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  1. Article ; Online: Engineering Cupriavidus necator H16 for the autotrophic production of (R)-1,3-butanediol.

    Gascoyne, Joshua Luke / Bommareddy, Rajesh Reddy / Heeb, Stephan / Malys, Naglis

    Metabolic engineering

    2021  Volume 67, Page(s) 262–276

    Abstract: Butanediols are widely used in the synthesis of polymers, specialty chemicals and important chemical intermediates. Optically pure R-form of 1,3-butanediol (1,3-BDO) is required for the synthesis of several industrial compounds and as a key intermediate ... ...

    Abstract Butanediols are widely used in the synthesis of polymers, specialty chemicals and important chemical intermediates. Optically pure R-form of 1,3-butanediol (1,3-BDO) is required for the synthesis of several industrial compounds and as a key intermediate of β-lactam antibiotic production. The (R)-1,3-BDO can only be produced by application of a biocatalytic process. Cupriavidus necator H16 is an established production host for biosynthesis of biodegradable polymer poly-3-hydroxybutryate (PHB) via acetyl-CoA intermediate. Therefore, the utilisation of acetyl-CoA or its upstream precursors offers a promising strategy for engineering biosynthesis of value-added products such as (R)-1,3-BDO in this bacterium. Notably, C. necator H16 is known for its natural capacity to fix carbon dioxide (CO
    MeSH term(s) Autotrophic Processes ; Butylene Glycols ; Carbon Cycle ; Cupriavidus necator/genetics
    Chemical Substances Butylene Glycols ; 1,3-butylene glycol (3XUS85K0RA)
    Language English
    Publishing date 2021-07-02
    Publishing country Belgium
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1470383-x
    ISSN 1096-7184 ; 1096-7176
    ISSN (online) 1096-7184
    ISSN 1096-7176
    DOI 10.1016/j.ymben.2021.06.010
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  2. Article ; Online: Mushroom-shaped structures formed in Acinetobacter baumannii biofilms grown in a roller bioreactor are associated with quorum sensing-dependent Csu-pilus assembly.

    Romero, Manuel / Mayer, Celia / Heeb, Stephan / Wattanavaekin, Krittanont / Cámara, Miguel / Otero, Ana / Williams, Paul

    Environmental microbiology

    2022  Volume 24, Issue 9, Page(s) 4329–4339

    Abstract: There is currently a need to develop simple biofilm models that facilitate investigation of the architecture/biology of mature bacterial biofilms in a consistent/standardized manner given their environmental and clinical importance and the need for new ... ...

    Abstract There is currently a need to develop simple biofilm models that facilitate investigation of the architecture/biology of mature bacterial biofilms in a consistent/standardized manner given their environmental and clinical importance and the need for new anti-biofilm interventions. This study introduces a novel biofilm culture system termed the rolling biofilm bioreactor (RBB). This easily operated system allows adherent microbial cells to be repeatedly exposed to air/solid/liquid interfaces optimizing biofilm growth. The RBB was exploited to investigate biofilm formation in Acinetobacter baumannii. High levels of A. baumannii biofilm biomass reproducibly accumulate in the RBB and, importantly, undergo a maturation step to form large mushroom-shaped structures that had not been observed in other models. Based on image analysis of biofilm development and genetic manipulation, we show how N-acylhomoserine lactone-dependent quorum sensing (QS) impacts on biofilm differentiation, composition and antibiotic tolerance. Our results indicate that extracellular DNA (eDNA) is a key matrix component in mature Acinetobacter biofilms as the mushroom-like structures consist of dense cellular masses encased in an eDNA mesh. Moreover, this study reveals the contribution of QS to A. baumannii biofilm differentiation through Csu pilus assembly regulation. Understanding the mechanisms of structural development of mature biofilms helps to identify new biofilm eradication and removal strategies.
    MeSH term(s) Acinetobacter baumannii ; Acyl-Butyrolactones ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Biofilms ; Bioreactors ; Quorum Sensing
    Chemical Substances Acyl-Butyrolactones ; Anti-Bacterial Agents ; Bacterial Proteins
    Language English
    Publishing date 2022-03-30
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1111/1462-2920.15985
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  3. Article ; Online: Alkyl-quinolone-dependent quorum sensing controls prophage-mediated autolysis in

    Giallonardi, Giulia / Letizia, Morgana / Mellini, Marta / Frangipani, Emanuela / Halliday, Nigel / Heeb, Stephan / Cámara, Miguel / Visca, Paolo / Imperi, Francesco / Leoni, Livia / Williams, Paul / Rampioni, Giordano

    Frontiers in cellular and infection microbiology

    2023  Volume 13, Page(s) 1183681

    Abstract: Pseudomonas ... ...

    Abstract Pseudomonas aeruginosa
    MeSH term(s) Humans ; Quinolones/pharmacology ; Quorum Sensing ; Pseudomonas aeruginosa/genetics ; Prophages ; Biofilms ; Autolysis
    Chemical Substances Quinolones
    Language English
    Publishing date 2023-05-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2023.1183681
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  4. Article ; Online: RsaL-driven negative regulation promotes heterogeneity in

    Mellini, Marta / Letizia, Morgana / Caruso, Lorenzo / Guiducci, Alessandra / Meneghini, Carlo / Heeb, Stephan / Williams, Paul / Cámara, Miguel / Visca, Paolo / Imperi, Francesco / Leoni, Livia / Rampioni, Giordano

    mBio

    2023  , Page(s) e0203923

    Abstract: In its canonical interpretation, quorum sensing (QS) allows single cells in a bacterial population to synchronize gene expression and hence perform specific tasks collectively once ... ...

    Abstract In its canonical interpretation, quorum sensing (QS) allows single cells in a bacterial population to synchronize gene expression and hence perform specific tasks collectively once the
    Language English
    Publishing date 2023-10-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mbio.02039-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Professor Dieter Haas (1945-2017).

    Heeb, Stephan / Càmara, Miguel / Filloux, Alain / Williams, Paul

    FEMS microbiology reviews

    2017  Volume 41, Issue 5, Page(s) 597–598

    Language English
    Publishing date 2017-08-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 283740-7
    ISSN 1574-6976 ; 0168-6445
    ISSN (online) 1574-6976
    ISSN 0168-6445
    DOI 10.1093/femsre/fux040
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    In stock of ZB MED Cologne/Königswinter

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  6. Article ; Online: Design, Synthesis, and Evaluation of New 1

    Soukarieh, Fadi / Mashabi, Alaa / Richardson, William / Oton, Eduard Vico / Romero, Manuel / Dubern, Jean-Frédéric / Robertson, Shaun N / Lucanto, Simone / Markham-Lee, Zoe / Sou, Tomás / Kukavica-Ibrulj, Irena / Levesque, Roger C / Bergstrom, Christel A S / Halliday, Nigel / Kellam, Barrie / Emsley, Jonas / Heeb, Stephan / Williams, Paul / Stocks, Michael J /
    Cámara, Miguel

    Journal of medicinal chemistry

    2024  Volume 67, Issue 2, Page(s) 1008–1023

    Abstract: Pseudomonas ... ...

    Abstract Pseudomonas aeruginosa
    MeSH term(s) Humans ; Pseudomonas Infections/drug therapy ; Pseudomonas Infections/microbiology ; Quorum Sensing ; Biofilms ; Quinolones/pharmacology ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Anti-Bacterial Agents/metabolism ; Imidazoles/pharmacology ; Imidazoles/therapeutic use ; Imidazoles/metabolism ; Pseudomonas aeruginosa/metabolism ; Bacterial Proteins ; Virulence Factors
    Chemical Substances Quinolones ; Anti-Bacterial Agents ; Imidazoles ; Bacterial Proteins ; Virulence Factors
    Language English
    Publishing date 2024-01-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 218133-2
    ISSN 1520-4804 ; 0022-2623
    ISSN (online) 1520-4804
    ISSN 0022-2623
    DOI 10.1021/acs.jmedchem.3c00973
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  7. Article ; Online: Combining Inducible Lectin Expression and Magnetic Glyconanoparticles for the Selective Isolation of Bacteria from Mixed Populations.

    Petch, Joshua E / Gurnani, Pratik / Yilmaz, Gokhan / Mastrotto, Francesca / Alexander, Cameron / Heeb, Stephan / Cámara, Miguel / Mantovani, Giuseppe

    ACS applied materials & interfaces

    2021  Volume 13, Issue 16, Page(s) 19230–19243

    Abstract: The selective isolation of bacteria from mixed populations has been investigated in varied applications ranging from differential pathogen identification in medical diagnostics and food safety to the monitoring of microbial stress dynamics in industrial ... ...

    Abstract The selective isolation of bacteria from mixed populations has been investigated in varied applications ranging from differential pathogen identification in medical diagnostics and food safety to the monitoring of microbial stress dynamics in industrial bioreactors. Selective isolation techniques are generally limited to the confinement of small populations in defined locations, may be unable to target specific bacteria, or rely on immunomagnetic separation, which is not universally applicable. In this proof-of-concept work, we describe a novel strategy combining inducible bacterial lectin expression with magnetic glyconanoparticles (MGNPs) as a platform technology to enable selective bacterial isolation from cocultures. An inducible mutant of the type 1 fimbriae, displaying the mannose-specific lectin FimH, was constructed in
    MeSH term(s) Bacterial Adhesion ; Escherichia coli/genetics ; Escherichia coli/isolation & purification ; Gene Expression ; Glycoproteins/chemistry ; Glycoproteins/metabolism ; Lectins/genetics ; Magnets/chemistry ; Nanoparticles/chemistry ; Polymers/chemistry
    Chemical Substances Glycoproteins ; Lectins ; Polymers
    Language English
    Publishing date 2021-04-14
    Publishing country United States
    Document type Journal Article
    ISSN 1944-8252
    ISSN (online) 1944-8252
    DOI 10.1021/acsami.1c00907
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  8. Article ; Online: Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China.

    Baker, Michelle / Zhang, Xibin / Maciel-Guerra, Alexandre / Babaarslan, Kubra / Dong, Yinping / Wang, Wei / Hu, Yujie / Renney, David / Liu, Longhai / Li, Hui / Hossain, Maqsud / Heeb, Stephan / Tong, Zhiqin / Pearcy, Nicole / Zhang, Meimei / Geng, Yingzhi / Zhao, Li / Hao, Zhihui / Senin, Nicola /
    Chen, Junshi / Peng, Zixin / Li, Fengqin / Dottorini, Tania

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 206

    Abstract: Sharing of genetic elements among different pathogens and commensals inhabiting same hosts and environments has significant implications for antimicrobial resistance (AMR), especially in settings with high antimicrobial exposure. We analysed 661 ... ...

    Abstract Sharing of genetic elements among different pathogens and commensals inhabiting same hosts and environments has significant implications for antimicrobial resistance (AMR), especially in settings with high antimicrobial exposure. We analysed 661 Escherichia coli and Salmonella enterica isolates collected within and across hosts and environments, in 10 Chinese chicken farms over 2.5 years using data-mining methods. Most isolates within same hosts possessed the same clinically relevant AMR-carrying mobile genetic elements (plasmids: 70.6%, transposons: 78%), which also showed recent common evolution. Supervised machine learning classifiers revealed known and novel AMR-associated mutations and genes underlying resistance to 28 antimicrobials, primarily associated with resistance in E. coli and susceptibility in S. enterica. Many were essential and affected same metabolic processes in both species, albeit with varying degrees of phylogenetic penetration. Multi-modal strategies are crucial to investigate the interplay of mobilome, resistance and metabolism in cohabiting bacteria, especially in ecological settings where community-driven resistance selection occurs.
    MeSH term(s) Animals ; Farms ; Chickens ; Escherichia coli/genetics ; Phylogeny ; China/epidemiology ; Salmonella enterica/genetics ; Anti-Infective Agents
    Chemical Substances Anti-Infective Agents
    Language English
    Publishing date 2024-01-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-44272-1
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  9. Article ; Online: Topology-Based Three-Dimensional Reconstruction of Delicate Skeletal Fossil Remains and the Quantification of Their Taphonomic Deformation

    Oliver E. Demuth / Juan Benito / Emanuel Tschopp / Stephan Lautenschlager / Heinrich Mallison / Niklaus Heeb / Daniel J. Field

    Frontiers in Ecology and Evolution, Vol

    2022  Volume 10

    Abstract: Taphonomic and diagenetic processes inevitably distort the original skeletal morphology of fossil vertebrate remains. Key aspects of palaeobiological datasets may be directly impacted by such morphological deformation, such as taxonomic diagnoses and ... ...

    Abstract Taphonomic and diagenetic processes inevitably distort the original skeletal morphology of fossil vertebrate remains. Key aspects of palaeobiological datasets may be directly impacted by such morphological deformation, such as taxonomic diagnoses and phylogenetic hypotheses, interpretations of the shape and orientation of anatomical structures, and assessments of interspecific and intraspecific variation. In order to overcome these ubiquitous challenges we present a novel reconstruction workflow combining retopology and retrodeformation, allowing the original morphology of both symmetrically and asymmetrically damaged areas of fossils to be reconstructed. As case studies, we present idealised three-dimensional reconstructions of the sternum of the crownward stem-bird Ichthyornis dispar, and cervical vertebrae of the diplodocid sauropod Galeamopus pabsti. Multiple Ichthyornis sterna were combined into a single, idealised composite representation through superimposition and alignment of retopologised models, and this composite was subsequently retrodeformed. The Galeamopus vertebrae were individually retrodeformed and symmetrised. Our workflow enabled us to quantify deformation of individual specimens with respect to our reconstructions, and to characterise global and local taphonomic deformation. Our workflow can be integrated with geometric morphometric approaches to enable quantitative morphological comparisons among multiple specimens, as well as quantitative interpolation of “mediotypes” of serially homologous elements such as missing vertebrae, haemal arches, or ribs.
    Keywords retrodeformation ; 3D modelling ; taphonomy ; reconstruction ; dinosaurs ; Ichthyornis ; Evolution ; QH359-425 ; Ecology ; QH540-549.5
    Subject code 590
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: Engineering Cupriavidus necator H16 for the autotrophic production of (R)-1,3-butanediol

    Gascoyne, Joshua Luke / Bommareddy, Rajesh Reddy / Heeb, Stephan / Malys, Naglis

    Metabolic engineering. 2021 Sept., v. 67

    2021  

    Abstract: Butanediols are widely used in the synthesis of polymers, specialty chemicals and important chemical intermediates. Optically pure R-form of 1,3-butanediol (1,3-BDO) is required for the synthesis of several industrial compounds and as a key intermediate ... ...

    Abstract Butanediols are widely used in the synthesis of polymers, specialty chemicals and important chemical intermediates. Optically pure R-form of 1,3-butanediol (1,3-BDO) is required for the synthesis of several industrial compounds and as a key intermediate of β-lactam antibiotic production. The (R)-1,3-BDO can only be produced by application of a biocatalytic process. Cupriavidus necator H16 is an established production host for biosynthesis of biodegradable polymer poly-3-hydroxybutryate (PHB) via acetyl-CoA intermediate. Therefore, the utilisation of acetyl-CoA or its upstream precursors offers a promising strategy for engineering biosynthesis of value-added products such as (R)-1,3-BDO in this bacterium. Notably, C. necator H16 is known for its natural capacity to fix carbon dioxide (CO₂) using hydrogen as an electron donor. Here, we report engineering of this facultative lithoautotrophic bacterium for heterotrophic and autotrophic production of (R)-1,3-BDO. Implementation of (R)-3-hydroxybutyraldehyde-CoA- and pyruvate-dependent biosynthetic pathways in combination with abolishing PHB biosynthesis and reducing flux through the tricarboxylic acid cycle enabled to engineer strain, which produced 2.97 g/L of (R)-1,3-BDO and achieved production rate of nearly 0.4 Cmol Cmol⁻¹ h⁻¹ autotrophically. This is first report of (R)-1,3-BDO production from CO₂.
    Keywords Cupriavidus necator ; acetyl coenzyme A ; bacteria ; biocatalysis ; biodegradability ; biosynthesis ; carbon dioxide ; hydrogen ; polymers ; tricarboxylic acid cycle ; value added
    Language English
    Dates of publication 2021-09
    Size p. 262-276.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 1470383-x
    ISSN 1096-7184 ; 1096-7176
    ISSN (online) 1096-7184
    ISSN 1096-7176
    DOI 10.1016/j.ymben.2021.06.010
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