DOCSLIB.ORG

Interspecies Interactions That Result in Bacillus Subtilis Forming Biofilms Are

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Interspecies Interactions That Result in Bacillus Subtilis Forming Biofilms Are Interspecies interactions that result in Bacillus subtilis PNAS PLUS forming biofilms are mediated mainly by members of its own genus Elizabeth A. Shanka, Vanja Klepac-Ceraja,1, Leonardo Collado-Torresa,2, Gordon E. Powersa,3, Richard Losickb, and Roberto Koltera,4 aDepartment of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; and bDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 Edited by James M. Tiedje, Michigan State University, East Lansing, MI, and approved October 10, 2011 (received for review March 9, 2011) Many different systems of bacterial interactions have been de- populations of motile cells, matrix-producing cells, and dormant scribed. However, relatively few studies have explored how spores (5, 6). interactions between different microorganisms might influence The regulation of the expression of the epsA-O and tapA bacterial development. To explore such interspecies interactions, operons has been studied extensively (10, 13–20). Both operons we focused on Bacillus subtilis, which characteristically develops are controlled indirectly by the master regulator, phosphory- into matrix-producing cannibals before entering sporulation. We lated Spo0A (Spo0A∼P) (11, 21, 22). This transcription factor investigated whether organisms from the natural environment of modulates the expression of a large number of genes depending B. subtilis—the soil—were able to alter the development of B. on its concentration (23, 24). Low levels of Spo0A∼Pleadtothe subtilis. To test this possibility, we developed a coculture micro- induction of transcription of the epsA-O and tapA operons, colony screen in which we used fluorescent reporters to identify resulting in the production of extracellular matrix and thus soil bacteria able to induce matrix production in B. subtilis. Most of biofilm formation (Fig. 1) (22). At high levels of Spo0A∼P, the bacteria that influence matrix production in B. subtilis are matrix genes are repressed, sporulation genes are induced, and members of the genus Bacillus, suggesting that such interactions these matrix-producing cells go on to become spores. MICROBIOLOGY may be predominantly with close relatives. The interactions The matrix-producing cells have a second important physio- we observed were mediated via two different mechanisms. One logical function: They are cannibals (Fig. 1) (25, 26). These cells resulted in increased expression of matrix genes via the activation produce two toxins, sporulation-delaying protein (SDP) and of a sensor histidine kinase, KinD. The second was kinase indepen- sporulation-killing factor (SKF) (25, 27). To survive, these cells dent and conceivably functions by altering the relative subpopula- also produce immunity proteins (28, 29). Both the toxin and tions of B. subtilis cell types by preferentially killing noncannibals. immunity genes are under the control of Spo0A∼P. These toxins These two mechanisms were grouped according to the inducing are able to kill B. subtilis cells not expressing immunity (those ’ B. subtilis strain s relatedness to . Our results suggest that bacte- that have not yet phosphorylated Spo0A) as well as other ria preferentially alter their development in response to secreted microbes (30). This killing presumably provides the matrix-pro- molecules from closely related bacteria and do so using mecha- ducing cannibal with nutrients and delays sporulation (25). The nisms that depend on the phylogenetic relatedness of the interact- production of biofilm matrix thus is linked intrinsically to this ing bacteria. mechanism of siblicide that prolongs the survival of this sub- population of B. subtilis cells (25, 26). ell–cell interactions are a feature common to all living sys- The levels of Spo0A∼P are controlled by the action of mem- Ctems. Bacteria are no exception, and numerous mechanisms brane-bound histidine sensor kinases (KinA, KinB, KinC, KinD, that use secreted products as signaling molecules are known (1, and KinE) that directly and indirectly phosphorylate Spo0A in 2). Among these, the so-called “quorum sensing” systems are response to still poorly defined environmental cues (31). The perhaps the best studied (3, 4). In quorum sensing, all bacterial activities of these kinases thus control differentiation in B. sub- cells within a population produce secreted molecules. Only when tilis (31–33). KinC has a role in defining the matrix-producing population densities are high is there a response to these com- cannibal subpopulation when it is activated by the self-produced pounds, thus allowing the bacteria to coordinate their behavior. molecule surfactin (34). Purified natural products functionally However, it is clear that there is much more to bacterial cell–cell related to surfactin but produced by other bacteria also induce interactions than simply counting numbers and coordinating matrix synthesis in B. subtilis in a KinC-dependent manner behavior. Secreted molecules also play key roles in microbial (34). In addition, nisin, an antimicrobial produced by Lactococcus development so that different cell fates can arise and coexist within a single-species population (5, 6). In addition, in settings where multiple species coexist, their interactions often are me- Author contributions: E.A.S., R.L., and R.K. designed research; E.A.S., L.C.-T., and G.E.P. diated through extracellular compounds. Development in one performed research; E.A.S. and V.K.-C. analyzed data; and E.A.S., R.L., and R.K. wrote microbe can be influenced by small molecules secreted by other the paper. species (7, 8). The authors declare no conflict of interest. We have been interested in understanding the role of in- This article is a PNAS Direct Submission. terspecies interactions in the well-studied developmental pro- Data deposition: The sequences reported in this paper have been deposited in the Gen- cesses that the soil bacterium Bacillus subtilis undergoes during Bank database (accession nos. JF501232–JF501388 and JF496856–JF496919). biofilm formation. Biofilms are aggregations of cells held to- 1Present address: Forsyth Institute, Cambridge, MA 02142. gether by an extracellular matrix (9, 10). The matrix has two main 2Present address: Winter Genomics, Mexico City, Mexico 07300. components, an exopolysaccharide synthesized by the products 3Present address: Stanford University School of Medicine, Stanford, CA 94305. fi of the epsA-O operon, and amyloid bers encoded by the prod- 4To whom correspondence should be addressed. E-mail: [email protected]. ucts of the tapA operon (formerly yqxM) (9, 11, 12). Within This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. biofilms, several different cell types coexist, including sub- 1073/pnas.1103630108/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1103630108 PNAS Early Edition | 1of8 Downloaded by guest on September 24, 2021 Pseudomonas (1) Matrix-producing Spores A cannibals Erwinia (1) Bacillus (2) Toxins Pasteuriaceae B. subtilis Incertae Sedis (1) Matrix [ Spo0A~P ] Unclassified Enterobacteriaceae (4) Fig. 1. Diagram illustrating the development of B. subtilis into matrix- Enterobacter (6) producing cannibals and then spores. At low Spo0A∼P levels B. subtilis activates genes required for the production of matrix and produces two cannibalism toxins. At high Spo0A∼P levels sporulation begins. Bacillus (2) B Paenibacillus (1) Pasteuriaceae lactis, induces a hypercannibalism phenotype in B. subtilis (26). Pseudomonas (2) Incertae Sedis (1) Thus, small molecules from numerous bacteria are capable of influencing differentiation in B. subtilis. This observation sug- Raoutella (1) gests that B. subtilis development may be influenced by the Buttiauxella (1) presence of other bacteria in natural settings. We therefore hypothesized that other soil microbes, when grown next to B. subtilis, might trigger its differentiation into Unclassified Enterobacter (3) matrix-producing cannibals. To investigate these possible in- Enterobacteriaceae (4) B. subtilis terspecies interactions, we developed a screen in which Fig. 2. The cultivable organisms growing under the microcolony coculture and soil microorganisms were cocultured. While the colonies screen conditions are phylogenetically diverse. Soil organisms were selected grew, we monitored B. subtilis differentiation into matrix pro- systematically from random fields of view of soil A and soil B (grown as for ducers using a fluorescent reporter. In this way we identified coculture screen) and were isolated. (A) The 16S rRNA gene from 71 isolates a large number of soil organisms that induced differentiation in from soil A and (B) 89 isolates from soil B were sequenced. The pie chart B. subtilis. The majority of these organisms were other members sectors are proportional to the number of representatives within each la- of the genus Bacillus. This result led us to explore how broadly beled group. The number of operational taxonomic units at the 99% level distributed the ability to induce matrix production is among a within that group is noted in parentheses. The darkly shaded exploded wedges represent the Firmicutes, whose representatives are all within the range of phylogenetically diverse Bacillus species. We found that class Bacillales. All other sequences were from Proteobacteria. many Bacillus species induce matrix production in B. subtilis, and the mechanisms they use are grouped according to their phylo- genetic relatedness to B. subtilis. We therefore suggest that the We conducted interspecies-interaction
Load more

Recommended publications
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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
    [Show full text]
  • Bacterial Degradation of Isoprene in the Terrestrial Environment Myriam
    Bacterial Degradation of Isoprene in the Terrestrial Environment Myriam El Khawand A thesis submitted to the University of East Anglia in fulfillment of the requirements for the degree of Doctor of Philosophy School of Environmental Sciences November 2014 ©This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that use of any information derive there from must be in accordance with current UK Copyright Law. In addition, any quotation or extract must include full attribution. Abstract Isoprene is a climate active gas emitted from natural and anthropogenic sources in quantities equivalent to the global methane flux to the atmosphere. 90 % of the emitted isoprene is produced enzymatically in the chloroplast of terrestrial plants from dimethylallyl pyrophosphate via the methylerythritol pathway. The main role of isoprene emission by plants is to reduce the damage caused by heat stress through stabilizing cellular membranes. Isoprene emission from microbes, animals, and humans has also been reported, albeit less understood than isoprene emission from plants. Despite large emissions, isoprene is present at low concentrations in the atmosphere due to its rapid reactions with other atmospheric components, such as hydroxyl radicals. Isoprene can extend the lifetime of potent greenhouse gases, influence the tropospheric concentrations of ozone, and induce the formation of secondary organic aerosols. While substantial knowledge exists about isoprene production and atmospheric chemistry, our knowledge of isoprene sinks is limited. Soils consume isoprene at a high rate and contain numerous isoprene-utilizing bacteria. However, Rhodococcus sp. AD45 is the only terrestrial isoprene-degrading bacterium characterized in any detail.
    [Show full text]
  • 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.
    [Show full text]
  • Integrated Management of Mi-1 Virulent Meloidogyne Incognita
    Türk. entomol. derg., 2019, 43 (2): 157-169 ISSN 1010-6960 DOI: http://dx.doi.org/10.16970/entoted.526844 E-ISSN 2536-491X Original article (Orijinal araştırma) Integrated management of Mi-1 virulent Meloidogyne incognita (Kofoid & White, 1919) Chitwood, 1949 (Tylenchida: Meloidogynidae) in greenhouse tomatoes1 Örtüaltı domates yetiştiriciliğinde Mi-1 virülent Meloidogyne incognita (Kofoid & White, 1919) Chitwood, 1949 (Tylenchida: Meloidogynidae)’ya karşı entegre mücadele Mustafa ÇATALKAYA2 Zübeyir DEVRAN2* Abstract The Mi-1 gene in tomato provides a safe and economical strategy for managing root-knot nematodes (RKN). However, the resistance conferred by the Mi-1 gene is not effective against virulent populations of RKNs. In this study, the efficacy of combining the dose effect of the Mi-1 gene with Bacillus firmus Bredemann & Wermer, 1933 (Bacillales: Bacillaceae) + fluopyram against Mi-1-virulent Meloidogyne incognita (Kofoid & White, 1919) Chitwood, 1949 (Tylenchida: Meloidogynidae) after soil solarization was assessed for tomatoes grown in a greenhouse. The study was conducted in a greenhouse in Kepez, Antalya between 2015 and 2016. The second-stage juveniles M. incognita were not detected in the soil for 2 months after solarization completed. The reactions of homozygous or heterozygous resistant tomato plants against Mi-1-virulent populations were not statistically different under greenhouse conditions. Furthermore, B. firmus + fluopyram controlled the RKN population when applied to the soil both during the planting period and when J2 count in the soil started to increase. This study suggests that the soil solarization should be combined with other management methods, and the dose effect of the Mi-1 gene is not important against virulent RKN populations.
    [Show full text]
  • Reorganising the Order Bacillales Through Phylogenomics
    Systematic and Applied Microbiology 42 (2019) 178–189 Contents lists available at ScienceDirect Systematic and Applied Microbiology jou rnal homepage: http://www.elsevier.com/locate/syapm Reorganising the order Bacillales through phylogenomics a,∗ b c Pieter De Maayer , Habibu Aliyu , Don A. Cowan a School of Molecular & Cell Biology, Faculty of Science, University of the Witwatersrand, South Africa b Technical Biology, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Germany c Centre for Microbial Ecology and Genomics, University of Pretoria, South Africa a r t i c l e i n f o a b s t r a c t Article history: Bacterial classification at higher taxonomic ranks such as the order and family levels is currently reliant Received 7 August 2018 on phylogenetic analysis of 16S rRNA and the presence of shared phenotypic characteristics. However, Received in revised form these may not be reflective of the true genotypic and phenotypic relationships of taxa. This is evident in 21 September 2018 the order Bacillales, members of which are defined as aerobic, spore-forming and rod-shaped bacteria. Accepted 18 October 2018 However, some taxa are anaerobic, asporogenic and coccoid. 16S rRNA gene phylogeny is also unable to elucidate the taxonomic positions of several families incertae sedis within this order. Whole genome- Keywords: based phylogenetic approaches may provide a more accurate means to resolve higher taxonomic levels. A Bacillales Lactobacillales suite of phylogenomic approaches were applied to re-evaluate the taxonomy of 80 representative taxa of Bacillaceae eight families (and six family incertae sedis taxa) within the order Bacillales.
    [Show full text]
  • Controlling the Meloidogyne Disease Complex in Ugandan Tomatoes
    Adrian Wolfgang BSc Controlling the Meloidogyne disease complex in Ugandan tomatoes MASTER’S THESIS To achieve the university degree of Master of Science Master degree program: Ecology and Evolutionary Biology Submitted to Karl-Franzens University Graz Supervisor Priv.-Doz. Mag. Dr.rer.nat. Günther Raspotnig Institute of Biology Graz, April 2018 In cooperation with: ❆✩✩✪✫❆✬✪✭ 2 AFFIDAVIT Ich erkläre ehrenwörtlich, dass ich die vorliegende Arbeit selbständig und ohne fremde Hilfe verfasst, andere als die angegebenen Quellen nicht benutzt und die den Quellen wörtlich oder inhaltlich entnommenen Stellen als solche kenntlich gemacht habe. Die Arbeit wurde bisher in gleicher oder ähnlicher Form keiner anderen inländischen oder ausländischen Prüfungsbehörde vorgelegt und auch noch nicht veröffentlicht. Die vorliegende Fassung entspricht der eingereichten elektronischen Version. I declare that I have authored this thesis independently, that I have not used other than the declared sources/resources, and that I have explicitly indicated all material which has been quoted either literally or by content from the sources used. The text document uploaded to UNIGRAZonline is identical to the present master’s thesis. ________________________ _____________________________________ Date Signature 3 Table of contents Table of contents ........................................................................................................................ 4 0.1 Abstract ..........................................................................................................................
    [Show full text]
  • POPULATION DYNAMICS of Pasteuria Penetrans in a PEANUT FIELD and DESCRIPTION of a Pasteuria ISOLATE INFECTING Mesocriconema Ornatum
    POPULATION DYNAMICS OF Pasteuria penetrans IN A PEANUT FIELD AND DESCRIPTION OF A Pasteuria ISOLATE INFECTING Mesocriconema ornatum By JOEY ISURITA ORAJAY A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2009 1 © 2009 Joey Isurita Orajay 2 To my Tatay and Nanay for their 50th wedding anniversary 3 ACKNOWLEDGMENTS This dissertation came in part out of long history of research done on Pasteuria penetrans in the Nematode Management Laboratory headed by Dr. Dickson. When I joined the research group in 2004, I have worked with a number of scientists and peers who made various contributions to honing my scientific perspectives and skills in conducting studies. I also got involved in several activities and organizations in the university that gave me chances to have productive interactions with a diverse group of people. To all of them, I wish to convey my sincerest appreciation. Foremost, I would like to express my gratitude to Dr. Donald W. Dickson, my major professor and dissertation adviser, for his unwavering support and constant guidance throughout my stay in his laboratory. I also thank him for instilling confidence in me by believing that I can do this research. His passion in nematology is truly worth emulating and it was such an honor for me to being part of his research team. I also express my gratefulness to the members of my advisory committee, Drs. James F. Preston, William T. Crow, Robin M. Giblin-Davis and Janet A.
    [Show full text]
  • Protein Profiling As a Tool for Identifying Environmental Aerobic Endospore-Forming Bacteria
    vv ISSN: 2640-8007 DOI: https://dx.doi.org/10.17352/ojb LIFE SCIENCES GROUP Received: 11 January, 2020 Research Article Accepted: 11 March, 2020 Published: 12 March, 2020 *Corresponding author: Marlene Teixeira De-Souza, Protein profi ling as a tool for Department of Cellular Biology, University of Brasilia, Darcy Ribeiro University Campus, 70.910-900 Brasilia, DF, Brazil, Tel: +55 61 3107-3044; identifying environmental E-mail: ORCiD: https://orcid.org/0000-0003-1538-2657 aerobic endospore-forming Keywords: Bacillales; Taxonomy; Phenotype; Genotype; MALDI-TOF-MS bacteria https://www.peertechz.com Paulo Henrique R Martins1, Luciano Paulino da Silva2, Juliana Capella de Orem1, Maria Inês A de Magalhães1, Danilo de Andrade Cavalcante1 and Marlene Teixeira De- Souza1* 1Department of Cellular Biology, University of Brasilia, Darcy Ribeiro University Campus, Brasilia, DF, Brazil 2Embrapa Genetic Resources and Biotechnology, Caixa Postal 02372, Brasilia, DF, Brazil Abstract Aerobic Endospore-Forming Bacteria (AEFB) are taxonomically and physiologically diverse, comprising species of genus Bacillus and related genera of industrial and medical importance. For taxonomic purpose, we applied the matrix-assisted laser desorption/ionization mass spectrometry with time-of-fl ight to identify 64 environmental AEFB (SDF for Solo do Distrito Federal) and compare the results with those obtained using 16S rRNA gene sequencing. Concordance between the two methods was observed for 93,75% samples at the genus level. Strains were clustered between 2 genera (family Bacillaceae): Bacillus, the most prevalent, and Lysinibacillus. Two other genera, Brevibacillus and Paenibacillus (family Paenibacillaceae) were also distinguished. Gene similarity discriminated an additional genus (Rummeliibacillus). At the species level, the genotyping method achieved superior capacity identifying 93,75% strains.
    [Show full text]
  • Gut Microbiota and Obesity: a Role for Probiotics
    nutrients Review Gut Microbiota and Obesity: A Role for Probiotics Ludovico Abenavoli 1,* , Emidio Scarpellini 2, Carmela Colica 3 , Luigi Boccuto 4,5 , Bahare Salehi 6 , Javad Sharifi-Rad 7 , Vincenzo Aiello 8, Barbara Romano 9, Antonino De Lorenzo 10 , Angelo A. Izzo 9 and Raffaele Capasso 11,* 1 Department of Health Sciences, University Magna Graecia, Campus “Salvatore Venuta”, 88100 Catanzaro, Italy 2 Clinical Nutrition Unit, and Internal Medicine Unit, “Madonna del Soccorso” General Hospital, Via Luciano Manara 7, 63074 San Benedetto del Tronto (AP), Italy; [email protected] 3 CNR, IBFM UOS, Università degli Studi “Magna Graecia” di Catanzaro, Campus “Salvatore Venuta”, 88100 Catanzaro, Italy; [email protected] 4 Greenwood Genetic Center, Greenwood, SC 29646, USA; [email protected] 5 Clemson University School of Health Research, Clemson, SC 29634, USA 6 Student Research Committee, School of Medicine, Bam University of Medical Sciences, Bam 44340847, Iran; [email protected] 7 Zabol Medicinal Plants Research Center, Zabol University of Medical Sciences, Zabol 61615585, Iran; javad.sharifi[email protected] 8 Department of Medical and Surgical Sciences, University of Magna Græcia, Viale Europa, Germaneto, 88100 Catanzaro, Italy; [email protected] 9 Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy; [email protected] (B.R.); [email protected] (A.A.I.) 10 Division of Clinical Nutrition and Nutrigenomic, Department of Biomedicine and Prevention, University of Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; [email protected] 11 Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici (NA), Italy * Correspondence: [email protected] (L.A.); [email protected] (R.C.); Tel.: +39-0961-369-4387 (L.A.); +39-081-678-664 (R.C.) Received: 10 August 2019; Accepted: 24 September 2019; Published: 7 November 2019 Abstract: Nowadays, obesity is one of the most prevalent human health problems.
    [Show full text]
  • Understanding Molecular Identification and Polyphasic
    Journal of Microbiological Methods 103 (2014) 80–100 Contents lists available at ScienceDirect Journal of Microbiological Methods journal homepage: www.elsevier.com/locate/jmicmeth Review Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms Surajit Das ⁎, Hirak R. Dash, Neelam Mangwani, Jaya Chakraborty, Supriya Kumari Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India article info abstract Article history: The major proportion of earth's biological diversity is inhabited by microorganisms and they play a useful role in Received 21 November 2013 diversified environments. However, taxonomy of microorganisms is progressing at a snail's pace, thus less than Received in revised form 22 May 2014 1% of the microbial population has been identified so far. The major problem associated with this is due to a lack Accepted 22 May 2014 of uniform, reliable, advanced, and common to all practices for microbial identification and systematic studies. Available online 2 June 2014 However, recent advances have developed many useful techniques taking into account the house-keeping Keywords: genes as well as targeting other gene catalogues (16S rRNA, rpoA, rpoB, gyrA, gyrB etc. in case of bacteria and β Bacteria 26S, 28S, -tubulin gene in case of fungi). Some uncultivable approaches using much advanced techniques like Fungi flow cytometry and gel based techniques have also been used to decipher microbial diversity. However, all Molecular identification these techniques have their corresponding pros and cons. In this regard, a polyphasic taxonomic approach is ad- Gene sequencing vantageous because it exploits simultaneously both conventional as well as molecular identification techniques.
    [Show full text]