Pasteuria Penetrans (Bacilli: Bacillales: Pasteuriaceae)1 Ruhiyyih Dyrdahl-Young and Peter Digennaro2
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Desulfuribacillus Alkaliarsenatis Gen. Nov. Sp. Nov., a Deep-Lineage
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Extremophiles (2012) 16:597–605 DOI 10.1007/s00792-012-0459-7 ORIGINAL PAPER Desulfuribacillus alkaliarsenatis gen. nov. sp. nov., a deep-lineage, obligately anaerobic, dissimilatory sulfur and arsenate-reducing, haloalkaliphilic representative of the order Bacillales from soda lakes D. Y. Sorokin • T. P. Tourova • M. V. Sukhacheva • G. Muyzer Received: 10 February 2012 / Accepted: 3 May 2012 / Published online: 24 May 2012 Ó The Author(s) 2012. This article is published with open access at Springerlink.com Abstract An anaerobic enrichment culture inoculated possible within a pH range from 9 to 10.5 (optimum at pH with a sample of sediments from soda lakes of the Kulunda 10) and a salt concentration at pH 10 from 0.2 to 2 M total Steppe with elemental sulfur as electron acceptor and for- Na? (optimum at 0.6 M). According to the phylogenetic mate as electron donor at pH 10 and moderate salinity analysis, strain AHT28 represents a deep independent inoculated with sediments from soda lakes in Kulunda lineage within the order Bacillales with a maximum of Steppe (Altai, Russia) resulted in the domination of a 90 % 16S rRNA gene similarity to its closest cultured Gram-positive, spore-forming bacterium strain AHT28. representatives. On the basis of its distinct phenotype and The isolate is an obligate anaerobe capable of respiratory phylogeny, the novel haloalkaliphilic anaerobe is suggested growth using elemental sulfur, thiosulfate (incomplete as a new genus and species, Desulfuribacillus alkaliar- T T reduction) and arsenate as electron acceptor with H2, for- senatis (type strain AHT28 = DSM24608 = UNIQEM mate, pyruvate and lactate as electron donor. -
Appendix III: OTU's Found to Be Differentially Abundant Between CD and Control Patients Via Metagenomeseq Analysis
Appendix III: OTU's found to be differentially abundant between CD and control patients via metagenomeSeq analysis OTU Log2 (FC CD / FDR Adjusted Phylum Class Order Family Genus Species Number Control) p value 518372 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 2.16 5.69E-08 194497 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 2.15 8.93E-06 175761 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 5.74 1.99E-05 193709 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 2.40 2.14E-05 4464079 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides NA 7.79 0.000123188 20421 Firmicutes Clostridia Clostridiales Lachnospiraceae Coprococcus NA 1.19 0.00013719 3044876 Firmicutes Clostridia Clostridiales Lachnospiraceae [Ruminococcus] gnavus -4.32 0.000194983 184000 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 2.81 0.000306032 4392484 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides NA 5.53 0.000339948 528715 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 2.17 0.000722263 186707 Firmicutes Clostridia Clostridiales NA NA NA 2.28 0.001028539 193101 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 1.90 0.001230738 339685 Firmicutes Clostridia Clostridiales Peptococcaceae Peptococcus NA 3.52 0.001382447 101237 Firmicutes Clostridia Clostridiales NA NA NA 2.64 0.001415109 347690 Firmicutes Clostridia Clostridiales Ruminococcaceae Oscillospira NA 3.18 0.00152075 2110315 Firmicutes Clostridia -
Analyzing the Early Stages of Clostridium Difficile Spore
ANALYZING THE EARLY STAGES OF CLOSTRIDIUM DIFFICILE SPORE GERMINATION A Dissertation by MICHAEL FRANCIS Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Chair of Committee, Joseph A. Sorg Committee Members, James L. Smith Matthew S. Sachs Paul D. Straight Head of Department, Thomas D. McKnight May 2017 Major Subject: Microbiology Copyright 2017 Michael Francis ABSTRACT Infections caused by Clostridium difficile have increased steadily over the past several years. While studies on C. difficile virulence and physiology have been hindered, in the past, by lack of genetic approaches and suitable animal models, newly developed technologies and animal models allow for improved experimental detail. One such advance was the generation of a mouse-model of C. difficile infection. This system was an important step forward in the analysis of the genetic requirements for colonization and infection. Equally important is understanding the differences that exist between mice and humans. One of these differences is the natural bile acid composition. Bile acid-mediated spore germination, a process whereby a dormant spore returns to active, vegetative growth, is an important step during C. difficile colonization. Mice produce several different bile acids that are not found in humans (muricholic acids) that have the potential to impact C. difficile spore germination. In order to understand potential effects of these different bile acids on C. difficile physiology, we characterized their effects on C. difficile spore germination and growth of vegetative cells. We found that the mouse-derived muricholic acids affect germination similarly to a previously-described inhibitor of germination, chenodeoxycholic acid. -
Distribution and Characteristics of Bacillus Bacteria Associated with Hydrobionts and the Waters of the Peter the Great Bay, Sea of Japan I
ISSN 0026-2617, Microbiology, 2008, Vol. 77, No. 4, pp. 497–503. © Pleiades Publishing, Ltd., 2008. Original Russian Text © I.A. Beleneva, 2008, published in Mikrobiologiya, 2008, Vol. 77, No. 4, pp. 558–565. EXPERIMENTAL ARTICLES Distribution and Characteristics of Bacillus Bacteria Associated with Hydrobionts and the Waters of the Peter the Great Bay, Sea of Japan I. A. Beleneva1 Zhirmunskii Institute of Marine Biology, Far East Division, Russian Academy of Sciences, ul. Pal’chevskogo, 17, Vladivostok 690041, Russia Received May 28, 2007 Abstract—Bacilli of the species Bacillus subtilis, B. pumilus, B. mycoides, B. marinus and B. licheniformis (a total of 53 strains) were isolated from 15 invertebrate species and the water of the Vostok Bay, Peter the Great Bay, Sea of Japan. Bacilli were most often isolated from bivalves (22.7%) and sea cucumbers (18.9%); they occurred less frequently in sea urchins and starfish (13.2 and 7.5%, respectively). Most of bacilli strains were isolated from invertebrates inhabiting silted sediments. No Bacillus spp. strains were isolated from invertebrates inhabiting stony and sandy environments. The species diversity of bacilli isolated from marine objects under study was low. Almost all bacterial isolates were resistant to lincomycin. Unlike B. pumilus, B. subtilis isolates were mostly resistant to benzylpenicillin and ampicillin. Antibiotic sensitivity of B. licheniformis strains was variable (two strains were resistant to benzylpenicillin and oxacillin, while one was sensitive). A significant fraction of isolated bacilli contained pigments. Pigmented strains were more often isolated from seawater sam- ples, while colorless ones predominated within hydrobionts. B. subtilis colonies had the broadest range of co- lors. -
Ultrastructure and Development of Pasteuria Sp. (S-1 Strain), an Obligate Endoparasite of Belonolaimus Longicaudatus (Nemata: Tylenchida) R
Journal of Nematology 33(4):227–238. 2001. © The Society of Nematologists 2001. Ultrastructure and Development of Pasteuria sp. (S-1 strain), an Obligate Endoparasite of Belonolaimus longicaudatus (Nemata: Tylenchida) R. M. Giblin-Davis,1 D. S. Williams,2 W. P. Wergin,3 D. W. Dickson,4 T. E. Hewlett,4 S. Bekal,5 and J. O. Becker5 Abstract: Pasteuria sp., strain S-1, is a gram-positive, obligate endoparasitic bacterium that uses the phytoparasitic sting nematode, Belonolaimus longicaudatus, as its host in Florida. The host attachment of S-1 appears to be specific to the genus Belonolaimus with development occurring only in juveniles and adults of B. longicaudatus. This bacterium is characterized from other described species of Pasteuria using ultrastructure of the mature endospore. Penetration, development, and sporogenesis were elucidated with TEM, LTSEM, and SEM and are similar to other nematode-specific Pasteuria. Recent analysis of 16S rDNA sequence homology confirms its congeneric ranking with other Pasteuria species and strains from nematodes and cladocerans, and corroborates ultrastructural, morphological, morphometric, and host-range evidence suggesting separate species status. Key words: Belonolaimus longicaudatus, development, obligate nematode endoparasitic bacterium, Pasteuria sp. (S-1 strain), sporo- genesis, sting nematode, ultrastructure. Investigators have identified four nominal species of al., 1989). Thus, traditional procedures for biochemical Pasteuria that are gram-positive, mycelial, endospore- characterization have not -
Resilience of Microbial Communities After Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms
microorganisms Article Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms Tim Piel 1,†, Giovanni Sandrini 1,†,‡, Gerard Muyzer 1 , Corina P. D. Brussaard 1,2 , Pieter C. Slot 1, Maria J. van Herk 1, Jef Huisman 1 and Petra M. Visser 1,* 1 Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; [email protected] (T.P.); [email protected] (G.S.); [email protected] (G.M.); [email protected] (C.P.D.B.); [email protected] (P.C.S.); [email protected] (M.J.v.H.); [email protected] (J.H.) 2 Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherland Institute for Sea Research, 1790 AB Den Burg, The Netherlands * Correspondence: [email protected]; Tel.: +31-20-5257073 † These authors have contributed equally to this work. ‡ Current address: Department of Technology & Sources, Evides Water Company, 3006 AL Rotterdam, The Netherlands. Abstract: Applying low concentrations of hydrogen peroxide (H2O2) to lakes is an emerging method to mitigate harmful cyanobacterial blooms. While cyanobacteria are very sensitive to H2O2, little Citation: Piel, T.; Sandrini, G.; is known about the impacts of these H2O2 treatments on other members of the microbial com- Muyzer, G.; Brussaard, C.P.D.; Slot, munity. In this study, we investigated changes in microbial community composition during two P.C.; van Herk, M.J.; Huisman, J.; −1 lake treatments with low H2O2 concentrations (target: 2.5 mg L ) and in two series of controlled Visser, P.M. -
LTER Proposal
Project Summary The KBS LTER Site: Long-term Ecological Research in Row-crop Agriculture Project Summary In 1987 we initiated the KBS Long-term Ecological Research Project in Row-crop Agriculture to examine basic ecological relationships in field-crop ecosystems typical of the US Midwest. Our goal was – and remains – to test the long-term hypothesis that agronomic management based on knowledge of ecological interactions in cropping systems can effectively replace management based on chemical inputs. We established a major field experiment comprising 11 different cropping systems and unmanaged successional communities, corresponding to different levels and types of ecological structure and disturbance and including biologically-based and conventional agricultural management. Within these systems we test hypotheses related to the patterns and processes that underlie ecosystem productivity and environmental performance. Working hypotheses are built around the general topic areas of plant community dynamics, soil microbial populations, insect predator-prey relationships, watershed and field- scale biogeochemistry, human interactions, and regional ecological processes. Intellectual Merit: With this proposal we build on past work to formulate an integrated model of agricultural landscapes that thoroughly incorporates the interactions between human and natural systems. Our overarching theme for this next research phase is “Farming for ecosystem services in a changing environment,” reflecting our desire to understand the full suite of ecosystem services associated with agriculture, including mitigation of undesirable environmental impacts. We propose to focus on responses of the coupled human and natural systems to changing external drivers, including climate change, agricultural intensification (land use alterations), and shifts in global markets. We use a pulse-press disturbance model to delineate the biophysical interactions in agriculture that produce ecosystem services vis a vis human systems. -
Probiotic Lactic Acid Bacteria Vs. Bacilli: Pros and Cons ARTHUR C
Probiotic lactic acid bacteria vs. bacilli: pros and cons ARTHUR C. OUWEHAND1*, SOFIA FORSSTEN1, MARKUS LEHTINEN1, ELIZABETH GALBRAITH2, ELLEN DAVIS2 *Corresponding author 1. Active Nutrition, DuPont Nutrition & Health, Sokeritehtaantie 20, 02460 Kantvik, Finland Arthur C. Ouwehand 2. Animal and Environmental Applications, DuPont Nutrition & Health, W227 N752 Westmound Drive, Waukesha, WI 53186, USA KEYWORDS: probiotic, lactic acid bacteria, Lactobacillus, Bifidobacterium, Bacillus, spores ABSTRACT: Both lactic acid bacteria (LAB) and bacilli are commercialised as probiotics; LAB are mainly utilised as live and active or dormant cells, while bacilli are utilised as spores. Belonging to very different genera, they have different technological properties. LAB have a longer history of use as probiotics and therefore have a broader base as far as health efficacy documentation is concerned. The question therefore sometimes arises; strains from which of these groups make better probiotics? Considering the fact that probiotics, by definition, have to be viable in sufficient numbers and have to have documented health benefits, this is not a relevant question. Any microbial strain has to fulfil these criteria in order to qualify as a probiotic. The current paper reviews and compares the available data for both groups of organisms. Pre - Probiotics INTRODUCTION In order to supply consumers with products that provide meaningful levels of probiotics, several requirements have There is no legal description of probiotics. However, the most to be fulfilled by probiotic strains selected for industrial commonly accepted definition is from a FAO/WHO working production. Quality-control must be vigilantly performed, group: “Live microorganisms which when administered in assuring identity, viability and absence of contaminants. -
Horizontal Gene Flow Into Geobacillus Is Constrained by the Chromosomal Organization of Growth and Sporulation
bioRxiv preprint doi: https://doi.org/10.1101/381442; this version posted August 2, 2018. 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 4.0 International license. Horizontal gene flow into Geobacillus is constrained by the chromosomal organization of growth and sporulation Alexander Esin1,2, Tom Ellis3,4, Tobias Warnecke1,2* 1Molecular Systems Group, Medical Research Council London Institute of Medical Sciences, London, United Kingdom 2Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom 3Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom 4Department of Bioengineering, Imperial College London, London, United Kingdom *corresponding author ([email protected]) 1 bioRxiv preprint doi: https://doi.org/10.1101/381442; this version posted August 2, 2018. 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 4.0 International license. Abstract Horizontal gene transfer (HGT) in bacteria occurs in the context of adaptive genome architecture. As a consequence, some chromosomal neighbourhoods are likely more permissive to HGT than others. Here, we investigate the chromosomal topology of horizontal gene flow into a clade of Bacillaceae that includes Geobacillus spp. Reconstructing HGT patterns using a phylogenetic approach coupled to model-based reconciliation, we discover three large contiguous chromosomal zones of HGT enrichment. -
Significance of Donor Human Milk
fmicb-09-01376 June 26, 2018 Time: 17:31 # 1 ORIGINAL RESEARCH published: 27 June 2018 doi: 10.3389/fmicb.2018.01376 Preterm Gut Microbiome Depending on Feeding Type: Significance of Donor Human Milk Anna Parra-Llorca1, María Gormaz1,2, Cristina Alcántara3, María Cernada1,2, Antonio Nuñez-Ramiro1,2, Máximo Vento1,2*† and Maria C. Collado3*† 1 Neonatal Research Group, Health Research Institute La Fe, University and Polytechnic Hospital La Fe, Valencia, Spain, 2 Division of Neonatology, University and Polytechnic Hospital La Fe, Valencia, Spain, 3 Department of Biotechnology, Institute of Agrochemistry and Food Technology, Spanish National Research Council, Valencia, Spain Preterm microbial colonization is affected by gestational age, antibiotic treatment, type of birth, but also by type of feeding. Breast milk has been acknowledged as the gold standard for human nutrition. In preterm infants breast milk has been associated with improved growth and cognitive development and a reduced risk of necrotizing enterocolitis and late onset sepsis. In the absence of their mother’s own milk (MOM), pasteurized donor human milk (DHM) could be the best available alternative due to its similarity to the former. However, little is known about the effect of DHM upon preterm Edited by: Sandra Torriani, microbiota and potential biological implications. Our objective was to determine the University of Verona, Italy impact of DHM upon preterm gut microbiota admitted in a referral neonatal intensive Reviewed by: care unit (NICU). A prospective observational cohort study in NICU of 69 neonates Carlotta De Filippo, <32 weeks of gestation and with a birth weight ≤1,500 g was conducted. -
Microbial Community Composition During Degradation of Organic Matter
TECHNISCHE UNIVERSITÄT MÜNCHEN Lehrstuhl für Bodenökologie Microbial community composition during degradation of organic matter Stefanie Elisabeth Wallisch Vollständiger Abdruck der von der Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigten Dissertation. Vorsitzender: Univ.-Prof. Dr. A. Göttlein Prüfer der Dissertation: 1. Hon.-Prof. Dr. M. Schloter 2. Univ.-Prof. Dr. S. Scherer Die Dissertation wurde am 14.04.2015 bei der Technischen Universität München eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt am 03.08.2015 angenommen. Table of contents List of figures .................................................................................................................... iv List of tables ..................................................................................................................... vi Abbreviations .................................................................................................................. vii List of publications and contributions .............................................................................. viii Publications in peer-reviewed journals .................................................................................... viii My contributions to the publications ....................................................................................... viii Abstract -
A Transcriptomic Snapshot of Early Molecular Communication Between Pasteuria Penetrans and Meloidogyne Incognita Victor Phani1, Vishal S
Phani et al. BMC Genomics (2018) 19:850 https://doi.org/10.1186/s12864-018-5230-8 RESEARCH ARTICLE Open Access A transcriptomic snapshot of early molecular communication between Pasteuria penetrans and Meloidogyne incognita Victor Phani1, Vishal S. Somvanshi1, Rohit N. Shukla2, Keith G. Davies3,4* and Uma Rao1* Abstract Background: Southern root-knot nematode Meloidogyne incognita (Kofoid and White, 1919), Chitwood, 1949 is a key pest of agricultural crops. Pasteuria penetrans is a hyperparasitic bacterium capable of suppressing the nematode reproduction, and represents a typical coevolved pathogen-hyperparasite system. Attachment of Pasteuria endospores to the cuticle of second-stage nematode juveniles is the first and pivotal step in the bacterial infection. RNA-Seq was used to understand the early transcriptional response of the root-knot nematode at 8 h post Pasteuria endospore attachment. Results: A total of 52,485 transcripts were assembled from the high quality (HQ) reads, out of which 582 transcripts were found differentially expressed in the Pasteuria endospore encumbered J2 s, of which 229 were up-regulated and 353 were down-regulated. Pasteuria infection caused a suppression of the protein synthesis machinery of the nematode. Several of the differentially expressed transcripts were putatively involved in nematode innate immunity, signaling, stress responses, endospore attachment process and post-attachment behavioral modification of the juveniles. The expression profiles of fifteen selected transcripts were validated to be true by the qRT PCR. RNAi based silencing of transcripts coding for fructose bisphosphate aldolase and glucosyl transferase caused a reduction in endospore attachment as compared to the controls, whereas, silencing of aspartic protease and ubiquitin coding transcripts resulted in higher incidence of endospore attachment on the nematode cuticle.