Thitiwut Vongkampang WEBB
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Genomics 98 (2011) 370–375
Genomics 98 (2011) 370–375 Contents lists available at ScienceDirect Genomics journal homepage: www.elsevier.com/locate/ygeno Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae Hiromi Nishida a,⁎, Teruhiko Beppu b, Kenji Ueda b a Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan b Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, Japan article info abstract Article history: The anaerobic thermophilic bacterial genus Dictyoglomus is characterized by the ability to produce useful Received 2 June 2011 enzymes such as amylase, mannanase, and xylanase. Despite the significance, the phylogenetic position of Accepted 1 August 2011 Dictyoglomus has not yet been clarified, since it exhibits ambiguous phylogenetic positions in a single gene Available online 7 August 2011 sequence comparison-based analysis. The number of substitutions at the diverging point of Dictyoglomus is insufficient to show the relationships in a single gene comparison-based analysis. Hence, we studied its Keywords: evolutionary trait based on whole-genome comparison. Both gene content and orthologous protein sequence Whole-genome comparison Dictyoglomus comparisons indicated that Dictyoglomus is most closely related to the phylum Thermotogae and it forms a Bacterial systematics monophyletic group with Coprothermobacter proteolyticus (a constituent of the phylum Firmicutes) and Coprothermobacter proteolyticus Thermotogae. Our findings indicate that C. proteolyticus does not belong to the phylum Firmicutes and that the Thermotogae phylum Dictyoglomi is not closely related to either the phylum Firmicutes or Synergistetes but to the phylum Thermotogae. © 2011 Elsevier Inc. -
Online Supplementary Figures of Chapter 3
Online Supplementary Figures of Chapter 3 Fabio Gori Figures 1-30 contain pie charts showing the population characterization re- sulting from the taxonomic assignment computed by the methods. On the simulated datasets the true population distribution is also shown. 1 MTR Bacillales (47.11%) Thermoanaerobacterales (0.76%) Clostridiales (33.58%) Lactobacillales (7.99%) Others (10.55%) LCA Bacillales (48.38%) Thermoanaerobacterales (0.57%) Clostridiales (32.14%) Lactobacillales (10.07%) Others (8.84%) True Distribution 333 386 Prochlorales (5.84%) 535 Bacillales (34.61%) Halanaerobiales (4.37%) Thermoanaerobacterales (10.29%) Clostridiales (28.75%) Lactobacillales (9.38%) 1974 Herpetosiphonales (6.77%) 1640 249 587 Figure 1: Population distributions (rank Order) of M1, coverage 0.1x, by MTR and LCA, and the true population distribution. 2 MTR Bacillus (47.34%) Clostridium (14.61%) Lactobacillus (8.71%) Anaerocellum (11.41%) Alkaliphilus (5.14%) Others (12.79%) LCA Bacillus (51.41%) Clostridium (8.08%) Lactobacillus (9.23%) Anaerocellum (15.79%) Alkaliphilus (5.17%) Others (10.31%) True Distribution 386 552 Herpetosiphon (6.77%) 333 Prochlorococcus (5.84%) 587 Bacillus (34.61%) Clostridium (19.07%) Lactobacillus (9.38%) 249 Halothermothrix (4.37%) Caldicellulosiruptor (10.29%) Alkaliphilus (9.68%) 535 1974 1088 Figure 2: Population distributions (rank Genus) of M1, coverage 0.1x, by MTR and LCA, and the true population distribution. 3 MTR Prochlorales (0.07%) Bacillales (47.97%) Thermoanaerobacterales (0.66%) Clostridiales (32.18%) Lactobacillales (7.76%) Others (11.35%) LCA Prochlorales (0.10%) Bacillales (49.02%) Thermoanaerobacterales (0.59%) Clostridiales (30.62%) Lactobacillales (9.50%) Others (10.16%) True Distribution 3293 3950 Prochlorales (5.65%) 5263 Bacillales (36.68%) Halanaerobiales (3.98%) Thermoanaerobacterales (10.56%) Clostridiales (27.34%) Lactobacillales (9.03%) 21382 Herpetosiphonales (6.78%) 15936 2320 6154 Figure 3: Population distributions (rank Order) of M1, coverage 1x, by MTR and LCA, and the true population distribution. -
Sporulation Evolution and Specialization in Bacillus
bioRxiv preprint doi: https://doi.org/10.1101/473793; this version posted March 11, 2019. 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 4.0 International license. Research article From root to tips: sporulation evolution and specialization in Bacillus subtilis and the intestinal pathogen Clostridioides difficile Paula Ramos-Silva1*, Mónica Serrano2, Adriano O. Henriques2 1Instituto Gulbenkian de Ciência, Oeiras, Portugal 2Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal *Corresponding author: Present address: Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands Phone: 0031 717519283 Email: [email protected] (Paula Ramos-Silva) Running title: Sporulation from root to tips Keywords: sporulation, bacterial genome evolution, horizontal gene transfer, taxon- specific genes, Bacillus subtilis, Clostridioides difficile 1 bioRxiv preprint doi: https://doi.org/10.1101/473793; this version posted March 11, 2019. 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 4.0 International license. Abstract Bacteria of the Firmicutes phylum are able to enter a developmental pathway that culminates with the formation of a highly resistant, dormant spore. Spores allow environmental persistence, dissemination and for pathogens, are infection vehicles. In both the model Bacillus subtilis, an aerobic species, and in the intestinal pathogen Clostridioides difficile, an obligate anaerobe, sporulation mobilizes hundreds of genes. -
Evidence of Horizontal Gene Transfer by Transposase Gene Analyses in Fervidobacterium Species
RESEARCH ARTICLE Evidence of horizontal gene transfer by transposase gene analyses in Fervidobacterium species Alba Cuecas1, Wirojne Kanoksilapatham2, Juan M. Gonzalez1* 1 Institute of Natural Resources and Agrobiology, Spanish Council for Research, IRNAS-CSIC, Avda. Rena Mercedes 10, Sevilla, Spain, 2 Department of Microbiology, Faculty of Science, Silpakorn University, Nakhon Pathom, Thailand * [email protected] a1111111111 a1111111111 a1111111111 a1111111111 Abstract a1111111111 Horizontal Gene Transfer (HGT) plays an important role in the physiology and evolution of microorganisms above all thermophilic prokaryotes. Some members of the Phylum Thermo- togae (i.e., Thermotoga spp.) have been reported to present genomes constituted by a mosaic of genes from a variety of origins. This study presents a novel approach to search OPEN ACCESS on the potential plasticity of Fervidobacterium genomes using putative transposase-encod- Citation: Cuecas A, Kanoksilapatham W, Gonzalez ing genes as the target of analysis. Transposases are key proteins involved in genomic JM (2017) Evidence of horizontal gene transfer by DNA rearrangements. A comprehensive comparative analysis, including phylogeny, non- transposase gene analyses in Fervidobacterium species. PLoS ONE 12(4): e0173961. https://doi. metric multidimensional scaling analysis of tetranucleotide frequencies, repetitive flanking org/10.1371/journal.pone.0173961 sequences and divergence estimates, was performed on the transposase genes detected Editor: Shihui Yang, National Renewable Energy -
Biochemical Characterization of Β-Xylan Acting Glycoside
BIOCHEMICAL CHARACTERIZATION OF β-XYLAN ACTING GLYCOSIDE HYDROLASES FROM THE THERMOPHILIC BACTERIUM Caldicellulosiruptor saccharolyticus Thesis Submitted to The School of Engineering of the UNIVERSITY OF DAYTON In Partial Fulfillment of the Requirements for The Degree of Master of Science in Chemical Engineering By Jin Cao Dayton, Ohio December, 2012 BIOCHEMICAL CHARACTERIZATION OF β-XYLAN ACTING GLYCOSIDE HYDROLASES FROM THE THERMOPHILIC BACTERIUM Caldicellulosiruptor saccharolyticus Name: Cao, Jin APPROVED BY: ______________________ ________________________ Donald A. Comfort, Ph.D. Amy Ciric, Ph.D. Advisory Committee Chairman Committee Member Research Advisor & Assistant Professor Lecturer Department of Department of Chemical & Materials Engineering Chemical & Materials Engineering ________________________ Karolyn Hansen, Ph.D. Committee Member Assistant Professor Department of Biology _______________________ ________________________ John G. Weber, Ph.D. Tony E. Saliba, Ph.D. Associate Dean Dean, School of Engineering School of Engineering & Wilke Distinguished Professor ii ABSTRACT BIOCHEMICAL CHARACTERIZATION OF Β-XYLAN ACTING GLYCOSIDE HYDROLASES FROM THE THERMOPHILIC BACTERIUM Caldicellulosiruptor saccharolyticus Name: Cao, Jin University of Dayton Research Advisor: Donald A. Comfort Fossil fuels have been the dominant source for energy around the world since the industrial revolution, however, with the increasing demand for energy and decreasing fossil fuel reserves alternative energy sources must be exploited. Bio-ethanol is a promising prospect for an alternative energy source to petroleum, especially when plant biomass is used as the replacement carbon source. This gives greater benefit for implementation of bioethanol as a viable alternative transport fuel than food stocks such as starch from corn. The implementation of this next generation of bioethanol requires more robust and environmentally friendly methods for degrading cellulose and hemicellulose, the two major components of plant biomass. -
Microbial Diversity and Cellulosic Capacity in Municipal Waste Sites By
Microbial diversity and cellulosic capacity in municipal waste sites by Rebecca Co A thesis presented to the University of Waterloo in fulfilment of the thesis requirement for the degree of Master of Science in Biology Waterloo, Ontario, Canada, 2019 © Rebecca Co 2019 Author’s Declaration This thesis consists of material all of which I authored or co-authored: see Statement of Contributions included in the thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii Statement of Contributions In Chapter 2, the sampling and DNA extraction and sequencing of samples (Section 2.2.1 - 2.2.2) were carried out by Dr. Aneisha Collins-Fairclough and Dr. Melessa Ellis. The work described in Section 2.2.3 Metagenomic pipeline and onwards was done by the thesis’s author. Sections 2.2.1 Sample collection – 2.2.4 16S rRNA gene community profile were previously published in Widespread antibiotic, biocide, and metal resistance in microbial communities inhabiting a municipal waste environment and anthropogenically impacted river by Aneisha M. Collins- Fairclough, Rebecca Co, Melessa C. Ellis, and Laura A. Hug. 2018. mSphere: e00346-18. The writing and analyses incorporated into this chapter are by the thesis's author. iii Abstract Cellulose is the most abundant organic compound found on earth. Cellulose’s recalcitrance to hydrolysis is a major limitation to improving the efficiency of industrial applications. The biofuel, pulp and paper, agriculture, and textile industries employ mechanical and chemical methods of breaking down cellulose. -
Genome Diversity of Spore-Forming Firmicutes MICHAEL Y
Genome Diversity of Spore-Forming Firmicutes MICHAEL Y. GALPERIN National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 ABSTRACT Formation of heat-resistant endospores is a specific Vibrio subtilis (and also Vibrio bacillus), Ferdinand Cohn property of the members of the phylum Firmicutes (low-G+C assigned it to the genus Bacillus and family Bacillaceae, Gram-positive bacteria). It is found in representatives of four specifically noting the existence of heat-sensitive vegeta- different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, tive cells and heat-resistant endospores (see reference 1). and Negativicutes, which all encode similar sets of core sporulation fi proteins. Each of these classes also includes non-spore-forming Soon after that, Robert Koch identi ed Bacillus anthracis organisms that sometimes belong to the same genus or even as the causative agent of anthrax in cattle and the species as their spore-forming relatives. This chapter reviews the endospores as a means of the propagation of this orga- diversity of the members of phylum Firmicutes, its current taxon- nism among its hosts. In subsequent studies, the ability to omy, and the status of genome-sequencing projects for various form endospores, the specific purple staining by crystal subgroups within the phylum. It also discusses the evolution of the violet-iodine (Gram-positive staining, reflecting the pres- Firmicutes from their apparently spore-forming common ancestor ence of a thick peptidoglycan layer and the absence of and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, an outer membrane), and the relatively low (typically ruminococci) in the course of their adaptation to the saprophytic less than 50%) molar fraction of guanine and cytosine lifestyle in a nutrient-rich environment. -
Development of Genetic Tools for Thermotoga Spp
DEVELOPMENT OF GENETIC TOOLS FOR THERMOTOGA SPP. Dongmei Han A Dissertation Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY December 2013 Committee: Dr. Zhaohui Xu, Advisor Dr. Lisa C. Chavers Graduate Faculty Representative Dr. George S. Bullerjahn Dr. Raymond A. Larsen Dr. Scott O. Rogers © 2013 Dongmei Han All Rights Reserved iii ABSTRACT Zhaohui Xu, Advisor Thermotoga spp. may serve as model systems for understanding life sustainability under hyperthermophilic conditions. They are also attractive candidates for producing biohydrogen in industry. However, a lack of genetic tools has hampered the investigation and application of these organisms. We improved the cultivation method of Thermotoga spp. for preparing and handling Thermotoga solid cultures under aerobic conditions. An embedded method achieved a plating efficiency of ~ 50%, and a soft SVO medium was introduced to bridge isolating single Thermotoga colonies from solid medium to liquid medium. The morphological change of T. neapolitana during the growth process was observed through scanning electron microscopy and transmission electron microscopy. At the early exponential phase, around OD600 0.1 – 0.2, the area of adhered region between toga and cell membrane was the largest, and it was suspected to be the optimal time for DNA uptake in transformation. The capacity of natural transformation was found in T. sp. RQ7, but not in T. maritima. A Thermotoga-E. coli shuttle vector pDH10 was constructed using pRQ7, a cryptic mini-plasmid isolated from T. sp. RQ7. Plasmid pDH10 was introduced to T. sp. RQ7 by liposome-mediated transformation, electroporation, and natural transformation, and to T. -
Genomic Insights from Monoglobus Pectinilyticus: a Pectin-Degrading Specialist Bacterium in the Human Colon
The ISME Journal (2019) 13:1437–1456 https://doi.org/10.1038/s41396-019-0363-6 ARTICLE Genomic insights from Monoglobus pectinilyticus: a pectin-degrading specialist bacterium in the human colon 1,2 1,3 4 2 2 5 Caroline C. Kim ● Genelle R. Healey ● William J. Kelly ● Mark L. Patchett ● Zoe Jordens ● Gerald W. Tannock ● 6 6 1 7,8,9 1 Ian M. Sims ● Tracey J. Bell ● Duncan Hedderley ● Bernard Henrissat ● Douglas I. Rosendale Received: 19 April 2018 / Revised: 7 January 2019 / Accepted: 19 January 2019 / Published online: 6 February 2019 © International Society for Microbial Ecology 2019 Abstract Pectin is abundant in modern day diets, as it comprises the middle lamellae and one-third of the dry carbohydrate weight of fruit and vegetable cell walls. Currently there is no specialized model organism for studying pectin fermentation in the human colon, as our collective understanding is informed by versatile glycan-degrading bacteria rather than by specialist pectin degraders. Here we show that the genome of Monoglobus pectinilyticus possesses a highly specialized glycobiome for pectin degradation, unique amongst Firmicutes known to be in the human gut. Its genome encodes a simple set of metabolic pathways relevant to pectin sugar utilization, and its predicted glycobiome comprises an unusual distribution of carbohydrate- 1234567890();,: 1234567890();,: active enzymes (CAZymes) with numerous extracellular methyl/acetyl esterases and pectate lyases. We predict the M. pectinilyticus degradative process is facilitated by cell-surface S-layer homology (SLH) domain-containing proteins, which proteomics analysis shows are differentially expressed in response to pectin. Some of these abundant cell surface proteins of M. -
Seasonal Patterns in Microbial Communities Inhabiting the Hot Springs of Tengchong, Yunnan Province†, China
bs_bs_banner Environmental Microbiology (2014) 16(6), 1579–1591 doi:10.1111/1462-2920.12311 Seasonal patterns in microbial communities inhabiting the hot springs of Tengchong, Yunnan Province†, China †Correction added after first online publication on 14 November 2013: In the title of the article, the word ‘Providence’ in ‘Yunnan Providence’ is now amended to ‘Province’. Brandon R. Briggs,1 Eoin L. Brodie,2 groups and 113 OTUs within 20 archaeal phylum-level Lauren M. Tom,2 Hailiang Dong,1,3* Hongchen Jiang,4 groups, which are additional 54 bacterial phyla and Qiuyuan Huang,1 Shang Wang,3 Weiguo Hou,3 11 archaeal phyla to those that were previously Geng Wu,4 Liuquin Huang,3 Brian P. Hedlund,5 described using pyrosequencing. Monsoon samples Chuanlun Zhang,6,7 Paul Dijkstra8 and (June 2011) showed increased concentrations of Bruce A. Hungate8 potassium, total organic carbon, ammonium, calcium, 1Department of Geology and Environmental Earth sodium and total nitrogen, and decreased ferrous iron Science, Miami University, Oxford, OH 45056, USA. relative to the dry season (January 2011). At the same 2Ecology Department, Earth Sciences Division, time, the highly ordered microbial communities Lawrence Berkeley National Laboratory, Berkeley, CA present in January gave way to poorly ordered com- 94720, USA. munities in June, characterized by higher richness of 3China University of Geosciences, State Key Laboratory Bacteria, including microbes related to mesophiles. of Biogeology and Environmental Geology, Beijing These seasonal changes in geochemistry and com- 100083, China. munity structure are likely due to high rainfall influx 4China University of Geosciences, State Key Laboratory during the monsoon season and indicate that sea- of Biogeology and Environmental Geology, Wuhan sonal dynamics occurs in high-temperature environ- 430074, China. -
Download (PDF)
A) Sm B) Sw C) Ss D) N1 114, Nitrospira 114, Nitrospira 24, Sytrophobacteraceae 146, Propionibacterineae 323, Firmicutes 26, Sytrophobacteraceae 161, Spirochaetaceae 228, Chloroflexi 333, Lactobacillales 67, KSB3 132, Acidobacteria 23, Sytrophobacteraceae 21, TM6 23, Sytrophobacteraceae 143, Actinobacteridae 209, Chloroflexi 132, Acidobacteria 85, Bacteroidales 348, Firmicutes 10, Rhodocyclales 301, Firmicutes 114, Nitrospira 146, Propionibacterineae 79, Bacteroidales 23, Sytrophobacteraceae 61, Epsilon proteobacteria 224, Chloroflexi 146, Propionibacterineae 85, Bacteroidales 209, Chloroflexi 87, Bacteroidales 152, Propionibacterineae 113, Flexibacteraceae 351, OD2 208, Chloroflexi 85, Bacteroidales 128, Planctomycetes 146, Propionibacterineae 213, Chloroflexi 186, Chlorobi 161, Spirochaetaceae 79, Bacteroidales 280, Clostridiaceae 250, Lachnospiraceae 138, others 196, Chloroflexi 114, Nitrospira 262, Lachnospiraceae 183, Chlorobi 213, Chloroflexi 24, Sytrophobacteraceae 340, Acidaminococcaceae 231, Chloroflexi 218, Chloroflexi 228, Chloroflexi 25, Sytrophobacteraceae 15, Rhodobacterales 333, Lactobacillales 25, Sytrophobacteraceae 13, Methylophilales 55, Desulfovibrionales 165, Spirochaetaceae 55, Desulfovibrionales 23, Sytrophobacteraceae 173, Spirochaetaceae 65, others 61, Epsilonproteobacteria 116, Verrucomicrobia-Chlamydiae 148, Propionibacterineae 1, Shewanella 132, Acidobacteria 158, Rubrobacteridae 157, Rubrobacteridae 2, Pseudomonadaceae 143, Actinobacteridae 83, Bacteroidales 85, Bacteroidales 3, Pseudomonadaceae 157, Rubrobacteridae -
Community Analysis of Plant Biomass-Degrading Microorganisms from Obsidian Pool, Yellowstone National Park
Microb Ecol DOI 10.1007/s00248-014-0500-8 ENVIRONMENTAL MICROBIOLOGY Community Analysis of Plant Biomass-Degrading Microorganisms from Obsidian Pool, Yellowstone National Park Tatiana A. Vishnivetskaya & Scott D. Hamilton-Brehm & Mircea Podar & Jennifer J. Mosher & Anthony V. Palumbo & Tommy J. Phelps & Martin Keller & James G. Elkins Received: 12 May 2014 /Accepted: 16 September 2014 # Springer Science+Business Media New York (outside the USA) 2014 Abstract The conversion of lignocellulosic biomass into (OBP), was examined for potential biomass-active microorgan- biofuels can potentially be improved by employing robust mi- isms using cultivation-independent and enrichment techniques. croorganisms and enzymes that efficiently deconstruct plant Analysis of 33,684 archaeal and 43,784 bacterial quality-filtered polysaccharides at elevated temperatures. Many of the geother- 16S rRNA gene pyrosequences revealed that archaeal diversity mal features of Yellowstone National Park (YNP) are surrounded in the main pool was higher than bacterial; however, in the by vegetation providing a source of allochthonic material to vegetated area, overall bacterial diversity was significantly support heterotrophic microbial communities adapted to utilize higher. Of notable interest was a flooded depression adjacent to plant biomass as a primary carbon and energy source. In this OBP supporting a stand of Juncus tweedyi, a heat-tolerant rush study, a well-known hot spring environment, Obsidian Pool commonly found growing near geothermal features in YNP. The microbial community from heated sediments surrounding the The submitted manuscript has been authored by a contractor of the U.S. plants was enriched in members of the Firmicutes including Government under contract DE-AC05-00OR22725. Accordingly, the potentially (hemi)cellulolytic bacteria from the genera U.S.