Iolabs· D Addgene 2018 Boston Bacterial Meeting - Schedule and Introduction
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Ecology and Evolution of Metabolic Cross-Feeding Interactions in Bacteria† Cite This: Nat
Natural Product Reports View Article Online REVIEW View Journal | View Issue Ecology and evolution of metabolic cross-feeding interactions in bacteria† Cite this: Nat. Prod. Rep.,2018,35,455 Glen D'Souza, ab Shraddha Shitut, ce Daniel Preussger,c Ghada Yousif,cde Silvio Waschina f and Christian Kost *ce Literature covered: early 2000s to late 2017 Bacteria frequently exchange metabolites with other micro- and macro-organisms. In these often obligate cross-feeding interactions, primary metabolites such as vitamins, amino acids, nucleotides, or growth factors are exchanged. The widespread distribution of this type of metabolic interactions, however, is at odds with evolutionary theory: why should an organism invest costly resources to benefit other individuals rather than using these metabolites to maximize its own fitness? Recent empirical work has fi fi Creative Commons Attribution 3.0 Unported Licence. shown that bacterial genotypes can signi cantly bene t from trading metabolites with other bacteria relative to cells not engaging in such interactions. Here, we will provide a comprehensive overview over the ecological factors and evolutionary mechanisms that have been identified to explain the evolution Received 25th January 2018 and maintenance of metabolic mutualisms among microorganisms. Furthermore, we will highlight DOI: 10.1039/c8np00009c general principles that underlie the adaptive evolution of interconnected microbial metabolic networks rsc.li/npr as well as the evolutionary consequences that result for cells living in such communities. 1 Introduction 2.5 Mechanisms of metabolite transfer This article is licensed under a 2 Metabolic cross-feeding interactions 2.5.1 Contact-independent mechanisms 2.1 Historical account 2.5.1.1 Passive diffusion 2.2 Classication of cross-feeding interactions 2.5.1.2 Active transport 2.2.1 Unidirectional by-product cross-feeding 2.5.1.3 Vesicle-mediated transport Open Access Article. -
Pulse Generation in the Quorum Machinery of Pseudomonas Aeruginosa
This is a repository copy of Pulse generation in the quorum machinery of Pseudomonas aeruginosa. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/116745/ Version: Published Version Article: Alfiniyah, Cicik Alfiniyah, Bees, Martin Alan and Wood, Andrew James orcid.org/0000- 0002-6119-852X (2017) Pulse generation in the quorum machinery of Pseudomonas aeruginosa. Bulletin of Mathematical Biology. pp. 1360-1389. ISSN 1522-9602 https://doi.org/10.1007/s11538-017-0288-z Reuse This article is distributed under the terms of the Creative Commons Attribution (CC BY) licence. This licence allows you to distribute, remix, tweak, and build upon the work, even commercially, as long as you credit the authors for the original work. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Bull Math Biol (2017) 79:1360–1389 DOI 10.1007/s11538-017-0288-z ORIGINAL ARTICLE Pulse Generation in the Quorum Machinery of Pseudomonas aeruginosa Cicik Alfiniyah1,2 · Martin A. Bees1 · A. Jamie Wood1,3 Received: 28 September 2016 / Accepted: 3 May 2017 / Published online: 19 May 2017 © The Author(s) 2017. This article is an open access publication Abstract Pseudomonas aeruginosa is a Gram-negative bacterium that is responsible for a wide range of infections in humans. -
Subtilase Sprp Exerts Pleiotropic Effects in Pseudomonas Aeruginosa
ORIGINAL RESEARCH Subtilase SprP exerts pleiotropic effects in Pseudomonas aeruginosa Alexander Pelzer1, Tino Polen2, Horst Funken1, Frank Rosenau3, Susanne Wilhelm1, Michael Bott2 & Karl-Erich Jaeger1 1Institute of Molecular Enzyme Technology, Research Centre Juelich, Heinrich-Heine-University Duesseldorf, D-52426 Juelich, Germany 2Institut of Bio- und Geosciences IBG-1: Biotechnology, Research Centre Juelich, D-52426 Juelich, Germany 3Institute of Pharmaceutical Biotechnology, Ulm-University, Albert-Einstein-Allee 11, D-89069 Ulm, Germany Keywords Abstract Biofilm, microarray, motility, orf PA1242, protease, Pseudomonas aeruginosa, The open reading frame PA1242 in the genome of Pseudomonas aeruginosa Pyoverdine. PAO1 encodes a putative protease belonging to the peptidase S8 family of sub- tilases. The respective enzyme termed SprP consists of an N-terminal signal Correspondence peptide and a so-called S8 domain linked by a domain of unknown function Karl-Erich Jaeger, Institute of Molecular (DUF). Presumably, this DUF domain defines a discrete class of Pseudomonas Enzyme Technology, Heinrich-Heine- proteins as homologous domains can be identified almost exclusively in pro- University Duesseldorf, Research Centre Juelich, D-52426 Juelich, Germany. teins of the genus Pseudomonas. The sprP gene was expressed in Escherichia coli Δ Tel: (+49)-2461-61-3716; Fax: (+49)-2461-61- and proteolytic activity was demonstrated. A P. aeruginosa sprP mutant was 2490; E-mail: [email protected] constructed and its gene expression pattern compared to the wild-type strain by genome microarray analysis revealing altered expression levels of 218 genes. Funding Information Apparently, SprP is involved in regulation of a variety of different cellular pro- 2021 As a member of the CLIB -Graduate cesses in P. -
With Synthetic Mucus, Researchers Take Aim at Antibiotic Resistance 26 April 2017
With synthetic mucus, researchers take aim at antibiotic resistance 26 April 2017 Researchers are pursuing an innovative and "Over millions of years, the mucus has evolved the unexpected new avenue in the quest to fight ability to keep a number of these problematic antibiotic resistance: synthetic mucus. By studying pathogenic microbes in check, preventing them and replicating mucus' natural ability to control from causing damage," said Ribbeck. "But the pathogenic bacteria, the scientists hope to find mucus does not kill the microbes. Instead, it tames new methods for combatting infections. them." Katharina Ribbeck, professor of tissue engineering In its new work, her team investigated how mucins, at the Massachusetts Institute of Technology, will the sugar-coated molecules that form the mucus present the work at the American Society for gel, influence the makeup of our internal microbial Biochemistry and Molecular Biology annual communities by constraining the formation of meeting during the Experimental Biology 2017 multicellular assemblies (also known as biofilms) by meeting, to be held April 22–26 in Chicago. the microbes. As a case study, the scientists looked at the mucins that are found in saliva, called "I am so excited about mucus because I am MUC5B. They grew two types of bacteria known to convinced it can help us find new strategies for compete in the mouth: Streptococcus mutans, protecting us from infections, in particular those which forms cavities, and Streptococcus sanguinis, that relate to an overgrowth of harmful microbes," a bacterium associated with healthy oral conditions. said Ribbeck. "My lab and others around the world They found that the harmful Streptococcus mutans have begun to engineer mucin-inspired polymers bacteria quickly outgrew Streptococcus sanguinis and [synthetic] mucus. -
Social Behaviour in Microorganisms 13
13 Social behaviour in microorganisms Kevin R. Foster OVERVIEW Sociobiology has come a long way. We now have Many species do all of this in surface-attached a solid base of evolutionary theory supported communities, known as biofilms, in which the by a myriad of empirical tests. It is perhaps less diversity of species and interactions reaches appreciated, however, that first discussions of bewildering heights. Grouping can even involve social behaviour and evolution in Darwin’s day differentiation and development, as in the spec- drew upon single-celled organisms. Since then, tacular multicellular escape responses of slime microbes have received short shrift, and their moulds and myxobacteria. Like any society, how- full spectrum of sociality has only recently come ever, microbes face conflict, and most groups to light. Almost everything that a microorgan- will involve instances of both cooperation and ism does has social consequences; simply divid- competition among their members. And, as in ing can consume another’s resources. Microbes any society, microbial conflicts are mediated by also secrete a wide range of products that affect three key processes: constraints on rebellion, others, including digestive enzymes, toxins, mol- coercion that enforces compliance, and kinship ecules for communication and DNA that allows whereby cells direct altruistic aid towards clone- genes to mix both within and among species. mates. 13.1 Introduction indeed sociology, microbes have featured in descrip- tions of social life. Prominent among these are the We must be prepared to learn some day, from the students writings of Herbert Spencer, the social philosopher of microscopical pond-life, facts of unconscious mutual sup- who coined the term survival of the fi ttest in the wake port, even from the life of micro-organisms. -
Quorum Sensing Modulates the Epibiotic-Parasitic Relationship
fmicb-09-02049 September 24, 2018 Time: 16:12 # 1 ORIGINAL RESEARCH published: 24 September 2018 doi: 10.3389/fmicb.2018.02049 Quorum Sensing Modulates the Epibiotic-Parasitic Relationship Between Actinomyces odontolyticus and Its Saccharibacteria epibiont, a Nanosynbacter lyticus Strain, TM7x Joseph K. Bedree1,2, Batbileg Bor2, Lujia Cen2, Anna Edlund3, Renate Lux4, Jeffrey S. McLean5, Wenyuan Shi2* and Xuesong He2* 1 Section of Oral Biology, Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States, 2 Department of Microbiology, The Forsyth Institute, Cambridge, MA, United States, 3 Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, United States, 4 Section of Periodontics, Division of Constitutive and Regenerative Sciences, School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States, 5 Department of Periodontics, School of Dentistry, University of Washington, Seattle, WA, United States Edited by: The ultra-small, obligate parasitic epibiont, TM7x, the first and only current member of Sebastian Fraune, Christian-Albrechts-Universität zu Kiel, the long-elusive Saccharibacteria (formerly the TM7 phylum) phylum to be cultivated, Germany was isolated in co-culture with its bacterial host, Actinomyces odontolyticus subspecies Reviewed by: actinosynbacter, XH001. Initial phenotypic characterization of the TM7x-associated Jürgen Tomasch, XH001 co-culture revealed enhanced biofilm formation in the presence of TM7x Helmholtz-Gemeinschaft Deutscher Forschungszentren (HZ), Germany compared to XH001 as monoculture. Genomic analysis and previously published Tim Miyashiro, transcriptomic profiling of XH001 also revealed the presence of a putative AI-2 quorum Pennsylvania State University, United States sensing (QS) operon, which was highly upregulated upon association of TM7x with *Correspondence: XH001. -
Ecological and Evolutionary Implications of Shape During Population Expansion
ECOLOGICAL AND EVOLUTIONARY IMPLICATIONS OF SHAPE DURING POPULATION EXPANSION Submitted by Christopher Lee Coles to the University of Exeter as a thesis for the degree of Doctor of Philosophy in Biological Sciences January 2015 This thesis is available for library use on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. I certify that all material in this thesis which is not my own work has been identified and that no material has previously been submitted and approved for the award of a degree by this or any other University. Signature: ................................... ~ 1 ~ In loving memory of Laura Joan Coles ~ 2 ~ Abstract The spatial spread of populations is one of the most visible and fundamental processes in population and community ecology. Due to the potential negative impacts of spatial spread of invasive populations, there has been intensive research into understanding the drivers of ecological spread, predicting spatial dynamics, and finding management strategies that best constrain or control population expansion. However, understanding the spread of populations has proved to be a formidable task and our ability to accurately predict the spread of these populations has to date been limited. Microbial populations, during their spread across agar plate environments, can exhibit a wide array of spatial patterns, ranging from relatively circular patterns to highly irregular, fractal-like patterns. Work analysing these patterns of spread has mainly focused on the underlying mechanistic processes responsible for these patterns, with relatively little investigation into the ecological and evolutionary drivers of these patterns. With the increased recognition of the links between microbial and macrobial species, it is possible that many of the ecological/evolutionary mechanisms responsible for these patterns of spread at a microbial level extrapolate to the spatial spread of populations in general. -
Phenotypic and Physiological Characterization of the Epibiotic Interaction Between Tm7x and Its Basibiont Actinomyces
HHS Public Access Author manuscript Author Manuscript Author ManuscriptMicrob Author ManuscriptEcol. Author manuscript; Author Manuscript available in PMC 2017 January 01. Published in final edited form as: Microb Ecol. 2016 January ; 71(1): 243–255. doi:10.1007/s00248-015-0711-7. Phenotypic and physiological characterization of the epibiotic interaction between TM7x and its basibiont Actinomyces Batbileg Bor1, Nicole Poweleit2, Justin S. Bois3, Lujia Cen1, Joseph K. Bedree1, Z. Hong Zhou2,4, Robert P. Gunsalus2, Renate Lux1, Jeffrey S. McLean5, Xuesong He1,*, and Wenyuan Shi1,* 1Section of Oral Biology, School of Dentistry, University of California, Los Angeles, CA 90095 2Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095 3Division of Biology and Biological Engineering, California Institute of Technology, MC 114-96, Pasadena, CA 91125 4California Nanosystems Institute, University of California, Los Angeles, California 90095 5Department of Periodontics, University of Washington, Seattle, WA 98195 Abstract Despite many examples of obligate epibiotic symbiosis (one organism living on the surface of another) in nature, such an interaction has rarely been observed between two bacteria. Here, we further characterize a newly reported interaction between a human oral obligate parasitic bacterium TM7x (cultivated member of Candidatus Saccharimonas formerly Candidate Phylum TM7), and its basibiont Actinomyces odontolyticus species (XH001), providing a model system to study epiparasitic symbiosis in the domain Bacteria. Detailed microscopic studies indicate that both partners display extensive morphological changes during symbiotic growth. XH001 cells manifested as short rods in monoculture, but displayed elongated and hyphal morphology when physically associated with TM7x. Interestingly, these dramatic morphological changes in XH001 were also induced in oxygen-depleted conditions, even in the absence of TM7x. -
Science in a New Light Last Experiment on the DORIS Synchrotron, P-CUBE Draws to a Close, and the Story Behind a New Crystal Harvesting Technology
The Newsletter of the European Molecular Biology Laboratory EMBL Issue 72 • December 2012 • www.embl.org/newsletter etcetera Science in a new light Last experiment on the DORIS synchrotron, P-CUBE draws to a close, and the story behind a new crystal harvesting technology Balancing act More than 300 scientists, journalists and members of the public convened at EMBL Heidelberg 9–10 November to discuss one of the most challenging DORIS retired, page 4 issues facing mankind: the increas- ing number of species of plants and animals under threat of extinction. The diverse programme for this year’s Science and Society conference brought together expertise from areas including research, policy, public health and philosophy. The event gave participants the opportunity to voice opinions, hopes and concerns in rela- Crystal harvesting, page 5 P-CUBE legacy, page 3 tion to biodiversity. See page 10 Reviews, rewards and renewals Important decisions made at Winter Council Meeting in November An eventful Winter Council Meeting took place in Hamburg, with delegates discussing and voting on a large number of lab-based issues. Highlights included the announcement of positive reviews of EMBL Heidelberg’s Genome Biology Unit and EMBL Monterotondo’s Mouse Biology Unit, a special contribution from the Luxembourg government to fund joint projects, agreement to take the next steps towards a new outstation, and the appointment of Claudio Sunkel as the new Chair of Council. Find out more on page 2 Meet the new John Kendrew The greatest story What sci-fi head of EMBL Award winner never told? stocking filler 7 Monterotondo 9 11 12 would you give? Winter Council Meeting: Reviews, rewards and renewals Delegates took part in an eventful Winter finance research projects jointly selected by Council Meeting in Hamburg, 27–28 Novem- EMBL and Luxembourg’s National Research ber, where they approved EMBL’s 2013 budget Fund (FNR). -
Metabolic Network Percolation Quantifies Biosynthetic Capabilities
RESEARCH ARTICLE Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome David B Bernstein1,2, Floyd E Dewhirst3,4, Daniel Segre` 1,2,5,6,7* 1Department of Biomedical Engineering, Boston University, Boston, United States; 2Biological Design Center, Boston University, Boston, United States; 3The Forsyth Institute, Cambridge, United States; 4Harvard School of Dental Medicine, Boston, United States; 5Bioinformatics Program, Boston University, Boston, United States; 6Department of Biology, Boston University, Boston, United States; 7Department of Physics, Boston University, Boston, United States Abstract The biosynthetic capabilities of microbes underlie their growth and interactions, playing a prominent role in microbial community structure. For large, diverse microbial communities, prediction of these capabilities is limited by uncertainty about metabolic functions and environmental conditions. To address this challenge, we propose a probabilistic method, inspired by percolation theory, to computationally quantify how robustly a genome-derived metabolic network produces a given set of metabolites under an ensemble of variable environments. We used this method to compile an atlas of predicted biosynthetic capabilities for 97 metabolites across 456 human oral microbes. This atlas captures taxonomically-related trends in biomass composition, and makes it possible to estimate inter-microbial metabolic distances that correlate with microbial co-occurrences. We also found a distinct cluster of fastidious/uncultivated taxa, including several Saccharibacteria (TM7) species, characterized by their abundant metabolic deficiencies. By embracing uncertainty, our approach can be broadly applied to understanding metabolic interactions in complex microbial ecosystems. *For correspondence: DOI: https://doi.org/10.7554/eLife.39733.001 [email protected] Competing interests: The authors declare that no Introduction competing interests exist. -
Co Crouzier Ribbeck Advmatin
DOI: 10.1002/ Article type: Full Paper Title: Probing the Role of Mucin-Bound Glycans in Bacterial Repulsion by Mucin Coatings Julia Y. Co†, Thomas Crouzier†, and Katharina Ribbeck* †These authors contributed equally to this work. J. Y. Co1,2, T. Crouzier1 PhD, and Assistant Professor K. Ribbeck1, PhD 1 Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA 2 Microbiology Graduate Program, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA *E-mail: [email protected] Keywords: Mucin coatings, bacterial attachment, Streptococcus pneumoniae, Staphylococcus aureus, deglycosylation The original version of this manuscript is available at http://onlinelibrary.wiley.com/doi/10.1002/admi.201500179/abstract Copyright WILEY-VCH Verlag GmbH & Co. KGaA, 69469 Weinheim, Germany, 2013. 1 Table of Contents Excerpt Mucin coatings suppress surface attachment by the bacteria Streptococcus pneumoniae and Staphylococcus aureus. Bacterial repulsion by mucin coatings is dependent on the presence of mucin-bound glycans. Upon mucin deglycosylation, the coatings display measurable changes in coating thickness and softness, as well as antifouling capacity. This study highlights the structural and functional role of glycans in mucin coatings. J. Y. Co†, T. Crouzier†, and K. Ribbeck* Probing the Role of Mucin-Bound Glycans in Bacterial Repulsion by Mucin Coatings Abstract Microbial colonization of implanted medical devices in humans can lead to device failure and life-threatening infections. One strategy to prevent this unwanted colonization is to coat devices with polymers that reduce bacterial attachment. This study investigates how mucins, a class of biopolymers found in mucus, can be used as surface coatings to prevent attachment of selected respiratory pathogens to polystyrene surfaces. -
A Preliminary Study of Chemical Profiles of Honey, Cerumen
foods Article A Preliminary Study of Chemical Profiles of Honey, Cerumen, and Propolis of the African Stingless Bee Meliponula ferruginea Milena Popova 1 , Dessislava Gerginova 1 , Boryana Trusheva 1 , Svetlana Simova 1, Alfred Ngenge Tamfu 2 , Ozgur Ceylan 3, Kerry Clark 4 and Vassya Bankova 1,* 1 Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; [email protected] (M.P.); [email protected] (D.G.); [email protected] (B.T.); [email protected] (S.S.) 2 Department of Chemical Engineering, School of Chemical Engineering and Mineral Industries, University of Ngaoundere, 454 Ngaoundere, Cameroon; [email protected] 3 Food Quality Control and Analysis Program, Ula Ali Kocman Vocational School, Mugla Sitki Kocman University, 48147 Ula Mugla, Turkey; [email protected] 4 Volunteer Advisor in Beekeeping and Bee Products with Canadian Executive Services Organization, P.O. Box 2090, Dawson Creek, BC V1G 4K8, Canada; [email protected] * Correspondence: [email protected]; Tel.: +359-2-9606-149 Abstract: Recently, the honey and propolis of stingless bees have been attracting growing atten- tion because of their health-promoting properties. However, studies on these products of African Meliponini are still very scarce. In this preliminary study, we analyzed the chemical composition of honey, two cerumen, and two resin deposits (propolis) samples of Meliponula ferruginea from Tanzania. The honey of M. ferruginea was profiled by NMR and indicated different long-term stability Citation: Popova, M.; Gerginova, D.; from Apis mellifera European (Bulgarian) honey. It differed significantly in sugar and organic acids Trusheva, B.; Simova, S.; Tamfu, A.N.; content and had a very high amount of the disaccharide trehalulose, known for its bioactivities.