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Gu S, Zhu F, Zhang L, Wen J. Mid-Long Chain Dicarboxylic Acid Production via Systems Metabolic Engineering: Progress and Prospects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5555-5573. [PMID: 38442481 DOI: 10.1021/acs.jafc.4c00002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Mid-to-long-chain dicarboxylic acids (DCAi, i ≥ 6) are organic compounds in which two carboxylic acid functional groups are present at the terminal position of the carbon chain. These acids find important applications as structural components and intermediates across various industrial sectors, including organic compound synthesis, food production, pharmaceutical development, and agricultural manufacturing. However, conventional petroleum-based DCA production methods cause environmental pollution, making sustainable development challenging. Hence, the demand for eco-friendly processes and renewable raw materials for DCA production is rising. Owing to advances in systems metabolic engineering, new tools from systems biology, synthetic biology, and evolutionary engineering can now be used for the sustainable production of energy-dense biofuels. Here, we explore systems metabolic engineering strategies for DCA synthesis in various chassis via the conversion of different raw materials into mid-to-long-chain DCAs. Subsequently, we discuss the future challenges in this field and propose synthetic biology approaches for the efficient production and successful commercialization of these acids.
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Affiliation(s)
- Shanna Gu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian 116045, China
| | - Fuzhou Zhu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
| | - Lin Zhang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian 116045, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
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2
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Dsouza FP, Dinesh S, Sharma S. Understanding the intricacies of microbial biofilm formation and its endurance in chronic infections: a key to advancing biofilm-targeted therapeutic strategies. Arch Microbiol 2024; 206:85. [PMID: 38300317 DOI: 10.1007/s00203-023-03802-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/04/2023] [Accepted: 12/16/2023] [Indexed: 02/02/2024]
Abstract
Bacterial biofilms can adhere to various surfaces in the environment with human beings being no exception. Enclosed in a self-secreted matrix which contains extracellular polymeric substances, biofilms are intricate communities of bacteria that play a significant role across various sectors and raise concerns for public health, medicine and industries. These complex structures allow free-floating planktonic cells to adopt multicellular mode of growth which leads to persistent infections. This is of great concern as biofilms can withstand external attacks which include antibiotics and immune responses. A more comprehensive and innovative approach to therapy is needed in view of the increasing issue of bacterial resistance brought on by the overuse of conventional antimicrobial medications. Thus, to oppose the challenges posed by biofilm-related infections, innovative therapeutic strategies are being explored which include targeting extracellular polymeric substances, quorum sensing, and persister cells. Biofilm-responsive nanoparticles show promising results by improving drug delivery and reducing the side effects. This review comprehensively examines the factors influencing biofilm formation, host immune defence mechanisms, infections caused by biofilms, diagnostic approaches, and biofilm-targeted therapies.
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Affiliation(s)
| | - Susha Dinesh
- Department of Bioinformatics, BioNome, Bengaluru, Karnataka, 560043, India.
| | - Sameer Sharma
- Department of Bioinformatics, BioNome, Bengaluru, Karnataka, 560043, India
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3
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Lima BP, Davies JR, Wickström C, Johnstone KF, Hall JW, Svensater G, Herzberg MC. Streptococcus gordonii Poised for Glycan Feeding through a MUC5B-Discriminating, Lipoteichoic Acid-Mediated Outside-In Signaling Circuit. J Bacteriol 2022; 204:e0011822. [PMID: 35652671 PMCID: PMC9210975 DOI: 10.1128/jb.00118-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/09/2022] [Indexed: 11/20/2022] Open
Abstract
Many oral bacteria employ cell wall-anchored adhesins to bind to the salivary films coating the teeth and mucosal surfaces. Surface binding prevents clearance and facilitates catabolism of salivary film glycoproteins. We asked whether Streptococcus gordonii adhesin expression changes in response to surface salivary cues using a eukaryote-like, outside-in recognition and signaling circuit. To determine whether the cues were discriminated, S. gordonii was tested during cell adhesion and biofilm formation on a MUC5B-rich or lower-molecular-mass salivary fraction or an uncoated abiotic surface. Cells were recovered and analyzed for differences in gene expression and proteins in cell wall fractions. In salivary-free conditions, planktonic S. gordonii presented three prominent cell wall LPXTG-motif proteins, SGO_1487, SGO_0890, and MbpA (mucin-binding protein A; SGO_0707). During biofilm formation on MUC5B-coated surfaces, MbpA, a MUC5B-binding protein, and key genes in the tagatose and quorum-sensing pathways were strongly promoted. The response to MUC5B required the two-component system (TCS), streptococcal regulator of adhesins sensor and regulator (SraSR, SGO_1180/81), lipoteichoic acid (LTA), and the homologous paired adhesins, SspA and SspB (SspAB). LTA appears to link the outside signal (MUC5B) to intramembrane SraSR. Tagatose pathway gene expression may poise cells to metabolize MUC5B glycans and, with a quorum-sensing gene (luxS), may direct formation of a consortium to facilitate glycan cross-feeding by S. gordonii. We now show that a Gram-positive bacterium discriminates specific surface environmental cues using an outside-in signaling mechanism to apparently optimize colonization of saliva-coated surfaces. IMPORTANCE All organisms throughout the tree of life sense and respond to their surface environments. To discriminate among mucosal surface environmental cues, we report that Streptococcus gordonii recognizes a high-molecular-weight mucin glycoprotein, MUC5B, using the paired adhesins SspAB and lipoteichoic acid; the latter bridges the outside signal to an intramembrane two-component system to transcriptionally regulate a MUC5B-specific adhesin and genes that may facilitate glycan catabolism.
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Affiliation(s)
- Bruno P. Lima
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Julia R. Davies
- Section for Oral Biology and Pathology, Faculty of Odontology, Malmö University, Malmö, Sweden
| | - Claes Wickström
- Section for Oral Biology and Pathology, Faculty of Odontology, Malmö University, Malmö, Sweden
| | - Karen F. Johnstone
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jeffrey W. Hall
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Gunnel Svensater
- Section for Oral Biology and Pathology, Faculty of Odontology, Malmö University, Malmö, Sweden
| | - Mark C. Herzberg
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
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Barcoto MO, Rodrigues A. Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation. Front Microbiol 2022; 13:812143. [PMID: 35685924 PMCID: PMC9171207 DOI: 10.3389/fmicb.2022.812143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Anthropogenic activities have extensively transformed the biosphere by extracting and disposing of resources, crossing boundaries of planetary threat while causing a global crisis of waste overload. Despite fundamental differences regarding structure and recalcitrance, lignocellulose and plastic polymers share physical-chemical properties to some extent, that include carbon skeletons with similar chemical bonds, hydrophobic properties, amorphous and crystalline regions. Microbial strategies for metabolizing recalcitrant polymers have been selected and optimized through evolution, thus understanding natural processes for lignocellulose modification could aid the challenge of dealing with the recalcitrant human-made polymers spread worldwide. We propose to look for inspiration in the charismatic fungal-growing insects to understand multipartite degradation of plant polymers. Independently evolved in diverse insect lineages, fungiculture embraces passive or active fungal cultivation for food, protection, and structural purposes. We consider there is much to learn from these symbioses, in special from the community-level degradation of recalcitrant biomass and defensive metabolites. Microbial plant-degrading systems at the core of insect fungicultures could be promising candidates for degrading synthetic plastics. Here, we first compare the degradation of lignocellulose and plastic polymers, with emphasis in the overlapping microbial players and enzymatic activities between these processes. Second, we review the literature on diverse insect fungiculture systems, focusing on features that, while supporting insects' ecology and evolution, could also be applied in biotechnological processes. Third, taking lessons from these microbial communities, we suggest multidisciplinary strategies to identify microbial degraders, degrading enzymes and pathways, as well as microbial interactions and interdependencies. Spanning from multiomics to spectroscopy, microscopy, stable isotopes probing, enrichment microcosmos, and synthetic communities, these strategies would allow for a systemic understanding of the fungiculture ecology, driving to application possibilities. Detailing how the metabolic landscape is entangled to achieve ecological success could inspire sustainable efforts for mitigating the current environmental crisis.
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Affiliation(s)
- Mariana O. Barcoto
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, Brazil
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Andre Rodrigues
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, Brazil
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
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5
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Kruppa O, Czermak P. Screening for Biofilm-Stimulating Factors in the Freshwater Planctomycete Planctopirus limnophila to Improve Sessile Growth in a Chemically Defined Medium. Microorganisms 2022; 10:microorganisms10040801. [PMID: 35456851 PMCID: PMC9028447 DOI: 10.3390/microorganisms10040801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/31/2022] [Accepted: 04/10/2022] [Indexed: 12/26/2022] Open
Abstract
Planctomycetes such as Planctopirus limnophila offer a promising source of bioactive molecules, particularly when they switch from planktonic to sessile growth, but little is known about the corresponding biosynthetic gene clusters and how they are activated. We therefore screened for factors that promote sessile growth and biofilm formation to enable the cultivation of P. limnophila in a fixed-bed reactor. We carried out screening in microtiter plates focusing on biofilm formation and changes in optical density in response to various C:N ratios, metal ions, and oxidative stress. We used MTT assays and crystal violet staining to quantify biofilm formation. Positive factors were then validated in a fixed-bed bioreactor. The initial screen showed that D1ASO medium supplemented with NH4Cl to achieve a C:N ratio of 5.7:1, as well as 50 µM FeSO4 or CuSO4, increased the biofilm formation relative to the control medium. Exposure to H2O2 did not affect cell viability but stimulated biofilm formation. However, the same results were not replicated in the fixed-bed bioreactor, probably reflecting conditions that are unique to this environment such as the controlled pH and more vigorous aeration. Although we were able to cultivate P. limnophila in a fixed-bed bioreactor using a chemically defined medium, the factors that stimulate biofilm formation and inhibit planktonic growth were only identified in microtiter plates and further evaluation is required to establish optimal growth conditions in the bioreactor system.
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Affiliation(s)
- Oscar Kruppa
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, 35390 Giessen, Germany;
| | - Peter Czermak
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, 35390 Giessen, Germany;
- Faculty of Biology and Chemistry, Justus-Liebig University of Giessen, 35390 Giessen, Germany
- Correspondence:
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Kulshreshtha G, D’Alba L, Dunn IC, Rehault-Godbert S, Rodriguez-Navarro AB, Hincke MT. Properties, Genetics and Innate Immune Function of the Cuticle in Egg-Laying Species. Front Immunol 2022; 13:838525. [PMID: 35281050 PMCID: PMC8914949 DOI: 10.3389/fimmu.2022.838525] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/31/2022] [Indexed: 01/13/2023] Open
Abstract
Cleidoic eggs possess very efficient and orchestrated systems to protect the embryo from external microbes until hatch. The cuticle is a proteinaceous layer on the shell surface in many bird and some reptile species. An intact cuticle forms a pore plug to occlude respiratory pores and is an effective physical and chemical barrier against microbial penetration. The interior of the egg is assumed to be normally sterile, while the outer eggshell cuticle hosts microbes. The diversity of the eggshell microbiome is derived from both maternal microbiota and those of the nesting environment. The surface characteristics of the egg, outer moisture layer and the presence of antimicrobial molecules composing the cuticle dictate constituents of the microbial communities on the eggshell surface. The avian cuticle affects eggshell wettability, water vapor conductance and regulates ultraviolet reflectance in various ground-nesting species; moreover, its composition, thickness and degree of coverage are dependent on species, hen age, and physiological stressors. Studies in domestic avian species have demonstrated that changes in the cuticle affect the food safety of eggs with respect to the risk of contamination by bacterial pathogens such as Salmonella and Escherichia coli. Moreover, preventing contamination of internal egg components is crucial to optimize hatching success in bird species. In chickens there is moderate heritability (38%) of cuticle deposition with a potential for genetic improvement. However, much less is known about other bird or reptile cuticles. This review synthesizes current knowledge of eggshell cuticle and provides insight into its evolution in the clade reptilia. The origin, composition and regulation of the eggshell microbiome and the potential function of the cuticle as the first barrier of egg defense are discussed in detail. We evaluate how changes in the cuticle affect the food safety of table eggs and vertical transmission of pathogens in the production chain with respect to the risk of contamination. Thus, this review provides insight into the physiological and microbiological characteristics of eggshell cuticle in relation to its protective function (innate immunity) in egg-laying birds and reptiles.
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Affiliation(s)
- Garima Kulshreshtha
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Liliana D’Alba
- Evolutionary Ecology, Naturalis Biodiversity Center, Leiden, Netherlands
| | - Ian C. Dunn
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Maxwell T. Hincke
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Department of Innovation in Medical Education, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
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7
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Urvoy M, Lami R, Dreanno C, Daudé D, Rodrigues AMS, Gourmelon M, L'Helguen S, Labry C. Quorum sensing disruption regulates hydrolytic enzyme and biofilm production in estuarine bacteria. Environ Microbiol 2021; 23:7183-7200. [PMID: 34528354 DOI: 10.1111/1462-2920.15775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/02/2021] [Accepted: 09/10/2021] [Indexed: 12/18/2022]
Abstract
Biofilms of heterotrophic bacteria cover organic matter aggregates and constitute hotspots of mineralization, primarily acting through extracellular hydrolytic enzyme production. Nevertheless, regulation of both biofilm and hydrolytic enzyme synthesis remains poorly investigated, especially in estuarine ecosystems. In this study, various bioassays, mass spectrometry and genomics approaches were combined to test the possible involvement of quorum sensing (QS) in these mechanisms. QS is a bacterial cell-cell communication system that relies notably on the emission of N-acylhomoserine lactones (AHLs). In our estuarine bacterial collection, we found that 28 strains (9%), mainly Vibrio, Pseudomonas and Acinetobacter isolates, produced at least 14 different types of AHLs encoded by various luxI genes. We then inhibited the AHL QS circuits of those 28 strains using a broad-spectrum lactonase preparation and tested whether biofilm production as well as β-glucosidase and leucine-aminopeptidase activities were impacted. Interestingly, we recorded contrasted responses, as biofilm production, dissolved and cell-bound β-glucosidase and leucine-aminopeptidase activities significantly increased in 4%-68% of strains but decreased in 0%-21% of strains. These findings highlight the key role of AHL-based QS in estuarine bacterial physiology and ultimately on biogeochemical cycles. They also point out the complexity of QS regulations within natural microbial assemblages.
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Affiliation(s)
- Marion Urvoy
- Ifremer, DYNECO, Plouzané, F-29280, France.,Université de Bretagne Occidentale, CNRS, IRD, Ifremer, UMR 6539, Laboratoire des Sciences de l'Environnement Marin (LEMAR), Plouzané, F-29280, France
| | - Raphaël Lami
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), 66650 Banyuls-sur-Mer, France
| | | | - David Daudé
- Gene&GreenTK, 19-21 Boulevard Jean Moulin, Marseille, 13005, France
| | - Alice M S Rodrigues
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), 66650 Banyuls-sur-Mer, France
| | | | - Stéphane L'Helguen
- Université de Bretagne Occidentale, CNRS, IRD, Ifremer, UMR 6539, Laboratoire des Sciences de l'Environnement Marin (LEMAR), Plouzané, F-29280, France
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8
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Pinto J, Lami R, Krasovec M, Grimaud R, Urios L, Lupette J, Escande ML, Sanchez F, Intertaglia L, Grimsley N, Piganeau G, Sanchez-Brosseau S. Features of the Opportunistic Behaviour of the Marine Bacterium Marinobacter algicola in the Microalga Ostreococcus tauri Phycosphere. Microorganisms 2021; 9:microorganisms9081777. [PMID: 34442856 PMCID: PMC8399681 DOI: 10.3390/microorganisms9081777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022] Open
Abstract
Although interactions between microalgae and bacteria are observed in both natural environment and the laboratory, the modalities of coexistence of bacteria inside microalgae phycospheres in laboratory cultures are mostly unknown. Here, we focused on well-controlled cultures of the model green picoalga Ostreococcus tauri and the most abundant member of its phycosphere, Marinobacter algicola. The prevalence of M. algicola in O. tauri cultures raises questions about how this bacterium maintains itself under laboratory conditions in the microalga culture. The results showed that M. algicola did not promote O. tauri growth in the absence of vitamin B12 while M. algicola depended on O. tauri to grow in synthetic medium, most likely to obtain organic carbon sources provided by the microalgae. M. algicola grew on a range of lipids, including triacylglycerols that are known to be produced by O. tauri in culture during abiotic stress. Genomic screening revealed the absence of genes of two particular modes of quorum-sensing in Marinobacter genomes which refutes the idea that these bacterial communication systems operate in this genus. To date, the ‘opportunistic’ behaviour of M. algicola in the laboratory is limited to several phytoplanktonic species including Chlorophyta such as O. tauri. This would indicate a preferential occurrence of M. algicola in association with these specific microalgae under optimum laboratory conditions.
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Affiliation(s)
- Jordan Pinto
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (J.P.); (M.K.); (J.L.); (F.S.); (N.G.); (G.P.)
| | - Raphaël Lami
- Sorbonne Université, CNRS, USR 3579 Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France;
| | - Marc Krasovec
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (J.P.); (M.K.); (J.L.); (F.S.); (N.G.); (G.P.)
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Régis Grimaud
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, 64000 Pau, France; (R.G.); (L.U.)
| | - Laurent Urios
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, 64000 Pau, France; (R.G.); (L.U.)
| | - Josselin Lupette
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (J.P.); (M.K.); (J.L.); (F.S.); (N.G.); (G.P.)
- Université de Bordeaux, CNRS, UMR 5200 Laboratoire de Biogenèse Membranaire, 33140 Villenave d’Ornon, France
| | - Marie-Line Escande
- Sorbonne Université, CNRS, FR 3724, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (M.-L.E.); (L.I.)
| | - Frédéric Sanchez
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (J.P.); (M.K.); (J.L.); (F.S.); (N.G.); (G.P.)
| | - Laurent Intertaglia
- Sorbonne Université, CNRS, FR 3724, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (M.-L.E.); (L.I.)
| | - Nigel Grimsley
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (J.P.); (M.K.); (J.L.); (F.S.); (N.G.); (G.P.)
| | - Gwenaël Piganeau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (J.P.); (M.K.); (J.L.); (F.S.); (N.G.); (G.P.)
| | - Sophie Sanchez-Brosseau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (J.P.); (M.K.); (J.L.); (F.S.); (N.G.); (G.P.)
- Correspondence:
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9
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Bunse C, Koch H, Breider S, Simon M, Wietz M. Sweet spheres: succession and CAZyme expression of marine bacterial communities colonizing a mix of alginate and pectin particles. Environ Microbiol 2021; 23:3130-3148. [PMID: 33876546 DOI: 10.1111/1462-2920.15536] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/06/2021] [Accepted: 04/15/2021] [Indexed: 12/24/2022]
Abstract
Polysaccharide particles are important substrates and microhabitats for marine bacteria. However, substrate-specific bacterial dynamics in mixtures of particle types with different polysaccharide composition, as likely occurring in natural habitats, are undescribed. Here, we studied the composition, functional diversity and gene expression of marine bacterial communities colonizing a mix of alginate and pectin particles. Amplicon, metagenome and metatranscriptome sequencing revealed that communities on alginate and pectin particles significantly differed from their free-living counterparts. Unexpectedly, microbial dynamics on alginate and pectin particles were similar, with predominance of amplicon sequence variants (ASVs) from Tenacibaculum, Colwellia, Psychrobium and Psychromonas. Corresponding metagenome-assembled genomes (MAGs) expressed diverse alginate lyases, several colocalized in polysaccharide utilization loci. Only a single, low-abundant MAG showed elevated transcript abundances of pectin-degrading enzymes. One specific Glaciecola ASV dominated the free-living fraction, possibly persisting on particle-derived oligomers through different glycoside hydrolases. Elevated ammonium uptake and metabolism signified nitrogen as an important factor for degrading carbon-rich particles, whereas elevated methylcitrate and glyoxylate cycles suggested nutrient limitation in surrounding waters. The bacterial preference for alginate, whereas pectin primarily served as colonization scaffold, illuminates substrate-driven dynamics within mixed polysaccharide pools. These insights expand our understanding of bacterial niche specialization and the biological carbon pump in macroalgae-rich habitats.
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Affiliation(s)
- Carina Bunse
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany.,Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Hanna Koch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.,Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Sven Breider
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany.,Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Matthias Wietz
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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10
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Burgos-Garay ML, Santiago AJ, Kartforosh L, Kotay S, Donlan RM. Supplemental nutrients stimulate the amplification of carbapenemase-producing Klebsiella pneumoniae (CPKP) in a sink drain in vitro biofilm reactor model. BIOFOULING 2021; 37:465-480. [PMID: 34210218 DOI: 10.1080/08927014.2021.1915998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 03/25/2021] [Accepted: 04/06/2021] [Indexed: 06/13/2023]
Abstract
Liquid wastes (LW) disposed in hospital handwashing sinks may affect colonization of sink P-traps by carbapenemase-producing Klebsiella pneumoniae (CPKP), causing CPKP dispersal into the patient care environment. This study aimed to determine the effect of LW on biofilm formation and CPKP colonization in a P-Trap model (PTM). PTMs containing polymicrobial biofilms grown in autoclaved municipal tap water (ATW) supplemented with 5% dextrose in water (D5W), nutritional shake (Shake), sugar-based soft drink (Soda), or ATW were inoculated with K. pneumoniae ST258 KPC+ (ST258) or K. pneumoniae CAV1016 (CAV1016) and sampled after 7, 14, and 21 d. Biofilm bio-volume, mean thickness, and heterotrophic plate counts were significantly reduced and roughness coefficient significantly increased by Soda compared with D5W, Shake, or ATW. CPKP were significantly reduced by Soda but significantly amplified by D5W (ST258; CAV1016, 7 d) and Shake (ST258) suggesting that reducing LW disposal in sinks may reduce CPKP dispersal into patient care environments.
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Affiliation(s)
- María L Burgos-Garay
- Division of Healthcare Quality Promotion, Clinical and Environmental Microbiology Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ariel J Santiago
- Division of Healthcare Quality Promotion, Clinical and Environmental Microbiology Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Leila Kartforosh
- Division of Healthcare Quality Promotion, Clinical and Environmental Microbiology Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shireen Kotay
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, VA, USA
| | - Rodney M Donlan
- Division of Healthcare Quality Promotion, Clinical and Environmental Microbiology Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
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11
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Lebov JF, Bohannan BJM. Msh Pilus Mutations Increase the Ability of a Free-Living Bacterium to Colonize a Piscine Host. Genes (Basel) 2021; 12:genes12020127. [PMID: 33498301 PMCID: PMC7909257 DOI: 10.3390/genes12020127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 02/07/2023] Open
Abstract
Symbioses between animals and bacteria are ubiquitous. To better understand these relationships, it is essential to unravel how bacteria evolve to colonize hosts. Previously, we serially passaged the free-living bacterium, Shewanella oneidensis, through the digestive tracts of germ-free larval zebrafish (Danio rerio) to uncover the evolutionary changes involved in the initiation of a novel symbiosis with a vertebrate host. After 20 passages, we discovered an adaptive missense mutation in the mshL gene of the msh pilus operon, which improved host colonization, increased swimming motility, and reduced surface adhesion. In the present study, we determined that this mutation was a loss-of-function mutation and found that it improved zebrafish colonization by augmenting S. oneidensis representation in the water column outside larvae through a reduced association with environmental surfaces. Additionally, we found that strains containing the mshL mutation were able to immigrate into host digestive tracts at higher rates per capita. However, mutant and evolved strains exhibited no evidence of a competitive advantage after colonizing hosts. Our results demonstrate that bacterial behaviors outside the host can play a dominant role in facilitating the onset of novel host associations.
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Affiliation(s)
- Jarrett F. Lebov
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA;
- Correspondence:
| | - Brendan J. M. Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA;
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12
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Fungus-growing insects host a distinctive microbiota apparently adapted to the fungiculture environment. Sci Rep 2020; 10:12384. [PMID: 32709946 PMCID: PMC7381635 DOI: 10.1038/s41598-020-68448-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 06/24/2020] [Indexed: 01/09/2023] Open
Abstract
Some lineages of ants, termites, and beetles independently evolved a symbiotic association with lignocellulolytic fungi cultivated for food, in a lifestyle known as fungiculture. Fungus-growing insects' symbiosis also hosts a bacterial community thought to integrate their physiology. Similarities in taxonomic composition support the microbiota of fungus-growing insects as convergent, despite differences in fungus-rearing by these insects. Here, by comparing fungus-growing insects to several hosts ranging diverse dietary patterns, we investigate whether the microbiota taxonomic and functional profiles are characteristic of the fungiculture environment. Compared to other hosts, the microbiota associated with fungus-growing insects presents a distinctive taxonomic profile, dominated by Gammaproteobacteria at class level and by Pseudomonas at genera level. Even with a functional profile presenting similarities with the gut microbiota of herbivorous and omnivorous hosts, some differentially abundant features codified by the microbiota of fungus-growing insects suggest these communities occupying microhabitats that are characteristic of fungiculture. These features include metabolic pathways involved in lignocellulose breakdown, detoxification of plant secondary metabolites, metabolism of simple sugars, fungal cell wall deconstruction, biofilm formation, antimicrobials biosynthesis, and metabolism of diverse nutrients. Our results suggest that the microbiota could be functionally adapted to the fungiculture environment, codifying metabolic pathways potentially relevant to the fungus-growing insects' ecosystems functioning.
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13
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Van Gaelen P, Springael D, Smets I. A high-throughput assay to quantify protein hydrolysis in aerobic and anaerobic wastewater treatment processes. Appl Microbiol Biotechnol 2020; 104:8037-8048. [PMID: 32700087 DOI: 10.1007/s00253-020-10751-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/09/2020] [Accepted: 06/16/2020] [Indexed: 12/01/2022]
Abstract
Proteins, an important fraction of the organic matter in wastewater, typically enter a treatment facility as high molecular weight components. These components are degraded by extracellular protein hydrolytic enzymes, denoted as proteases. Adequate protein hydrolysis monitoring is crucial, since protein hydrolysis is often a rate-limiting step in wastewater treatment. However, current monitoring tools lack a high sample throughput and reliable quantification. Here, we present an improved assay for high-throughput protein hydrolysis rate measurements in wastewater treatment applications. A BODIPY FL casein model substrate was implemented in a microplate format for continuous fluorescent quantification. Case studies on a conventional and a high-rate aerobic municipal wastewater treatment plant and a lab-scale, two-stage, anaerobic reactor provided proof-of-concept. The assay presented in this study can help to obtain monitoring-based process insights, which will in turn allow improving biological performance of wastewater treatment installations in the future. KEY POINTS: • Protein hydrolysis is a crucial step in biological wastewater treatment. • Quantification of the protein hydrolysis rate enables in-depth process knowledge. • BODIPY FL casein is a suitable model substrate for a protein hydrolysis assay. • High sample throughput was obtained with fluorescent hydrolysis quantification. Graphical abstract.
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Affiliation(s)
- Pieter Van Gaelen
- Bio- and Chemical Systems Technology, Reactor Engineering and Safety (CREaS), Department of Chemical Engineering, KU Leuven, Celestijnenlaan 200F, PO box 2424, B-3001, Leuven, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, Department of Earth and Environmental sciences, KU Leuven, Kasteelpark Arenberg 20, B-3001, Leuven, Belgium
| | - Ilse Smets
- Bio- and Chemical Systems Technology, Reactor Engineering and Safety (CREaS), Department of Chemical Engineering, KU Leuven, Celestijnenlaan 200F, PO box 2424, B-3001, Leuven, Belgium.
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14
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Brethauer S, Shahab RL, Studer MH. Impacts of biofilms on the conversion of cellulose. Appl Microbiol Biotechnol 2020; 104:5201-5212. [PMID: 32337627 PMCID: PMC7275028 DOI: 10.1007/s00253-020-10595-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 12/02/2022]
Abstract
Abstract Lignocellulose is a widely available renewable carbon source and a promising feedstock for the production of various chemicals in biorefineries. However, its recalcitrant nature is a major hurdle that must be overcome to enable economic conversion processes. Deconstruction of lignocellulose is part of the global carbon cycle, and efficient microbial degradation systems have evolved that might serve as models to improve commercial conversion processes. Biofilms—matrix encased, spatially organized clusters of microbial cells and the predominating lifestyle in nature—have been recognized for their essential role in the degradation of cellulose in nature, e.g., in soils or in the digestive tracts of ruminant animals. Cellulolytic biofilms allow for a high concentration of enzymes at the boundary layer between the solid substrate and the liquid phase and the more complete capture of hydrolysis products directly at the hydrolysis site, which is energetically favorable. Furthermore, enhanced expression of genes for carbohydrate active enzymes as a response to the attachment on solid substrate has been demonstrated for cellulolytic aerobic fungi and anerobic bacteria. In natural multispecies biofilms, the vicinity of different microbial species allows the creation of efficient food webs and synergistic interactions thereby, e.g., avoiding the accumulation of inhibiting metabolites. In this review, these topics are discussed and attempts to realize the benefits of biofilms in targeted applications such as the consolidated bioprocessing of lignocellulose are highlighted. Key Points Multispecies biofilms enable efficient lignocellulose destruction in the biosphere. Cellulose degradation by anaerobic bacteria often occurs by monolayered biofilms. Fungal biofilms immobilize enzymes and substrates in an external digestion system. Surface attached cultures typically show higher expression of cellulolytic enzymes.
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Affiliation(s)
- Simone Brethauer
- School of Agricultural, Forest and Food Sciences, Laboratory of Biofuels and Biochemicals, Bern University of Applied Sciences (BFH), 3052, Zollikofen, Switzerland
| | - Robert L Shahab
- School of Agricultural, Forest and Food Sciences, Laboratory of Biofuels and Biochemicals, Bern University of Applied Sciences (BFH), 3052, Zollikofen, Switzerland
| | - Michael H Studer
- School of Agricultural, Forest and Food Sciences, Laboratory of Biofuels and Biochemicals, Bern University of Applied Sciences (BFH), 3052, Zollikofen, Switzerland.
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15
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Masangkay FR, Milanez GD, Tsiami A, Somsak V, Kotepui M, Tangpong J, Karanis P. First report of Cryptosporidium hominis in a freshwater sponge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 700:134447. [PMID: 31677419 DOI: 10.1016/j.scitotenv.2019.134447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
Identification of Cryptosporidium oocyst is essential in ensuring water quality fit for human use, consumption, and recreation. This communication proposes the supplemental analysis of substrate-associated biofilms, in particular, freshwater sponges in improving case finding of waterborne-protozoan pathogens (WBPP) in environmental aquatic samples. In this study, a small portion of a mature freshwater sponge under the Genus Spongilla was subjected to microscopic and molecular analysis to identify the presence of Cryptosporidium. Microscopic screening with modified Kinyoun's staining (MK) and microscopic confirmation using direct antibody fluorescent testing (IFT) returned with Cryptosporidium spp. positive findings. Molecular investigation resulted in the confirmation of Cryptosporidium hominis upon sequencing of PCR products and phylogenetic analysis. This is the first report of a pathogenic protozoan, C. hominis isolated from a freshwater sponge. The results of this study provide evidence of the value of expanding water quality assessment strategies to the analysis of substrate-associated biofilms and sponges in improving case finding of WBPP in natural aquatic environments.
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Affiliation(s)
- Frederick R Masangkay
- Biomedical Sciences Program, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand; Department of Medical Technology, Institute of Arts and Sciences, Far Eastern University-Manila, Manila 1015, Philippines.
| | - Giovanni D Milanez
- Biomedical Sciences Program, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand; Department of Medical Technology, Institute of Arts and Sciences, Far Eastern University-Manila, Manila 1015, Philippines
| | - Amalia Tsiami
- London Geller College of Hospitality and Tourism, University of West London, St Mary's Road, Ealing, London W5 5RF, United Kingdom
| | - Voravuth Somsak
- Biomedical Sciences Program, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Manas Kotepui
- Biomedical Sciences Program, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Jitbanjong Tangpong
- Biomedical Sciences Program, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand.
| | - Panagiotis Karanis
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; University of Nicosia Medical School, Anatomy Centre, P.O. Box 24005, CY-1700, Nicosia, 2408, Cyprus
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