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Actinobacterial Diversity of the Ethiopian Rift Valley Lakes
ACTINOBACTERIAL DIVERSITY OF THE ETHIOPIAN RIFT VALLEY LAKES By Gerda Du Plessis Submitted in partial fulfillment of the requirements for the degree of Magister Scientiae (M.Sc.) in the Department of Biotechnology, University of the Western Cape Supervisor: Prof. D.A. Cowan Co-Supervisor: Dr. I.M. Tuffin November 2011 DECLARATION I declare that „The Actinobacterial diversity of the Ethiopian Rift Valley Lakes is my own work, that it has not been submitted for any degree or examination in any other university, and that all the sources I have used or quoted have been indicated and acknowledged by complete references. ------------------------------------------------- Gerda Du Plessis ii ABSTRACT The class Actinobacteria consists of a heterogeneous group of filamentous, Gram-positive bacteria that colonise most terrestrial and aquatic environments. The industrial and biotechnological importance of the secondary metabolites produced by members of this class has propelled it into the forefront of metagenomic studies. The Ethiopian Rift Valley lakes are characterized by several physical extremes, making it a polyextremophilic environment and a possible untapped source of novel actinobacterial species. The aims of the current study were to identify and compare the eubacterial diversity between three geographically divided soda lakes within the ERV focusing on the actinobacterial subpopulation. This was done by means of a culture-dependent (classical culturing) and culture-independent (DGGE and ARDRA) approach. The results indicate that the eubacterial 16S rRNA gene libraries were similar in composition with a predominance of α-Proteobacteria and Firmicutes in all three lakes. Conversely, the actinobacterial 16S rRNA gene libraries were significantly different and could be used to distinguish between sites. -
Clostridium Aerotolerans Sp
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Apr. 1987, p. 102-105 Vol. 37, No. 2 0020-7713/87/020102-04$02.OO/O Copyright 0 1987, International Union of Microbiological Societies Clostridium aerotolerans sp. nov. a Xylanolytic Bacterium from Corn Stover and from the Rumina of Sheep Fed Corn Stover N. 0. VAN GYLSWYK" AND J. J. T. K. VAN DER TOORN Anaerobic Microbiology Division, Laboratory for Molecular and Cell Biology, Onderstepoort 01 10, South Africa Two strains of sporeforming, xylan-digesting, rod-shaped bacteria were isolated from a lo-* dilution of rumen ingesta taken from two sheep fed a corn stover ration. To determine the source of these strains, we examined the corn stover and isolated two strains of similar bacteria from it. The four strains were remarkably tolerant to oxygen although they did not grow in liquid medium that was shaken while exposed to air. They fermented a wide variety of carbon sources and produced formic, acetic, and lactic acids, ethanol, carbon dioxide, and hydrogen from xylan. The deoxyribonucleic acid base composition was 40 mol% guanine plus cytosine. The name proposed for these strains is Clostridiurn aerotolerans; the type strain is strain XSA62 (ATCC 43524). Two strains of sporeforming bacteria were found among a in which glucose (5 g/liter) replaced xylan. Spores were large number of bacteria isolated from colonies that pro- stained with malachite green (10). Motility was determined duced clearing zones in xylan (3%) agar medium inoculated after cells were grown overnight on maintenance slants. with a loh8 dilution of rumen ingesta from sheep fed corn Growth in basal medium containing cellobiose (5 g/liter) stover diets (14) as briefly described by van der Toorn and from which reducing agent (cysteine and sulfide) had been vim Gylswyk (15). -
Bacillus Crassostreae Sp. Nov., Isolated from an Oyster (Crassostrea Hongkongensis)
International Journal of Systematic and Evolutionary Microbiology (2015), 65, 1561–1566 DOI 10.1099/ijs.0.000139 Bacillus crassostreae sp. nov., isolated from an oyster (Crassostrea hongkongensis) Jin-Hua Chen,1,2 Xiang-Rong Tian,2 Ying Ruan,1 Ling-Ling Yang,3 Ze-Qiang He,2 Shu-Kun Tang,3 Wen-Jun Li,3 Huazhong Shi4 and Yi-Guang Chen2 Correspondence 1Pre-National Laboratory for Crop Germplasm Innovation and Resource Utilization, Yi-Guang Chen Hunan Agricultural University, 410128 Changsha, PR China [email protected] 2College of Biology and Environmental Sciences, Jishou University, 416000 Jishou, PR China 3The Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, 650091 Kunming, PR China 4Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA A novel Gram-stain-positive, motile, catalase- and oxidase-positive, endospore-forming, facultatively anaerobic rod, designated strain JSM 100118T, was isolated from an oyster (Crassostrea hongkongensis) collected from the tidal flat of Naozhou Island in the South China Sea. Strain JSM 100118T was able to grow with 0–13 % (w/v) NaCl (optimum 2–5 %), at pH 5.5–10.0 (optimum pH 7.5) and at 5–50 6C (optimum 30–35 6C). The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant respiratory quinone was menaquinone-7 and the major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0,C16 : 0 and C16 : 1v11c. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown glycolipid and an unknown phospholipid. The genomic DNA G+C content was 35.9 mol%. -
Developing a Genetic Manipulation System for the Antarctic Archaeon, Halorubrum Lacusprofundi: Investigating Acetamidase Gene Function
www.nature.com/scientificreports OPEN Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Received: 27 May 2016 Accepted: 16 September 2016 investigating acetamidase gene Published: 06 October 2016 function Y. Liao1, T. J. Williams1, J. C. Walsh2,3, M. Ji1, A. Poljak4, P. M. G. Curmi2, I. G. Duggin3 & R. Cavicchioli1 No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms. -
Botulism: Guidance for Health Care Providers Key Medical and Public Health Interventions After Identification of a Suspected Case
Virginia Department of Health Botulism: Guidance for Health Care Providers Key Medical and Public Health Interventions after Identification of a Suspected Case Table of Contents 1. Epidemiology ........................................................................................................................................ 1 2. Clinical Manifestations .......................................................................................................................... 2 3. Laboratory Testing and Diagnosis ......................................................................................................... 3 4. Treatment ............................................................................................................................................. 6 5. Post-exposure Prophylaxis .................................................................................................................... 6 6. Vaccination ........................................................................................................................................... 6 7. Infection Control ................................................................................................................................... 6 8. Decontamination .................................................................................................................................. 7 9. Postmortem Practices ........................................................................................................................... 7 10. Public Health -
Heat Resistant Thermophilic Endospores in Cold Estuarine Sediments
Heat resistant thermophilic endospores in cold estuarine sediments Emma Bell Thesis submitted for the degree of Doctor of Philosophy School of Civil Engineering and Geosciences Faculty of Science, Agriculture and Engineering February 2016 Abstract Microbial biogeography explores the spatial and temporal distribution of microorganisms at multiple scales and is influenced by environmental selection and passive dispersal. Understanding the relative contribution of these factors can be challenging as their effects can be difficult to differentiate. Dormant thermophilic endospores in cold sediments offer a natural model for studies focusing on passive dispersal. Understanding distributions of these endospores is not confounded by the influence of environmental selection; rather their occurrence is due exclusively to passive transport. Sediment heating experiments were designed to investigate the dispersal histories of various thermophilic spore-forming Firmicutes in the River Tyne, a tidal estuary in North East England linking inland tributaries with the North Sea. Microcosm incubations at 50-80°C were monitored for sulfate reduction and enriched bacterial populations were characterised using denaturing gradient gel electrophoresis, functional gene clone libraries and high-throughput sequencing. The distribution of thermophilic endospores among different locations along the estuary was spatially variable, indicating that dispersal vectors originating in both warm terrestrial and marine habitats contribute to microbial diversity in estuarine and marine environments. In addition to their persistence in cold sediments, some endospores displayed a remarkable heat-resistance surviving multiple rounds of autoclaving. These extremely heat-resistant endospores are genetically similar to those detected in deep subsurface environments, including geothermal groundwater investigated from a nearby terrestrial borehole drilled to >1800 m depth with bottom temperatures in excess of 70°C. -
A Metagenomic Β-Glucuronidase Uncovers a Core Adaptive Function of the Human Intestinal Microbiome
A metagenomic β-glucuronidase uncovers a core adaptive function of the human intestinal microbiome Karine Gloux, Olivier Berteau, Hanane El oumami, Fabienne Béguet, Marion Leclerc, and Joël Doré1 Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1319 Micalis, F-78352 Jouy en Josas, France Edited by Todd R. Klaenhammer, North Carolina State University, Raleigh, NC, and approved June 1, 2010 (received for review February 4, 2010) In the human gastrointestinal tract, bacterial β-D-glucuronidases (BG; XIVa), major reservoirs of BG-positive bacteria (11), are dys- E.C. 3.2.1.31) are involved both in xenobiotic metabolism and in some biosis markers in Crohn’s disease (12–15) and in intestinal carci- of the beneficial effects of dietary compounds. Despite their biolog- nogenesis (16). Nevertheless, the relative contribution of bacterial ical significance, investigations are hampered by the fact that only strains to the global intestinal BG activity remains unclear, and a few BGs have so far been studied. A functional metagenomic the molecular bases are essentially unknown. approach was therefore performed on intestinal metagenomic In the human digestive tract, bacterial BGs are known to be libraries using chromogenic glucuronides as probes. Using this strat- distributed among the Enterobacteriaceae family in some Firmi- egy, 19 positive metagenomic clones were identified but only one cutes genera (Lactobacillus, Streptococcus, Clostridium, Rumino- exhibited strong β-D-glucuronidase activity when subcloned into an coccus, Roseburia, and Faecalibacterium) and in a specific species expression vector. The cloned gene encoded a β-D-glucuronidase of Actinobacteria (Bifidobacterium dentium) (11, 17, 18). On (called H11G11-BG) that had distant amino acid sequence homolo- the basis of their sequence, BGs are highly homologous to gies and an additional C terminus domain compared with known β-galactosidases and only a few of them have been investigated β fi -D-glucuronidases. -
Dysbiosis of Small Intestinal Microbiota in Liver Cirrhosis and Its
www.nature.com/scientificreports OPEN Dysbiosis of small intestinal microbiota in liver cirrhosis and its association with etiology Received: 31 May 2016 Yanfei Chen1, Feng Ji2, Jing Guo1, Ding Shi1, Daiqiong Fang1 & Lanjuan Li1 Accepted: 22 August 2016 Cirrhosis-associated duodenal dysbiosis is not yet clearly defined. In this research, duodenal Published: 30 September 2016 mucosal microbiota was analyzed in 30 cirrhotic patients and 28 healthy controls using 16S rRNA gene pyrosequencing methods. The principal coordinate analysis revealed that cirrhotic patients were colonized by remarkable different duodenal mucosal microbiota in comparison with controls. At the genus level, Veillonella, Megasphaera, Dialister, Atopobium, and Prevotella were found overrepresented in cirrhotic duodenum. And the duodenal microbiota of healthy controls was enriched with Neisseria, Haemophilus, and SR1 genera incertae sedis. On the other hand, based on predicted metagenomes analyzed, gene pathways related to nutrient absorption (e.g. sugar and amino acid metabolism) were highly abundant in cirrhosis duodenal microbiota, and functional modules involved in bacterial proliferation and colonization (e.g. bacterial motility proteins and secretion system) were overrepresented in controls. When considering the etiology of cirrhosis, two operational taxonomic units (OTUs), OTU-23 (Neisseria) and OTU-36 (Gemella), were found discriminative between hepatitis- B-virus related cirrhosis and primary biliary cirrhosis. The results suggest that the structure of duodenal mucosa microbiota in cirrhotic patients is dramatically different from healthy controls. The duodenum dysbiosis might be related to alterations of oral microbiota and changes in duodenal micro- environment. Gut microbiota and bacterial translocation (BT) play an important role in the pathogenesis of complications of cirrhosis1. -
Assessing Lyme Disease Relevant Antibiotics Through Gut Bacteroides Panels
Assessing Lyme Disease Relevant Antibiotics through Gut Bacteroides Panels by Sohum Sheth Abstract: Lyme borreliosis is the most prevalent vector-borne disease in the United States caused by the transmission of bacteria Borrelia burgdorferi harbored by the Ixodus scapularis ticks (Sharma, Brown, Matluck, Hu, & Lewis, 2015). Antibiotics currently used to treat Lyme disease include oral doxycycline, amoxicillin, and ce!riaxone. Although the current treatment is e"ective in most cases, there is need for the development of new antibiotics against Lyme disease, as the treatment does not work in 10-20% of the population for unknown reasons (X. Wu et al., 2018). Use of antibiotics in the treatment of various diseases such as Lyme disease is essential; however, the downside is the development of resistance and possibly deleterious e"ects on the human gut microbiota composition. Like other organs in the body, gut microbiota play an essential role in the health and disease state of the body (Ianiro, Tilg, & Gasbarrini, 2016). Of importance in the microbiome is the genus Bacteroides, which accounts for roughly one-third of gut microbiome composition (H. M. Wexler, 2007). $e purpose of this study is to investigate how antibiotics currently used for the treatment of Lyme disease in%uences the Bacteroides cultures in vitro and compare it with a new antibiotic (antibiotic X) identi&ed in the laboratory to be e"ective against B. burgdorferi. Using microdilution broth assay, minimum inhibitory concentration (MIC) was tested against nine di"erent strains of Bacteroides. Results showed that antibiotic X has a higher MIC against Bacteroides when compared to amoxicillin, ce!riaxone, and doxycycline, making it a promising new drug for further investigation and in vivo studies. -
Modulation of the Gut Microbiota Alters the Tumour-Suppressive Efficacy of Tim-3 Pathway Blockade in a Bacterial Species- and Host Factor-Dependent Manner
microorganisms Article Modulation of the Gut Microbiota Alters the Tumour-Suppressive Efficacy of Tim-3 Pathway Blockade in a Bacterial Species- and Host Factor-Dependent Manner Bokyoung Lee 1,2, Jieun Lee 1,2, Min-Yeong Woo 1,2, Mi Jin Lee 1, Ho-Joon Shin 1,2, Kyongmin Kim 1,2 and Sun Park 1,2,* 1 Department of Microbiology, Ajou University School of Medicine, Youngtongku Wonchondong San 5, Suwon 442-749, Korea; [email protected] (B.L.); [email protected] (J.L.); [email protected] (M.-Y.W.); [email protected] (M.J.L.); [email protected] (H.-J.S.); [email protected] (K.K.) 2 Department of Biomedical Sciences, The Graduate School, Ajou University, Youngtongku Wonchondong San 5, Suwon 442-749, Korea * Correspondence: [email protected]; Tel.: +82-31-219-5070 Received: 22 August 2020; Accepted: 9 September 2020; Published: 11 September 2020 Abstract: T cell immunoglobulin and mucin domain-containing protein-3 (Tim-3) is an immune checkpoint molecule and a target for anti-cancer therapy. In this study, we examined whether gut microbiota manipulation altered the anti-tumour efficacy of Tim-3 blockade. The gut microbiota of mice was manipulated through the administration of antibiotics and oral gavage of bacteria. Alterations in the gut microbiome were analysed by 16S rRNA gene sequencing. Gut dysbiosis triggered by antibiotics attenuated the anti-tumour efficacy of Tim-3 blockade in both C57BL/6 and BALB/c mice. Anti-tumour efficacy was restored following oral gavage of faecal bacteria even as antibiotic administration continued. In the case of oral gavage of Enterococcus hirae or Lactobacillus johnsonii, transferred bacterial species and host mouse strain were critical determinants of the anti-tumour efficacy of Tim-3 blockade. -
Food Waste Composting and Microbial Community Structure Profiling
processes Review Food Waste Composting and Microbial Community Structure Profiling Kishneth Palaniveloo 1,* , Muhammad Azri Amran 1, Nur Azeyanti Norhashim 1 , Nuradilla Mohamad-Fauzi 1,2, Fang Peng-Hui 3, Low Hui-Wen 3, Yap Kai-Lin 3, Looi Jiale 3, Melissa Goh Chian-Yee 3, Lai Jing-Yi 3, Baskaran Gunasekaran 3,* and Shariza Abdul Razak 4,* 1 Institute of Ocean and Earth Sciences, Institute for Advanced Studies Building, University of Malaya, Wilayah Persekutuan Kuala Lumpur 50603, Malaysia; [email protected] (M.A.A.); [email protected] (N.A.N.) 2 Institute of Biological Sciences, Faculty of Science, University of Malaya, Wilayah Persekutuan Kuala Lumpur 50603, Malaysia; [email protected] 3 Faculty of Applied Science, UCSI University (South Wing), Cheras, Wilayah Persekutuan Kuala Lumpur 56000, Malaysia; [email protected] (F.P.-H.); [email protected] (L.H.-W.); [email protected] (Y.K.-L.); [email protected] (L.J.); [email protected] (M.G.C.-Y.); [email protected] (L.J.-Y.) 4 Nutrition and Dietetics Program, School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia * Correspondence: [email protected] (K.P.); [email protected] (B.G.); [email protected] (S.A.R.); Tel.: +60-3-7967-4640 (K.P.); +60-16-323-4159 (B.G.); +60-19-964-4043 (S.A.R.) Received: 20 May 2020; Accepted: 16 June 2020; Published: 22 June 2020 Abstract: Over the last decade, food waste has been one of the major issues globally as it brings a negative impact on the environment and health. -
Clostridium Amazonitimonense, Clostridium Me
ORIGINAL ARTICLE Taxonogenomic description of four new Clostridium species isolated from human gut: ‘Clostridium amazonitimonense’, ‘Clostridium merdae’, ‘Clostridium massilidielmoense’ and ‘Clostridium nigeriense’ M. T. Alou1, S. Ndongo1, L. Frégère1, N. Labas1, C. Andrieu1, M. Richez1, C. Couderc1, J.-P. Baudoin1, J. Abrahão2, S. Brah3, A. Diallo1,4, C. Sokhna1,4, N. Cassir1, B. La Scola1, F. Cadoret1 and D. Raoult1,5 1) Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France, 2) Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil, 3) Hopital National de Niamey, BP 247, Niamey, Niger, 4) Campus Commun UCAD-IRD of Hann, Route des pères Maristes, Hann Maristes, BP 1386, CP 18524, Dakar, Senegal and 5) Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia Abstract Culturomics investigates microbial diversity of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. The present study allowed identification of four putative new Clostridium sensu stricto species: ‘Clostridium amazonitimonense’ strain LF2T, ‘Clostridium massilidielmoense’ strain MT26T, ‘Clostridium nigeriense’ strain Marseille-P2414T and ‘Clostridium merdae’ strain Marseille-P2953T, which we describe using the concept of taxonogenomics. We describe the main characteristics of each bacterium and present their complete genome sequence and annotation. © 2017 Published by Elsevier Ltd. Keywords: ‘Clostridium amazonitimonense’, ‘Clostridium massilidielmoense’, ‘Clostridium merdae’, ‘Clostridium nigeriense’, culturomics, emerging bacteria, human microbiota, taxonogenomics Original Submission: 18 August 2017; Revised Submission: 9 November 2017; Accepted: 16 November 2017 Article published online: 22 November 2017 intestine [1,4–6].