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Ndiaye A, Coulombe K, Fliss I, Filteau M. High-throughput ecological interaction mapping of dairy microorganisms. Int J Food Microbiol 2025; 427:110965. [PMID: 39522360 DOI: 10.1016/j.ijfoodmicro.2024.110965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 10/03/2024] [Accepted: 11/03/2024] [Indexed: 11/16/2024]
Abstract
To engineer efficient microbial management strategies in the food industry, a comprehensive understanding of microbial interactions is crucial. Microorganisms live in communities where they influence each other in several ways. Although much attention has been paid to the production of antagonistic metabolites in lactic acid bacteria (LAB), research that accounts for the complexity of their ecological interactions and their dynamics remains limited. This study explores binary interactions within a mock community of 94 strains, including 23 LAB from culture collections and 71 isolated from dairy products. Using a colony-picking robot and image analysis, bidirectional interactions were measured at high throughput on solid media, where one test strain was challenged against other mock community members as the target strains. Assays of 15 test strains (14 LAB and one yeast) yielded 1,142 bidirectionally mapped interactions, classified by ecological type over seven days. The results showed variation in the strength, directionality, and type of interactions depending on the origin of the target strains. Cooperation rates increased for strains isolated from raw milk to pasteurized milk and cheese, while exploitation was more common in raw milk strains. Cooperating strains also exhibited more similar ecological behaviors than competing strains, suggesting the presence of microbial cliques. Interestingly, Lactococcus cremoris ATCC 19257 developed pink-red pigmentation when co-cultured with Pseudomonas aeruginosa. Overall, these findings present an unprecedented exploratory data set that significantly improves our understanding of microbial interactions at the system level, with potential applications in strain selection for food processes such as fermentation, bioprotection, and probiotics.
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Affiliation(s)
- Amadou Ndiaye
- Département des Sciences des aliments, Université Laval, Québec, QC, Canada; Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Karl Coulombe
- Département des Sciences des aliments, Université Laval, Québec, QC, Canada; Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
| | - Ismail Fliss
- Département des Sciences des aliments, Université Laval, Québec, QC, Canada; Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
| | - Marie Filteau
- Département des Sciences des aliments, Université Laval, Québec, QC, Canada; Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.
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2
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Beizman-Magen Y, Orevi T, Kashtan N. Hydration conditions as a critical factor in antibiotic-mediated bacterial competition outcomes. Appl Environ Microbiol 2024:e0200424. [PMID: 39714150 DOI: 10.1128/aem.02004-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Accepted: 11/27/2024] [Indexed: 12/24/2024] Open
Abstract
Antibiotic secretion plays a pivotal role in bacterial interference competition; yet, the impact of environmental hydration conditions on such competition is not well understood. Here, we investigate how hydration conditions affect interference competition among bacteria, studying the interactions between the antibiotic-producing Bacillus velezensis FZB42 and two bacterial strains susceptible to its antibiotics: Xanthomonas euvesicatoria 85-10 and Pseudomonas syringae DC3000. Our results show that wet-dry cycles significantly modify the response of the susceptible bacteria to both the supernatant and cells of the antibiotic-producing bacteria, compared to constantly wet conditions. Notably, X. euvesicatoria shows increased protection against both the cells and supernatants of B. velezensis under wet-dry cycles, while P. syringae cells become more susceptible under wet-dry cycles. In addition, we observed a reciprocal interaction between P. syringae and B. velezensis, where P. syringae inhibits B. velezensis under wet conditions. Our findings highlight the important role of hydration conditions in shaping bacterial interference competition, providing valuable insights into the microbial ecology of water-unsaturated surfaces, with implications for applications such as biological control of plant pathogens and mitigating antibiotic resistance.IMPORTANCEOur study reveals that hydration conditions, particularly wet-dry cycles, significantly influence antibiotic-mediated competition between bacterial species. We revealed that the effectiveness of antibiotics produced by Bacillus velezensis against two susceptible bacterial species: Xanthomonas and Pseudomonas varies based on these hydration conditions. Unlike traditional laboratory environments, many real-world habitats, such as soil, plant surfaces, and even animal skin, undergo frequent wet-dry cycles. These conditions affect bacterial competition dynamics and outcomes, with wet-dry cycles providing increased protection for some bacteria while making others more susceptible. Our findings highlight the importance of considering environmental hydration when studying microbial interactions and developing biological control strategies. This research has important implications for improving agricultural practices and understanding natural microbial ecosystems.
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Affiliation(s)
- Yana Beizman-Magen
- Institute of Environmental Sciences, Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food, and Environment, Hebrew University, Rehovot, Israel
| | - Tomer Orevi
- Institute of Environmental Sciences, Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food, and Environment, Hebrew University, Rehovot, Israel
| | - Nadav Kashtan
- Institute of Environmental Sciences, Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food, and Environment, Hebrew University, Rehovot, Israel
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Kumar NG, Grosser MR, Wan S, Schator D, Ahn E, Jedel E, Nieto V, Evans DJ, Fleiszig SMJ. Contact Lens Wear Alters Transcriptional Responses to Pseudomonas aeruginosa in Both the Corneal Epithelium and the Bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.03.626720. [PMID: 39677621 PMCID: PMC11643048 DOI: 10.1101/2024.12.03.626720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
Abstract
Purpose Healthy corneas resist colonization by virtually all microbes yet contact lens wear can predispose the cornea to sight-threatening infection with Pseudomonas aeruginosa. Here, we explored how lens wear changes corneal epithelium transcriptional responses to P. aeruginosa and its impact on bacterial gene expression. Methods Male and female C57BL/6J mice were fitted with a contact lens on one eye for 24 h. After lens removal, corneas were immediately challenged for 4 h with P. aeruginosa. A separate group of naïve mice were similarly challenged with bacteria. Bacteria-challenged eyes were compared to uninoculated naive controls as was lens wear alone. Total RNA-sequencing determined corneal epithelium and bacterial gene expression. Results Prior lens wear profoundly altered the corneal response to P. aeruginosa, including: upregulated pattern-recognition receptors (tlr3, nod1), downregulated lectin pathway of complement activation (masp1), amplified upregulation of tcf7, gpr55, ifi205, wfdc2 (immune defense) and further suppression of efemp1 (corneal stromal integrity). Without lens wear, P. aeruginosa upregulated mitochondrial and ubiquinone metabolism genes. Lens wear alone upregulated axl, grn, tcf7, gpr55 (immune defense) and downregulated Ca2+-dependent genes necab1, snx31 and npr3. P. aeruginosa exposure to prior lens wearing vs. naïve corneas upregulated bacterial genes of virulence (popD), its regulation (rsmY, PA1226) and antimicrobial resistance (arnB, oprR). Conclusion Prior lens wear impacts corneal epithelium gene expression altering its responses to P. aeruginosa and how P. aeruginosa responds to it favoring virulence, survival and adaptation. Impacted genes and associated networks provide avenues for research to better understand infection pathogenesis.
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Affiliation(s)
- Naren G. Kumar
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA USA
| | - Melinda R Grosser
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA USA
| | - Stephanie Wan
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA USA
| | - Daniel Schator
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA USA
| | - Eugene Ahn
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA USA
| | - Eric Jedel
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA USA
- Graduate Program in Infectious Diseases and Immunity, University of California, Berkeley, CA USA
| | - Vincent Nieto
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA USA
| | - David J. Evans
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA USA
- College of Pharmacy, Touro University California, Vallejo, CA USA
| | - Suzanne M. J. Fleiszig
- Herbert Wertheim School of Optometry & Vision Science, University of California, Berkeley, CA USA
- Graduate Groups in Vision Science and Microbiology, University of California, Berkeley, CA USA
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4
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Yang C, Xue B, Yuan Q, Wang S, Su H. Algorithm of spatial-temporal simulation for environment-strain interactions in strain-strain consortia based on resource competition mechanism. Comput Struct Biotechnol J 2024; 23:2861-2871. [PMID: 39100804 PMCID: PMC11296241 DOI: 10.1016/j.csbj.2024.06.033] [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: 01/25/2024] [Revised: 06/26/2024] [Accepted: 06/26/2024] [Indexed: 08/06/2024] Open
Abstract
Interaction simulation for co-culture systems is important for optimizing culture conditions and improving yields. For industrial production, the environment significantly affects the spatial-temporal microbial interactions. However, the current research on polymicrobial interactions mainly focuses on interaction patterns among strains, and neglects the environment influence. Based on the resource competition relationship between two strains, this research set up the modules of cellular physicochemical properties, nutrient uptake and metabolite release, cellular survival, cell swimming and substrate diffusion, and investigated the spatial-temporal strain-environment interactions through module coupling and data mining. Furthermore, in an Escherichia coli-Saccharomyces cerevisiae consortium, the total net reproduction rate decreased as glucose was consumed. E. coli gradually dominated favorable positions due to its higher glucose utilization capacity, reaching 100 % abundance with a competitive strength of 0.86 for glucose. Conversely, S. cerevisiae decreased to 0 % abundance with a competitive strength of 0.14. The simulation results of environment influence on strain competitiveness showed that inoculation ratio and dissolved oxygen strongly influenced strain competitiveness. Specifically, strain competitiveness increased with higher inoculation ratio, whereas E. coli competitiveness increased as dissolved oxygen increased, in contrast to S. cerevisiae. On the other hand, substrate diffusion condition, micronutrients and toxins had minimal influence on strain competitiveness. This method offers a straightforward procedure without featured downscaling and provides novel insights into polymicrobial interaction simulation.
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Affiliation(s)
- Chen Yang
- State Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Bioprocess, and Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, People’s Republic of China
| | - Boyuan Xue
- State Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Bioprocess, and Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, People’s Republic of China
| | - Qianqian Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Bioprocess, and Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, People’s Republic of China
| | - Shaojie Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Bioprocess, and Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, People’s Republic of China
| | - Haijia Su
- State Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Bioprocess, and Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, People’s Republic of China
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5
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Ouertani A, Mollet C, Boughanmi Y, de Pomyers H, Mosbah A, Ouzari HI, Cherif A, Gigmes D, Maresca M, Mabrouk K. Screening of antimicrobial activity in venom: Exploring key parameters. Toxicon 2024; 251:108135. [PMID: 39433258 DOI: 10.1016/j.toxicon.2024.108135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 09/20/2024] [Accepted: 10/18/2024] [Indexed: 10/23/2024]
Abstract
The escalating challenge of antibiotic resistance significantly threatens global health, underscoring the critical need for new antimicrobial agents. Venoms, increasingly recognized as reservoirs of bioactive compounds with diverse pharmacological effects, have been the focus of recent research. This work evaluates the use of various screening methodologies in assessing the antimicrobial activities of 185 venoms against some gram positive and gram negative bacteria, including E. coli ATCC 8739, B. subtilis ATCC 6633, P. aeruginosa ATCC 9027, and S. aureus ATCC 6538P species and explores the influence of settings on the findings. Furthermore, the research explored the possibility of purifying antimicrobial molecules from venoms through HPLC. Several fractions demonstrated antimicrobial activity against the tested strains. Our results reveal that the measured antimicrobial efficacy of venoms varies according to:i) venom concentration, ii) the detection method, including microdilution and radial diffusion assays, and iii) the choice of culture medium, specifically LB or MH. This strategy has allowed us, for the first time, to identify antimicrobial activity in: i) Bitis arietans venom against P. aeruginosa ATCC 9027, ii) Naja nubiae and Bothrops lanceolatus against B. subtilis ATCC 6633, P. aeruginosa ATCC 9027, and S. aureus ATCC 6538P, and iii) Hadogenes zuluanus, Mesobuthus caucasicus, Nebo hierichonticus, Opistophthalmus wahlbergii scorpions, and Mylabris quadripunctata beetles against S. aureus ATCC 6538P. These findings highlight venoms potential as effective antimicrobial resources and improve our understanding of key factors critical for an accurate detection of venoms antimicrobial properties.
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Affiliation(s)
- Awatef Ouertani
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, 2020, Ariana, Tunisia
| | - Chloé Mollet
- Aix Marseille Univ, CNRS, ICR, UMR 7273, 13397, Marseille, Cedex 20, France; LATOXAN SAS, 845 avenue Pierre Brossolette, 26800, Portes-les-Valence, France
| | - Yasmine Boughanmi
- Aix Marseille Univ, CNRS, ICR, UMR 7273, 13397, Marseille, Cedex 20, France; LATOXAN SAS, 845 avenue Pierre Brossolette, 26800, Portes-les-Valence, France
| | - Harold de Pomyers
- LATOXAN SAS, 845 avenue Pierre Brossolette, 26800, Portes-les-Valence, France
| | - Amor Mosbah
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, 2020, Ariana, Tunisia
| | - Hadda-Imene Ouzari
- Université Tunis El Manar, FST, LMBA (LR03ES03), 2092, Campus Universitaire, Tunis, Tunisia
| | - Ameur Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, 2020, Ariana, Tunisia
| | - Didier Gigmes
- Aix Marseille Univ, CNRS, ICR, UMR 7273, 13397, Marseille, Cedex 20, France
| | - Marc Maresca
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13013, Marseille, France
| | - Kamel Mabrouk
- Aix Marseille Univ, CNRS, ICR, UMR 7273, 13397, Marseille, Cedex 20, France.
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6
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Harris CG, Semprini L, Rochefort WE, Fogg KC. Statistical optimization of cell-hydrogel interactions for green microbiology - a tutorial review. RSC SUSTAINABILITY 2024; 2:3750-3768. [PMID: 39464839 PMCID: PMC11499971 DOI: 10.1039/d4su00400k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Accepted: 10/14/2024] [Indexed: 10/29/2024]
Abstract
In this tutorial mini-review, we explore the application of Design of Experiments (DOE) as a powerful statistical tool in biotechnology. Specifically, we review the optimization of hydrogel materials for diverse microbial applications related to green microbiology, the use of microbes to promote sustainability. Hydrogels, three-dimensional polymers networks with high water retention capabilities, are pivotal in the immobilization of microorganisms and provide a customizable environment essential for directing microbial fate. We focus on the application of DOE to precisely tailor hydrogel compositions for a range of fungi and bacteria either used for the sustainable production of chemical compounds, or the elimination of hazardous substances. We examine a variety of DOE design strategies such as central composite designs, Box-Behnken designs, and optimal designs, and discuss their strategic implementation across diverse hydrogel formulations. Our analysis explores the integral role of DOE in refining hydrogels derived from a spectrum of polymers, including natural and synthetic polymers. We illustrate how DOE facilitates nuanced control over hydrogel properties that cannot be achieved using a standard one factor at a time approach. Furthermore, this review reveals a conserved finding across different materials and applications: there are significant interactions between hydrogel parameters and cell behavior. This highlights the intricacies of cell-hydrogel interactions and the impact on hydrogel material properties and cellular functions. Lastly, this review not only highlights DOE's efficacy in streamlining the optimization of cell-hydrogel processes but also positions it as a critical tool in advancing our understanding of cell-hydrogel dynamics, potentially leading to innovative advancements in biotechnological applications and bioengineering solutions.
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Affiliation(s)
- Conor G Harris
- School of Chemical, Biological, and Environmental Engineering, Oregon State University Corvallis OR 97331 USA +1 541-737-1777
| | - Lewis Semprini
- School of Chemical, Biological, and Environmental Engineering, Oregon State University Corvallis OR 97331 USA +1 541-737-1777
| | - Willie E Rochefort
- School of Chemical, Biological, and Environmental Engineering, Oregon State University Corvallis OR 97331 USA +1 541-737-1777
| | - Kaitlin C Fogg
- School of Chemical, Biological, and Environmental Engineering, Oregon State University Corvallis OR 97331 USA +1 541-737-1777
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7
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Lichtenegger AS, Posadas-Cantera S, Badr MT, Häcker G. Comparison of the diversity of anaerobic-cultured gut bacterial communities on different culture media using 16S rDNA sequencing. J Microbiol Methods 2024; 224:106988. [PMID: 38977080 DOI: 10.1016/j.mimet.2024.106988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/10/2024]
Abstract
The gut microbiome is a dense and diverse community of different microorganisms that deeply influence human physiology and that have important interactions with pathogens. For the correct antibiotic treatment of infections, with its twin goals of effective inhibition of the pathogen and limitation of collateral damage to the microbiome, the identification of infectious organisms is key. Microbiological culturing is still the mainstay of pathogen identification, and anaerobic species are among the most demanding bacterial communities to culture. This study aimed to evaluate the impact of growth media on the culture of an-aerobic bacteria from human stool samples. Stool samples from eight human subjects were cultured each on a yeast extract cysteine blood agar (HCB) and a modified peptone-yeast extract-glucose (MPYG) plate and subjected to Illumina NGS analysis after DNA extraction and amplification. The results showed tight clustering of sequencing samples belonging to the same human subject. Various differences in bacterial richness and evenness could be observed between the two media, with HCB plates supporting the growth of a more diverse microbial community, and MPYG plates improving the growth rates of certain taxa. No statistical significance was observed between the groups. This study highlights the importance of choosing the appropriate growth media for anaerobic bacterial culture and adjusting culture conditions to target specific pathological conditions. HCB plates are suitable for standard microbiological diagnostics, while MPYG plates may be more appropriate for targeting specific conditions. This work emphasizes the role of next-generation sequencing in supporting future research in clinical microbiology.
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Affiliation(s)
- Anne Sophie Lichtenegger
- Institute of Medical Microbiology and Hygiene, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.
| | - Sara Posadas-Cantera
- Institute of Medical Microbiology and Hygiene, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Mohamed Tarek Badr
- Institute of Medical Microbiology and Hygiene, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Georg Häcker
- Institute of Medical Microbiology and Hygiene, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
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8
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Shao Z, Gu S, Zhang X, Xue J, Yan T, Guo S, Pommier T, Jousset A, Yang T, Xu Y, Shen Q, Wei Z. Siderophore interactions drive the ability of Pseudomonas spp . consortia to protect tomato against Ralstonia solanacearum. HORTICULTURE RESEARCH 2024; 11:uhae186. [PMID: 39247881 PMCID: PMC11377186 DOI: 10.1093/hr/uhae186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 07/01/2024] [Indexed: 09/10/2024]
Abstract
The soil-borne bacterial pathogen Ralstonia solanacearum causes significant losses in Solanaceae crop production worldwide, including tomato, potato, and eggplant. To efficiently prevent outbreaks, it is essential to understand the complex interactions between pathogens and the microbiome. One promising mechanism for enhancing microbiome functionality is siderophore-mediated competition, which is shaped by the low iron availability in the rhizosphere. This study explores the critical role of iron competition in determining microbiome functionality and its potential for designing high-performance microbiome engineering strategies. We investigated the impact of siderophore-mediated interactions on the efficacy of Pseudomonas spp. consortia in suppressing R. solanacearum , both in vitro and in vivo. Our findings show that siderophore production significantly enhances the inhibitory effects of Pseudomonas strains on pathogen growth, while other metabolites are less effective under iron-limited conditions. Moreover, siderophores play a crucial role in shaping interactions within the consortia, ultimately determining the level of protection against bacterial wilt disease. This study highlights the key role of siderophores in mediating consortium interactions and their impact on tomato health. Our results also emphasize the limited efficacy of other secondary metabolites in iron-limited environments, underscoring the importance of siderophore-mediated competition in maintaining tomato health and suppressing disease.
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Affiliation(s)
- Zhengying Shao
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaohua Gu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xiaoni Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiao Xue
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Tao Yan
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Saisai Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Thomas Pommier
- Setec Energie Environnement, 97/101 bvd Vivier Merle, Lyon 69003, France
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianjie Yang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
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9
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Chiba M, Miri S, Yousuf B, Esmail GA, Leao L, Li Y, Hincke M, Minic Z, Mottawea W, Hammami R. Dual bacteriocin and extracellular vesicle-mediated inhibition of Campylobacter jejuni by the potential probiotic candidate Ligilactobacillus salivarius UO.C249. Appl Environ Microbiol 2024; 90:e0084524. [PMID: 39078127 PMCID: PMC11337818 DOI: 10.1128/aem.00845-24] [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: 05/01/2024] [Accepted: 07/03/2024] [Indexed: 07/31/2024] Open
Abstract
Campylobacter jejuni (C. jejuni) is one of the most common causes of foodborne infections worldwide and a major contributor to diarrheal diseases. This study aimed to explore the ability of commensal gut bacteria to control C. jejuni infection. Bacterial strains from the intestinal mucosa of broilers were screened in vitro against C. jejuni ATCC BAA1153. The cell-free supernatant (CFS) of Ligilactobacillus salivarius UO.C249 showed potent dose-dependent antimicrobial activity against the pathogen, likely due to the presence of bacteriocin-like moieties, as confirmed by protease treatment. Genome and exoproteome analyses revealed the presence of known bacteriocins, including Abp118. The genome of Lg. salivarius UO.C249 harbors a 1.8-Mb chromosome and a 203-kb megaplasmid. The strain was susceptible to several antibiotics and had a high survival rate in the simulated chicken gastrointestinal tract (GIT). Post-protease treatment revealed residual inhibitory activity, suggesting alternative antimicrobial mechanisms. Short-chain fatty acid (SCFA) quantification confirmed non-inhibitory levels of acetic (24.4 ± 1.2 mM), isovaleric (34 ± 1.0 µM), and butyric (32 ± 2.5 µM) acids. Interestingly, extracellular vesicles (EVs) isolated from the CFS of Lg. salivarius UO.C249 were found to inhibit C. jejuni ATCC BAA-1153. Proteome profiling of these EVs revealed the presence of unique proteins distinct from bacteriocins identified in CFS. The majority of the identified proteins in EVs are located in the membrane and play roles in transmembrane transport and peptidoglycan degradation, peptidase, proteolysis, and hydrolysis. These findings suggest that although bacteriocins are a primary antimicrobial mechanism, EV production also contributes to the inhibitory activity of Lg. salivarius UO.C249 against C. jejuni. IMPORTANCE Campylobacter jejuni (C. jejuni) is a major cause of gastroenteritis and a global public health concern. The increasing antibiotic resistance and lack of effective alternatives in livestock production pose serious challenges for controlling C. jejuni infections. Therefore, alternative strategies are needed to control this pathogen, especially in the poultry industry where it is prevalent and can be transmitted to humans through contaminated food products. In this study, Ligilactobacillus salivarius UO.C249 isolated from broiler intestinal mucosa inhibited C. jejuni and exhibited important probiotic features. Beyond bacteriocins, Lg. salivarius UO.C249 secretes antimicrobial extracellular vesicles (EVs) with a unique protein set distinct from bacteriocins that are involved in transmembrane transport and peptidoglycan degradation. Our findings suggest that beyond bacteriocins, EV production is also a distinct inhibitory signaling mechanism used by Lg. salivarius UO.C249 to control C. jejuni. These findings hold promise for the application of probiotic EVs for pathogen control.
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Affiliation(s)
- Mariem Chiba
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Saba Miri
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Basit Yousuf
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Galal Ali Esmail
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Luana Leao
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Yingxi Li
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Maxwell Hincke
- Department of Innovation in Medical Education, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Zoran Minic
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Walid Mottawea
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Riadh Hammami
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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10
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Wu F, Yuan C, Ruan C, Zheng M, Liu L, Wang G, Chen G. Coagulation promotes the spread of antibiotic resistance genes in secondary effluents. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 355:124245. [PMID: 38810683 DOI: 10.1016/j.envpol.2024.124245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 05/04/2024] [Accepted: 05/26/2024] [Indexed: 05/31/2024]
Abstract
Wastewater treatment plants (WWTPs) are biological hotspots receiving the residual antibiotics and antibiotic resistant bacteria/genes (ARB/ARGs) that greatly influence the spread of antibiotic resistance in the environment. A common method used in WWTPs for the purification of secondary effluent is coagulation. Notwithstanding the increasing health concern of antibiotic resistance in WWTPs, the impact of coagulation on the emergence and spread of antibiotic resistance remains unclear. To shed light on this, our study investigated the behavior of four representative ARB types (tetracycline, sulfamethoxazole, clindamycin, and ciprofloxacin resistance) during the coagulation process in a model wastewater treatment plant. Our search showed a significant reduction in the presence of ARBs after either PAC or FeCl3 coagulation, with removal efficiencies of 95% and 90%, respectively. However, after 4 days of storage, ARB levels in the coagulated effluent increased by 6-138 times higher than the original secondary effluent. It suggests a potential resurgence and spread of antibiotic resistance after coagulation. Detailed studies suggest that coagulants, particularly PAC, may facilitate the transfer of ARGs among different bacterial species by the enhanced cell-cell contact during coagulation-induced bacterial aggregation. This transfer is further enhanced by the factors such as auxiliary mixing, longer incubation time and ideal operating temperatures. In addition, both PAC and FeCl3 affected gene expression associated with bacterial conjugation, leading to an increase in conjugation efficiency. In conclusion, while coagulation serves as a purification method, it might inadvertently boost the spread of ARGs during tertiary wastewater treatment. This underscores the importance of implementing subsequent measures to mitigate this effect. Our findings provide a deeper understanding of the challenges posed by bacterial antibiotic resistance in wastewater and pave the way for devising more effective ARB and ARG management strategies.
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Affiliation(s)
- Fazhu Wu
- Department of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Chao Yuan
- Department of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Chujin Ruan
- Department of Soil and Water Sciences, China Agricultural University, Beijing, 100193, China; Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, 8600, Switzerland
| | - Mengqi Zheng
- Department of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Li Liu
- Department of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Gang Wang
- Department of Soil and Water Sciences, China Agricultural University, Beijing, 100193, China
| | - Guowei Chen
- Department of Civil Engineering, Hefei University of Technology, Hefei, 230009, China.
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11
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Leinweber A, Laffont C, Lardi M, Eberl L, Pessi G, Kümmerli R. RNA-Seq reveals that Pseudomonas aeruginosa mounts growth medium-dependent competitive responses when sensing diffusible cues from Burkholderia cenocepacia. Commun Biol 2024; 7:995. [PMID: 39143311 PMCID: PMC11324955 DOI: 10.1038/s42003-024-06618-3] [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: 05/05/2023] [Accepted: 07/23/2024] [Indexed: 08/16/2024] Open
Abstract
Most habitats host diverse bacterial communities, offering opportunities for inter-species interactions. While competition might often dominate such interactions, little is known about whether bacteria can sense competitors and mount adequate responses. The competition sensing hypothesis proposes that bacteria can use cues such as nutrient stress and cell damage to prepare for battle. Here, we tested this hypothesis by measuring transcriptome changes in Pseudomonas aeruginosa exposed to the supernatant of its competitor Burkholderia cenocepacia. We found that P. aeruginosa exhibited significant growth-medium-dependent transcriptome changes in response to competition. In an iron-rich medium, P. aeruginosa upregulated genes encoding the type-VI secretion system and the siderophore pyoverdine, whereas genes encoding phenazine toxins and hydrogen cyanide were upregulated under iron-limited conditions. Moreover, general stress response and quorum sensing regulators were upregulated upon supernatant exposure. Altogether, our results reveal nuanced competitive responses of P. aeruginosa when confronted with B. cenocepacia supernatant, integrating both environmental and social cues.
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Affiliation(s)
- Anne Leinweber
- Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Clémentine Laffont
- Department of Quantitative Biomedicine, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.
| | - Martina Lardi
- Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Rolf Kümmerli
- Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.
- Department of Quantitative Biomedicine, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.
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12
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Sachdeva S, Sarethy IP. Diving into freshwater microbial metabolites: Pioneering research and future prospects. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024:1-19. [PMID: 38887995 DOI: 10.1080/09603123.2024.2351153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 04/30/2024] [Indexed: 06/20/2024]
Abstract
In practically every facet of life, especially nutrition, agriculture, and healthcare, microorganisms offer a prospective origin for abundant natural substances and products. Among these microorganisms, bacteria also possess the capability to rapidly acclimate to diverse environments, utilize varied resources, and effectively respond to environmental fluctuations, including those influenced by human activities like pollution and climate change. The ever-changing environment of freshwater bodies influences bacterial communities, offering opportunities for improving health and environmental conservation that remain unexplored. Herein, the study discusses the bacterial taxa along with specialised metabolites with antioxidant, antibacterial, and anticancer activity that have been identified from freshwater environments, thus achieving Sustainable Development Goals addressing health and wellbeing (SDG-3), economic growth (SDG-8) along with industrial development (SDG-9). The present review is intended as a compendium for research teams working in the fields of medicinal chemistry, organic chemistry, clinical research, and natural product chemistry.
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Affiliation(s)
- Saloni Sachdeva
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Indira P Sarethy
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
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13
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Partipilo G, Bowman EK, Palmer EJ, Gao Y, Ridley RS, Alper HS, Keitz BK. Single-Cell Phenotyping of Extracellular Electron Transfer via Microdroplet Encapsulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598847. [PMID: 38915652 PMCID: PMC11195189 DOI: 10.1101/2024.06.13.598847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Electroactive organisms contribute to metal cycling, pollutant removal, and other redox-driven environmental processes. Studying this phenomenon in high-throughput is challenging since extracellular reduction cannot easily be traced back to its cell of origin within a mixed population. Here, we describe the development of a microdroplet emulsion system to enrich EET-capable organisms. We validated our system using the model electroactive organism S. oneidensis and describe the tooling of a benchtop microfluidic system for oxygen-limited processes. We demonstrated enrichment of EET-capable phenotypes from a mixed wild-type and EET-knockout population. As a proof-of-concept application, bacteria were collected from iron sedimentation from Town Lake (Austin, TX) and subjected to microdroplet enrichment. We observed an increase in EET-capable organisms in the sorted population that was distinct when compared to a population enriched in a bulk culture more closely akin to traditional techniques for discovering EET-capable bacteria. Finally, two bacterial species, C. sakazakii and V. fessus not previously shown to be electroactive, were further cultured and characterized for their ability to reduce channel conductance in an organic electrochemical transistor (OECT) and to reduce soluble Fe(III). We characterized two bacterial species not previously shown to exhibit electrogenic behavior. Our results demonstrate the utility of a microdroplet emulsions for identifying putative EET-capable bacteria and how this technology can be leveraged in tandem with existing methods.
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Affiliation(s)
- Gina Partipilo
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Emily K. Bowman
- Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, 78712
| | - Emma J. Palmer
- Civil, Architectural, and Environmental Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Yang Gao
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Rodney S. Ridley
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Benjamin K. Keitz
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
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14
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Capasso C, Supuran CT. Overview on bacterial carbonic anhydrase genetic families. Enzymes 2024; 55:1-29. [PMID: 39222988 DOI: 10.1016/bs.enz.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Bacterial carbonic anhydrases (BCAs, EC 4.2.1.1) are indispensable enzymes in microbial physiology because they facilitate the hydration of carbon dioxide (CO2) to bicarbonate ions (HCO3-) and protons (H+), which are crucial for various metabolic processes and cellular homeostasis. Their involvement spans from metabolic pathways, such as photosynthesis, respiration, to organic compounds production, which are pivotal for bacterial growth and survival. This chapter elucidates the diversity of BCA genetic families, categorized into four distinct classes (α, β, γ, and ι), which may reflect bacterial adaptation to environmental niches and their metabolic demands. The diversity of BCAs is essential not only for understanding their physiological roles but also for exploring their potential in biotechnology. Knowledge of their diversity enables researchers to develop innovative biocatalysts for industrial applications, including carbon capture technologies to convert CO2 emissions into valuable products. Additionally, BCAs are relevant to biomedical research and drug development because of their involvement in bacterial pathogenesis and microbial survival within the host. Understanding the diversity and function of BCAs can aid in designing targeted therapeutics that interfere with bacterial metabolism and potentially reduce the risk of infections.
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Affiliation(s)
- Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, CNR, Napoli, Italy.
| | - Claudiu T Supuran
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Firenze, Italy
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15
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Murray-Nerger LA, Maestri D, Liu X, Li Z, Tempera I, Teng M, Gewurz BE. The DNA loop release factor WAPL suppresses Epstein-Barr virus latent membrane protein expression to maintain the highly restricted latency I program. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593401. [PMID: 38766209 PMCID: PMC11100819 DOI: 10.1101/2024.05.09.593401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Epstein-Barr virus (EBV) uses latency programs to colonize the memory B-cell reservoir, and each program is associated with human malignancies. However, knowledge remains incomplete of epigenetic mechanisms that maintain the highly restricted latency I program, present in memory and Burkitt lymphoma cells, in which EBNA1 is the only EBV-encoded protein expressed. Given increasing appreciation that higher order chromatin architecture is an important determinant of viral and host gene expression, we investigated roles of Wings Apart-Like Protein Homolog (WAPL), a host factor that unloads cohesins to control DNA loop size and that was discovered as an EBNA2-associated protein. WAPL knockout (KO) in Burkitt cells de-repressed LMP1 and LMP2A expression but not other EBV oncogenes to yield a viral program reminiscent of EBV latency II, which is rarely observed in B-cells. WAPL KO also increased LMP1/2A levels in latency III lymphoblastoid cells. WAPL KO altered EBV genome architecture, triggering formation of DNA loops between the LMP promoter region and the EBV origins of lytic replication (oriLyt). Hi-C analysis further demonstrated that WAPL KO reprograms EBV genomic DNA looping. LMP1 and LMP2A de-repression correlated with decreased histone repressive marks at their promoters. We propose that EBV coopts WAPL to negatively regulate latent membrane protein expression to maintain Burkitt latency I. Author Summary EBV is a highly prevalent herpesvirus etiologically linked to multiple lymphomas, gastric and nasopharyngeal carcinomas, and multiple sclerosis. EBV persists in the human host in B-cells that express a series of latency programs, each of which is observed in a distinct type of human lymphoma. The most restricted form of EBV latency, called latency I, is observed in memory cells and in most Burkitt lymphomas. In this state, EBNA1 is the only EBV-encoded protein expressed to facilitate infected cell immunoevasion. However, epigenetic mechanisms that repress expression of the other eight EBV-encoded latency proteins remain to be fully elucidated. We hypothesized that the host factor WAPL might have a role in restriction of EBV genes, as it is a major regulator of long-range DNA interactions by negatively regulating cohesin proteins that stabilize DNA loops, and WAPL was found in a yeast 2-hybrid screen for EBNA2-interacting host factors. Using CRISPR together with Hi-ChIP and Hi-C DNA architecture analyses, we uncovered WAPL roles in suppressing expression of LMP1 and LMP2A, which mimic signaling by CD40 and B-cell immunoglobulin receptors, respectively. These proteins are expressed together with EBNA1 in the latency II program. We demonstrate that WAPL KO changes EBV genomic architecture, including allowing the formation of DNA loops between the oriLyt enhancers and the LMP promoter regions. Collectively, our study suggests that WAPL reinforces Burkitt latency I by preventing the formation of DNA loops that may instead support the latency II program.
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16
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Silva-Andrade C, Rodriguez-Fernández M, Garrido D, Martin AJM. Using metabolic networks to predict cross-feeding and competition interactions between microorganisms. Microbiol Spectr 2024; 12:e0228723. [PMID: 38506512 PMCID: PMC11064492 DOI: 10.1128/spectrum.02287-23] [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: 06/07/2023] [Accepted: 02/06/2024] [Indexed: 03/21/2024] Open
Abstract
Understanding the interactions between microorganisms and their impact on bacterial behavior at the community level is a key research topic in microbiology. Different methods, relying on experimental or mathematical approaches based on the diverse properties of bacteria, are currently employed to study these interactions. Recently, the use of metabolic networks to understand the interactions between bacterial pairs has increased, highlighting the relevance of this approach in characterizing bacteria. In this study, we leverage the representation of bacteria through their metabolic networks to build a predictive model aimed at reducing the number of experimental assays required for designing bacterial consortia with specific behaviors. Our novel method for predicting cross-feeding or competition interactions between pairs of microorganisms utilizes metabolic network features. Machine learning classifiers are employed to determine the type of interaction from automatically reconstructed metabolic networks. Several algorithms were assessed and selected based on comprehensive testing and careful separation of manually compiled data sets obtained from literature sources. We used different classification algorithms, including K Nearest Neighbors, XGBoost, Support Vector Machine, and Random Forest, tested different parameter values, and implemented several data curation approaches to reduce the biological bias associated with our data set, ultimately achieving an accuracy of over 0.9. Our method holds substantial potential to advance the understanding of community behavior and contribute to the development of more effective approaches for consortia design.IMPORTANCEUnderstanding bacterial interactions at the community level is critical for microbiology, and leveraging metabolic networks presents an efficient and effective approach. The introduction of this novel method for predicting interactions through machine learning classifiers has the potential to advance the field by reducing the number of experimental assays required and contributing to the development of more effective bacterial consortia.
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Affiliation(s)
- Claudia Silva-Andrade
- Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - María Rodriguez-Fernández
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alberto J. M. Martin
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Escuela de Ingeniería, Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
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17
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Zhang S, Hung J, Yen TN, Huang S. Mutualistic interactions of lactate-producing lactobacilli and lactate-utilizing Veillonella dispar: Lactate and glutamate cross-feeding for the enhanced growth and short-chain fatty acid production. Microb Biotechnol 2024; 17:e14484. [PMID: 38801349 PMCID: PMC11129673 DOI: 10.1111/1751-7915.14484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024] Open
Abstract
The human gut hosts numerous ecological niches for microbe-microbe and host-microbe interactions. Gut lactate homeostasis in humans is crucial and relies on various bacteria. Veillonella spp., gut lactate-utilizing bacteria, and lactate-producing bacteria were frequently co-isolated. A recent clinical trial has revealed that lactate-producing bacteria in humans cross-feed lactate to Veillonella spp.; however, their interspecies interaction mechanisms remain unclear. Veillonella dispar, an obligate anaerobe commonly found in the human gut and oral cavity, ferments lactate into acetate and propionate. In our study, we investigated the interaction between V. dispar ATCC 17748T and three representative phylogenetically distant strains of lactic acid bacteria, Lactobacillus acidophilus ATCC 4356T, Lacticaseibacillus paracasei subsp. paracasei ATCC 27216T, and Lactiplantibacillus plantarum ATCC 10241. Bacterial growth, viability, metabolism and gene level adaptations during bacterial interaction were examined. V. dispar exhibited the highest degree of mutualism with L. acidophilus. During co-culture of V. dispar with L. acidophilus, both bacteria exhibited enhanced growth and increased viability. V. dispar demonstrated an upregulation of amino acid biosynthesis pathways and the aspartate catabolic pathway. L. acidophilus also showed a considerable number of upregulated genes related to growth and lactate fermentation. Our results support that V. dispar is able to enhance the fermentative capability of L. acidophilus by presumably consuming the produced lactate, and that L. acidophilus cross-feed not only lactate, but also glutamate, to V. dispar during co-culture. The cross-fed glutamate enters the central carbon metabolism in V. dispar. These findings highlight an intricate metabolic relationship characterized by cross-feeding of lactate and glutamate in parallel with considerable gene regulation within both L. acidophilus (lactate-producing) and V. dispar (lactate-utilizing). The mechanisms of mutualistic interactions between a traditional probiotic bacterium and a potential next-generation probiotic bacterium were elucidated in the production of short-chain fatty acids.
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Affiliation(s)
- Shi‐Min Zhang
- Program in Molecular MedicineNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Jia‐He Hung
- School of MedicineNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Tran Ngoc Yen
- Institute of Microbiology and ImmunologyNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Shir‐Ly Huang
- Institute of Microbiology and ImmunologyNational Yang Ming Chiao Tung UniversityTaipeiTaiwan
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18
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Li C, Han G, Huang L, Lu Y, Xia Y, Zhang N, Liu Q, Xu J. Metagenomic Analyses Reveal Gut Microbial Profiles of Cnaphalocrocis medinalis Driven by the Infection of Baculovirus CnmeGV. Microorganisms 2024; 12:757. [PMID: 38674701 PMCID: PMC11052019 DOI: 10.3390/microorganisms12040757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/20/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
The composition of microbiota in the digestive tract gut is essential for insect physiology, homeostasis, and pathogen infection. Little is known about the interactions between microbiota load and oral infection with baculoviruses. CnmeGV is an obligative baculovirus to Cnaphalocrocis medinalis. We investigated the impact of CnmeGV infection on the structure of intestinal microbes of C. medinalis during the initial infection stage. The results revealed that the gut microbiota profiles were dynamically driven by pathogen infection of CnmeGV. The numbers of all the OTU counts were relatively higher at the early and later stages, while the microbial diversity significantly increased early but dropped sharply following the infection. The compositional abundance of domain bacteria Firmicutes developed substantially higher. The significantly enriched and depleted species can be divided into four groups at the species level. Fifteen of these species were ultimately predicted as the biomarkers of CnmeGV infection. CnmeGV infection induces significant enrichment of alterations in functional genes related to metabolism and the immune system, encompassing processes such as carbohydrate, amino acid, cofactor, and vitamin metabolism. Finally, the study may provide an in-depth analysis of the relationship between host microbiota, baculovirus infection, and pest control of C. medinalis.
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Affiliation(s)
| | | | | | | | | | | | | | - Jian Xu
- National Experimental Station of Yangzhou for Agricultural Microbiology, Jiangsu Lixiahe Institute of Agricultural Sciences, Yangzhou 225008, China; (C.L.); (G.H.); (L.H.); (Y.L.); (Y.X.); (N.Z.); (Q.L.)
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19
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Carnicero-Mayo Y, Sáenz de Miera LE, Ferrero MÁ, Navasa N, Casqueiro J. Modeling Dynamics of Human Gut Microbiota Derived from Gluten Metabolism: Obtention, Maintenance and Characterization of Complex Microbial Communities. Int J Mol Sci 2024; 25:4013. [PMID: 38612823 PMCID: PMC11012253 DOI: 10.3390/ijms25074013] [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: 02/28/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Western diets are rich in gluten-containing products, which are frequently poorly digested. The human large intestine harbors microorganisms able to metabolize undigested gluten fragments that have escaped digestion by human enzymatic activities. The aim of this work was obtaining and culturing complex human gut microbial communities derived from gluten metabolism to model the dynamics of healthy human large intestine microbiota associated with different gluten forms. For this purpose, stool samples from six healthy volunteers were inoculated in media containing predigested gluten or predigested gluten plus non-digested gluten. Passages were carried out every 24 h for 15 days in the same medium and community composition along time was studied via V3-V4 16S rDNA sequencing. Diverse microbial communities were successfully obtained. Moreover, communities were shown to be maintained in culture with stable composition for 14 days. Under non-digested gluten presence, communities were enriched in members of Bacillota, such as Lachnospiraceae, Clostridiaceae, Streptococcaceae, Peptoniphilaceae, Selenomonadaceae or Erysipelotrichaceae, and members of Actinomycetota, such as Bifidobacteriaceae and Eggerthellaceae. Contrarily, communities exposed to digested gluten were enriched in Pseudomonadota. Hence, this study shows a method for culture and stable maintenance of gut communities derived from gluten metabolism. This method enables the analysis of microbial metabolism of gluten in the gut from a community perspective.
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Affiliation(s)
- Yaiza Carnicero-Mayo
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24007 León, Spain;
| | - Luis E. Sáenz de Miera
- Área de Genética, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24007 León, Spain;
| | - Miguel Ángel Ferrero
- Área de Bioquímica y Biología Molecular, Facultad de Veterinaria, Universidad de León, 24007 León, Spain; (M.Á.F.); (N.N.)
| | - Nicolás Navasa
- Área de Bioquímica y Biología Molecular, Facultad de Veterinaria, Universidad de León, 24007 León, Spain; (M.Á.F.); (N.N.)
| | - Javier Casqueiro
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24007 León, Spain;
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20
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Li S, Young T, Archer S, Lee K, Alfaro AC. Gut microbiome resilience of green-lipped mussels, Perna canaliculus, to starvation. Int Microbiol 2024; 27:571-580. [PMID: 37523041 PMCID: PMC10991064 DOI: 10.1007/s10123-023-00397-3] [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: 03/12/2023] [Revised: 06/14/2023] [Accepted: 07/03/2023] [Indexed: 08/01/2023]
Abstract
Host gut microbiomes play an important role in animal health and resilience to conditions, such as malnutrition and starvation. These host-microbiome relationships are poorly understood in the marine mussel Perna canaliculus, which experiences significant variations in food quantity and quality in coastal areas. Prolonged starvation may be a contributory factor towards incidences of mass mortalities in farmed mussel populations, resulting in highly variable production costs and unreliable market supplies. Here, we examine the gut microbiota of P. canaliculus in response to starvation and subsequent re-feeding using high-throughput amplicon sequencing of the 16S rRNA gene. Mussels showed no change in bacterial species richness when subjected to a 14-day starvation, followed by re-feeding/recovery. However, beta bacteria diversity revealed significant shifts (PERMANOVA p-value < 0.001) in community structure in the starvation group and no differences in the subsequent recovery group (compared to the control group) once they were re-fed, highlighting their recovery capability and resilience. Phylum-level community profiles revealed an elevation in dominance of Proteobacteria (ANCOM-BC p-value <0.001) and Bacteroidota (ANCOM-BC p-value = 0.04) and lower relative abundance of Cyanobacteria (ANCOM-BC p-value = 0.01) in the starvation group compared to control and recovery groups. The most abundant genus-level shifts revealed relative increases of the heterotroph Halioglobus (p-value < 0.05) and lowered abundances of the autotroph Synechococcus CC9902 in the starvation group. Furthermore, a SparCC correlation network identified co-occurrence of a cluster of genera with elevated relative abundance in the starved mussels that were positively correlated with Synechococcus CC9902. The findings from this work provide the first insights into the effect of starvation on the resilience capacity of Perna canaliculus gut microbiota, which is of central importance to understanding the effect of food variation and limitation in farmed mussels.
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Affiliation(s)
- Siming Li
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Tim Young
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
- The Centre for Biomedical and Chemical Sciences, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Stephen Archer
- Department of Environmental Science, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Kevin Lee
- Department of Environmental Science, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand.
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21
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Romdhane S, Huet S, Spor A, Bru D, Breuil MC, Philippot L. Manipulating the physical distance between cells during soil colonization reveals the importance of biotic interactions in microbial community assembly. ENVIRONMENTAL MICROBIOME 2024; 19:18. [PMID: 38504378 PMCID: PMC10953230 DOI: 10.1186/s40793-024-00559-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/03/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND Microbial communities are of tremendous importance for ecosystem functioning and yet we know little about the ecological processes driving the assembly of these communities in the environment. Here, we used an unprecedented experimental approach based on the manipulation of physical distance between neighboring cells during soil colonization to determine the role of bacterial interactions in soil community assembly. We hypothesized that experimentally manipulating the physical distance between bacterial cells will modify the interaction strengths leading to differences in microbial community composition, with increasing distance between neighbors favoring poor competitors. RESULTS We found significant differences in both bacterial community diversity, composition and co-occurrence networks after soil colonization that were related to physical distancing. We show that reducing distances between cells resulted in a loss of bacterial diversity, with at least 41% of the dominant OTUs being significantly affected by physical distancing. Our results suggest that physical distancing may differentially modulate competitiveness between neighboring species depending on the taxa present in the community. The mixing of communities that assembled at high and low cell densities did not reveal any "home field advantage" during coalescence. This confirms that the observed differences in competitiveness were due to biotic rather than abiotic filtering. CONCLUSIONS Our study demonstrates that the competitiveness of bacteria strongly depends on cell density and community membership, therefore highlighting the fundamental role of microbial interactions in the assembly of soil communities.
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Affiliation(s)
- Sana Romdhane
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France.
| | - Sarah Huet
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
| | - Aymé Spor
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
| | - David Bru
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
| | - Marie-Christine Breuil
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
| | - Laurent Philippot
- Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, F-21000, Dijon, France
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22
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Musa OI, Akande SA, Ijah UJJ, Abioye OP, Maude AM, Samuel JO, Mustapha A, Abdulrahim AM, Gusdanis ACG. Biofilms communities in the soil: characteristic and interactions using mathematical model. Res Microbiol 2024; 175:104149. [PMID: 37923049 DOI: 10.1016/j.resmic.2023.104149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/17/2023] [Accepted: 10/22/2023] [Indexed: 11/07/2023]
Abstract
There are many different kinds of microorganisms in the soil, and many of them are biofilms because they can make supracellular compounds. Surface-associated microorganisms in a biofilm are encased in a hydrated extracellular polymeric substance that aids in adherence and survival. Numerous different kinds of microorganisms call the soil home. Strong interactions with and among species are made possible by biofilms; this, in turn, might increase the effectiveness with which organic compounds and poisons in soil are degraded. This encouraged us to take a close look at soil biofilm ecosystems, which we do in this paper. In this research, we will look at how soil biofilms arise and how that affects the composition of microbial communities and their function in the soil. Recent years have seen an uptick in interest in questions about biofilm structure and the social interactions of various bacteria. Many concepts elucidating the underlying mathematics of biofilm growth are also presented. Since biofilms are so widespread, this breakthrough in soil biofilm inquiry might help scientists understand soil microbiomes better. Mathematical models further extrapolate the relationships between microbial communities and gives a more precise information as to what is happening in a biofilm. Biofilms can help plants cope with a variety of environmental challenges. Soil quality, plant nourishment, plant protection, bioremediation, and climate change are all influenced by the interplay of biofilm communities. Thus, biofilms play an important role in the development of environmentally friendly and sustainable agriculture.
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Affiliation(s)
- Ojeba Innocent Musa
- Department of Microbiology, Skyline University Nigeria, Kano State, Nigeria.
| | | | | | - Olabisi Peter Abioye
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Asmau Mohammed Maude
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Job Oloruntoba Samuel
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Adamu Mustapha
- Department of Microbiology, Federal University of Technology, Minna Niger State, Nigeria
| | - Al-Musbahu Abdulrahim
- Department of Mathematics, Federal University of Technology, Minna Niger State, Nigeria
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23
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Yin R, Cheng J, Lin J. The role of the type VI secretion system in the stress resistance of plant-associated bacteria. STRESS BIOLOGY 2024; 4:16. [PMID: 38376647 PMCID: PMC10879055 DOI: 10.1007/s44154-024-00151-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/26/2024] [Indexed: 02/21/2024]
Abstract
The type VI secretion system (T6SS) is a powerful bacterial molecular weapon that can inject effector proteins into prokaryotic or eukaryotic cells, thereby participating in the competition between bacteria and improving bacterial environmental adaptability. Although most current studies of the T6SS have focused on animal bacteria, this system is also significant for the adaptation of plant-associated bacteria. This paper briefly introduces the structure and biological functions of the T6SS. We summarize the role of plant-associated bacterial T6SS in adaptability to host plants and the external environment, including resistance to biotic stresses such as host defenses and competition from other bacteria. We review the role of the T6SS in response to abiotic factors such as acid stress, oxidation stress, and osmotic stress. This review provides an important reference for exploring the functions of the T6SS in plant-associated bacteria. In addition, characterizing these anti-stress functions of the T6SS may provide new pathways toward eliminating plant pathogens and controlling agricultural losses.
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Affiliation(s)
- Rui Yin
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Sciences, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Juanli Cheng
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Sciences, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Jinshui Lin
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Sciences, Yan'an University, Yan'an, 716000, Shaanxi, China.
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24
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Alvarez-Aponte ZI, Govindaraju AM, Hallberg ZF, Nicolas AM, Green MA, Mok KC, Fonseca-García C, Coleman-Derr D, Brodie EL, Carlson HK, Taga ME. Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates. THE ISME JOURNAL 2024; 18:wrae068. [PMID: 38648288 PMCID: PMC11287214 DOI: 10.1093/ismejo/wrae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/15/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids-the vitamin B12 family of cofactors-are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microorganisms involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12 over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12 at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.
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Affiliation(s)
- Zoila I Alvarez-Aponte
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Alekhya M Govindaraju
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Zachary F Hallberg
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Alexa M Nicolas
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Myka A Green
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Kenny C Mok
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Citlali Fonseca-García
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, United States
| | - Devin Coleman-Derr
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, United States
| | - Eoin L Brodie
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Hans K Carlson
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States
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25
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Hedin KA, Mirhakkak MH, Vaaben TH, Sands C, Pedersen M, Baker A, Vazquez-Uribe R, Schäuble S, Panagiotou G, Wellejus A, Sommer MOA. Saccharomyces boulardii enhances anti-inflammatory effectors and AhR activation via metabolic interactions in probiotic communities. THE ISME JOURNAL 2024; 18:wrae212. [PMID: 39488793 PMCID: PMC11631509 DOI: 10.1093/ismejo/wrae212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2024] [Revised: 10/17/2024] [Accepted: 11/01/2024] [Indexed: 11/04/2024]
Abstract
Metabolic exchanges between strains in gut microbial communities shape their composition and interactions with the host. This study investigates the metabolic synergy between potential probiotic bacteria and Saccharomyces boulardii, aiming to enhance anti-inflammatory effects within a multi-species probiotic community. By screening a collection of 85 potential probiotic bacterial strains, we identified two strains that demonstrated a synergistic relationship with S. boulardii in pairwise co-cultivation. Furthermore, we computationally predicted cooperative communities with symbiotic relationships between S. boulardii and these bacteria. Experimental validation of 28 communities highlighted the role of S. boulardii as a key player in microbial communities, significantly boosting the community's cell number and production of anti-inflammatory effectors, thereby affirming its essential role in improving symbiotic dynamics. Based on our observation, one defined community significantly activated the aryl hydrocarbon receptor-a key regulator of immune response-280-fold more effectively than the community without S. boulardii. This study underscores the potential of microbial communities for the design of more effective probiotic formulations.
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Affiliation(s)
- Karl Alex Hedin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Mohammad H Mirhakkak
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Troels Holger Vaaben
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Carmen Sands
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Mikael Pedersen
- National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Adam Baker
- Human Health Biosolution, Novonesis, Hørsholm 2970, Denmark
| | - Ruben Vazquez-Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- Center for Microbiology, VIB-KU Leuven, Leuven 3001, Belgium
| | - Sascha Schäuble
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
| | - Gianni Panagiotou
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute (Leibniz-HKI), Jena 07745, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University, Jena 07743, Germany
- Jena University Hospital, Friedrich Schiller University, Jena 07743, Germany
- Department of Medicine, University of Hong Kong, Hong Kong (SAR), China
| | - Anja Wellejus
- Human Health Biosolution, Novonesis, Hørsholm 2970, Denmark
| | - Morten Otto Alexander Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
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26
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Booth SC, Meacock OJ, Foster KR. Cell motility empowers bacterial contact weapons. THE ISME JOURNAL 2024; 18:wrae141. [PMID: 39073907 PMCID: PMC11482024 DOI: 10.1093/ismejo/wrae141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 05/02/2024] [Accepted: 07/24/2024] [Indexed: 07/31/2024]
Abstract
Many bacteria kill competitors using short-range weapons, such as the Type VI secretion system and contact dependent inhibition (CDI). Although these weapons can deliver powerful toxins, they rely on direct contact between attacker and target cells. We hypothesized that movement enables attackers to contact more targets and thus greatly empower their weapons. To explore this, we developed individual-based and continuum models of contact-dependent combat which show that motility greatly improves toxin delivery through two underlying processes. First, genotypic mixing increases the inter-strain contact probability of attacker and sensitive cells. Second, target switching ensures attackers constantly attack new cells, instead of repeatedly hitting the same cell. We test our predictions with the pathogen Pseudomonas aeruginosa, using genetically engineered strains to study the interaction between CDI and twitching motility. As predicted, we find that motility works synergistically with CDI, in some cases increasing weapon efficacy up to 10,000-fold compared with non-motile scenarios. Moreover, we demonstrate that both mixing processes occur using timelapse single-cell microscopy and quantify their relative importance by combining experimental data with our model. Our work shows how bacteria can combine cell movement with contact-based weapons to launch powerful attacks on their competitors.
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Affiliation(s)
- Sean C Booth
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Oliver J Meacock
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX13RE, United Kingdom
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27
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Pushkareva E, Elster J, Kudoh S, Imura S, Becker B. Microbial community composition of terrestrial habitats in East Antarctica with a focus on microphototrophs. Front Microbiol 2024; 14:1323148. [PMID: 38249463 PMCID: PMC10797080 DOI: 10.3389/fmicb.2023.1323148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024] Open
Abstract
The Antarctic terrestrial environment harbors a diverse community of microorganisms, which have adapted to the extreme conditions. The aim of this study was to describe the composition of microbial communities in a diverse range of terrestrial environments (various biocrusts and soils, sands from ephemeral wetlands, biofilms, endolithic and hypolithic communities) in East Antarctica using both molecular and morphological approaches. Amplicon sequencing of the 16S rRNA gene revealed the dominance of Chloroflexi, Cyanobacteria and Firmicutes, while sequencing of the 18S rRNA gene showed the prevalence of Alveolata, Chloroplastida, Metazoa, and Rhizaria. This study also provided a comprehensive assessment of the microphototrophic community revealing a diversity of cyanobacteria and eukaryotic microalgae in various Antarctic terrestrial samples. Filamentous cyanobacteria belonging to the orders Oscillatoriales and Pseudanabaenales dominated prokaryotic community, while members of Trebouxiophyceae were the most abundant representatives of eukaryotes. In addition, the co-occurrence analysis showed a prevalence of positive correlations with bacterial taxa frequently co-occurring together.
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Affiliation(s)
- Ekaterina Pushkareva
- Department of Biology, Botanical Institute, University of Cologne, Cologne, Germany
| | - Josef Elster
- Institute of Botany, Academy of Sciences of the Czech Republic, Třeboň, Czechia
- Centre for Polar Ecology, University of South Bohemia, České Budějovice, Czechia
| | - Sakae Kudoh
- Department of Polar Science, The Graduate University for Advanced Studies, SOKENDAI, Tachikawa, Japan
- National Institute of Polar Research, Research Organization of Information and Systems, Tachikawa, Japan
| | - Satoshi Imura
- Department of Polar Science, The Graduate University for Advanced Studies, SOKENDAI, Tachikawa, Japan
- National Institute of Polar Research, Research Organization of Information and Systems, Tachikawa, Japan
| | - Burkhard Becker
- Department of Biology, Botanical Institute, University of Cologne, Cologne, Germany
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28
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Le Bras C, Rault L, Jacquet N, Daniel N, Chuat V, Valence F, Bellanger A, Bousarghin L, Blat S, Le Loir Y, Le Huërou-Luron I, Even S. Two human milk-like synthetic bacterial communities displayed contrasted impacts on barrier and immune responses in an intestinal quadricellular model. ISME COMMUNICATIONS 2024; 4:ycad019. [PMID: 38415201 PMCID: PMC10897888 DOI: 10.1093/ismeco/ycad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 02/29/2024]
Abstract
The human milk (HM) microbiota, a highly diverse microbial ecosystem, is thought to contribute to the health benefits associated with breast-feeding, notably through its impact on infant gut microbiota. Our objective was to further explore the role of HM bacteria on gut homeostasis through a "disassembly/reassembly" strategy. HM strains covering the diversity of HM cultivable microbiota were first characterized individually and then assembled in synthetic bacterial communities (SynComs) using two human cellular models, peripheral blood mononuclear cells and a quadricellular model mimicking intestinal epithelium. Selected HM bacteria displayed a large range of immunomodulatory properties and had variable effects on epithelial barrier, allowing their classification in functional groups. This multispecies characterization of HM bacteria showed no clear association between taxonomy and HM bacteria impacts on epithelial immune and barrier functions, revealing the entirety and complexity of HM bacteria potential. More importantly, the assembly of HM strains into two SynComs of similar taxonomic composition but with strains exhibiting distinct individual properties, resulted in contrasting impacts on the epithelium. These impacts of SynComs partially diverged from the predicted ones based on individual bacteria. Overall, our results indicate that the functional properties of the HM bacterial community rather than the taxonomic composition itself could play a crucial role in intestinal homeostasis of infants.
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Affiliation(s)
- Charles Le Bras
- STLO, INRAE, Institut Agro, Rennes, 35042, France
- Institut NuMeCan, INRAE, INSERM, Univ Rennes, Rennes-Saint Gilles, 35590, France
| | - Lucie Rault
- STLO, INRAE, Institut Agro, Rennes, 35042, France
| | | | | | | | | | | | - Latifa Bousarghin
- Institut NuMeCan, INRAE, INSERM, Univ Rennes, Rennes-Saint Gilles, 35590, France
| | - Sophie Blat
- Institut NuMeCan, INRAE, INSERM, Univ Rennes, Rennes-Saint Gilles, 35590, France
| | - Yves Le Loir
- STLO, INRAE, Institut Agro, Rennes, 35042, France
| | | | - Sergine Even
- STLO, INRAE, Institut Agro, Rennes, 35042, France
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29
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Dogsa I, Mandic-Mulec I. Multiscale spatial segregation analysis in digital images of biofilms. Biofilm 2023; 6:100157. [PMID: 37790733 PMCID: PMC10542597 DOI: 10.1016/j.bioflm.2023.100157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023] Open
Abstract
Quantifying the degree of spatial segregation of two bacterial strains in mixed biofilms is an important topic in microbiology. Spatial segregation is dependent on spatial scale as two strains may appear to be well mixed if observed from a distance, but a closer look can reveal strong separation. Typically, this information is encoded in a digital image that represents the binary system, e.g., a microscopy image of a two species biofilm. To decode spatial segregation information, we have developed quantitative measures for evaluating the degree of the spatial scale-dependent segregation of two bacterial strains in a digital image. The constructed algorithm is based on the new segregation measures and overcomes drawbacks of existing approaches for biofilm segregation analysis. The new approach is implemented in a freely available software and was successfully applied to biofilms of two strains and bacterial suspensions for detection of the different spatial scale-dependent segregation levels.
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Affiliation(s)
- Iztok Dogsa
- Chair of Microbiology, Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000, Ljubljana, EU, Slovenia
| | - Ines Mandic-Mulec
- Chair of Microbiology, Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000, Ljubljana, EU, Slovenia
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30
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Hwang HG, Ye DY, Jung GY. Biosensor-guided discovery and engineering of metabolic enzymes. Biotechnol Adv 2023; 69:108251. [PMID: 37690614 DOI: 10.1016/j.biotechadv.2023.108251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
A variety of chemicals have been produced through metabolic engineering approaches, and enhancing biosynthesis performance can be achieved by using enzymes with high catalytic efficiency. Accordingly, a number of efforts have been made to discover enzymes in nature for various applications. In addition, enzyme engineering approaches have been attempted to suit specific industrial purposes. However, a significant challenge in enzyme discovery and engineering is the efficient screening of enzymes with the desired phenotype from extensive enzyme libraries. To overcome this bottleneck, genetically encoded biosensors have been developed to specifically detect target molecules produced by enzyme activity at the intracellular level. Especially, the biosensors facilitate high-throughput screening (HTS) of targeted enzymes, expanding enzyme discovery and engineering strategies with advances in systems and synthetic biology. This review examines biosensor-guided HTS systems and highlights studies that have utilized these tools to discover enzymes in diverse areas and engineer enzymes to enhance their properties, such as catalytic efficiency, specificity, and stability.
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Affiliation(s)
- Hyun Gyu Hwang
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea.
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31
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Wang A, He M, Liu H, Ouyang W, Liu X, Li Q, Lin C, Liu X. Distribution heterogeneity of sediment bacterial community in the river-lake system impacted by nonferrous metal mines: Diversity, composition and co-occurrence patterns. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 338:122715. [PMID: 37821043 DOI: 10.1016/j.envpol.2023.122715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/03/2023] [Accepted: 10/07/2023] [Indexed: 10/13/2023]
Abstract
Metal(loid) pollution caused by mining activities can affect microbial communities. However, knowledge of the diversity, composition, and co-occurrence patterns of bacterial communities in aquatic systems impacted by nonferrous metal mines. Here, the metal(loid) contents and bacterial communities in sediments from the Zijiang River (tributary to mainstream) to Dongting Lake were investigated by geochemical and molecular biology methods. The results indicated that the river sediments had lower pH and higher ecological risk of metal(loid)s than the lake sediment. The diversity and composition of bacterial communities in river sediments significantly (p < 0.05) differed from those in lake sediments, showing distributional heterogeneity. The biomarkers of tributary, mainstream, and lake sediments were mainly members of Deltaproteobacteria, Firmicutes, and Nitrospirae, respectively, reflecting species sorting in different habitats. Multivariate statistical analysis demonstrated that total and bioavailable Sb, As, and Zn were positively correlated with bacterial community richness. pH, TOC, TN, and Zn were crucial factors in shaping the distribution difference of bacterial communities. Environment-bacteria network analysis indicated that pH, SO42-, and total and bioavailable As and Sb greatly influenced the bacterial composition at the genus level. Bacteria-bacteria network analysis manifested that the co-occurrence network in mainstream sediments with a higher risk of metal(loid) pollution exhibited higher modularity and connectivity, which might be the survival mechanism for bacterial communities adapted to metal(loid) pollution. This study can provide a theoretical basis for understanding the ecological status of aquatic systems.
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Affiliation(s)
- Aihua Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Mengchang He
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Huiji Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Wei Ouyang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China; Advanced Interdisciplinary Institute of Environment and Ecology, Beijing Normal University, Zhuhai, 519087, China.
| | - Xinyi Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Qin Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Chunye Lin
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Xitao Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
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Angoshtari R, Scribner KT, Marsh TL. The impact of primary colonizers on the community composition of river biofilm. PLoS One 2023; 18:e0288040. [PMID: 37956125 PMCID: PMC10642824 DOI: 10.1371/journal.pone.0288040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 06/19/2023] [Indexed: 11/15/2023] Open
Abstract
As a strategy for minimizing microbial infections in fish hatcheries, we have investigated how putatively probiotic bacterial populations influence biofilm formation. All surfaces that are exposed to the aquatic milieu develop a microbial community through the selective assembly of microbial populations into a surface-adhering biofilm. In the investigations reported herein, we describe laboratory experiments designed to determine how initial colonization of a surface by nonpathogenic isolates from sturgeon eggs influence the subsequent assembly of populations from a pelagic river community, into the existing biofilm. All eight of the tested strains altered the assembly of river biofilm in a strain-specific manner. Previously formed isolate biofilm was challenged with natural river populations and after 24 hours, two strains and two-isolate combinations proved highly resistant to invasion, comprising at least 80% of the biofilm community, four isolates were intermediate in resistance, accounting for at least 45% of the biofilm community and two isolates were reduced to 4% of the biofilm community. Founding biofilms of Serratia sp, and combinations of Brevundimonas sp.-Hydrogenophaga sp. and Brevundimonas sp.-Acidovorax sp. specifically blocked populations of Aeromonas and Flavobacterium, potential fish pathogens, from colonizing the biofilm. In addition, all isolate biofilms were effective at blocking invading populations of Arcobacter. Several strains, notably Deinococcus sp., recruited specific low-abundance river populations into the top 25 most abundant populations within biofilm. The experiments suggest that relatively simple measures can be used to control the assembly of biofilm on the eggs surface and perhaps offer protection from pathogens. In addition, the methodology provides a relatively rapid way to detect potentially strong ecological interactions between bacterial populations in the formation of biofilms.
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Affiliation(s)
- Roshan Angoshtari
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States of America
| | - Kim T. Scribner
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, United States of America
| | - Terence L. Marsh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States of America
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Cecchini L, Barmaz C, Cea MJC, Baeschlin H, Etter J, Netzer S, Bregy L, Marchukov D, Trigo NF, Meier R, Hirschi J, Wyss J, Wick A, Zingg J, Christensen S, Radan AP, Etter A, Müller M, Kaess M, Surbek D, Yilmaz B, Macpherson AJ, Sokollik C, Misselwitz B, Ganal-Vonarburg SC. The Bern Birth Cohort (BeBiCo) to study the development of the infant intestinal microbiota in a high-resource setting in Switzerland: rationale, design, and methods. BMC Pediatr 2023; 23:560. [PMID: 37946167 PMCID: PMC10637001 DOI: 10.1186/s12887-023-04198-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 07/17/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Microbiota composition is fundamental to human health with the intestinal microbiota undergoing critical changes within the first two years of life. The developing intestinal microbiota is shaped by maternal seeding, breast milk and its complex constituents, other nutrients, and the environment. Understanding microbiota-dependent pathologies requires a profound understanding of the early development of the healthy infant microbiota. METHODS Two hundred and fifty healthy pregnant women (≥20 weeks of gestation) from the greater Bern area will be enrolled at Bern University hospital's maternity department. Participants will be followed as mother-baby pairs at delivery, week(s) 1, 2, 6, 10, 14, 24, 36, 48, 96, and at years 5 and 10 after birth. Clinical parameters describing infant growth and development, morbidity, and allergic conditions as well as socio-economic, nutritional, and epidemiological data will be documented. Neuro-developmental outcomes and behavior will be assessed by child behavior checklists at and beyond 2 years of age. Maternal stool, milk, skin and vaginal swabs, infant stool, and skin swabs will be collected at enrolment and at follow-up visits. For the primary outcome, the trajectory of the infant intestinal microbiota will be characterized by 16S and metagenomic sequencing regarding composition, metabolic potential, and stability during the first 2 years of life. Secondary outcomes will assess the cellular and chemical composition of maternal milk, the impact of nutrition and environment on microbiota development, the maternal microbiome transfer at vaginal or caesarean birth and thereafter on the infant, and correlate parameters of microbiota and maternal milk on infant growth, development, health, and mental well-being. DISCUSSION The Bern birth cohort study will provide a detailed description and normal ranges of the trajectory of microbiota maturation in a high-resource setting. These data will be compared to data from low-resource settings such as from the Zimbabwe-College of Health-Sciences-Birth-Cohort study. Prospective bio-sampling and data collection will allow studying the association of the microbiota with common childhood conditions concerning allergies, obesity, neuro-developmental outcomes , and behaviour. Trial registration The trial has been registered at www. CLINICALTRIALS gov , Identifier: NCT04447742.
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Affiliation(s)
- Luca Cecchini
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland
| | - Colette Barmaz
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland
| | - Maria José Coloma Cea
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland
| | - Hannah Baeschlin
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland
| | - Julian Etter
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland
| | - Stefanie Netzer
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland
| | - Leonie Bregy
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland
| | - Dmitrij Marchukov
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland
| | - Nerea Fernandez Trigo
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland
| | - Rachel Meier
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland
| | - Jasmin Hirschi
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland
| | - Jacqueline Wyss
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland
| | - Andrina Wick
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland
| | - Joelle Zingg
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland
| | - Sandro Christensen
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland
| | - Anda-Petronela Radan
- Department of Obstetrics and Gynaecology, Bern University Hospital, Inselspital, University of Bern, Friedbühlstrasse 19, 3010, Bern, Switzerland
| | - Annina Etter
- Department of Obstetrics and Gynaecology, Bern University Hospital, Inselspital, University of Bern, Friedbühlstrasse 19, 3010, Bern, Switzerland
| | - Martin Müller
- Department of Obstetrics and Gynaecology, Bern University Hospital, Inselspital, University of Bern, Friedbühlstrasse 19, 3010, Bern, Switzerland
| | - Michael Kaess
- University Hospital of Child and Adolescent Psychiatry and Psychotherapy, University of Bern, Bolligenstrasse 111, Haus A, 3000, Bern, Switzerland
| | - Daniel Surbek
- Department of Obstetrics and Gynaecology, Bern University Hospital, Inselspital, University of Bern, Friedbühlstrasse 19, 3010, Bern, Switzerland
| | - Bahtiyar Yilmaz
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland
| | - Andrew J Macpherson
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland
| | - Christiane Sokollik
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital, Inselspital, University of Bern, Freiburgstrasse 15, 3010, Bern, Switzerland
| | - Benjamin Misselwitz
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland.
| | - Stephanie C Ganal-Vonarburg
- Department for BioMedical Research (DBMR), Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Freiburgstr. 18, 3010, Bern, Switzerland
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Svet L, Parijs I, Isphording S, Lories B, Marchal K, Steenackers HP. Competitive interactions facilitate resistance development against antimicrobials. Appl Environ Microbiol 2023; 89:e0115523. [PMID: 37819078 PMCID: PMC10617502 DOI: 10.1128/aem.01155-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 10/13/2023] Open
Abstract
While the evolution of antimicrobial resistance is well studied in free-living bacteria, information on resistance development in dense and diverse biofilm communities is largely lacking. Therefore, we explored how the social interactions in a duo-species biofilm composed of the brewery isolates Pseudomonas rhodesiae and Raoultella terrigena influence the adaptation to the broad-spectrum antimicrobial sulfathiazole. Previously, we showed that the competition between these brewery isolates enhances the antimicrobial tolerance of P. rhodesiae. Here, we found that this enhanced tolerance in duo-species biofilms is associated with a strongly increased antimicrobial resistance development in P. rhodesiae. Whereas P. rhodesiae was not able to evolve resistance against sulfathiazole in monospecies conditions, it rapidly evolved resistance in the majority of the duo-species communities. Although the initial presence of R. terrigena was thus required for P. rhodesiae to acquire resistance, the resistance mechanisms did not depend on the presence of R. terrigena. Whole genome sequencing of resistant P. rhodesiae clones showed no clear mutational hot spots. This indicates that the acquired resistance phenotype depends on complex interactions between low-frequency mutations in the genetic background of the strains. We hypothesize that the increased tolerance in duo-species conditions promotes resistance by enhancing the selection of partially resistant mutants and opening up novel evolutionary trajectories that enable such genetic interactions. This hypothesis is reinforced by experimentally excluding potential effects of increased initial population size, enhanced mutation rate, and horizontal gene transfer. Altogether, our observations suggest that the community mode of life and the social interactions therein strongly affect the accessible evolutionary pathways toward antimicrobial resistance.IMPORTANCEAntimicrobial resistance is one of the most studied bacterial properties due to its enormous clinical and industrial relevance; however, most research focuses on resistance development of a single species in isolation. In the present study, we showed that resistance evolution of brewery isolates can differ greatly between single- and mixed-species conditions. Specifically, we observed that the development of antimicrobial resistance in certain species can be significantly enhanced in co-culture as compared to the single-species conditions. Overall, the current study emphasizes the need of considering the within bacterial interactions in microbial communities when evaluating antimicrobial treatments and resistance evolution.
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Affiliation(s)
- Luka Svet
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), Leuven, Belgium
| | - Ilse Parijs
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), Leuven, Belgium
| | - Simon Isphording
- Department of Plant Biotechnology and Bioinformatics, Data Integration and Biological Networks, UGent, Technologiepark 15, Gent, Belgium
| | - Bram Lories
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), Leuven, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Data Integration and Biological Networks, UGent, Technologiepark 15, Gent, Belgium
| | - Hans P. Steenackers
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), Leuven, Belgium
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Kiousi DE, Karadedos DM, Sykoudi A, Repanas P, Kamarinou CS, Argyri AA, Galanis A. Development of a Multiplex PCR Assay for Efficient Detection of Two Potential Probiotic Strains Using Whole Genome-Based Primers. Microorganisms 2023; 11:2553. [PMID: 37894211 PMCID: PMC10609308 DOI: 10.3390/microorganisms11102553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Probiotics are microorganisms that exert strain-specific health-promoting effects on the host. Τhey are employed in the production of functional dairy or non-dairy food products; still, their detection in these complex matrices is a challenging task. Several culture-dependent and culture-independent methods have been developed in this direction; however, they present low discrimination at the strain level. Here, we developed a multiplex PCR assay for the detection of two potential probiotic lactic acid bacteria (LAB) strains, Lactiplantibacillus plantarum L125 and Lp. pentosus L33, in monocultures and yogurt samples. Unique genomic regions were identified via comparative genomic analysis and were used to produce strain-specific primers. Then, primer sets were selected that produced distinct electrophoretic DNA banding patterns in multiplex PCR for each target strain. This method was further implemented for the detection of the two strains in yogurt samples, highlighting its biotechnological applicability. Moreover, it can be applied with appropriate modifications to detect any bacterial strain with available WGS.
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Affiliation(s)
- Despoina E. Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Dimitrios M. Karadedos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Anastasia Sykoudi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Panagiotis Repanas
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Christina S. Kamarinou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece;
| | - Anthoula A. Argyri
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece;
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
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Balaraman V, Indran SV, Li Y, Meekins DA, Jakkula LU, Liu H, Hays MP, Souza-Neto JA, Gaudreault NN, Hardwidge PR, Wilson WC, Weber F, Richt JA. Identification of host factors for Rift Valley Fever Phlebovirus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.559935. [PMID: 37808812 PMCID: PMC10557628 DOI: 10.1101/2023.09.28.559935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Background Rift Valley fever phlebovirus (RVFV) is a zoonotic pathogen that causes Rift Valley fever (RVF) in livestock and humans. Currently, there is no licensed human vaccine or antiviral drug to control RVF. Although multiple species of animals and humans are vulnerable to RVFV infection, host factors affecting susceptibility are not well understood. Methodology To identify the host factors or genes essential for RVFV replication, we conducted a CRISPR-Cas9 knock-out screen in human A549 cells. We then validated the putative genes using siRNA-mediated knockdowns and CRISPR-Cas9-mediated knockout studies, respectively. The role of a candidate gene in the virus replication cycle was assessed by measuring intracellular viral RNA accumulation, and the virus titers by plaque assay or TCID50 assay. Findings We identified approximately 900 genes with potential involvement in RVFV infection and replication. Further evaluation of the effect of six genes on viral replication using siRNA-mediated knockdowns found that silencing two genes (WDR7 and LRP1) significantly impaired RVFV replication. For further analysis, we focused on the WDR7 gene since the role of LRP1 in RVFV replication was previously described in detail. Knock-out A549 cell lines were generated and used to dissect the effect of WRD7 on RVFV and another bunyavirus, La Crosse encephalitis virus (LACV). We observed significant effects of WDR7 knock-out cells on both intracellular RVFV RNA levels and viral titers. At the intracellular RNA level, WRD7 affected RVFV replication at a later phase of its replication cycle (24h) when compared to LACV which was affected an earlier replication phase (12h). Conclusion In summary, we have identified WDR7 as an essential host factor for the replication of two relevant bunyaviruses, RVFV and LACV. Future studies will investigate the mechanistic role by which WDR7 facilitates Phlebovirus replication.
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Affiliation(s)
- Velmurugan Balaraman
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Sabarish V. Indran
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Yonghai Li
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - David A. Meekins
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Laxmi U.M.R. Jakkula
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Heidi Liu
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Micheal P. Hays
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Jayme A. Souza-Neto
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Natasha N. Gaudreault
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Philip R. Hardwidge
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - William C. Wilson
- United States Department of Agriculture, Agricultural Research Service, National Bio and Agro-Defense Facility, Foreign Arthropod-Borne Animal Diseases Research Unit, Manhattan, Kansas, United States of America
| | - Friedemann Weber
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany
| | - Juergen A. Richt
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
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Hoang DQ, Wilson LR, Scheftgen AJ, Suen G, Currie CR. Disturbance-Diversity Relationships of Microbial Communities Change Based on Growth Substrate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554838. [PMID: 37662195 PMCID: PMC10473689 DOI: 10.1101/2023.08.25.554838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Disturbance events can impact ecological community dynamics. Understanding how communities respond to disturbances, and how those responses can vary, is a challenge in microbial ecology. In this study, we grew a previously enriched specialized microbial community on either cellulose or glucose as a sole carbon source, and subjected them to one of five different disturbance regimes of varying frequencies ranging from low to high. Using 16S rRNA gene amplicon sequencing, we show that community structure is largely driven by substrate, but disturbance frequency affects community composition and successional dynamics. When grown on cellulose, bacteria in the genera Cellvibrio, Lacunisphaera, and Asticaccacaulis are the most abundant microbes. However, Lacunisphaera is only abundant in the lower disturbance frequency treatments, while Asticaccaulis is more abundant in the highest disturbance frequency treatment. When grown on glucose, the most abundant microbes are two Pseudomonas sequence variants, and a Cohnella sequence variant that is only abundant in the highest disturbance frequency treatment. Communities grown on cellulose exhibited a greater range of diversity (0.67-1.99 Shannon diversity and 1.38-5.25 Inverse Simpson diversity) that peak at the intermediate disturbance frequency treatment, or 1 disturbance every 3 days. Communities grown on glucose, however, ranged from 0.49-1.43 Shannon diversity and 1.37- 3.52 Inverse Simpson with peak diversity at the greatest disturbance frequency treatment. These results demonstrate that the dynamics of a microbial community can vary depending on substrate and the disturbance frequency, and may potentially explain the variety of diversity-disturbance relationships observed in microbial ecosystems.
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Affiliation(s)
- Don Q Hoang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lindsay R Wilson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Andrew J Scheftgen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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Soto MJ, Pérez J, Muñoz-Dorado J, Contreras-Moreno FJ, Moraleda-Muñoz A. Transcriptomic response of Sinorhizobium meliloti to the predatory attack of Myxococcus xanthus. Front Microbiol 2023; 14:1213659. [PMID: 37405170 PMCID: PMC10315480 DOI: 10.3389/fmicb.2023.1213659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/01/2023] [Indexed: 07/06/2023] Open
Abstract
Bacterial predation impacts microbial community structures, which can have both positive and negative effects on plant and animal health and on environmental sustainability. Myxococcus xanthus is an epibiotic soil predator with a broad range of prey, including Sinorhizobium meliloti, which establishes nitrogen-fixing symbiosis with legumes. During the M. xanthus-S. meliloti interaction, the predator must adapt its transcriptome to kill and lyse the target (predatosome), and the prey must orchestrate a transcriptional response (defensome) to protect itself against the biotic stress caused by the predatory attack. Here, we describe the transcriptional changes taking place in S. meliloti in response to myxobacterial predation. The results indicate that the predator induces massive changes in the prey transcriptome with up-regulation of protein synthesis and secretion, energy generation, and fatty acid (FA) synthesis, while down-regulating genes required for FA degradation and carbohydrate transport and metabolism. The reconstruction of up-regulated pathways suggests that S. meliloti modifies the cell envelop by increasing the production of different surface polysaccharides (SPSs) and membrane lipids. Besides the barrier role of SPSs, additional mechanisms involving the activity of efflux pumps and the peptide uptake transporter BacA, together with the production of H2O2 and formaldehyde have been unveiled. Also, the induction of the iron-uptake machinery in both predator and prey reflects a strong competition for this metal. With this research we complete the characterization of the complex transcriptional changes that occur during the M. xanthus-S. meliloti interaction, which can impact the establishment of beneficial symbiosis with legumes.
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Affiliation(s)
- María José Soto
- Departamento de Biotecnología y Protección Ambiental, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Juana Pérez
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - José Muñoz-Dorado
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | | | - Aurelio Moraleda-Muñoz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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Kang J, Song G, Wang X, Qiu W, Pei F, Ling H, Ping W, Ge J. Aerobic composting with sauerkraut fermentation waste water: Increasing the stability and complexity of bacterial community and changing bacterial community assembly processes. BIORESOURCE TECHNOLOGY 2023; 376:128883. [PMID: 36921638 DOI: 10.1016/j.biortech.2023.128883] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Aerobic composting renders the sauerkraut fermentation waste water harmless while adding soluble nutrients. Unravelling the bacterial community assembly processes, changes in community robustness and community cohesion and the relationship between them under composting treatment of sauerkraut fermentation waste water is an interesting topic. Sauerkraut fermentation waste water was used for composting, which increased bacterial linkages, community robustness, competitive behaviour during warming periods and cooperative behaviour during cooling periods, and the control of community assembly processes shifts from deterministic processes (variable selection) to stochastic processes (decentralised limitation). At the same time, the influence of community robustness and community cohesion on community assembly processes was increased. Community cohesion and robustness were significantly correlated with community function. These results indicate that community robustness and community cohesion are critical for the biological handling of hazardous substances.
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Affiliation(s)
- Jie Kang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Gang Song
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Xu Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Wei Qiu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Fangyi Pei
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Hongzhi Ling
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Wenxiang Ping
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Jingping Ge
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China.
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Lemke M, DeSalle R. The Next Generation of Microbial Ecology and Its Importance in Environmental Sustainability. MICROBIAL ECOLOGY 2023; 85:781-795. [PMID: 36826587 PMCID: PMC10156817 DOI: 10.1007/s00248-023-02185-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/24/2023] [Indexed: 05/04/2023]
Abstract
Collectively, we have been reviewers for microbial ecology, genetics and genomics studies that include environmental DNA (eDNA), microbiome studies, and whole bacterial genome biology for Microbial Ecology and other journals for about three decades. Here, we wish to point out trends and point to areas of study that readers, especially those moving into the next generation of microbial ecology research, might learn and consider. In this communication, we are not saying the work currently being accomplished in microbial ecology and restoration biology is inadequate. What we are saying is that a significant milestone in microbial ecology has been reached, and approaches that may have been overlooked or were unable to be completed before should be reconsidered in moving forward into a new more ecological era where restoration of the ecological trajectory of systems has become critical. It is our hope that this introduction, along with the papers that make up this special issue, will address the sense of immediacy and focus needed to move into the next generation of microbial ecology study.
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Affiliation(s)
- Michael Lemke
- Department of Biology, University of Illinois at Springfield, Springfield, IL, USA.
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.
| | - Rob DeSalle
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
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Zhang Y, Cai Y, Chen Z. Community-specific diffusion characteristics determine resistance of biofilms to oxidative stress. SCIENCE ADVANCES 2023; 9:eade2610. [PMID: 36961890 DOI: 10.1126/sciadv.ade2610] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Biofilms are multicellular communities with a spatial structure. Different from single-cell scale diffusion in planktonic systems, the diffusion distance becomes the dimension of multicellular clusters in a biofilm. Such differences in diffusion behavior affect the tolerance and response to exogenous stress. Here, we found that at the same doses of exogenous hydrogen peroxide (H2O2), planktonic Escherichia coli were completely killed within two hours, whereas the biofilm resumed growth in six hours by building a catalase barrier to block H2O2 penetration, despite the growth burden. Unexpectedly, when we changed the carbon source from glucose to glycerol, H2O2 instantly counterintuitively boosted biofilm growth due to supplemental oxygen, which was the growth-limiting factor. We further demonstrated that the energy metabolism modes determined the growth-limiting factor, which then determined the two patterns of biofilms resistances to H2O2.
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Affiliation(s)
- Yuzhen Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yumin Cai
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zhaoyuan Chen
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo 315020, China
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Atwah B, Iqbal MS, Kabrah S, Kabrah A, Alghamdi S, Tabassum A, Baghdadi MA, Alzahrani H. Susceptibility of Diabetic Patients to COVID-19 Infections: Clinico-Hematological and Complications Analysis. Vaccines (Basel) 2023; 11:vaccines11030561. [PMID: 36992148 DOI: 10.3390/vaccines11030561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Background: Coronavirus disease 2019 has become a global health threat resulting in a catastrophic spread and more than 3.8 million deaths worldwide. It has been suggested that there is a negative influence of diabetes mellites (DM), which is a complex chronic disease, on COVID-19 severe outcomes. Other factors in diabetic patients may also contribute to COVID-19 disease outcomes, such as older age, obesity, hyperglycaemia, hypertension, and other chronic conditions. Methods: A cohort study was conducted on the demographics, clinical information, and laboratory findings of the hospitalised COVID-19 with DM and non-DM patients were obtained from the medical records in King Faisal Specialist Hospital and Research Centre, Saudi Arabia. Results: Among the study population, 108 patients had DM, and 433 were non-DM patients. Patients with DM were more likely to present symptoms such as fever (50.48%), anorexia (19.51%), dry cough (47.96%), shortness of breath (35.29%), chest pain (16.49%), and other symptoms. There was a significant decrease in the mean of haematological and biochemical parameters, such as haemoglobin, calcium, and alkaline phosphate in people with diabetes compared to non-diabetics and a considerable increase in other parameters, such as glucose, potassium, and cardiac troponin. Conclusions: According to the findings of this study, patients who have diabetes have a greater risk of developing more severe symptoms associated with COVID-19 disease. This could result in more patients being admitted to the intensive care unit as well as higher mortality rates.
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Affiliation(s)
- Banan Atwah
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mohammad Shahid Iqbal
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Saeed Kabrah
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ahmed Kabrah
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Aisha Tabassum
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mohammed A Baghdadi
- Research Center, King Faisal Specialist Hospital and Research Centre (KFSH&RC), Jeddah 23431, Saudi Arabia
| | - Hissah Alzahrani
- Mathematical Sciences Department, Faculty of Applied Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
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Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis. mSystems 2023; 8:e0057422. [PMID: 36537799 PMCID: PMC9948732 DOI: 10.1128/msystems.00574-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Microbial community analysis of aquatic environments showed that an important component of its microbial diversity consists of bacteria with cell sizes of ~0.1 μm. Such small bacteria can show genomic reductions and metabolic dependencies with other bacteria. However, so far, no study has investigated if such bacteria exist in terrestrial environments like soil. Here, we isolated soil bacteria that passed through a 0.1-μm filter. The complete genome of one of the isolates was sequenced and the bacterium was identified as Hylemonella gracilis. A set of coculture assays with phylogenetically distant soil bacteria with different cell and genome sizes was performed. The coculture assays revealed that H. gracilis grows better when interacting with other soil bacteria like Paenibacillus sp. AD87 and Serratia plymuthica. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct cell-cell contact. Our study indicates that in soil there are bacteria that can pass through a 0.1-μm filter. These bacteria may have been overlooked in previous research on soil microbial communities. Such small bacteria, exemplified here by H. gracilis, can induce transcriptional and metabolomic changes in other bacteria upon their interactions in soil. In vitro, the studied interspecific interactions allowed utilization of growth substrates that could not be utilized by monocultures, suggesting that biochemical interactions between substantially different sized soil bacteria may contribute to the symbiosis of soil bacterial communities. IMPORTANCE Analysis of aquatic microbial communities revealed that parts of its diversity consist of bacteria with cell sizes of ~0.1 μm. Such bacteria can show genomic reductions and metabolic dependencies with other bacteria. So far, no study investigated if such bacteria exist in terrestrial environments such as soil. Here, we show that such bacteria also exist in soil. The isolated bacteria were identified as Hylemonella gracilis. Coculture assays with phylogenetically different soil bacteria revealed that H. gracilis grows better when cocultured with other soil bacteria. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct contact. Our study revealed that bacteria are present in soil that can pass through 0.1-μm filters. Such bacteria may have been overlooked in previous research on soil microbial communities and may contribute to the symbiosis of soil bacterial communities.
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Lee YH, Kim H, Heo DW, Ahn IS, Auh QS. Volatile sulfide compounds and oral microorganisms on the inner surface of masks in individuals with halitosis during COVID-19 pandemic. Sci Rep 2023; 13:2487. [PMID: 36781937 PMCID: PMC9924882 DOI: 10.1038/s41598-023-29080-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 01/30/2023] [Indexed: 02/15/2023] Open
Abstract
Mask-wearing is still recommended owing to the continuing impact of the COVID-19 pandemic. Within the closed chamber created by the mask, people are increasingly self-aware of their oral malodor. In this prospective and cross-sectional study, we aimed to measure volatile sulfide compound (VSC) levels in patients with halitosis and investigate the oral microbiome profile on the inner surface of their KF94 masks. We also investigated which oral microbiota increases VSC levels and whether the oral microbiomes of oral saliva and mask are correlated. A total of 50 subjects (41 women, average age 38.12 ± 12.58 years old) were included in the study, 25 healthy subjects and 25 patients with halitosis who wore masks for more than 3 h. The dominant bacterial species, bacterial profile, and Shannon diversity index of whole unstimulated saliva and the inner surface of the mask were investigated. The bacterial 16S ribosomal RNA genes of the major oral bacterial species were analyzed using real-time PCR. Gas chromatography was used to measure hydrogen sulfide (H2S) and methyl mercaptan (CH3SH), which are representative VSCs. The total bacterial DNA copy number was significantly higher in the saliva sample than in the mask sample (p < 0.001), and the average value was 276 times greater. Shannon diversity index was also significantly higher in saliva than in the inner surface of the mask (2.62 ± 0.81 vs. 1.15 ± 1.52, p < 0.001). The most common Gram-negative and Gram-positive species in the masks were Porphyromonas gingivalis (Pg) and Lactobacillus casei (Lc), respectively. The bacterial species with significant positive correlations between saliva and mask samples were Prevotella intermedia (Pi) (r = 0.324, p = 0.022), Eikenella corrodens (r = 0.309, p = 0.029), Lc (r = 0.293, p = 0.039), and Parvimonas micra (Pm) (r = 0.366, p = 0.009). The mean value of CH3SH was significantly higher in the halitosis group than in the non-halitosis group (17.84 ± 29.00 vs. 3.84 ± 10.57 ppb, p = 0.031). In the halitosis group, the DNA copy numbers and VSC levels showed highly positive correlation coefficients in the order Pg, Treponema denticola (Td), Tannerella forsythia (Tf), Pi, and Prevotella nigrescens (Pn) (all p < 0.05). Regarding bacterial profiles of the mask, Td was strongly correlated with CH3SH (r = 0.414, p = 0.040) and total VSCs (r = 0.374, p = 0.033) only in halitosis group. Mask-wearing time was strongly correlated with total VSCs, H2S, and CH3SH (all r > 0.8, p < 0.001). Oral bacteria, whose association with halitosis has been identified, increased VSC levels in mask-wearing subjects during the COVID-19 pandemic, particularly the number of Gram-negative anaerobes such as Pg and Td. Mask-wearing time was a major factor in increasing VSC levels. The study results suggest that people with halitosis could control these Gram-negative bacteria by improving oral hygiene and regularly changing masks.
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Affiliation(s)
- Yeon-Hee Lee
- Department of Orofacial Pain and Oral Medicine, Kyung Hee University School of Dentistry, Kyung Hee University Medical Center, #613 Hoegi-Dong, Dongdaemun-Gu, Seoul, 02447, South Korea.
| | - Hyeongrok Kim
- Life Science Institute, Denomics Inc. 518, 5 Digital-Ro 26-Gil, Guro-Gu, Seoul, 08389, South Korea
| | - Dae Wook Heo
- Life Science Institute, Denomics Inc. 518, 5 Digital-Ro 26-Gil, Guro-Gu, Seoul, 08389, South Korea
| | - In-Suk Ahn
- Life Science Institute, Denomics Inc. 518, 5 Digital-Ro 26-Gil, Guro-Gu, Seoul, 08389, South Korea
| | - Q-Schick Auh
- Department of Orofacial Pain and Oral Medicine, Kyung Hee University School of Dentistry, Kyung Hee University Medical Center, #613 Hoegi-Dong, Dongdaemun-Gu, Seoul, 02447, South Korea
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Devi P, Kumari P, Yadav A, Tarai B, Budhiraja S, Shamim U, Pandey R. Transcriptionally active nasopharyngeal commensals and opportunistic microbial dynamics define mild symptoms in the COVID 19 vaccination breakthroughs. PLoS Pathog 2023; 19:e1011160. [PMID: 36800345 PMCID: PMC9937460 DOI: 10.1371/journal.ppat.1011160] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/27/2023] [Indexed: 02/18/2023] Open
Abstract
The development of COVID 19 vaccines as an effort to mitigate the outbreak, has saved millions of lives globally. However, vaccination breakthroughs have continuously challenged the vaccines' effectiveness and provided incentives to explore facets holding potential to alter vaccination-induced immunity and protection from subsequent infection, especially VOCs (Variants Of Concern). We explored the functional dynamics of nasopharyngeal transcriptionally active microbes (TAMs) between vaccination breakthroughs and unvaccinated SARS-CoV-2 infected individuals. Microbial taxonomic communities were differentially altered with skewed enrichment of bacterial class/genera of Firmicutes and Gammaproteobacteria with grossly reduced phylum Bacteroidetes in vaccination breakthrough individuals. The Bacillus genus was abundant in Firmicutes in vaccination breakthrough whereas Prevotella among Bacteroides dominated the unvaccinated. Also, Pseudomonas and Salmonella of Gammaproteobacteria were overrepresented in vaccination breakthrough, whilst unvaccinated showed presence of several genera, Achromobacter, Bordetella, Burkholderia, Neisseria, Hemophilus, Salmonella and Pseudomonas, belonging to Proteobacteria. At species level, the microbiota of vaccination breakthrough exhibited relatively higher abundance of unique commensals, in comparison to potential opportunistic microbes enrichment in unvaccinated patients' microbiota. Functional metabolic pathways like amino acid biosynthesis, sulphate assimilation, fatty acid and beta oxidation, associated with generation of SCFAs (short chain fatty acids), were enriched in vaccination breakthroughs. Majorly, metabolic pathways of LCFAs biosynthesis (long chain fatty acids; oleate, dodecenoate, palmitoleate, gondoate) were found associated with the unvaccinated. Our research highlights that vaccination decreases the microbial diversity in terms of depleting opportunistic pathogens and increasing the preponderance of commensals with respect to unvaccinated patients. Metabolic pathway analysis substantiates the shift in diversity to functionally modulate immune response generation, which may be related to mild clinical manifestations and faster recovery times during vaccination breakthroughs.
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Affiliation(s)
- Priti Devi
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Pallawi Kumari
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Aanchal Yadav
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Bansidhar Tarai
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Sandeep Budhiraja
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Uzma Shamim
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Alker AT, Aspiras AE, Dunbar TL, Farrell MV, Fedoriouk A, Jones JE, Mikhail SR, Salcedo GY, Moore BS, Shikuma NJ. A modular plasmid toolkit applied in marine Proteobacteria reveals functional insights during bacteria-stimulated metamorphosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526474. [PMID: 36778221 PMCID: PMC9915575 DOI: 10.1101/2023.01.31.526474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A conspicuous roadblock to studying marine bacteria for fundamental research and biotechnology is a lack of modular synthetic biology tools for their genetic manipulation. Here, we applied, and generated new parts for, a modular plasmid toolkit to study marine bacteria in the context of symbioses and host-microbe interactions. To demonstrate the utility of this plasmid system, we genetically manipulated the marine bacterium Pseudoalteromonas luteoviolacea , which stimulates the metamorphosis of the model tubeworm, Hydroides elegans . Using these tools, we quantified constitutive and native promoter expression, developed reporter strains that enable the imaging of host-bacteria interactions, and used CRISPR interference (CRISPRi) to knock down a secondary metabolite and a host-associated gene. We demonstrate the broader utility of this modular system for rapidly creating and iteratively testing genetic tractability by modifying marine bacteria that are known to be associated with diverse host-microbe symbioses. These efforts enabled the successful transformation of twelve marine strains across two Proteobacteria classes, four orders and ten genera. Altogether, the present study demonstrates how synthetic biology strategies enable the investigation of marine microbes and marine host-microbe symbioses with broader implications for environmental restoration and biotechnology.
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Dahal S, Hurst GB, Chourey K, Engle NL, Burdick LH, Morrell-Falvey JL, Tschaplinski TJ, Doktycz MJ, Pelletier DA. Mechanism for Utilization of the Populus-Derived Metabolite Salicin by a Pseudomonas- Rahnella Co-Culture. Metabolites 2023; 13:metabo13020140. [PMID: 36837758 PMCID: PMC9959693 DOI: 10.3390/metabo13020140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/30/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Pseudomonas fluorescens GM16 associates with Populus, a model plant in biofuel production. Populus releases abundant phenolic glycosides such as salicin, but P. fluorescens GM16 cannot utilize salicin, whereas Pseudomonas strains are known to utilize compounds similar to the aglycone moiety of salicin-salicyl alcohol. We propose that the association of Pseudomonas to Populus is mediated by another organism (such as Rahnella aquatilis OV744) that degrades the glucosyl group of salicin. In this study, we demonstrate that in the Rahnella-Pseudomonas salicin co-culture model, Rahnella grows by degrading salicin to glucose 6-phosphate and salicyl alcohol which is secreted out and is subsequently utilized by P. fluorescens GM16 for its growth. Using various quantitative approaches, we elucidate the individual pathways for salicin and salicyl alcohol metabolism present in Rahnella and Pseudomonas, respectively. Furthermore, we were able to establish that the salicyl alcohol cross-feeding interaction between the two strains on salicin medium is carried out through the combination of their respective individual pathways. The research presents one of the potential advantages of salicyl alcohol release by strains such as Rahnella, and how phenolic glycosides could be involved in attracting multiple types of bacteria into the Populus microbiome.
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Affiliation(s)
- Sanjeev Dahal
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN 37996, USA
- Department of Chemical Engineering, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Gregory B. Hurst
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Karuna Chourey
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Leah H. Burdick
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | | | | | - Mitchel J. Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Dale A. Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
- Correspondence:
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Wiesinger A, Wenderlein J, Ulrich S, Hiereth S, Chitimia-Dobler L, Straubinger RK. Revealing the Tick Microbiome: Insights into Midgut and Salivary Gland Microbiota of Female Ixodes ricinus Ticks. Int J Mol Sci 2023; 24:ijms24021100. [PMID: 36674613 PMCID: PMC9864629 DOI: 10.3390/ijms24021100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/09/2023] Open
Abstract
The ectoparasite Ixodes ricinus is an important vector for many tick-borne diseases (TBD) in the northern hemisphere, such as Lyme borreliosis, rickettsiosis, human granulocytic anaplasmosis, or tick-borne encephalitis virus. As climate change will lead to rising temperatures in the next years, we expect an increase in tick activity, tick population, and thus in the spread of TBD. Consequently, it has never been more critical to understand relationships within the microbial communities in ticks that might contribute to the tick's fitness and the occurrence of TBD. Therefore, we analyzed the microbiota in different tick tissues such as midgut, salivary glands, and residual tick material, as well as the microbiota in complete Ixodes ricinus ticks using 16S rRNA gene amplicon sequencing. By using a newly developed DNA extraction protocol for tick tissue samples and a self-designed mock community, we were able to detect endosymbionts and pathogens that have been described in the literature previously. Further, this study displayed the usefulness of including a mock community during bioinformatic analysis to identify essential bacteria within the tick.
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Affiliation(s)
- Anna Wiesinger
- Chair of Bacteriology and Mycology, Institute for Infectious Diseases and Zoonosis, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Jasmin Wenderlein
- Chair of Bacteriology and Mycology, Institute for Infectious Diseases and Zoonosis, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Sebastian Ulrich
- Chair of Bacteriology and Mycology, Institute for Infectious Diseases and Zoonosis, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Stephanie Hiereth
- Chair of Bacteriology and Mycology, Institute for Infectious Diseases and Zoonosis, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Lidia Chitimia-Dobler
- Bundeswehr Institute of Microbiology (InstMikroBioBw), Neuherbergstraße 11, 80937 Munich, Germany
| | - Reinhard K. Straubinger
- Chair of Bacteriology and Mycology, Institute for Infectious Diseases and Zoonosis, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
- Correspondence:
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Hardy A, Kever L, Frunzke J. Antiphage small molecules produced by bacteria - beyond protein-mediated defenses. Trends Microbiol 2023; 31:92-106. [PMID: 36038409 DOI: 10.1016/j.tim.2022.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/27/2022] [Accepted: 08/01/2022] [Indexed: 11/15/2022]
Abstract
Bacterial populations face the constant threat of viral predation exerted by bacteriophages ('phages'). In response, bacteria have evolved a wide range of defense mechanisms against phage challenges. Yet the vast majority of antiphage defense systems described until now are mediated by proteins or RNA complexes acting at the single-cell level. Here, we review small molecule-based defense strategies against phage infection, with a focus on the antiphage molecules described recently. Importantly, inhibition of phage infection by excreted small molecules has the potential to protect entire bacterial communities, highlighting the ecological significance of these antiphage strategies. Considering the immense repertoire of bacterial metabolites, we envision that the list of antiphage small molecules will be further expanded in the future.
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Affiliation(s)
- Aël Hardy
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Larissa Kever
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Julia Frunzke
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany.
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Extracellular DNAses Facilitate Antagonism and Coexistence in Bacterial Competitor-Sensing Interference Competition. Appl Environ Microbiol 2022; 88:e0143722. [PMID: 36374088 PMCID: PMC9746292 DOI: 10.1128/aem.01437-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Over the last 4 decades, the rate of discovery of novel antibiotics has decreased drastically, ending the era of fortuitous antibiotic discovery. A better understanding of the biology of bacteriogenic toxins potentially helps to prospect for new antibiotics. To initiate this line of research, we quantified antagonists from two different sites at two different depths of soil and found the relative number of antagonists to correlate with the bacterial load and carbon-to-nitrogen (C/N) ratio of the soil. Consecutive studies show the importance of antagonist interactions between soil isolates and the lack of a predicted role for nutrient availability and, therefore, support an in situ role in offense for the production of toxins in environments of high bacterial loads. In addition, the production of extracellular DNAses (exDNases) and the ability to antagonize correlate strongly. Using an in domum-developed probabilistic cellular automaton model, we studied the consequences of exDNase production for both coexistence and diversity within a dynamic equilibrium. Our model demonstrates that exDNase-producing isolates involved in amensal interactions act to stabilize a community, leading to increased coexistence within a competitor-sensing interference competition environment. Our results signify that the environmental and biological cues that control natural-product formation are important for understanding antagonism and community dynamics, structure, and function, permitting the development of directed searches and the use of these insights for drug discovery. IMPORTANCE Ever since the first observation of antagonism by microorganisms by Ernest Duchesne (E. Duchesne, Contribution à l'étude de la concurrence vitale chez les microorganisms. Antagonism entre les moisissures et les microbes, These pour obtenir le grade de docteur en medicine, Lyon, France, 1897), many scientists successfully identified and applied bacteriogenic bioactive compounds from soils to cure infection. Unfortunately, overuse of antibiotics and the emergence of clinical antibiotic resistance, combined with a lack of discovery, have hampered our ability to combat infections. A deeper understanding of the biology of toxins and the cues leading to their production may elevate the success rate of the much-needed discovery of novel antibiotics. We initiated this line of research and discovered that bacterial reciprocal antagonism is associated with exDNase production in isolates from environments with high bacterial loads, while diversity may increase in environments of lower bacterial loads.
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