• Activity and composition of methanotrophic bacterial communities in planted rice soil studied by flux measurements, analyses of pmoA gene and stable isotope probing of phospholipid fatty acids.

      Shrestha, Minita; Abraham, Wolf-Rainer; Shrestha, Pravin Malla; Noll, Matthias; Conrad, Ralf; Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Strasse, D-35043, Marburg, Germany. (2008-02)
      Methanotrophs in the rhizosphere of rice field ecosystems attenuate the emissions of CH(4) into the atmosphere and thus play an important role for the global cycle of this greenhouse gas. Therefore, we measured the activity and composition of the methanotrophic community in the rhizosphere of rice microcosms. Methane oxidation was determined by measuring the CH(4) flux in the presence and absence of difluoromethane as a specific inhibitor for methane oxidation. Methane oxidation started on day 24 and reached the maximum on day 32 after transplantation. The total methanotrophic community was analysed by terminal restriction fragment length polymorphism (T-RFLP) and cloning/sequencing of the pmoA gene, which encodes a subunit of particulate methane monooxygenase. The metabolically active methanotrophic community was analysed by stable isotope probing of microbial phospholipid fatty acids (PLFA-SIP) using (13)C-labelled CH(4) directly added to the rhizospheric region. Rhizospheric soil and root samples were collected after exposure to (13)CH(4) for 8 and 18 days. Both T-RFLP/cloning and PLFA-SIP approaches showed that type I and type II methanotrophic populations changed over time with respect to activity and population size in the rhizospheric soil and on the rice roots. However, type I methanotrophs were more active than type II methanotrophs at both time points indicating they were of particular importance in the rhizosphere. PLFA-SIP showed that the active methanotrophic populations exhibit a pronounced spatial and temporal variation in rice microcosms.
    • Adaptation of microbial communities in soil contaminated with polychlorinated biphenyls, leading to the transformation of more highly chlorinated congeners in biofilm communities

      Macedo, A.J.; Neu, T. R.; Kuhlicke, U.; Abraham, W.-R.; 'Helmholtz Zentrum für Infektionsforschung (Cambridge University Press, 2006)
    • Adenosine in the inflamed gut: a Janus faced compound.

      Estrela, A B; Abraham, W-R; Helmholtz Center for Infection Research, Chemical Microbiology, Inhoffenstrasse 7, 38124 Braunschweig, Germany. (2011)
      The purine ribonucleoside adenosine (Ado) has been recognized for its regulatory functions in situations of cellular stress like ischemia, hypoxia and inflammation. The importance of extracellular Ado as a modulator in the immune system is a theme of great appreciation and the focus of recent increasing interest in the field of gastrointestinal inflammation. In this review, the different aspects of Ado signaling during inflammatory responses in the gut are discussed, considering the contribution of the four known Ado receptors (ARs; A(1), A(2A), A(2B), and A(3)), their mechanisms and expression patterns. Activation of these receptors in epithelial cells as well as in immune cells recruited to the inflamed intestinal mucosa determines the overall effect, ranging from a protective, anti-inflammatory modulation to a strong pro-inflammatory induction. Here we present the current advances in agonists and antagonists development and their potential therapeutic application studied in animal models of intestinal inflammation. In addition, alternative complementary approaches to manipulate such a complex signaling system are discussed, for example, the use of AR allosteric modulators or interference with Ado metabolism. Special features of the gut environment are taken into account: the contribution of diet components; the involvement of Ado in intestinal infections; the interactions with the gut microbiome, particularly, the recent exciting finding that an intestinal bacterium can directly produce extracellular Ado in response to host defense mechanisms in an inflammation scenario. Understanding each component of this dynamic system will broaden the possibilities for applying Ado signaling as a therapeutic target in gut inflammation.
    • Antimicrobial and biofilm inhibiting diketopiperazines.

      de Carvalho, M P; Abraham, W-R; Helmholtz Center for Infection Research, Chemical Microbiology, Inhoffenstrasse 7, 38124 Braunschweig, Germany. wolf-rainer.abraham@helmholtz-hzi.de. (2012-07-01)
      Diketopiperazines are the smallest cyclic peptides known. 90% of Gram-negative bacteria produce diketopiperazines and they have also been isolated from Gram-positive bacteria, fungi and higher organisms. Biosynthesis of cyclodipeptides can be achieved by dedicated nonribosomal peptide synthetases or by a novel type of synthetases named cyclopeptide synthases. Since the first report in 1924 a large number of bioactive diketopiperazines was discovered spanning activities as antitumor, antiviral, antifungal, antibacterial, antiprion, antihyperglycemic or glycosidase inhibitor agents. As infections are of increasing concern for human health and resistances against existing antibiotics are growing this review focuses on the antimicrobial activities of diketopiperazines. The antibiotic bicyclomycin is a diketopiperazine and structure activity studies revealed the unique nature of this compound which was finally developed for clinical applications. The antimicrobial activities of a number of other diketopiperazines along with structure activity relationships are discussed. Here a special focus is on the activity-toxicity problem of many compounds setting tight limitations to their application as drugs. Not only these classical antimicrobial activities but also proposed action in modulating bacterial communication as a new target to control biofilms will be evaluated. Pathogens organized in biofilms are difficult to eradicate because of the increase of their tolerance for antibiotics for several orders. Diketopiperazines were reported to modulate LuxR-mediated quorum-sensing systems of bacteria, and they are considered to influence cell-cell signaling offering alternative ways of biofilm control by interfering with microbial communication. Concluding the review we will finally discuss the potential of diketopiperazines in the clinic to erase biofilm infections.
    • Applications and impacts of stable isotope probing for analysis of microbial interactions.

      Abraham, Wolf-Rainer; group of Chemical microbiology, Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany. (2014-06)
      Probing the interactions between microbes and their environment with stable isotopes became a powerful technique over the last years. While quadruple mass spectrometry or isotope ratio mass spectrometry (IRMS) require at least 300,000 bacterial cells, analysis at the single-cell level is possible with secondary ion mass spectrometry (SIMS) or Raman microspectrometry. While SIMS needs enrichments of more than 0.1 and Raman microscopy of more than 25 at.-%, IRMS can deal with 0.0001 at.-%. To find out who eats what, one has to discern between the different species in a community. Several methods have been introduced to discern between the different taxa in microbial communities, e.g., by using fatty acids as biomarkers, density centrifugation of DNA/RNA, or fluorescent in situ hybridization (FISH) with phylogenetic probes. While the biomarker approach can be coupled with the high sensitivity of the IRMS, the DNA approach gives in general a better phylogenetic resolution of the metabolic active microbes. A combination of both is the separation via coupling of FISH-probes to magnetic beads or fluorescent assisted cell sorting (FACS) of stained cells leading to fractions which can be analyzed by IRMS. Applying these techniques over a time course can reveal the metabolic kinetics and food webs. In this review, the different methods are presented with examples and their advantages and disadvantages are discussed. An outlook on the combination of the various techniques and their applications in microbial ecology is given.
    • Arvoredol: An unusual chlorinated and biofilm inhibiting polyketide from a marine Penicillium sp. of the Brazilian coast

      Scopel, Marina; Mothes, Beatriz; Lerner, Clea B.; Henriques, Am?lia T.; Macedo, Alexandre J.; Abraham, Wolf-Rainer; Helmholtz Centre for infection research, Inhoffenstr. 7., 38124 Braunschweig, Germany. (2017-06)
      Penicillium sp. F37 has been isolated from the marine sponge Axinella corrugata and shown to be closely related to Penicillium maximae. From the culture of Penicillium sp. F37 arvoredol, a novel chlorinated polyketide with 6,7-dihydro-4(5H)-benzofuranone moiety has been isolated and characterized by spectroscopic methods Arvoredol prevented biofilm formation of the human pathogen Staphylococcus epidermidis at a concentration of 125 μg mL−1 by 40%. It was also active against colorectal carcinoma HCT116 cells with a MIC of 7.9 μg mL−1. © 2017 Phytochemical Society of Europe
    • Asticcacaulis benevestitus sp. nov., a psychrotolerant, dimorphic, prosthecate bacterium from tundra wetland soil.

      Vasilyeva, Lina V; Omelchenko, Marina V; Berestovskaya, Yulia Y; Lysenko, Anatolii M; Abraham, Wolf-Rainer; Dedysh, Svetlana N; Zavarzin, George A; S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/2, Moscow 117312, Russia. (2006-09)
      A Gram-negative, aerobic, heterotrophic, non-pigmented, dimorphic prosthecate bacterium was isolated from tundra wetland soil and designated strain Z-0023(T). Cells of this strain had a dimorphic life cycle and developed a non-adhesive stalk at a site not coincident with the centre of the cell pole, a characteristic typical of representatives of the genus Asticcacaulis. A highly distinctive feature of cells of strain Z-0023(T) was the presence of a conical, bell-shaped sheath when grown at low temperature. This prosthecate bacterium was a psychrotolerant, moderately acidophilic organism capable of growth between 4 and 28 degrees Celsius (optimum 15-20 degrees Celsius) and between pH 4.5 and 8.0 (optimum 5.6-6.0). The major phospholipid fatty acid was 18 : 1omega7c and the major phospholipids were phosphatidylglycerols. The G+C content of the DNA was 60.4 mol%. On the basis of 16S rRNA gene sequence similarity, strain Z-0023(T) was most closely related to Asticcacaulis biprosthecium (98 % similarity), Asticcacaulis taihuensis (98 %) and Asticcacaulis excentricus (95 %). However, low levels of DNA-DNA relatedness to these organisms and a number of distinctive features of the tundra wetland isolate indicated that it represented a novel species of the genus Asticcacaulis, for which the name Asticcacaulis benevestitus sp. nov. is proposed. The type strain is Z-0023(T) (=DSM 16100(T)=ATCC BAA-896(T)).
    • Bioactive Compounds Produced by Hypoxylon fragiforme against Staphylococcus aureus Biofilms.

      Yuyama, Kamila Tomoko; Chepkirui, Clara; Wendt, Lucile; Fortkamp, Diana; Stadler, Marc; Abraham, Wolf-Rainer; Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2017-12-12)
      Treating infections organized in biofilms is a challenge due to the resistance of the pathogens against antibiotics and host immune cells. Many fungi grow in a wet environment, favorable for the growth of bacterial biofilms, and we speculated that fungi possess some strategies to control these bacterial biofilms. A fungus identified as Hypoxylon fragiforme, was collected in the Harz Mountains, Germany, and its mycelial culture was fermented in different culture media for 67 days to test its biological potential against bacterial biofilms. Sclerin, sclerin diacid and its 3-methyl monoester (methyl 1-(5-hydroxy-6-carboxylic-2,3,4-trimethylphenyl) propionate) are here described for the first time from this fungus. Sclerin and its diacid interfered with the biofilm formation of the pathogen Staphylococcus aureus, inhibiting 86% and 80% of the biofilm at 256 μg mL-1, respectively, but not killing the bacterium. Interestingly, the monomethylester of sclerin diacid was inactive. Although these compounds did not possess any activity against a pre-formed biofilm, they prevented its formation at subtoxic concentrations. Furthermore, sclerin and its diacid displayed a high specificity against Staphylococcus aureus, indicating a good strategy against pathogenic biofilms when combined with antibiotics.
    • Brevundimonas vancanneytii sp. nov., isolated from blood of a patient with endocarditis.

      Estrela, Andréia B; Abraham, Wolf-Rainer; Helmholtz Center for Infection Research, Chemical Microbiology, Inhoffenstrasse 7, 38124 Braunschweig, Germany. (2010-09)
      A Gram-negative, rod-shaped, non-spore-forming bacterial strain, designated LMG 2337(T), was isolated from the blood of a patient with endocarditis and characterized. The strain was affiliated with the alphaproteobacterial genus Brevundimonas, with Brevundimonas diminuta LMG 2089(T) (98.3 % 16S rRNA gene sequence similarity) and Brevundimonas terrae KSL-145(T) (97.5 %) as its closest relatives. This affiliation was supported by chemotaxonomic data: the G+C content was 66.3 mol %, the major polar lipids were phosphatidyl diacylglycerol, sulfoquinovosyl diacylglycerol and phosphatidyl glucopyranosyl diacylglycerol and the major fatty acids were summed feature 7 (one or more of C(18 : 1)ω 7c, C(18 : 1)ω 9t and C(18 : 1)ω 12t) and C(16 : 0). Strain LMG 2337(T) displayed an unusually broad substrate spectrum. The results from DNA-DNA hybridization and physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain LMG 2337(T) from all of the type strains of hitherto-described Brevundimonas species. The strain therefore represents a novel species, for which the name Brevundimonas vancanneytii sp. nov. is proposed, with type strain LMG 2337(T) (=CCUG 1797(T) =ATCC 14736(T)).
    • Cauliform bacteria lacking phospholipids from an abyssal hydrothermal vent: proposal of Glycocaulis abyssi gen. nov., sp. nov., belonging to the family Hyphomonadaceae.

      Abraham, Wolf-Rainer; Lünsdorf, Heinrich; Vancanneyt, Marc; Smit, John; Helmholtz Center for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany. wolf-rainer.abraham@helmholtz-hzi.de (2013-06)
      Cauliform bacteria are prosthecate bacteria often specialized for oligotrophic environments. A polyphasic approach, comprising 16S rRNA gene sequencing, lipid analysis and salt tolerance characterizations, was used to clarify the taxonomy of one isolate, strain MCS 33(T), obtained from above the hot water plume of a deep-sea hydrothermal vent near Vancouver island, Canada. Cells contained no detectable phospholipids or sulpholipids, but did contain 1,2-di-O-acyl-3-O-α-D-glucopyranosylglycerol, 1,2-di-O-acyl-3-O-α-D-glucopyranuronosylglycerol and the novel lipid 1,2-di-O-acyl-3-[O-α-D-glucopyranuronosyl]glycerol-6'-N-glycine. It is assumed that the various glucoronosyl lipids are replacing, at least partially, the phospholipids in their various tasks in the cell cycle. The G+C content of the genomic DNA of strain MCS 33(T) was 62.8 mol%, and Q10 was the predominant respiratory ubiquinone. The 16S rRNA gene sequence of this chemoheterotrophic, aerobic, moderately halophilic strain showed only a low similarity of 94.4% to that of Oceanicaulis alexandrii C116-18(T), and both strains also differed based on their lipids. Although the novel strain was isolated from seawater sampled near a hydrothermal vent, its optimum temperature for growth was 30 °C. The main cellular fatty acids were C18:1ω7c, C18:0 and the unknown fatty acid ECL 11.798, and the main hydroxy fatty acid was C12:0 3-OH. The strain is proposed to represent a novel species of a new genus, Glycocaulis abyssi gen. nov., sp. nov. The type strain of the type species is MCS 33(T) (=LMG 27140(T)=CCUG 62981(T)).
    • Chemische Funktionalisierung und Materialoptimierung dentaler Implantat-Abutments zur Reduktion der oralen Biofilmbildung

      Stiesch, Meike; Menzel, Henning; Abraham, Wolf-Rainer; Müller, Peter Paul; Dempwolf, Wiebke; Pfaffenroth, Cornelia; Kohorst, Phillip; Winkel, Andreas; Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany. (Druckerei der Medizinischen Hochschule, 2012-07-06)
    • cis-2-Alkenoic acids as promising drugs for the control of biofilm infections.

      Yuyama, Kamila Tomoko; Abraham, Wolf-Rainer; Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2016-05-06)
      Microbes attached to surfaces and form biofilms where they are difficult to eradicate. Here they are embedded in a complex matrix of polymers and are much less sensitive against antibiotics or the immune system.
    • Combining Biofilm-Controlling Compounds and Antibiotics as a Promising New Way to Control Biofilm Infections.

      Estrela, Andréia Bergamo; Abraham, Wolf-Rainer; Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2010-05-11)
      Many bacteria grow on surfaces forming biofilms. In this structure, they are well protected and often high dosages of antibiotics cannot clear infectious biofilms. The formation and stabilization of biofilms are mediated by diffusible autoinducers (e.g. N-acyl homoserine lactones, small peptides, furanosyl borate diester). Metabolites interfering with this process have been identified in plants, animals and microbes, and synthetic analogues are known. Additionally, this seems to be not the only way to control biofilms. Enzymes capable of cleaving essential components of the biofilm matrix, e.g. polysaccharides or extracellular DNA, and thus weakening the biofilm architecture have been identified. Bacteria also have mechanisms to dissolve their biofilms and return to planktonic lifestyle. Only a few compounds responsible for the signalling of these processes are known, but they may open a completely novel line of biofilm control. All these approaches lead to the destruction of the biofilm but not the killing of the pathogens. Therefore, a combination of biofilm-destroying compounds and antibiotics to handle biofilm infections is proposed. In this article, different approaches to combine biofilm-controlling compounds and antibiotics to fight biofilm infections are discussed, as well as the balance between biofilm formation and virulence.
    • Community-based degradation of 4-chorosalicylate tracked on the single cell level.

      Pawelczyk, Sonja; Abraham, Wolf-Rainer; Harms, Hauke; Müller, Susann; University of Oxford, Department of Biochemistry, South Parks Road, OX1 3QU, Oxford, UK. (2008-09)
      4-Chlorosalicylate (4-CS) can be degraded completely by a bacterial consortium consisting of Pseudomonas reinekei (MT1), Achromobacter spanius (MT3) and Pseudomonas veronii (MT4). The fourth species Wautersiella falsenii (MT2) is thought to act as a 'necrotizer' of the community. Single cell approaches were used to follow every species' degradation activity within the community by assuming that growth and proliferation are activity markers for the utilization of 4-CS and its degradation pathway intermediates as carbon and energy sources. A primary/secondary antibody staining technique for species differentiation was applied and a species-resolved determination of proliferation activity by flow cytometry undertaken. Degradation was followed by quantifying 4-CS and the resulting intermediates by HPLC. A good correlation of HPLC bulk data with the proliferation activity states of every species within the community was found. It was also assumed that reduced activity of strain MT4 and increased proliferation of strain MT2 might have caused an observed breakdown of the consortium grown in the bioreactor. The double staining technique provided the chance to follow bacterial cell states and their roles in mixed cultures without applying labelled substrates. It is therefore in line with single cell techniques already successfully applied in biotechnology for developing strategies to optimize microbially catalyzed production processes.
    • Coprinuslactone protects the edible mushroom Coprinus comatus against biofilm infections by blocking both quorum-sensing and MurA.

      de Carvalho, Maira P; Gulotta, Giuseppe; do Amaral, Matheus W; Lünsdorf, Heinrich; Sasse, Florenz; Abraham, Wolf-Rainer; Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2016-10-03)
      Pathogens embedded in biofilms are involved in many infections and are very difficult to treat with antibiotics because of higher resistance compared to planktonic cells. Therefore, new approaches for their control are urgently needed. One way to search for biofilm dispersing compounds is to look at defense strategies of organisms exposed to wet environments, which makes them prone to biofilm infections. It is reasonable to assume that mushrooms have developed mechanisms to control biofilms on their sporocarps (fruiting bodies). A preliminary screening for biofilms on sporocarps revealed several species with few or no bacteria on their sporocarps. From the edible mushroom Coprinus comatus where no bacteria on the sporocarp could be detected (3R,4S)-2-methylene-3,4-dihydroxypentanoic acid 1,4-lactone, named coprinuslactone, was isolated. Coprinuslactone interfered with quorum-sensing and dispersed biofilms of Pseudomonas aeruginosa, where it also reduced the formation of the pathogenicity factors pyocyanin and rhamnolipid B. Coprinuslactone also damaged Staphylococcus aureus cells in biofilms at subtoxic concentrations. Furthermore, it inhibited UDP-N-acetylglucosamine enolpyruvyl transferase (MurA), essential for bacterial cell wall synthesis. These two modes of action ensure the inhibition of a broad spectrum of pathogens on the fruiting body but may also be useful for future clinical applications. This article is protected by copyright. All rights reserved.
    • Cytochalasans Act as Inhibitors of Biofilm Formation of Staphylococcus Aureus.

      Yuyama, Kamila Tomoko; Wendt, Lucile; Surup, Frank; Kretz, Robin; Chepkirui, Clara; Wittstein, Kathrin; Boonlarppradab, Chollaratt; Wongkanoun, Sarunyou; Luangsa-Ard, Jennifer; Stadler, Marc; Abraham, Wolf-Rainer; HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany. (MDPI, 2018-10-30)
      During the course of our ongoing work to discover new inhibitors of biofilm formation of Staphylococcus aureus from fungal sources, we observed biofilm inhibition by cytochalasans isolated from cultures of the ascomycete Hypoxylon fragiforme for the first time. Two new compounds were purified by a bioassay-guided fractionation procedure; their structures were elucidated subsequently by nuclear magnetic resonance (NMR) spectroscopy and high-resolution mass spectrometry (HR-MS). This unexpected finding prompted us to test further cytochalasans from other fungi and from commercial sources for comparison. Out of 21 cytochalasans, 13 showed significant inhibition of Staphylococcus aureus biofilm formation at subtoxic levels. These findings indicate the potential of cytochalasans as biofilm inhibitors for the first time, also because the minimum inhibitory concentrations (MIC) are independent of the anti-biofilm activities. However, cytochalasans are known to be inhibitors of actin, making some of them very toxic for eukaryotic cells. Since the chemical structures of the tested compounds were rather diverse, the inclusion of additional derivatives, as well as the evaluation of their selectivity against mammalian cells vs. the bacterium, will be necessary as next step in order to develop structure-activity relationships and identify the optimal candidates for development of an anti-biofilm agent. View Full-Text
    • Different implants have different biofilm communities-lessons for implant optimization

      Abraham, Wolf-Rainer; Dept. of chemical microbiology, Helmholtz Centre for infection research, D-38124 Braunschweig, Germany. (Walter de Gruyter GmbH & Co. KG, 2014-12-09)
    • Dipeptide cis-cyclo(Leucyl-Tyrosyl) produced by sponge associated Penicillium sp. F37 inhibits biofilm formation of the pathogenic Staphylococcus epidermidis.

      Scopel, Marina; Abraham, Wolf-Rainer; Henriques, Amélia T; Macedo, Alexandre J; Faculdade de Farmácia, Departamento de Produção de Matéria-Prima, Universidade Federal do Rio Grande do Sul, Av. Ipiranga, 2752, 90610-000 Porto Alegre, Brazil. (2013-02-01)
      Infections associated to microbial biofilms are involved in 80% of human infections and became a challenge concerning public health. Infections related to Staphylococcus epidermidis biofilms are presently commonly associated to medical devices, increasing treatment costs for this type of infection. Alternatives to eliminate this kind of disease have been employed in screening programs using diverse marine-derived fungi source of bioactive compounds capable to combat biofilm formation. In this work was isolated the dipeptide cis-cyclo(Leucyl-Tyrosyl) from a sponge associated Penicillium sp. possessing a remarkable inhibition up to 85% of biofilm formation without interfering with bacterial growth, confirmed by scanning electron microscopy. This is the first demonstration that cis-cyclo(Leucyl-Tyrosyl) is able to specifically inhibit biofilm formation adding another aspect to the broad spectrum of bioactivities of cyclic dipeptides.
    • Diversity and Activity of Bacterial Biofilm Communities Growing on Hexachlorocyclohexane

      Gebreil, Ahmed Shawky; Abraham, Wolf-Rainer; Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2016-08-03)
    • Fumitremorgins and Relatives - from Tremorgenic Compounds to Valuable Anti-Cancer Drugs.

      Abraham, Wolf-Rainer; Hemholtz Centre for infection research, Inhoffenstr.7, 38124 Braunschweig, Germany. (2017-07-24)
      Fumitremorgins are mycotoxins but can also inhibit cancer cells and reverse their drug resistance.