1
|
Li H, E W, Zhao D, Liu H, Pei J, Du B, Liu K, Zhu X, Wang C. Response of Paenibacillus polymyxa SC2 to the stress of polymyxin B and a key ABC transporter YwjA involved. Appl Microbiol Biotechnol 2024; 108:17. [PMID: 38170316 DOI: 10.1007/s00253-023-12916-3] [Citation(s) in RCA: 1] [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] [Revised: 09/24/2023] [Accepted: 10/04/2023] [Indexed: 01/05/2024]
Abstract
Polymyxins are cationic peptide antibiotics and regarded as the "final line of defense" against multidrug-resistant bacterial infections. Meanwhile, some polymyxin-resistant strains and the corresponding resistance mechanisms have also been reported. However, the response of the polymyxin-producing strain Paenibacillus polymyxa to polymyxin stress remains unclear. The purpose of this study was to investigate the stress response of gram-positive P. polymyxa SC2 to polymyxin B and to identify functional genes involved in the stress response process. Polymyxin B treatment upregulated the expression of genes related to basal metabolism, transcriptional regulation, transport, and flagella formation and increased intracellular ROS levels, flagellar motility, and biofilm formation in P. polymyxa SC2. Adding magnesium, calcium, and iron alleviated the stress of polymyxin B on P. polymyxa SC2, furthermore, magnesium and calcium could improve the resistance of P. polymyxa SC2 to polymyxin B by promoting biofilm formation. Meanwhile, functional identification of differentially expressed genes indicated that an ABC superfamily transporter YwjA was involved in the stress response to polymyxin B of P. polymyxa SC2. This study provides an important reference for improving the resistance of P. polymyxa to polymyxins and increasing the yield of polymyxins. KEY POINTS: • Phenotypic responses of P. polymyxa to polymyxin B was performed and indicated by RNA-seq • Forming biofilm was a key strategy of P. polymyxa to alleviate polymyxin stress • ABC transporter YwjA was involved in the stress resistance of P. polymyxa to polymyxin B.
Collapse
Affiliation(s)
- Hui Li
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Wenhui E
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Dongying Zhao
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Haiyang Liu
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Jian Pei
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Binghai Du
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Kai Liu
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Xueming Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Chengqiang Wang
- College of Life Sciences, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China.
| |
Collapse
|
2
|
Li Y, Liang X, Chen N, Yuan X, Wang J, Wu Q, Ding Y. The promotion of biofilm dispersion: a new strategy for eliminating foodborne pathogens in the food industry. Crit Rev Food Sci Nutr 2024:1-25. [PMID: 39054781 DOI: 10.1080/10408398.2024.2354524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Food safety is a critical global concern due to its direct impact on human health and overall well-being. In the food processing environment, biofilm formation by foodborne pathogens poses a significant problem as it leads to persistent and high levels of food contamination, thereby compromising the quality and safety of food. Therefore, it is imperative to effectively remove biofilms from the food processing environment to ensure food safety. Unfortunately, conventional cleaning methods fall short of adequately removing biofilms, and they may even contribute to further contamination of both equipment and food. It is necessary to develop alternative approaches that can address this challenge in food industry. One promising strategy in tackling biofilm-related issues is biofilm dispersion, which represents the final step in biofilm development. Here, we discuss the biofilm dispersion mechanism of foodborne pathogens and elucidate how biofilm dispersion can be employed to control and mitigate biofilm-related problems. By shedding light on these aspects, we aim to provide valuable insights and solutions for effectively addressing biofilm contamination issues in food industry, thus enhancing food safety and ensuring the well-being of consumers.
Collapse
Affiliation(s)
- Yangfu Li
- State Key Laboratory of Applied Microbiology Southern China, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xinmin Liang
- State Key Laboratory of Applied Microbiology Southern China, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Department of Food Science & Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Nuo Chen
- State Key Laboratory of Applied Microbiology Southern China, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaoming Yuan
- State Key Laboratory of Applied Microbiology Southern China, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Department of Food Science & Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yu Ding
- Department of Food Science & Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| |
Collapse
|
3
|
Yunus J, Wan Dagang WRZ, Jamaluddin H, Jemon K, Mohamad SE, Jonet MA. Bacterial biofilm growth and perturbation by serine protease from Bacillus sp. Arch Microbiol 2024; 206:138. [PMID: 38436775 DOI: 10.1007/s00203-024-03857-0] [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: 12/19/2023] [Revised: 01/16/2024] [Accepted: 01/21/2024] [Indexed: 03/05/2024]
Abstract
In nature, bacteria are ubiquitous and can be categorized as beneficial or harmless to humans, but most bacteria have one thing in common which is their ability to produce biofilm. Biofilm is encased within an extracellular polymeric substance (EPS) which provides resistance against antimicrobial agents. Protease enzymes have the potential to degrade or promote the growth of bacterial biofilms. In this study, the effects of a recombinant intracellular serine protease from Bacillus sp. (SPB) on biofilms from Staphylococcus aureus, Acinetobacter baumannii, and Pseudomonas aeruginosa were analyzed. SPB was purified using HisTrap HP column and concentrated using Amicon 30 ultra-centrifugal filter. SPB was added with varying enzyme activity and assay incubation period after biofilms were formed in 96-well plates. SPB was observed to have contrasting effects on different bacterial biofilms, where biofilm degradations were observed for both 7-day-old A. baumannii (37.26%) and S. aureus (71.51%) biofilms. Meanwhile, SPB promoted growth of P. aeruginosa biofilm up to 176.32%. Compatibility between protein components in S. aureus biofilm with SPB as well as a simpler membrane structure morphology led to higher biofilm degradation for S. aureus compared to A. baumannii. However, SPB promoted growth of P. aeruginosa biofilm due likely to its degrading protein factors that are responsible for biofilm detachment and dispersion, thus resulting in more multi-layered biofilm formation. Commercial protease Savinase which was used as a comparison showed degradation for all three bacterial biofilms. The results obtained are unique and will expand our understanding on the effects that bacterial proteases have toward biofilms.
Collapse
Affiliation(s)
- Julia Yunus
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Wan Rosmiza Zana Wan Dagang
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
| | - Haryati Jamaluddin
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
| | - Khairunadwa Jemon
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Shaza Eva Mohamad
- Department of Environmental Engineering and Green Technology (EGT), Malaysia Japan International Institute of Technology (MJIIT), Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia
| | - Mohd Anuar Jonet
- Structural And Applied Genomics Centre, Malaysia Genome and Vaccine Institute (MGVI), National Institute of Biotechnology Malaysia (NIBM), Jalan Bangi, 43000, Kajang, Selangor, Malaysia
| |
Collapse
|
4
|
Domínguez-Maqueda M, García-Márquez J, Tapia-Paniagua ST, González-Fernández C, Cuesta A, Espinosa-Ruíz C, Esteban MÁ, Alarcón FJ, Balebona MC, Moriñigo MÁ. Evaluation of the Differential Postbiotic Potential of Shewanella putrefaciens Pdp11 Cultured in Several Growing Conditions. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:1-18. [PMID: 38153608 PMCID: PMC10869407 DOI: 10.1007/s10126-023-10271-y] [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: 01/21/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023]
Abstract
The increased knowledge of functional foods has led to the development of a new generation of health products, including those containing probiotics and products derived from them. Shewanella putrefaciens Pdp11 (SpPdp11) is a strain described as a probiotic that exerts important beneficial effects on several farmed fish. However, the use of live probiotic cells in aquaculture has limitations such as uncertain survival and shelf life, which can limit their efficacy. In addition, its efficacy can vary across species and hosts. When probiotics are administered orally, their activity can be affected by the environment present in the host and by interactions with the intestinal microbiota. Furthermore, live cells can also produce undesired substances that may negatively impact the host as well as the risk of potential virulence reversion acquired such as antibiotic resistance. Therefore, new alternatives emerged such as postbiotics. Currently, there is no knowledge about the postbiotic potential of SpPdp11 in the aquaculture industry. Postbiotic refers to the use of bacterial metabolites, including extracellular products (ECPs), to improve host physiology. However, the production of postbiotic metabolites can be affected by various factors such as cultivation conditions, which can affect bacterial metabolism. Thus, the objective of this study was to evaluate the postbiotic potential of ECPs from SpPdp11 under different cultivation conditions, including culture media, temperature, growth phase, and salinity. We analyzed their hydrolytic, antibacterial, antiviral, and cytotoxic capacity on several fish cell lines. The results obtained have demonstrated how each ECP condition can exert a different hydrolytic profile, reduce the biofilm formation by bacterial pathogens relevant to fish, lower the titer of nervous necrosis virus (NNV), and exert a cytotoxic effect on different fish cell lines. In conclusion, the ECPs obtained from SpPdp11 have different capacities depending on the cultivation conditions used. These conditions must be considered in order to recover the maximum number of beneficial capacities or to choose the appropriate conditions for specific activities.
Collapse
Affiliation(s)
- Marta Domínguez-Maqueda
- Departamento de Microbiología, Facultad de Ciencias, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, Málaga, Spain
| | - Jorge García-Márquez
- Departamento de Microbiología, Facultad de Ciencias, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, Málaga, Spain
| | - Silvana T Tapia-Paniagua
- Departamento de Microbiología, Facultad de Ciencias, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, Málaga, Spain.
| | - Carmen González-Fernández
- Departamento de Biología Celular e Histología, Facultad de Ciencias, Universidad de Murcia, Murcia, Spain
| | - Alberto Cuesta
- Departamento de Biología Celular e Histología, Facultad de Ciencias, Universidad de Murcia, Murcia, Spain
| | - Cristóbal Espinosa-Ruíz
- Departamento de Biología Celular e Histología, Facultad de Ciencias, Universidad de Murcia, Murcia, Spain
| | - María Ángeles Esteban
- Departamento de Biología Celular e Histología, Facultad de Ciencias, Universidad de Murcia, Murcia, Spain
| | - Francisco Javier Alarcón
- Departamento de Biología y Geología, Universidad de Almería, Ceimar-Universidad de Almería, Almería, Spain
| | - María Carmen Balebona
- Departamento de Microbiología, Facultad de Ciencias, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, Málaga, Spain
| | - Miguel Ángel Moriñigo
- Departamento de Microbiología, Facultad de Ciencias, Instituto Andaluz de Biotecnología y Desarrollo Azul (IBYDA), Universidad de Málaga, Ceimar-Universidad de Málaga, Málaga, Spain
| |
Collapse
|
5
|
Keshapaga UR, Jathoth K, Singh SS, Gogada R, Burgula S. Characterization of high-yield Bacillus subtilis cysteine protease for diverse industrial applications. Braz J Microbiol 2023; 54:739-752. [PMID: 37157054 PMCID: PMC10235272 DOI: 10.1007/s42770-023-00992-6] [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: 10/20/2022] [Accepted: 04/25/2023] [Indexed: 05/10/2023] Open
Abstract
Bacterial proteases have extensive applications in various fields of industrial microbiology. In this study, protease-producing organisms were screened on skimmed milk agar media using serial dilution. Through microbial biomass production, biochemical tests, protease-specific activity, and 16 s RNA gene sequencing, the isolates were identified as Bacillus subtilis and submitted to NCBI. The strain accession numbers were designated as A1 (MT903972), A2 (MT903996), A4 (MT904091), and A5 (MT904796). The strain A4 Bacillus subtilis showed highest protease-specific activity as 76,153.84 U/mg. A4 Bacillus subtilis was unaffected by Ca2+, Cu2+, Fe2+, Hg2+, Mg2+, Na, Fe2+, and Zn2+ but was inhibited by 80% by Mn2+ (5 mM). The protease activity was inhibited by up to 30% by iodoacetamide (5 mM). These findings confirm the enzyme to be a cysteine protease which was further confirmed by MALDI-TOF. The identified protease showed 71% sequence similarity with Bacillus subtilis cysteine protease. The crude cysteine protease significantly aided in fabric stain removal when added to a generic detergent. It also aided in the recovery of silver from used X-ray films and de-hairing of goat skin hides and showed decent application in meat tenderization. Thus, the isolated cysteine protease has high potential for industrial applications.
Collapse
Affiliation(s)
- Usha Rani Keshapaga
- Department of Microbiology, University College of Science, Osmania University, Tarnaka, Hyderabad, 500 007, Telangana, India
| | - Kalyani Jathoth
- Department of Microbiology, University College of Science, Osmania University, Tarnaka, Hyderabad, 500 007, Telangana, India
| | - Surya Satyanarayana Singh
- Department of Biochemistry , University College of Science, Osmania University , Tarnaka, Hyderabad, 500 007, Telangana, India
| | - Raghu Gogada
- Department of Biochemistry , University College of Science, Osmania University , Tarnaka, Hyderabad, 500 007, Telangana, India
| | - Sandeepta Burgula
- Department of Microbiology, University College of Science, Osmania University, Tarnaka, Hyderabad, 500 007, Telangana, India.
| |
Collapse
|
6
|
Flemming HC, van Hullebusch ED, Neu TR, Nielsen PH, Seviour T, Stoodley P, Wingender J, Wuertz S. The biofilm matrix: multitasking in a shared space. Nat Rev Microbiol 2023; 21:70-86. [PMID: 36127518 DOI: 10.1038/s41579-022-00791-0] [Citation(s) in RCA: 179] [Impact Index Per Article: 179.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2022] [Indexed: 01/20/2023]
Abstract
The biofilm matrix can be considered to be a shared space for the encased microbial cells, comprising a wide variety of extracellular polymeric substances (EPS), such as polysaccharides, proteins, amyloids, lipids and extracellular DNA (eDNA), as well as membrane vesicles and humic-like microbially derived refractory substances. EPS are dynamic in space and time and their components interact in complex ways, fulfilling various functions: to stabilize the matrix, acquire nutrients, retain and protect eDNA or exoenzymes, or offer sorption sites for ions and hydrophobic substances. The retention of exoenzymes effectively renders the biofilm matrix an external digestion system influencing the global turnover of biopolymers, considering the ubiquitous relevance of biofilms. Physico-chemical and biological interactions and environmental conditions enable biofilm systems to morph into films, microcolonies and macrocolonies, films, ridges, ripples, columns, pellicles, bubbles, mushrooms and suspended aggregates - in response to the very diverse conditions confronting a particular biofilm community. Assembly and dynamics of the matrix are mostly coordinated by secondary messengers, signalling molecules or small RNAs, in both medically relevant and environmental biofilms. Fully deciphering how bacteria provide structure to the matrix, and thus facilitate and benefit from extracellular reactions, remains the challenge for future biofilm research.
Collapse
Affiliation(s)
- Hans-Curt Flemming
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
| | | | - Thomas R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Thomas Seviour
- Aarhus University Centre for Water Technology, Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Paul Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA.,Department of Orthopaedics, The Ohio State University, Columbus, OH, USA
| | - Jost Wingender
- University of Duisburg-Essen, Biofilm Centre, Department of Aquatic Microbiology, Essen, Germany
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| |
Collapse
|
7
|
Vera-Santander VE, Hernández-Figueroa RH, Jiménez-Munguía MT, Mani-López E, López-Malo A. Health Benefits of Consuming Foods with Bacterial Probiotics, Postbiotics, and Their Metabolites: A Review. Molecules 2023; 28:molecules28031230. [PMID: 36770898 PMCID: PMC9920731 DOI: 10.3390/molecules28031230] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/11/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Over the years, probiotics have been extensively studied within the medical, pharmaceutical, and food fields, as it has been revealed that these microorganisms can provide health benefits from their consumption. Bacterial probiotics comprise species derived from lactic acid bacteria (LAB) (genus Lactobacillus, Leuconostoc, and Streptococcus), the genus Bifidobacterium, and strains of Bacillus and Escherichia coli, among others. The consumption of probiotic products is increasing due to the current situation derived from the pandemic caused by COVID-19. Foods with bacterial probiotics and postbiotics are premised on being healthier than those not incorporated with them. This review aims to present a bibliographic compilation related to the incorporation of bacterial probiotics in food and to demonstrate through in vitro and in vivo studies or clinical trials the health benefits obtained with their metabolites and the consumption of foods with bacterial probiotics/postbiotics. The health benefits that have been reported include effects on the digestive tract, metabolism, antioxidant, anti-inflammatory, anticancer, and psychobiotic properties, among others. Therefore, developing food products with bacterial probiotics and postbiotics is a great opportunity for research in food science, medicine, and nutrition, as well as in the food industry.
Collapse
|
8
|
Leggieri PA, Valentine MT, O'Malley MA. Biofilm disruption enhances growth rate and carbohydrate-active enzyme production in anaerobic fungi. BIORESOURCE TECHNOLOGY 2022; 358:127361. [PMID: 35609749 DOI: 10.1016/j.biortech.2022.127361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/07/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Anaerobic gut fungi (AGF) are lignocellulose degraders that naturally form biofilms in the rumen of large herbivores and in standard culture techniques. While biofilm formation enhances biomass degradation and carbohydrate-active enzyme (CAZyme) production in some bacteria and aerobic fungi, gene expression and metabolism in AGF biofilms have not been compared to non-biofilm cultures. Here, using the tunable morphology of the non-rhizoidal AGF, Caecomyces churrovis, the impacts of biofilm formation on AGF gene expression, metabolic flux, growth rate, and xylan degradation rate are quantified to inform future industrial scale-up efforts. Contrary to previous findings, C. churrovis upregulated catabolic CAZymes in stirred culture relative to biofilm culture. Using a de novo transcriptome, 197 new transcripts with predicted CAZyme function were identified. Stirred cultures grew and degraded xylan significantly faster than biofilm-forming cultures with negligible differences in primary metabolic flux, offering a way to accelerate AGF biomass valorization without altering the fermentation product profile. The rhizoidal AGF, Neocallimastix lanati, also grew faster with stirring on a solid plant substrate, suggesting that the advantages of stirred C. churrovis cultures may apply broadly to other AGF.
Collapse
Affiliation(s)
- Patrick A Leggieri
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.
| | - Megan T Valentine
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106, USA.
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA; Joint BioEnergy Institute (JBEI), Emeryville, CA 94608, USA.
| |
Collapse
|
9
|
Danilova IV, Rudakova NL, Vasilyeva YA, Gilmutdinova AI, Diadkina IV, Khasanov DI, Sharipova MR. Optimization of Electroporation Conditions for Bacillus pumilus 3–19 Strain. BIONANOSCIENCE 2022. [DOI: 10.1007/s12668-022-00982-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
10
|
Tatta ER, Imchen M, Moopantakath J, Kumavath R. Bioprospecting of microbial enzymes: current trends in industry and healthcare. Appl Microbiol Biotechnol 2022; 106:1813-1835. [PMID: 35254498 DOI: 10.1007/s00253-022-11859-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/15/2022] [Accepted: 02/26/2022] [Indexed: 12/13/2022]
Abstract
Microbial enzymes have an indispensable role in producing foods, pharmaceuticals, and other commercial goods. Many novel enzymes have been reported from all domains of life, such as plants, microbes, and animals. Nonetheless, industrially desirable enzymes of microbial origin are limited. This review article discusses the classifications, applications, sources, and challenges of most demanded industrial enzymes such as pectinases, cellulase, lipase, and protease. In addition, the production of novel enzymes through protein engineering technologies such as directed evolution, rational, and de novo design, for the improvement of existing industrial enzymes is also explored. We have also explored the role of metagenomics, nanotechnology, OMICs, and machine learning approaches in the bioprospecting of novel enzymes. Overall, this review covers the basics of biocatalysts in industrial and healthcare applications and provides an overview of existing microbial enzyme optimization tools. KEY POINTS: • Microbial bioactive molecules are vital for therapeutic and industrial applications. • High-throughput OMIC is the most proficient approach for novel enzyme discovery. • Comprehensive databases and efficient machine learning models are the need of the hour to fast forward de novo enzyme design and discovery.
Collapse
Affiliation(s)
- Eswar Rao Tatta
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (PO.), Kasaragod, Kerala, 671320, India
| | - Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (PO.), Kasaragod, Kerala, 671320, India
| | - Jamseel Moopantakath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (PO.), Kasaragod, Kerala, 671320, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (PO.), Kasaragod, Kerala, 671320, India.
| |
Collapse
|
11
|
Pudova DS, Toymentseva AA, Gogoleva NE, Shagimardanova EI, Mardanova AM, Sharipova MR. Comparative Genome Analysis of Two Bacillus pumilus Strains Producing High Level of Extracellular Hydrolases. Genes (Basel) 2022; 13:genes13030409. [PMID: 35327964 PMCID: PMC8950961 DOI: 10.3390/genes13030409] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
Whole-genome sequencing of a soil isolate Bacillus pumilus, strain 7P, and its streptomycin-resistant derivative, B. pumilus 3-19, showed genome sizes of 3,609,117 bp and 3,609,444 bp, respectively. Annotation of the genome showed 3794 CDS (3204 with predicted function) and 3746 CDS (3173 with predicted function) in the genome of strains 7P and 3-19, respectively. In the genomes of both strains, the prophage regions Bp1 and Bp2 were identified. These include 52 ORF of prophage proteins in the Bp1 region and 38 prophages ORF in the Bp2 region. Interestingly, more than 50% of Bp1 prophage proteins are similar to the proteins of the phi105 in B. subtilis. The DNA region of Bp2 has 15% similarity to the DNA of the Brevibacillus Jimmer phage. Degradome analysis of the genome of both strains revealed 148 proteases of various classes. These include 60 serine proteases, 48 metalloproteases, 26 cysteine proteases, 4 aspartate proteases, 2 asparagine proteases, 3 threonine proteases, and 2 unclassified proteases. Likewise, three inhibitors of proteolytic enzymes were found. Comparative analysis of variants in the genomes of strains 7P and 3-19 showed the presence of 81 nucleotide variants in the genome 3-19. Among them, the missense mutations in the rpsL, comA, spo0F genes and in the upstream region of the srlR gene were revealed. These nucleotide polymorphisms may have affected the streptomycin resistance and overproduction of extracellular hydrolases of the 3-19 strain. Finally, a plasmid DNA was found in strain 7P, which is lost in its derivative, strain 3-19. This plasmid contains five coding DNA sequencing (CDS), two regulatory proteins and three hypothetical proteins.
Collapse
|
12
|
Sharipova MR, Mardanova AM, Rudakova NL, Pudova DS. Bistability and Formation of the Biofilm Matrix as Adaptive Mechanisms during the Stationary Phase of Bacillus subtilis. Microbiology (Reading) 2021. [DOI: 10.1134/s002626172006017x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
|
13
|
The ABC-Type Efflux Pump MacAB Is Involved in Protection of Serratia marcescens against Aminoglycoside Antibiotics, Polymyxins, and Oxidative Stress. mSphere 2021; 6:6/2/e00033-21. [PMID: 33692192 PMCID: PMC8546677 DOI: 10.1128/msphere.00033-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Serratia marcescens is an emerging pathogen with increasing clinical importance due to its intrinsic resistance to several classes of antibiotics. The chromosomally encoded drug efflux pumps contribute to antibiotic resistance and represent a major challenge for the treatment of bacterial infections. The ABC-type efflux pump MacAB was previously linked to macrolide resistance in Escherichia coli and Salmonella enterica serovar Typhimurium. The role of the MacAB homolog in antibiotic resistance of S. marcescens is currently unknown. We found that an S. marcescens mutant lacking the MacAB pump did not show increased sensitivity to the macrolide antibiotic erythromycin but was significantly more sensitive to aminoglycoside antibiotics and polymyxins. We also showed that, in addition to its role in drug efflux, the MacAB efflux pump is required for swimming motility and biofilm formation. We propose that the motility defect of the ΔmacAB mutant is due, at least in part, to the loss of functional flagella on the bacterial surface. Furthermore, we found that the promoter of the MacAB efflux pump was active during the initial hours of growth in laboratory medium and that its activity was further elevated in the presence of hydrogen peroxide. Finally, we demonstrate a complete loss of ΔmacAB mutant viability in the presence of peroxide, which is fully restored by complementation. Thus, the S. marcescens MacAB efflux pump is essential for survival during oxidative stress and is involved in protection from polymyxins and aminoglycoside antibiotics. IMPORTANCE The opportunistic pathogen Serratia marcescens can cause urinary tract infections, respiratory infections, meningitis, and sepsis in immunocompromised individuals. These infections are challenging to treat due to the intrinsic resistance of S. marcescens to an extensive array of antibiotics. Efflux pumps play a crucial role in protection of bacteria from antimicrobials. The MacAB efflux pump, previously linked to efflux of macrolides in Escherichia coli and protection from oxidative stress in Salmonella enterica serovar Typhimurium, is not characterized in S. marcescens. We show the role of the MacAB efflux pump in S. marcescens protection from aminoglycoside antibiotics and polymyxins, modulation of bacterial motility, and biofilm formation, and we illustrate the essential role for this pump in bacterial survival during oxidative stress. Our findings make the MacAB efflux pump an attractive target for inhibition to gain control over S. marcescens infections.
Collapse
|
14
|
Luo HZ, Zhou JW, Sun B, Jiang H, Tang S, Jia AQ. Inhibitory effect of norharmane on Serratia marcescens NJ01 quorum sensing-mediated virulence factors and biofilm formation. BIOFOULING 2021; 37:145-160. [PMID: 33682541 DOI: 10.1080/08927014.2021.1874942] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/22/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Serratia marcescens NJ01, a Gram-negative bacterium, can infect tomato leaves and cause chlorosis and wilting. The present study evaluated the quorum sensing (QS) and biofilm inhibitory effects of seven carboline compounds against S. marcescens NJ01 at 20 μg ml-1, and subsequently focused the study on norharmane as this had the best inhibitory activity. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis confirmed the down-regulation of QS and biofilm related genes bsmA, bsmB, fimA, fimC, flhD, pigA, pigC and shlA on exposure to norharmane. Fourier-Transform Infrared Spectroscopy (FT-IR) analysis showed a reduction in the major components of the exopolysaccharide (EPS) matrix such as nucleic acids, proteins and fatty acids, which are involved in forming the tertiary structure of biofilms. Norharmane exposure also enhanced the susceptibility of the biofilm to ofloxacin. Hence, norharmane has the potential for use as an antibiotic adjuvant to enhance the efficacy of conventional antibiotics to reduce pathogenic bacterial infections.
Collapse
Affiliation(s)
- Huai-Zhi Luo
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
- School Life and Pharmaceutical Sciences, Engineering Research Center for Utilization of Tropical Polysaccharide Resources, Ministry of Education, Hainan University, Haikou, China
| | - Jin-Wei Zhou
- School of Food (Biological) Engineering, Xuzhou University of Technology, Xuzhou, China
| | - Bing Sun
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Huan Jiang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Shi Tang
- School Life and Pharmaceutical Sciences, Engineering Research Center for Utilization of Tropical Polysaccharide Resources, Ministry of Education, Hainan University, Haikou, China
| | - Ai-Qun Jia
- School Life and Pharmaceutical Sciences, Engineering Research Center for Utilization of Tropical Polysaccharide Resources, Ministry of Education, Hainan University, Haikou, China
| |
Collapse
|
15
|
Qian WD, Huang J, Zhang JN, Li XC, Kong Y, Wang T, Li YD. Antimicrobial and Antibiofilm Activities and Mechanism of Action of Chelerythrine Against Carbapenem-Resistant Serratia marcescens In Vitro. Microb Drug Resist 2021; 27:1105-1116. [PMID: 33439767 DOI: 10.1089/mdr.2020.0207] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aim: To evaluate the antimicrobial and antibiofilm effects of chelerythrine (CHE) against carbapenem-resistant Serratia marcescens (CRSM). Materials and Methods: The minimum inhibitory concentration (MIC) of CHE against CRSM was determined using the agar dilution method. Changes in intracellular adenosine triphosphate (ATP) concentration, intracellular pH, cell membrane potential, and cell membrane integrity were investigated to assess the influence of CHE on the cell membrane. The effects of CHE on cell morphology were observed by field emission scanning electron microscopy (FESEM) and transmission electron microscopy. The antibiofilm formation of CHE was measured by crystal violet staining and visualized with confocal laser scanning microscopy (CLSM) and FESEM. The influence of CHE on biofilm components was further investigated using CLSM specific combined with double-dyeing methods. Results: Our results showed that CHE had an MIC at 125 μg/mL against CRSM was capable of inhibiting the growth of CRSM and destroying its cell membrane integrity, as well as obviously changing the cell morphology. Sub-MIC CHE displayed robust inhibitory effects against CRSM biofilm formation by mediating the production of biofilm components. In addition, CLSM- and FESEM-mediated evaluation of the damage of biofilm cells and biofilm persistence revealed that at high concentrations, CHE could compromise the cells within biofilms and remove preformed biofilms. Conclusion: CHE shows promise as a natural antimicrobial substance against biofilm-positive CRSM, with the potential to serve as an alternative therapeutic agent.
Collapse
Affiliation(s)
- Wei-Dong Qian
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, P.R. China
| | - Jie Huang
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, P.R. China
| | - Jia-Ning Zhang
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, P.R. China
| | - Xin-Cheng Li
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, P.R. China
| | - Yi Kong
- Department of Clinical Laboratory Medicine, Jining First Peoples' Hospital, Jining, P.R. China
| | - Ting Wang
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, P.R. China
| | - Yong-Dong Li
- Ningbo Municipal Center for Disease Control and Prevention, Ningbo, P.R. China
| |
Collapse
|
16
|
Weldrick PJ, Hardman MJ, Paunov VN. Superenhanced Removal of Fungal Biofilms by Protease‐Functionalized Amphotericin B Nanocarriers. ADVANCED NANOBIOMED RESEARCH 2021. [DOI: 10.1002/anbr.202000027] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Paul J. Weldrick
- Department of Chemistry and Biochemistry University of Hull Hull HU6 7RX UK
| | - Matthew J. Hardman
- Department of Chemistry and Biochemistry University of Hull Hull HU6 7RX UK
| | - Vesselin N. Paunov
- Department of Chemistry and Biochemistry University of Hull Hull HU6 7RX UK
| |
Collapse
|
17
|
Characterization of Enterococcus faecalis in different culture conditions. Sci Rep 2020; 10:21867. [PMID: 33318537 PMCID: PMC7736865 DOI: 10.1038/s41598-020-78998-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 12/03/2020] [Indexed: 02/07/2023] Open
Abstract
The aim of this study was to investigate how carbohydrates (glucose or sucrose) affect the characteristics of Enterococcus faecalis (E. faecalis) planktonic and biofilm in vitro. For this study, E. faecalis was cultured in tryptone-yeast extract broth with 0% glucose + 0% sucrose, 0.5% glucose, 1% glucose, 0.5% sucrose, or 1% sucrose. Viability of E. faecalis was examined by colony forming unit counting assays. Biofilm formation was assessed by measuring extracellular DNA (eDNA), a component of the biofilm matrix. Quantitative real-time PCR (qRT-PCR) was performed to investigate the expression of virulence-associated genes. Field emission scanning electron microscopy analysis, confocal laser scanning microscopy analysis, and crystal violet colorimetric assay were conducted to study E. faecalis biofilms. E. faecalis showed the highest viability and eDNA levels in 1% sucrose medium in biofilms. The result of qRT-PCR showed that the virulence-associated genes expressed highest in 1% sucrose-grown biofilms and in 1% glucose-grown planktonic cultures. E. faecalis showed highly aggregated biofilms and higher bacteria and exopolysaccharide (EPS) bio-volume in sucrose than in 0% glucose + 0% sucrose or glucose. The results indicate that the production of eDNA and EPS and expression of virulence-associated genes in E. faecalis are affected by the concentration of carbohydrates in biofilm or planktonic culture.
Collapse
|
18
|
Hernández-Granados MJ, Franco-Robles E. Postbiotics in human health: Possible new functional ingredients? Food Res Int 2020; 137:109660. [DOI: 10.1016/j.foodres.2020.109660] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 08/25/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023]
|
19
|
Danilova I, Sharipova M. The Practical Potential of Bacilli and Their Enzymes for Industrial Production. Front Microbiol 2020; 11:1782. [PMID: 32849401 PMCID: PMC7417770 DOI: 10.3389/fmicb.2020.01782] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/07/2020] [Indexed: 12/14/2022] Open
Abstract
Bacillus spp. are an affordable source of enzymes due to their wide distribution, safety in work, ease of cultivation, and susceptibility to genetic transformations. Researchers are particularly interested in proteolytic enzymes, which constitute one of the most diverse groups of microbial proteins in terms of properties. Despite the long history of their research, this group of enzymes continue to show great potential for practical application in the biomedical industry, as well as in the agricultural industry. Thus, the unique properties of bacillary proteinases, such as stability in a wide range of temperatures and pH, high specificity, biodegradability of a wide range of substrates, and the high potential of sequenced Bacillus genomes are a powerful foundation for the development of new biotechnologies. The current review aims to discuss recent studies on various enzymes in particular, proteinases produced by bacteria of the genus Bacillus, along with their prospective practical applications. This article also presents an interpretive summary of the recent developments on the usage of probiotic Bacillus strains as potential feed additives.
Collapse
Affiliation(s)
- Iuliia Danilova
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Margarita Sharipova
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| |
Collapse
|
20
|
Toushik SH, Mizan MFR, Hossain MI, Ha SD. Fighting with old foes: The pledge of microbe-derived biological agents to defeat mono- and mixed-bacterial biofilms concerning food industries. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2020.03.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
21
|
Weldrick PJ, Hardman MJ, Paunov VN. Enhanced Clearing of Wound-Related Pathogenic Bacterial Biofilms Using Protease-Functionalized Antibiotic Nanocarriers. ACS APPLIED MATERIALS & INTERFACES 2019; 11:43902-43919. [PMID: 31718141 DOI: 10.1021/acsami.9b16119] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biofilms are prevalent in chronic wounds and once formed are very hard to remove, which is associated with poor outcomes and high mortality rates. Biofilms are comprised of surface-attached bacteria embedded in an extracellular polymeric substance (EPS) matrix, which confers increased antibiotic resistance and host immune evasion. Therefore, disruption of this matrix is essential to tackle the biofilm-embedded bacteria. Here, we propose a novel nanotechnology to do this, based on protease-functionalized nanogel carriers of antibiotics. Such active antibiotic nanocarriers, surface coated with the protease Alcalase 2.4 L FG, "digest" their way through the biofilm EPS matrix, reach the buried bacteria, and deliver a high dose of antibiotic directly on their cell walls, which overwhelms their defenses. We demonstrated their effectiveness against six wound biofilm-forming bacteria, Staphylococcus aureus, Pseudomonas aeruginosa, Staphylococcus epidermidis, Klebsiella pneumoniae, Escherichia coli, and Enterococcus faecalis. We confirmed a 6-fold decrease in the biofilm mass and a substantial reduction in bacterial cell density using fluorescence, atomic force, and scanning electron microscopy. Additionally, we showed that co-treatments of ciprofloxacin and Alcalase-coated Carbopol nanogels led to a 3-log reduction in viable biofilm-forming cells when compared to ciprofloxacin treatments alone. Encapsulating an equivalent concentration of ciprofloxacin into the Alcalase-coated nanogel particles boosted their antibacterial effect much further, reducing the bacterial cell viability to below detectable amounts after 6 h of treatment. The Alcalase-coated nanogel particles were noncytotoxic to human adult keratinocyte cells (HaCaT), inducing a very low apoptotic response in these cells. Overall, we demonstrated that the Alcalase-coated nanogels loaded with a cationic antibiotic elicit very strong biofilm-clearing effects against wound-associated biofilm-forming pathogenic bacteria. This nanotechnology approach has the potential to become a very powerful treatment of chronically infected wounds with biofilm-forming bacteria.
Collapse
Affiliation(s)
- Paul J Weldrick
- Department of Chemistry and Biochemistry , University of Hull , Hull HU6 7RX , U.K
| | - Matthew J Hardman
- Centre for Atherothrombosis and Metabolic Disease , Hull York Medical School , Hull HU6 7RX , U.K
| | - Vesselin N Paunov
- Department of Chemistry and Biochemistry , University of Hull , Hull HU6 7RX , U.K
| |
Collapse
|
22
|
Yu M, Chua SL. Demolishing the great wall of biofilms in Gram‐negative bacteria: To disrupt or disperse? Med Res Rev 2019; 40:1103-1116. [DOI: 10.1002/med.21647] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/03/2019] [Accepted: 11/07/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Miao Yu
- Department of Applied Biology and Chemical TechnologyThe Hong Kong Polytechnic University, KowloonHong Kong SAR China
- State Key Laboratory of Chemical Biology and Drug DiscoveryThe Hong Kong Polytechnic University, KowloonHong Kong SAR China
| | - Song Lin Chua
- Department of Applied Biology and Chemical TechnologyThe Hong Kong Polytechnic University, KowloonHong Kong SAR China
- State Key Laboratory of Chemical Biology and Drug DiscoveryThe Hong Kong Polytechnic University, KowloonHong Kong SAR China
| |
Collapse
|
23
|
Kobayashi K, Ikemoto Y. Biofilm-associated toxin and extracellular protease cooperatively suppress competitors in Bacillus subtilis biofilms. PLoS Genet 2019; 15:e1008232. [PMID: 31622331 PMCID: PMC6818787 DOI: 10.1371/journal.pgen.1008232] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/29/2019] [Accepted: 10/04/2019] [Indexed: 12/17/2022] Open
Abstract
In nature, most bacteria live in biofilms where they compete with their siblings and other species for space and nutrients. Some bacteria produce antibiotics in biofilms; however, since the diffusion of antibiotics is generally hindered in biofilms by extracellular polymeric substances, i.e., the biofilm matrix, their function remains unclear. The Bacillus subtilis yitPOM operon is a paralog of the sdpABC operon, which produces the secreted peptide toxin SDP. Unlike sdpABC, yitPOM is induced in biofilms by the DegS-DegU two-component regulatory system. High yitPOM expression leads to the production of a secreted toxin called YIT. Expression of yitQ, which lies upstream of yitPOM, confers resistance to the YIT toxin, suggesting that YitQ is an anti-toxin protein for the YIT toxin. The alternative sigma factor SigW also contributes to YIT toxin resistance. In a mutant lacking yitQ and sigW, the YIT toxin specifically inhibits biofilm formation, and the extracellular neutral protease NprB is required for this inhibition. The requirement for NprB is eliminated by Δeps and ΔbslA mutations, either of which impairs production of biofilm matrix polymers. Overexpression of biofilm matrix polymers prevents the action of the SDP toxin but not the YIT toxin. These results indicate that, unlike the SDP toxin and many conventional antibiotics, the YIT toxin can pass through layers of biofilm matrix polymers to attack cells within biofilms with assistance from NprB. When the wild-type strain and the YIT-sensitive mutant were grown together on a solid medium, the wild-type strain formed biofilms that excluded the YIT-sensitive mutant. This observation suggests that the YIT toxin protects B. subtilis biofilms against competitors. Several bacteria are known to produce antibiotics in biofilms. We propose that some bacteria including B. subtilis may have evolved specialized antibiotics that can function within biofilms. Biofilms are multicellular aggregates of bacteria that are formed on various living and non-living surfaces. Biofilms often cause serious problems, including food contamination and infectious diseases. Since bacteria in biofilms exhibit increased tolerance or resistance to antimicrobials, new agents and treatments for combating biofilm-related problems are required. In this study, we demonstrated that B. subtilis produces a secreted peptide antibiotic called the YIT toxin and its resistant proteins in biofilms. A mutant lacking the resistance genes was defective in biofilm formation. This effect resulted from the ability of the YIT toxin to pass through the biofilm defense barrier and to attack biofilm cells. Thus, unlike many conventional antibiotics, the YIT toxin can penetrate biofilms and suppress the growth of YIT toxin-sensitive cells within biofilms. Some bacteria produce antibiotics in biofilms, some of which can alter the bacterial composition in the biofilms. Taking these observations into consideration, our findings suggest that some bacteria produce special antibiotics that are effective against bacteria in biofilms, and these antibiotics might serve as anti-biofilm agents.
Collapse
Affiliation(s)
- Kazuo Kobayashi
- Division of Biological Science, Nara Institute of Science & Technology, Ikoma, Nara, Japan
- * E-mail:
| | - Yukako Ikemoto
- Division of Biological Science, Nara Institute of Science & Technology, Ikoma, Nara, Japan
| |
Collapse
|
24
|
Cattò C, Secundo F, James G, Villa F, Cappitelli F. α-Chymotrypsin Immobilized on a Low-Density Polyethylene Surface Successfully Weakens Escherichia coli Biofilm Formation. Int J Mol Sci 2018; 19:E4003. [PMID: 30545074 PMCID: PMC6321288 DOI: 10.3390/ijms19124003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 11/23/2018] [Accepted: 12/10/2018] [Indexed: 12/25/2022] Open
Abstract
The protease α-chymotrypsin (α-CT) was covalently immobilized on a low-density polyethylene (LDPE) surface, providing a new non-leaching material (LDPE-α-CT) able to preserve surfaces from biofilm growth over a long working timescale. The immobilized enzyme showed a transesterification activity of 1.24 nmol/h, confirming that the immobilization protocol did not negatively affect α-CT activity. Plate count viability assays, as well as confocal laser scanner microscopy (CLSM) analysis, showed that LDPE-α-CT significantly impacts Escherichia coli biofilm formation by (i) reducing the number of adhered cells (-70.7 ± 5.0%); (ii) significantly affecting biofilm thickness (-81.8 ± 16.7%), roughness (-13.8 ± 2.8%), substratum coverage (-63.1 ± 1.8%), and surface to bio-volume ratio (+7.1 ± 0.2-fold); and (iii) decreasing the matrix polysaccharide bio-volume (80.2 ± 23.2%). Additionally, CLSM images showed a destabilized biofilm with many cells dispersing from it. Notably, biofilm stained for live and dead cells confirmed that the reduction in the biomass was achieved by a mechanism that did not affect bacterial viability, reducing the chances for the evolution of resistant strains.
Collapse
Affiliation(s)
- Cristina Cattò
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milano 20133, Italy.
| | - Francesco Secundo
- Institute of Chemistry of Molecular Recognition, National Research Council, Milano 20131, Italy.
| | - Garth James
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA.
| | - Federica Villa
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milano 20133, Italy.
| | - Francesca Cappitelli
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milano 20133, Italy.
| |
Collapse
|
25
|
Nahar S, Mizan MFR, Ha AJW, Ha SD. Advances and Future Prospects of Enzyme-Based Biofilm Prevention Approaches in the Food Industry. Compr Rev Food Sci Food Saf 2018; 17:1484-1502. [DOI: 10.1111/1541-4337.12382] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/22/2018] [Accepted: 06/27/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Shamsun Nahar
- Dept. of Food Science and Technology; Chung-Ang Univ.; Anseong Gyeonggi-Do 456-756 Republic of Korea
| | | | - Angela Jie-won Ha
- Dept. of Food Science and Technology; Chung-Ang Univ.; Anseong Gyeonggi-Do 456-756 Republic of Korea
| | - Sang-Do Ha
- Dept. of Food Science and Technology; Chung-Ang Univ.; Anseong Gyeonggi-Do 456-756 Republic of Korea
| |
Collapse
|