candidatus Prosiliicoccus Vernus, a Spring Phytoplankton Bloom
Systematic and Applied Microbiology 42 (2019) 41–53 Contents lists available at ScienceDirect Systematic and Applied Microbiology j ournal homepage: www.elsevier.de/syapm Candidatus Prosiliicoccus vernus, a spring phytoplankton bloom associated member of the Flavobacteriaceae ∗ T. Ben Francis, Karen Krüger, Bernhard M. Fuchs, Hanno Teeling, Rudolf I. Amann Max Planck Institute for Marine Microbiology, Bremen, Germany a r t i c l e i n f o a b s t r a c t Keywords: Microbial degradation of algal biomass following spring phytoplankton blooms has been characterised as Metagenome assembled genome a concerted effort among multiple clades of heterotrophic bacteria. Despite their significance to overall Helgoland carbon turnover, many of these clades have resisted cultivation. One clade known from 16S rRNA gene North Sea sequencing surveys at Helgoland in the North Sea, was formerly identified as belonging to the genus Laminarin Ulvibacter. This clade rapidly responds to algal blooms, transiently making up as much as 20% of the Flow cytometric sorting free-living bacterioplankton. Sequence similarity below 95% between the 16S rRNA genes of described Ulvibacter species and those from Helgoland suggest this is a novel genus. Analysis of 40 metagenome assembled genomes (MAGs) derived from samples collected during spring blooms at Helgoland support this conclusion. These MAGs represent three species, only one of which appears to bloom in response to phytoplankton. MAGs with estimated completeness greater than 90% could only be recovered for this abundant species. Additional, less complete, MAGs belonging to all three species were recovered from a mini-metagenome of cells sorted via flow cytometry using the genus specific ULV995 fluorescent rRNA probe. -
Distinct Microbial Assemblages Associated with Genetic Selection for High- and Low- Muscle Yield in Rainbow Trout
Distinct microbial assemblages associated with genetic selection for high- and low- muscle yield in rainbow trout Pratima Chapagain Middle Tennessee State University Donald Walker Middle Tennessee State University Tim Leeds USDA-ARS National Center for Cool and Cold Water Aquaculture Beth M Cleveland USDA-ARS National Center for Cool and Cold Water Aquaculture Mohamed Salem ( [email protected] ) Department of Animal and Avian Sciences, University of Maryland, college park https://orcid.org/0000- 0003-2142-6716 Research article Keywords: Aquaculture, Gut microbe function, Microbiota, Selective Breeding, Muscle yield, llet, ARS-FY- H, ARS-FY-L Posted Date: November 10th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-26816/v3 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published on November 23rd, 2020. See the published version at https://doi.org/10.1186/s12864-020-07204-7. Page 1/22 Abstract Background Fish gut microbial assemblages play a crucial role in the growth rate, metabolism, and immunity of the host. We hypothesized that the gut microbiota of rainbow trout was correlated with breeding program based genetic selection for muscle yield. To test this hypothesis, fecal samples from 19 sh representing an F2 high-muscle genetic line (ARS-FY-H) and 20 sh representing an F1 low-muscle yield genetic line (ARS-FY-L) were chosen for microbiota proling using the 16S rRNA gene. Signicant differences in microbial population between these two genetic lines might represent the effect of host genetic selection in structuring the gut microbiota of the host. -
Prokaryotic Community Structure and Respiration During Longterm
Prokaryotic community structure and respiration during long-term incubations Federico Baltar1, Markus V. Lindh1, Arkadi Parparov2, Tom Berman2 & Jarone Pinhassi1 1Marine Microbiology, School of Natural Sciences, Linnaeus University, Barlastgatan 11, SE-391 82, Kalmar, Sweden 2The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research IL-14102, Tiberias, Israel Keywords Abstract Bacterioplankton, biological oxygen demand, community composition, incubation, Despite the importance of incubation assays for studies in microbial ecology that fre- respiration. quently require long confinement times, few reports are available in which changes in the assemblage structure of aquatic prokaryotes were monitored during long- Correspondence term incubations. We measured rates of dissolved organic carbon degradation and Federico Baltar, Marine Microbiology, School of microbial respiration by consumption of dissolved oxygen (DO) in four experi- Natural Sciences, Linnaeus University, Barlastgatan 11, SE-391 82 Kalmar, Sweden. ments with Lake Kinneret near-surface water and, concomitantly, we analyzed the Tel: +46-480-447315; Fax: +46-480-447305; variability in prokaryotic community structure during long-term dark bottle incu- E-mail: [email protected] bations. During the first 24 h, there were only minor changes in bacterial community composition. Thereafter there were marked changes in the prokaryotic community Supported by the European Science Foundation EuroEEFG project MOCA, the structure during the incubations. In contrast, oxygen consumption rates (a proxy Crafoord Foundation, and the Swedish for both respiration and dissolved organic carbon degradation rates) remained sta- Research Council. ble for up to 10–23 days. This study is one of the first to examine closely the phylo- Received: 17 February 2012; Revised: 20 April genetic changes that occur in the microbial community of untreated freshwater 2012; Accepted: 23 April 2012 during long-term (days) incubations in dark, sealed containers. -
Penaeus Monodon
www.nature.com/scientificreports OPEN Bacterial analysis in the early developmental stages of the black tiger shrimp (Penaeus monodon) Pacharaporn Angthong1,3, Tanaporn Uengwetwanit1,3, Sopacha Arayamethakorn1, Panomkorn Chaitongsakul2, Nitsara Karoonuthaisiri1 & Wanilada Rungrassamee1* Microbial colonization is an essential process in the early life of animal hosts—a crucial phase that could help infuence and determine their health status at the later stages. The establishment of bacterial community in a host has been comprehensively studied in many animal models; however, knowledge on bacterial community associated with the early life stages of Penaeus monodon (the black tiger shrimp) is still limited. Here, we examined the bacterial community structures in four life stages (nauplius, zoea, mysis and postlarva) of two black tiger shrimp families using 16S rRNA amplicon sequencing by a next-generation sequencing. Although the bacterial profles exhibited diferent patterns in each developmental stage, Bacteroidetes, Proteobacteria, Actinobacteria and Planctomycetes were identifed as common bacterial phyla associated with shrimp. Interestingly, the bacterial diversity became relatively stable once shrimp developed to postlarvae (5-day-old and 15-day- old postlarval stages), suggesting an establishment of the bacterial community in matured shrimp. To our knowledge, this is the frst report on bacteria establishment and assembly in early developmental stages of P. monodon. Our fndings showed that the bacterial compositions could be shaped by diferent host developmental stages where the interplay of various host-associated factors, such as physiology, immune status and required diets, could have a strong infuence. Te shrimp aquaculture industry is one of the key sectors to supply food source to the world’s growing pop- ulation. -
OMICS Driven Microbial Ecology Hunt for a Core Microbiome
Environmental Microbiology, Volume 14, Issue 1, January 2012 VOLUME 14 NUMBER 1 JANUARY 2012 www.env-micro.com ISSN 1462-2912 Contents environmental microbiology Correspondence 140 Microbial rhodopsins on leaf surfaces of terrestrial plants N. Atamna-Ismaeel, O. M. Finkel, F. Glaser, I. Sharon, R. Schneider, 1 Omics for understanding microbial functional dynamics A. F. Post, J. L. Spudich, C. von Mering, J. A. Vorholt, D. Iluz, O. Béjà & J. K. Jansson, J. D. Neufeld, M. A. Moran & J. A. Gilbert S. Belkin 147 Photoautotrophic symbiont and geography are major factors affecting highly Minireviews structured and diverse bacterial communities in the lichen microbiome 4 Beyond the Venn diagram: the hunt for a core microbiome B. P. Hodkinson, N. R. Gottel, C. W. Schadt & F. Lutzoni A. Shade & J. Handelsman 162 Phosphate transporters in marine phytoplankton and their viruses: environmental cross-domain commonalities in viral-host gene exchanges 13 Targeted metagenomics: a high-resolution metagenomics approach for specifi c A. Monier, R. M. Welsh, C. Gentemann, G. Weinstock, E. Sodergren, gene clusters in complex microbial communities E. V. Armbrust, J. A. Eisen & A. Z. Worden H. Suenaga 177 Complete genome of Candidatus Chloracidobacterium thermophilum, a chlorophyll-based photoheterotroph belonging to the phylum Acidobacteria Research articles A. M. Garcia Costas, Z. Liu, L. P. Tomsho, S. C. Schuster, D. M. Ward & 23 Microbial metatranscriptomics in a permanent marine oxygen minimum zone D. A. Bryant F. J. Stewart, O. Ulloa & E. F. DeLong 191 Transcriptional responses of surface water marine microbial assemblages 41 Genome content of uncultivated marine Roseobacters in the surface ocean to deep-sea water amendment microbiology H. -
Life in the Cold Biosphere: the Ecology of Psychrophile
Life in the cold biosphere: The ecology of psychrophile communities, genomes, and genes Jeff Shovlowsky Bowman A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2014 Reading Committee: Jody W. Deming, Chair John A. Baross Virginia E. Armbrust Program Authorized to Offer Degree: School of Oceanography i © Copyright 2014 Jeff Shovlowsky Bowman ii Statement of Work This thesis includes previously published and submitted work (Chapters 2−4, Appendix 1). The concept for Chapter 3 and Appendix 1 came from a proposal by JWD to NSF PLR (0908724). The remaining chapters and appendices were conceived and designed by JSB. JSB performed the analysis and writing for all chapters with guidance and editing from JWD and co- authors as listed in the citation for each chapter (see individual chapters). iii Acknowledgements First and foremost I would like to thank Jody Deming for her patience and guidance through the many ups and downs of this dissertation, and all the opportunities for fieldwork and collaboration. The members of my committee, Drs. John Baross, Ginger Armbrust, Bob Morris, Seelye Martin, Julian Sachs, and Dale Winebrenner provided valuable additional guidance. The fieldwork described in Chapters 2, 3, and 4, and Appendices 1 and 2 would not have been possible without the help of dedicated guides and support staff. In particular I would like to thank Nok Asker and Lewis Brower for giving me a sample of their vast knowledge of sea ice and the polar environment, and the crew of the icebreaker Oden for a safe and fascinating voyage to the North Pole. -
Exploiting Marine Biodiversity the Potential Of
EXPLOITING MARINE BIODIVERSITY: THE POTENTIAL OF UNCULTIVABLE MICROORGANISMS FOR THE IDENTIFICATION OF NOVEL ANTIMICROBIAL COMPOUNDS Fortunato Palma Esposito Dottorato in Biotecnologie – XXX° ciclo Università di Napoli Federico II Dottorato in Biotecnologie – XXX° ciclo Università di Napoli Federico II EXPLOITING MARINE BIODIVERSITY: THE POTENTIAL OF UNCULTIVABLE MICROORGANISMS FOR THE IDENTIFICATION OF NOVEL ANTIMICROBIAL COMPOUNDS Fortunato Palma Esposito Dottorando: Fortunato Palma Esposito Relatore: Prof. Giovanni Sannia Correlatore: Dott. Donatella de Pascale Coordinatore: Prof. Giovanni Sannia “The important thing is not to stop questioning. Curiosity has its own reason for existence. One cannot help but be in awe when he contemplates the mysteries of eternity, of life, of the marvelous structure of reality. It is enough if one tries merely to comprehend a little of this mystery each day.” Albert Einstein INDEX Summary 1 Riassunto 3 General Introduction 9 1. The antibiotic resistance crisis 10 1.1 Mechanisms of Antibiotic resistance 13 2. Bioprospecting of natural products from marine an d extreme environments 15 2.1 Antarctic bacteria 16 2.2 Marine fungi 16 3. Microbial uncultivability 17 4. The unexpressed potential of genome 18 5. Marine Biotechnology 19 6. Aim of the project 19 7. References 20 Chapter 1. Bacteria from the extreme: a source of antimicrobial compounds 25 Abstract 27 1.1 Introduction 27 1.2 Materials and methods 28 1.3 Results 31 1.4 Discussion 38 1.5 References 40 1.6 Supplementary materials 43 Chapter 2. Isolation of an Antarctic bacterium Aequorivita sp. by Miniaturized Culture Chip as a producer of novel bioactive compounds 47 Abstract 49 2.1 Introduction 49 2.2 Materials and methods 50 2.3 Results 53 2.4 Discussion 61 2.5 References 64 2.6 Supplementary materials 67 Chapter 3.