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Papademas P, Paramithiotis S, Aspri M, Bintsis T, Anagnostopoulos DA, Tsaltas D. Editorial: Microbial communities in fermented products: current knowledge and future prospects. Front Microbiol 2024; 15:1408480. [PMID: 38737411 PMCID: PMC11082372 DOI: 10.3389/fmicb.2024.1408480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 04/10/2024] [Indexed: 05/14/2024] Open
Affiliation(s)
- Photis Papademas
- Department of Agricultural Sciences, Biotechnology & Food Science, Faculty of Geotechnical Sciences and Environmental Management, Cyprus University of Technology, Limassol, Cyprus
| | - Spiros Paramithiotis
- Department of Biological Applications and Technology, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Maria Aspri
- Department of Agricultural Sciences, Biotechnology & Food Science, Faculty of Geotechnical Sciences and Environmental Management, Cyprus University of Technology, Limassol, Cyprus
| | - Thomas Bintsis
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitrios A. Anagnostopoulos
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Dimitrios Tsaltas
- Department of Agricultural Sciences, Biotechnology & Food Science, Faculty of Geotechnical Sciences and Environmental Management, Cyprus University of Technology, Limassol, Cyprus
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Wu S, Lu J, Li C, Du H, Xu Y. Pediococcus spp. -mediated competition interaction within Daqu microbiota determines the temperature formation and metabolic profiles. Appl Environ Microbiol 2024; 90:e0179023. [PMID: 38506521 PMCID: PMC11022566 DOI: 10.1128/aem.01790-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 01/08/2024] [Indexed: 03/21/2024] Open
Abstract
Fermented microbiota is critical to the formation of microenvironment and metabolic profiles in spontaneous fermentation. Microorganisms generate a diverse array of metabolites concurrent with the release of heat energy. In the case of Daqu fermentation, the peak temperature exceeded 60°C, forming a typical high-temperature fermentation system known as high-temperature Daqu. However, microorganisms that cause the quality variation in Daqu and how they affect the functional microbiota and microenvironment in the fermentation process are not yet clear. This study adopted high-throughput sequencing and monitored the dynamic fluctuations of metabolites and environmental factors to identify the pivotal microorganism responsible for the alterations in interaction patterns of functional keystone taxa and quality decline in the fermentation system of different operational areas during the in situ fermentation process that had been mainly attributed to operational taxonomic unit (OTU)_22 (Pediococcus acidilactici). Additionally, we used isothermal microcalorimetry, plate inhibition experiments, and in vitro simulation fermentation experiments to explore the impact of Pediococcus spp. on heat generation, microorganisms, and metabolite profiles. Results showed the heat peak generated by Pediococcus spp. was significantly lower than that of Bacillus spp., filamentous fungi, and yeast. In addition, the preferential growth of P. acidilactici strain AA3 would obviously affect other strains to colonize through competition, and its metabolites made a significant impact on filamentous fungi. The addition of P. acidilactici strain AA3 in simulated fermentation would cause the loss of pyrazines and acids in metabolites. These evidences showed that the overgrowth of Pediococcus spp. greatly influenced the formation of high temperatures and compounds in solid-state fermentation systems. Our work illustrated the vital impact of interaction variability mediated by Pediococcus spp. for microbial assembly and metabolites, as well as in forming temperature. These results emphasized the functional role of Daqu microbiota in metabolites and heat production and the importance of cooperation in improving the fermentation quality.IMPORTANCEThe stable and high-quality saccharifying and fermenting starter in traditional solid-state fermentation was the prerequisite for liquor brewing. An imbalance of microbial homeostasis in fermentation can adversely impact production quality. Identification of such critical microorganisms and verifying their associations with other fermentation parameters pose a challenge in a traditional fermentation environment. To enhance the quality of spontaneous fermented products, strategies such as bioaugmentation or the control of harmful microorganisms would be employed. This work started with the differences in high-temperature Daqu metabolites to explore a series of functional microorganisms that could potentially contribute to product disparities, and found that the differences in interactions facilitated directly or indirectly by Pediococcus spp. seriously affected the development of microbial communities and metabolites, as well as the formation of the microenvironment. This study not only identified functional microbiota in Daqu that affected fermentation quality, but also demonstrated how microorganisms interact to affect the fermentation system, which would provide guidance for microbial supervision in the actual production process. Besides, the application of isothermal microcalorimetry in this study was helpful for us to understand the heat production capacity of microorganisms and their adaptability to the environment. This study presented a commendable framework for improving and controlling the quality of traditional fermentation and inspired further investigations in similar systems.
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Affiliation(s)
- Shenglu Wu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Jun Lu
- Guizhou Guotai Liquor Group Co. Ltd., Zunyi, Guizhou, China
| | - Changwen Li
- Guizhou Guotai Liquor Group Co. Ltd., Zunyi, Guizhou, China
| | - Hai Du
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
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3
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Watanabe D. Sake yeast symbiosis with lactic acid bacteria and alcoholic fermentation. Biosci Biotechnol Biochem 2024; 88:237-241. [PMID: 38006236 DOI: 10.1093/bbb/zbad167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
The yeast Saccharomyces cerevisiae plays a pivotal role in the production of fermented foods by converting sugars in ingredients into ethanol through alcoholic fermentation. However, how accurate is our understanding of its biological significance? Although yeast is essential to produce alcoholic beverages and bioethanol, yeast does not yield ethanol for humankind. Yeast obtains energy in the form of ATP for its own vital processes through alcoholic fermentation, which generates ethanol as a byproduct. The production of ethanol may have more significance for yeast, since many other organisms do not produce ethanol, a highly toxic substance, to obtain energy. The key to address this issue has not been found using conventional microbiology, where yeasts are isolated and cultured in pure form. This review focuses on a possible novel role of yeast alcohol fermentation, which is revealed through our recent studies of microbial interactions.
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Affiliation(s)
- Daisuke Watanabe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
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Toquet M, Bataller E, Toledo-Perona R, Gomis J, Contreras A, Sánchez A, Jiménez-Trigos E, Gómez-Martín Á. In Vitro Interaction between Mycoplasma agalactiae and Small Ruminants' Endogenous Bacterial Strains of Enterococcus spp. and Coagulase-Negative Staphylococcus. Microorganisms 2024; 12:406. [PMID: 38399811 PMCID: PMC10891560 DOI: 10.3390/microorganisms12020406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Recently, an antimicrobial effect on Mycoplasma agalactiae (Ma), the main etiological agent of contagious agalactia (CA), was reported in vitro with strains of Enterococcus spp. from ovine and caprine milk. The aim of this work was to evaluate the interaction of Ma with the same Enterococcus spp. isolated from other anatomical locations (vagina) and other bacterial populations present in milk, such as coagulase-negative staphylococci (CNS). The vaginal Enterococcus strains and the raw milk CNS were isolated from sheep and goats. Experimental in vitro conditions were prepared to assess the growth of Ma with and without the presence of these strains. The selected vaginal strains were identified as Enterococcus (E.) hirae and E. mundtii, and the strains of CNS were identified as Staphylococcus petrasii. Different interactions of Ma with ovine and caprine wild vaginal strains of Enterococcus and dairy strains of CNS are described for the first time: Ma can grow exponentially during 15 h with the selected strains, although with certain strains, its optimal growth can be negatively affected (p < 0.05). The colonization and/or excretion of Ma could, therefore, be influenced by certain endogenous bacterial strains. Our results increase the knowledge about possible bacterial ecology dynamics surrounding CA.
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Affiliation(s)
- Marion Toquet
- Microbiological Agents Associated with Animal Reproduction (ProVaginBIO) Research Group, Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Carrer Tirant lo Blanc, 7, 46115 Valencia, Spain
| | - Esther Bataller
- Microbiological Agents Associated with Animal Reproduction (ProVaginBIO) Research Group, Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Carrer Tirant lo Blanc, 7, 46115 Valencia, Spain
| | - Raquel Toledo-Perona
- Microbiological Agents Associated with Animal Reproduction (ProVaginBIO) Research Group, Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Carrer Tirant lo Blanc, 7, 46115 Valencia, Spain
| | - Jesús Gomis
- Microbiological Agents Associated with Animal Reproduction (ProVaginBIO) Research Group, Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Carrer Tirant lo Blanc, 7, 46115 Valencia, Spain
| | - Antonio Contreras
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Murcia, Campus de Espinardo, 30100 Murcia, Spain
| | - Antonio Sánchez
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Murcia, Campus de Espinardo, 30100 Murcia, Spain
| | - Estrella Jiménez-Trigos
- Microbiological Agents Associated with Animal Reproduction (ProVaginBIO) Research Group, Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Carrer Tirant lo Blanc, 7, 46115 Valencia, Spain
| | - Ángel Gómez-Martín
- Microbiological Agents Associated with Animal Reproduction (ProVaginBIO) Research Group, Departamento Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Carrer Tirant lo Blanc, 7, 46115 Valencia, Spain
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Wang B, Deng J, Donati V, Merali N, Frampton AE, Giovannetti E, Deng D. The Roles and Interactions of Porphyromonas gingivalis and Fusobacterium nucleatum in Oral and Gastrointestinal Carcinogenesis: A Narrative Review. Pathogens 2024; 13:93. [PMID: 38276166 PMCID: PMC10820765 DOI: 10.3390/pathogens13010093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
Epidemiological studies have spotlighted the intricate relationship between individual oral bacteria and tumor occurrence. Porphyromonas gingivalis and Fusobacteria nucleatum, which are known periodontal pathogens, have emerged as extensively studied participants with potential pathogenic abilities in carcinogenesis. However, the complex dynamics arising from interactions between these two pathogens were less addressed. This narrative review aims to summarize the current knowledge on the prevalence and mechanism implications of P. gingivalis and F. nucleatum in the carcinogenesis of oral squamous cell carcinoma (OSCC), colorectal cancer (CRC), and pancreatic ductal adenocarcinoma (PDAC). In particular, it explores the clinical and experimental evidence on the interplay between P. gingivalis and F. nucleatum in affecting oral and gastrointestinal carcinogenesis. P. gingivalis and F. nucleatum, which are recognized as keystone or bridging bacteria, were identified in multiple clinical studies simultaneously. The prevalence of both bacteria species correlated with cancer development progression, emphasizing the potential impact of the collaboration. Regrettably, there was insufficient experimental evidence to demonstrate the synergistic function. We further propose a hypothesis to elucidate the underlying mechanisms, offering a promising avenue for future research in this dynamic and evolving field.
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Affiliation(s)
- Bing Wang
- Department of Medical Oncology, Amsterdam University Medical Center, Cancer Center Amsterdam, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (B.W.); (J.D.); (V.D.); (E.G.)
| | - Juan Deng
- Department of Medical Oncology, Amsterdam University Medical Center, Cancer Center Amsterdam, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (B.W.); (J.D.); (V.D.); (E.G.)
| | - Valentina Donati
- Department of Medical Oncology, Amsterdam University Medical Center, Cancer Center Amsterdam, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (B.W.); (J.D.); (V.D.); (E.G.)
- Unit of Pathological Anatomy 2, Azienda Ospedaliero-Universitaria Pisana, 56100 Pisa, Italy
| | - Nabeel Merali
- Minimal Access Therapy Training Unit (MATTU), Royal Surrey County Hospital, NHS Foundation Trust, Egerton Road, Guildford GU2 7XX, UK; (N.M.); (A.E.F.)
- Department of Hepato-Pancreato-Biliary (HPB) Surgery, Royal Surrey County Hospital, NHS Foundation Trust, Egerton Road, Guildford GU2 7XX, UK
- Section of Oncology, Department of Clinical and Experimental Medicine, Faculty of Health Medical Science, University of Surrey, Guilford GU2 7WG, UK
| | - Adam E. Frampton
- Minimal Access Therapy Training Unit (MATTU), Royal Surrey County Hospital, NHS Foundation Trust, Egerton Road, Guildford GU2 7XX, UK; (N.M.); (A.E.F.)
- Department of Hepato-Pancreato-Biliary (HPB) Surgery, Royal Surrey County Hospital, NHS Foundation Trust, Egerton Road, Guildford GU2 7XX, UK
- Section of Oncology, Department of Clinical and Experimental Medicine, Faculty of Health Medical Science, University of Surrey, Guilford GU2 7WG, UK
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam University Medical Center, Cancer Center Amsterdam, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (B.W.); (J.D.); (V.D.); (E.G.)
- Fondazione Pisana per la Scienza, 56100 Pisa, Italy
| | - Dongmei Deng
- Department of Prevention Dentistry, Academic Center for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universitreit Amsterdam, 1081 LA Amsterdam, The Netherlands
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Chen X, Gao M, Wang L, Qiang G, Wu Y, Huang H, Kang G. A synthetic microbial consortium protects against obesity by regulating vitamin B6 metabolism. Gut Microbes 2024; 16:2304901. [PMID: 38269591 PMCID: PMC10813659 DOI: 10.1080/19490976.2024.2304901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
Constructing synthetic microbial consortia is a challenging task but holds enormous potential for various applications. Our previous droplet-based microfluidic approach allowed for the isolation of bacteria that could utilize metabolites from an engineered bacterium BsS-RS06551 with anti-obesity potential, facilitating the construction of synthetic microbial consortia. Here, we identified a strain of Bifidobacterium pseudocatenulatum JJ3 that interacted with BsS-RS06551, and in vitro coculture showed that BsS-RS06551 was likely to interact with JJ3 through five dipeptides. Pathway analysis revealed that the vitamin B6 metabolism pathway was enriched in the coculture of BsS-RS06551 and JJ3 compared with the individual culture of BsS-RS06551. Additionally, we confirmed that the administration of JJ3 significantly alleviated obesity and related disorders in mice fed a high-fat diet. Notably, continuous ingestion of the synthetic microbial consortium comprising BsS-RS06551 and JJ3 not only exhibited a more pronounced impact on alleviating obesity compared to the individual administration of BsS-RS06551 or JJ3 but also enriched the population of Bifidobacterium longum and perturbed the vitamin B6 metabolism pathway in the gut. Synthetic microbial consortia represent a promising frontier for synthetic biology, and our strategy provides guidance for constructing and applying such consortia.
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Affiliation(s)
- Xiuzhao Chen
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Mengxue Gao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Lina Wang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Guifen Qiang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College and Beijing Key Laboratory of Drug Target and Screening Research, Beijing, China
| | - Yili Wu
- Oujiang Laboratory, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - He Huang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Guangbo Kang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
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Srinivasan A, Sajeevan A, Rajaramon S, David H, Solomon AP. Solving polymicrobial puzzles: evolutionary dynamics and future directions. Front Cell Infect Microbiol 2023; 13:1295063. [PMID: 38145044 PMCID: PMC10748482 DOI: 10.3389/fcimb.2023.1295063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/03/2023] [Indexed: 12/26/2023] Open
Abstract
Polymicrobial infections include various microorganisms, often necessitating different treatment methods than a monomicrobial infection. Scientists have been puzzled by the complex interactions within these communities for generations. The presence of specific microorganisms warrants a chronic infection and impacts crucial factors such as virulence and antibiotic susceptibility. Game theory is valuable for scenarios involving multiple decision-makers, but its relevance to polymicrobial infections is limited. Eco-evolutionary dynamics introduce causation for multiple proteomic interactions like metabolic syntropy and niche segregation. The review culminates both these giants to form evolutionary dynamics (ED). There is a significant amount of literature on inter-bacterial interactions that remain unsynchronised. Such raw data can only be moulded by analysing the ED involved. The review culminates the inter-bacterial interactions in multiple clinically relevant polymicrobial infections like chronic wounds, CAUTI, otitis media and dental carries. The data is further moulded with ED to analyse the niche colonisation of two notoriously competitive bacteria: S.aureus and P.aeruginosa. The review attempts to develop a future trajectory for polymicrobial research by following recent innovative strategies incorporating ED to curb polymicrobial infections.
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Affiliation(s)
| | | | | | | | - Adline Princy Solomon
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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Wang M, Zhao K, Li X, Xie BB. Insights into the composition and assembly mechanism of microbial communities on intertidal microsand grains. Front Microbiol 2023; 14:1308767. [PMID: 38098661 PMCID: PMC10719935 DOI: 10.3389/fmicb.2023.1308767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023] Open
Abstract
Introduction Marine microorganisms are essential in marine ecosystems and have always been of interest. Currently, most marine microbial communities are studied at the bulk scale (millimeters to centimeters), and the composition, function and underlying assembly mechanism of microbial communities at the microscale (sub-100 micrometers) are unclear. Methods The microbial communities on microsand grains (40-100 µm, n = 150) from marine sediment were investigated and compared with those on macrosand grains (400-1000 µm, n = 60) and bulk sediments (n = 5) using amplicon sequencing technology. Results The results revealed a significant difference between microsand grains and macrosand grains. Microsand grains had lower numbers of operational taxonomic units (OTUs(97%)) and predicted functional genes than macrosand grains and bulk-scale samples. Microsand grains also showed greater intersample differences in the community composition and predicted functional genes than macrosand grains, suggesting a high level of heterogeneity of microbial communities at the microscale. Analyses based on ecological models indicated that stochastic processes dominated the assembly of microbial communities on sand grains. Consistently, cooccurrence network analyses showed that most microbial cooccurrence associations on sand grains were highly unstable. Metagenomic sequencing and further genome-scale metabolic modeling revealed that only a small number (1.3%) of microbe pairs showed high cooperative potential. Discussion This study explored the microbial community of marine sediments at the sub-100 µm scale, broadening the knowledge of the structure and assembly mechanism of marine microbial communities.
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Affiliation(s)
| | | | | | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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Liu X, Ma Y, Wu J, Wang P, Wang Y, Wang A, Yin Q, Ma H, Chan LL, Wu B. Characterizing the Influence of a Heterotrophic Bicosoecid Flagellate Pseudobodo sp. on the Dinoflagellate Gambierdiscus balechii. Toxins (Basel) 2023; 15:657. [PMID: 37999520 PMCID: PMC10674679 DOI: 10.3390/toxins15110657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023] Open
Abstract
Microbial interactions including competition, mutualism, commensalism, parasitism, and predation, which can be triggered by nutrient acquisition and chemical communication, are universal phenomena in the marine ecosystem. The interactions may influence the microbial population density, metabolism, and even their environmental functions. Herein, we investigated the interaction between a heterotrophic bicosoecid flagellate, Pseudobodo sp. (Bicoecea), and a dinoflagellate, Gambierdiscus balechii (Dinophyceae), which is a well-known ciguatera food poisoning (CFP) culprit. The presence of Pseudobodo sp. inhibited the algal proliferation and decreased the cardiotoxicity of zebrafish in the algal extract exposure experiment. Moreover, a significant difference in microbiome abundance was observed in algal cultures with and without Pseudobodo sp. Chemical analysis targeting toxins was performed by using liquid chromatography-tandem mass spectrometry (LC-MS/MS) combined with molecular networking (MN), showing a significant alteration in the cellular production of gambierone analogs and some super-carbon chain compounds. Taken together, our results demonstrated the impact of heterotrophic flagellate on the photosynthetic dinoflagellates, revealing the complex dynamics of algal toxin production and the ecological relationships related to dinoflagellates in the marine environment.
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Affiliation(s)
- Xiaowan Liu
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR 999077, China; (X.L.); (J.W.); (H.M.)
| | - Yihan Ma
- Ocean College, Zhejiang University, Zhoushan 321000, China; (Y.M.); (Y.W.); (A.W.); (Q.Y.)
| | - Jiajun Wu
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR 999077, China; (X.L.); (J.W.); (H.M.)
- Shenzhen Key Laboratory for the Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Pengbin Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China;
- The Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai 536000, China
| | - Yinuo Wang
- Ocean College, Zhejiang University, Zhoushan 321000, China; (Y.M.); (Y.W.); (A.W.); (Q.Y.)
| | - Anli Wang
- Ocean College, Zhejiang University, Zhoushan 321000, China; (Y.M.); (Y.W.); (A.W.); (Q.Y.)
| | - Qizhao Yin
- Ocean College, Zhejiang University, Zhoushan 321000, China; (Y.M.); (Y.W.); (A.W.); (Q.Y.)
| | - Haiying Ma
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR 999077, China; (X.L.); (J.W.); (H.M.)
| | - Leo Lai Chan
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR 999077, China; (X.L.); (J.W.); (H.M.)
- Shenzhen Key Laboratory for the Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Bin Wu
- Ocean College, Zhejiang University, Zhoushan 321000, China; (Y.M.); (Y.W.); (A.W.); (Q.Y.)
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Li L, Hu Z, Tan G, Fan J, Chen Y, Xiao Y, Wu S, Zhi Q, Liu T, Yin H, Tang Q. Enhancing plant growth in biofertilizer-amended soil through nitrogen-transforming microbial communities. Front Plant Sci 2023; 14:1259853. [PMID: 38034579 PMCID: PMC10683058 DOI: 10.3389/fpls.2023.1259853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023]
Abstract
Biofertilizers have immense potential for enhancing agricultural productivity. However, there is still a need for clarification regarding the specific mechanisms through which these biofertilizers improve soil properties and stimulate plant growth. In this research, a bacterial agent was utilized to enhance plant growth and investigate the microbial modulation mechanism of soil nutrient turnover using metagenomic technology. The results demonstrated a significant increase in soil fast-acting nitrogen (by 46.7%) and fast-acting phosphorus (by 88.6%) upon application of the bacterial agent. This finding suggests that stimulated soil microbes contribute to enhanced nutrient transformation, ultimately leading to improved plant growth. Furthermore, the application of the bacterial agent had a notable impact on the accumulation of key genes involved in nitrogen cycling. Notably, it enhanced nitrification genes (amo, hao, and nar), while denitrification genes (nir and nor) showed a slight decrease. This indicates that ammonium oxidation may be the primary pathway for increasing fast-acting nitrogen in soils. Additionally, the bacterial agent influenced the composition and functional structure of the soil microbial community. Moreover, the metagenome-assembled genomes (MAGs) obtained from the soil microbial communities exhibited complementary metabolic processes, suggesting mutual nutrient exchange. These MAGs contained widely distributed and highly abundant genes encoding plant growth promotion (PGP) traits. These findings emphasize how soil microbial communities can enhance vegetation growth by increasing nutrient availability and regulating plant hormone production. This effect can be further enhanced by introducing inoculated microbial agents. In conclusion, this study provides novel insights into the mechanisms underlying the beneficial effects of biofertilizers on soil properties and plant growth. The significant increase in nutrient availability, modulation of key genes involved in nitrogen cycling, and the presence of MAGs encoding PGP traits highlight the potential of biofertilizers to improve agricultural practices. These findings have important implications for enhancing agricultural sustainability and productivity, with positive societal and environmental impacts.
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Affiliation(s)
- Liangzhi Li
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Zhengrong Hu
- Hunan Tobacco Research Institute, Changsha, China
| | - Ge Tan
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Jianqiang Fan
- Technology Center, China Tobacco Fujian Industrial Co., Ltd., Xiamen, Fujian, China
| | - Yiqiang Chen
- Technology Center, China Tobacco Fujian Industrial Co., Ltd., Xiamen, Fujian, China
| | - Yansong Xiao
- Chenzhou Tobacco Company of Hunan Province, Chenzhou, China
| | - Shaolong Wu
- Hunan Tobacco Research Institute, Changsha, China
| | - Qiqi Zhi
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Tianbo Liu
- Hunan Tobacco Research Institute, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Qianjun Tang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
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11
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Juříková T, Mácha H, Lupjanová V, Pluháček T, Marešová H, Papoušková B, Luptáková D, Patil RH, Benada O, Grulich M, Palyzová A. The Deciphering of Growth-Dependent Strategies for Quorum-Sensing Networks in Pseudomonas aeruginosa. Microorganisms 2023; 11:2329. [PMID: 37764173 PMCID: PMC10534576 DOI: 10.3390/microorganisms11092329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/31/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Pseudomonas aeruginosa is recognized as a significant cause of morbidity and mortality among nosocomial pathogens. In respiratory infections, P. aeruginosa acts not only as a single player but also collaborates with the opportunistic fungal pathogen Aspergillus fumigatus. This study introduced a QS molecule portfolio as a potential new biomarker that affects the secretion of virulence factors and biofilm formation. The quantitative levels of QS molecules, including 3-o-C12-HSL, 3-o-C8-HSL, C4-HSL, C6-HSL, HHQ, PQS, and PYO, measured using mass spectrometry in a monoculture, indicated metabolic changes during the transition from planktonic to sessile cells. In the co-cultures with A. fumigatus, the profile of abundant QS molecules was reduced to 3-o-C12-HSL, C4-HSL, PQS, and PYO. A decrease in C4-HSL by 50% to 170.6 ± 11.8 ng/mL and an increase 3-o-C12-HSL by 30% up to 784.4 ± 0.6 ng/mL were detected at the stage of the coverage of the hyphae with bacteria. Using scanning electron microscopy, we showed the morphological stages of the P. aeruginosa biofilm, such as cell aggregates, maturated biofilm, and cell dispersion. qPCR quantification of the genome equivalents of both microorganisms suggested that they exhibited an interplay strategy rather than antagonism. This is the first study demonstrating the quantitative growth-dependent appearance of QS molecule secretion in a monoculture of P. aeruginosa and a co-culture with A. fumigatus.
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Affiliation(s)
- Tereza Juříková
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; (T.J.); (H.M.); (V.L.); (H.M.); (D.L.); (R.H.P.); (O.B.); (M.G.)
| | - Hynek Mácha
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; (T.J.); (H.M.); (V.L.); (H.M.); (D.L.); (R.H.P.); (O.B.); (M.G.)
- Department of Analytical Chemistry, Faculty of Science, Palacky University, 17. Listopadu 12, 771 46 Olomouc, Czech Republic; (T.P.); (B.P.)
| | - Vanda Lupjanová
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; (T.J.); (H.M.); (V.L.); (H.M.); (D.L.); (R.H.P.); (O.B.); (M.G.)
| | - Tomáš Pluháček
- Department of Analytical Chemistry, Faculty of Science, Palacky University, 17. Listopadu 12, 771 46 Olomouc, Czech Republic; (T.P.); (B.P.)
| | - Helena Marešová
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; (T.J.); (H.M.); (V.L.); (H.M.); (D.L.); (R.H.P.); (O.B.); (M.G.)
| | - Barbora Papoušková
- Department of Analytical Chemistry, Faculty of Science, Palacky University, 17. Listopadu 12, 771 46 Olomouc, Czech Republic; (T.P.); (B.P.)
| | - Dominika Luptáková
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; (T.J.); (H.M.); (V.L.); (H.M.); (D.L.); (R.H.P.); (O.B.); (M.G.)
| | - Rutuja H. Patil
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; (T.J.); (H.M.); (V.L.); (H.M.); (D.L.); (R.H.P.); (O.B.); (M.G.)
- Department of Analytical Chemistry, Faculty of Science, Palacky University, 17. Listopadu 12, 771 46 Olomouc, Czech Republic; (T.P.); (B.P.)
| | - Oldřich Benada
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; (T.J.); (H.M.); (V.L.); (H.M.); (D.L.); (R.H.P.); (O.B.); (M.G.)
| | - Michal Grulich
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; (T.J.); (H.M.); (V.L.); (H.M.); (D.L.); (R.H.P.); (O.B.); (M.G.)
| | - Andrea Palyzová
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; (T.J.); (H.M.); (V.L.); (H.M.); (D.L.); (R.H.P.); (O.B.); (M.G.)
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12
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Mao X, Chen H, Peng X, Zhao X, Yu Z, Xu D. Dysbiosis of vaginal and cervical microbiome is associated with uterine fibroids. Front Cell Infect Microbiol 2023; 13:1196823. [PMID: 37743857 PMCID: PMC10513091 DOI: 10.3389/fcimb.2023.1196823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023] Open
Abstract
Dysbiosis of the female reproductive tract is closely associated with gynecologic diseases. Here, we aim to explore the association between dysbiosis in the genital tract and uterine fibroids (UFs) to further provide new insights into UF etiology. We present an observational study to profile vaginal and cervical microbiome from 29 women with UFs and 38 healthy women, and 125 samples were obtained and sequenced. By comparing the microbial profiles between different parts of the reproductive tract, there is no significant difference in microbial diversity between healthy subjects and UF patients. However, alpha diversity of UF patients was negatively correlated with the number of fibroids. Increased Firmicutes were observed in both the cervical and vaginal microbiome of UF patients at the phylum level. In differential analysis of relative abundance, some genera were shown to be significantly enriched (e.g., Erysipelatoclostridium, Mucispirillum, and Finegoldia) and depleted (e.g., Erysipelotrichaceae UCG-003 and Sporolactobacillus) in UF patients. Furthermore, the microbial co-occurrence networks of UF patients showed lower connectivity and complexity, suggesting reduced interactions and stability of the cervical and vaginal microbiota in UF patients. In summary, our findings revealed the perturbation of microbiome in the presence of UFs and a distinct pattern of characteristic vaginal and cervical microbiome involved in UFs, offering new options to further improve prevention and management strategies.
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Affiliation(s)
- Xuetao Mao
- Department of Gynecology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hao Chen
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, China
| | - Xuan Peng
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Xingping Zhao
- Department of Gynecology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zheng Yu
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Dabao Xu
- Department of Gynecology, The Third Xiangya Hospital, Central South University, Changsha, China
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Shi T, Wang J, Dong J, Hu P, Guo Q. Periodontopathogens Porphyromonas gingivalis and Fusobacterium nucleatum and Their Roles in the Progression of Respiratory Diseases. Pathogens 2023; 12:1110. [PMID: 37764918 PMCID: PMC10535846 DOI: 10.3390/pathogens12091110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/18/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
The intricate interplay between oral microbiota and the human host extends beyond the confines of the oral cavity, profoundly impacting the general health status. Both periodontal diseases and respiratory diseases show high prevalence worldwide and have a marked influence on the quality of life for the patients. Accumulating studies are establishing a compelling association between periodontal diseases and respiratory diseases. Here, in this review, we specifically focus on the key periodontal pathogenic bacteria Porphyromonas gingivalis and Fusobacterium nucleatum and dissect their roles in the onset and course of respiratory diseases, mainly pneumonia, chronic obstructive pulmonary disease, lung cancer, and asthma. The mechanistic underpinnings and molecular processes on how P. gingivalis and F. nucleatum contribute to the progression of related respiratory diseases are further summarized and analyzed, including: induction of mucus hypersecretion and chronic airway inflammation; cytotoxic effects to disrupt the morphology and function of respiratory epithelial cells; synergistic pathogenic effects with respiratory pathogens like Streptococcus pneumoniae and Pseudomonas aeruginosa. By delving into the complex relationship to periodontal diseases and periodontopathogens, this review helps unearth novel insights into the etiopathogenesis of respiratory diseases and inspires the development of potential therapeutic avenues and preventive strategies.
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Affiliation(s)
- Tao Shi
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Jiale Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Jiajia Dong
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
- State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Pingyue Hu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Qiang Guo
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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Maatouk M, Rolain JM, Bittar F. Using Genomics to Decipher the Enigmatic Properties and Survival Adaptation of Candidate Phyla Radiation. Microorganisms 2023; 11:1231. [PMID: 37317205 DOI: 10.3390/microorganisms11051231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 06/16/2023] Open
Abstract
Microbial ecology is a critical field for understanding the composition, diversity, and functions of microorganisms in various environmental and health-related processes. The discovery of Candidate Phyla Radiation (CPR) through culture-independent methods has introduced a new division of microbes characterized by a symbiotic/parasitic lifestyle, small cell size, and small genome. Despite being poorly understood, CPRs have garnered significant attention in recent years due to their widespread detection in a variety of environmental and clinical samples. These microorganisms have been found to exhibit a high degree of genetic diversity compared to other microbes. Several studies have shed light on their potential importance in global biogeochemical cycles and their impact on various human activities. In this review, we provide a systematic overview of the discovery of CPRs. We then focus on describing how the genomic characteristics of CPRs have helped them interact with and adapt to other microbes in different ecological niches. Future works should focus on discovering the metabolic capacities of CPRs and, if possible, isolating them to obtain a better understanding of these microorganisms.
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Affiliation(s)
- Mohamad Maatouk
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Jean-Marc Rolain
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Fadi Bittar
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
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15
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Lee KW, Shin JS, Lee CM, Han HY, O Y, Kim HW, Cho TJ. Gut-on-a-Chip for the Analysis of Bacteria-Bacteria Interactions in Gut Microbial Community: What Would Be Needed for Bacterial Co-Culture Study to Explore the Diet-Microbiota Relationship? Nutrients 2023; 15:nu15051131. [PMID: 36904133 PMCID: PMC10005057 DOI: 10.3390/nu15051131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
Bacterial co-culture studies using synthetic gut microbiomes have reported novel research designs to understand the underlying role of bacterial interaction in the metabolism of dietary resources and community assembly of complex microflora. Since lab-on-a-chip mimicking the gut (hereafter "gut-on-a-chip") is one of the most advanced platforms for the simulative research regarding the correlation between host health and microbiota, the co-culture of the synthetic bacterial community in gut-on-a-chip is expected to reveal the diet-microbiota relationship. This critical review analyzed recent research on bacterial co-culture with perspectives on the ecological niche of commensals, probiotics, and pathogens to categorize the experimental approaches for diet-mediated management of gut health as the compositional and/or metabolic modulation of the microbiota and the control of pathogens. Meanwhile, the aim of previous research on bacterial culture in gut-on-a-chip has been mainly limited to the maintenance of the viability of host cells. Thus, the integration of study designs established for the co-culture of synthetic gut consortia with various nutritional resources into gut-on-a-chip is expected to reveal bacterial interspecies interactions related to specific dietary patterns. This critical review suggests novel research topics for co-culturing bacterial communities in gut-on-a-chip to realize an ideal experimental platform mimicking a complex intestinal environment.
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Affiliation(s)
- Ki Won Lee
- Department of Food and Biotechnology, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| | - Jin Song Shin
- Department of Food Regulatory Science, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| | - Chan Min Lee
- Department of Food and Biotechnology, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| | - Hea Yeon Han
- Department of Food and Biotechnology, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| | - Yun O
- Department of Food Regulatory Science, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| | - Hye Won Kim
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tae Jin Cho
- Department of Food and Biotechnology, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
- Department of Food Regulatory Science, College of Science and Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
- Correspondence: ; Tel.: +82-44-860-1433
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Naik B, Kumar V, Rizwanuddin S, Chauhan M, Choudhary M, Gupta AK, Kumar P, Kumar V, Saris PEJ, Rather MA, Bhuyan S, Neog PR, Mishra S, Rustagi S. Genomics, Proteomics, and Metabolomics Approaches to Improve Abiotic Stress Tolerance in Tomato Plant. Int J Mol Sci 2023; 24. [PMID: 36769343 DOI: 10.3390/ijms24033025] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
To explore changes in proteins and metabolites under stress circumstances, genomics, proteomics, and metabolomics methods are used. In-depth research over the previous ten years has gradually revealed the fundamental processes of plants' responses to environmental stress. Abiotic stresses, which include temperature extremes, water scarcity, and metal toxicity brought on by human activity and urbanization, are a major cause for concern, since they can result in unsustainable warming trends and drastically lower crop yields. Furthermore, there is an emerging reliance on agrochemicals. Stress is responsible for physiological transformations such as the formation of reactive oxygen, stomatal opening and closure, cytosolic calcium ion concentrations, metabolite profiles and their dynamic changes, expression of stress-responsive genes, activation of potassium channels, etc. Research regarding abiotic stresses is lacking because defense feedbacks to abiotic factors necessitate regulating the changes that activate multiple genes and pathways that are not properly explored. It is clear from the involvement of these genes that plant stress response and adaptation are complicated processes. Targeting the multigenicity of plant abiotic stress responses caused by genomic sequences, transcripts, protein organization and interactions, stress-specific and cellular transcriptome collections, and mutant screens can be the first step in an integrative approach. Therefore, in this review, we focused on the genomes, proteomics, and metabolomics of tomatoes under abiotic stress.
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Xu Y, Wu M, Zhao D, Zheng J, Dai M, Li X, Li W, Zhang C, Sun B. Simulated Fermentation of Strong-Flavor Baijiu through Functional Microbial Combination to Realize the Stable Synthesis of Important Flavor Chemicals. Foods 2023; 12:foods12030644. [PMID: 36766173 PMCID: PMC9913964 DOI: 10.3390/foods12030644] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/19/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The solid-state fermentation of Baijiu is complicated by the co-fermentation of many microorganisms. The instability of the composition and abundance of the microorganisms in the fermentation process leads to fluctuations of product quality, which is one of the bottleneck problems faced by the Strong-flavor Baijiu industry. In this study, we established a combination of functional microorganisms for the stable fermentation of the main flavor compounds of Baijiu, including medium and long-chain fatty acid ethyl esters such as hexanoic acid, ethyl ester; butanoic acid, ethyl ester; octanoic acid, ethyl ester; acetic acid, ethyl ester; 9,12-octadecadienoic acid, ethyl ester; and decanoic acid, ethyl ester in the fermented grains. Our study investigated the effects of microbial combinations on the fermentation from three aspects: microbial composition, microbial interactions, and microbial association with flavor compounds. The results showed that the added functional microorganisms (Lactobacillus, Clostridium, Caproiciproducens, Saccharomyces, and Aspergillus) became the dominant species in the fermentation system and formed positive interactions with other microorganisms, while the negative interactions between microorganisms were significantly reduced in the fermentation systems that contained both Daqu and functional microorganisms. The redundancy analysis showed that the functional microorganisms (Lactobacillus, Saccharomyces, Clostridium, Cloacibacterium, Chaenothecopsis, Anaerosporobacter, and Sporolactobacillus) showed strong positive correlations with the main flavor compounds (hexanoic acid, ethyl ester; lactic acid, ethyl ester; butanoic acid, ethyl ester; acetic acid, ethyl ester; and octanoic acid, ethyl ester). These results indicated that it was feasible to produce Baijiu with a functional microbial combination, and that this could promote stable Baijiu production.
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Affiliation(s)
- Youqiang Xu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- Correspondence: (Y.X.); (X.L.)
| | - Mengqin Wu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Dong Zhao
- Wuliangye Yibin Co., Ltd., Yibin 644000, China
| | - Jia Zheng
- Wuliangye Yibin Co., Ltd., Yibin 644000, China
| | - Mengqi Dai
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Xiuting Li
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 102401, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University (BTBU), Beijing 100048, China
- Correspondence: (Y.X.); (X.L.)
| | - Weiwei Li
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Chengnan Zhang
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Baoguo Sun
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 102401, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University (BTBU), Beijing 100048, China
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Abstract
In natural product research, microbial metabolites have tremendous potential to provide new therapeutic agents since extremely diverse chemical structures can be found in the nearly infinite microbial population. Conventionally, these specialized metabolites are screened by single-strain cultures. However, owing to the lack of biotic and abiotic interactions in monocultures, the growth conditions are significantly different from those encountered in a natural environment and result in less diversity and the frequent re-isolation of known compounds. In the last decade, several methods have been developed to eventually understand the physiological conditions under which cryptic microbial genes are activated in an attempt to stimulate their biosynthesis and elicit the production of hitherto unexpressed chemical diversity. Among those, co-cultivation is one of the most efficient ways to induce silenced pathways, mimicking the competitive microbial environment for the production and holistic regulation of metabolites, and has become a golden methodology for metabolome expansion. It does not require previous knowledge of the signaling mechanism and genome nor any special equipment for cultivation and data interpretation. Several reviews have shown the potential of co-cultivation to produce new biologically active leads. However, only a few studies have detailed experimental, analytical, and microbiological strategies for efficiently inducing bioactive molecules by co-culture. Therefore, we reviewed studies applying co-culture to induce secondary metabolite pathways to provide insights into experimental variables compatible with high-throughput analytical procedures. Mixed-fermentation publications from 1978 to 2022 were assessed regarding types of co-culture set-ups, metabolic induction, and interaction effects.
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Akram S, Ahmed A, He P, He P, Liu Y, Wu Y, Munir S, He Y. Uniting the Role of Endophytic Fungi against Plant Pathogens and Their Interaction. J Fungi (Basel) 2023; 9. [PMID: 36675893 DOI: 10.3390/jof9010072] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/21/2022] [Accepted: 12/25/2022] [Indexed: 01/06/2023] Open
Abstract
Endophytic fungi are used as the most common microbial biological control agents (MBCAs) against phytopathogens and are ubiquitous in all plant parts. Most of the fungal species have roles against a variety of plant pathogens. Fungal endophytes provide different services to be used as pathogen control agents, using an important aspect in the form of enhanced plant growth and induced systemic resistance, produce a variety of antifungal secondary metabolites (lipopeptides, antibiotics and enzymes) through colonization, and compete with other pathogenic microorganisms for growth factors (space and nutrients). The purpose of this review is to highlight the biological control potential of fungal species with antifungal properties against different fungal plant pathogens. We focused on the introduction, biology, isolation, identification of endophytic fungi, and their antifungal activity against fungal plant pathogens. The endosymbionts have developed specific genes that exhibited endophytic behavior and demonstrated defensive responses against pathogens such as antibiosis, parasitism, lytic enzyme and competition, siderophore production, and indirect responses by induced systemic resistance (ISR) in the host plant. Finally, different microscopic detection techniques to study microbial interactions (endophytic and pathogenic fungal interactions) in host plants are briefly discussed.
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Sun B, Barnes AD. Editorial: Soil-root-microbe interactions promote soil and plant health. Front Microbiol 2023; 14:1155234. [PMID: 36950170 PMCID: PMC10025551 DOI: 10.3389/fmicb.2023.1155234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Affiliation(s)
- Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- *Correspondence: Bo Sun
| | - Andrew D. Barnes
- Te Aka Mātuatua - School of Science, University of Waikato, Hamilton, New Zealand
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Ge W, Ren Y, Dong C, Shao Q, Bai Y, He Z, Yao T, Zhang Y, Zhu G, Deshmukh SK, Han Y. New perspective: Symbiotic pattern and assembly mechanism of Cantharellus cibarius-associated bacteria. Front Microbiol 2023; 14:1074468. [PMID: 36876069 PMCID: PMC9978014 DOI: 10.3389/fmicb.2023.1074468] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Cantharellus cibarius, an ectomycorrhizal fungus belonging to the Basidiomycetes, has significant medicinal and edible value, economic importance, and ecological benefits. However, C. cibarius remains incapable of artificial cultivation, which is thought to be due to the presence of bacteria. Therefore, much research has focused on the relationship between C. cibarius and bacteria, but rare bacteria are frequently overlooked, and symbiotic pattern and assembly mechanism of the bacterial community associated with C. cibarius remain unknown. In this study, the assembly mechanism and driving factors of both abundant and rare bacterial communities of C. cibarius were revealed by the null model. The symbiotic pattern of the bacterial community was examined using a co-occurrence network. Metabolic functions and phenotypes of the abundant and rare bacteria were compared using METAGENassist2, and the impacts of abiotic variables on the diversity of abundant and rare bacteria were examined using partial least squares path modeling. In the fruiting body and mycosphere of C. cibarius, there was a higher proportion of specialist bacteria compared with generalist bacteria. Dispersal limitation dominated the assembly of abundant and rare bacterial communities in the fruiting body and mycosphere. However, pH, 1-octen-3-ol, and total phosphorus of the fruiting body were the main driving factors of bacterial community assembly in the fruiting body, while available nitrogen and total phosphorus of the soil affected the assembly process of the bacterial community in the mycosphere. Furthermore, bacterial co-occurrence patterns in the mycosphere may be more complex compared with those in the fruiting body. Unlike the specific potential functions of abundant bacteria, rare bacteria may provide supplementary or unique metabolic pathways (such as sulfite oxidizer and sulfur reducer) to enhance the ecological function of C. cibarius. Notably, while volatile organic compounds can reduce mycosphere bacterial diversity, they can increase fruiting body bacterial diversity. Findings from this study further, our understanding of C. cibarius-associated microbial ecology.
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Affiliation(s)
- Wei Ge
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Yulian Ren
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Chunbo Dong
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Qiuyu Shao
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Yanmin Bai
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Zhaoying He
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Ting Yao
- Analysis and Test Center, Huangshan University, Huangshan, China
| | - Yanwei Zhang
- School of Biological Sciences, Guizhou Education University, Guiyang, Guizhou, China
| | - Guosheng Zhu
- Guizhou Key Laboratory of Edible Fungi Breeding, Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Sunil Kumar Deshmukh
- TERI-Deakin Nano Biotechnology Centre, The Energy and Resources Institute, New Delhi, India
| | - Yanfeng Han
- Institute of Fungus Resources, Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
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22
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Sun R, Wang X, Alhaj Hamoud Y, Lu M, Shaghaleh H, Zhang W, Zhang C, Ma C. Dynamic variation of bacterial community assemblage and functional profiles during rice straw degradation. Front Microbiol 2023; 14:1173442. [PMID: 37125169 PMCID: PMC10140369 DOI: 10.3389/fmicb.2023.1173442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
Bacteria is one of the most important drivers of straw degradation. However, the changes in bacterial community assemblage and straw-decomposing profiles during straw decomposition are not well understood. Based on cultivation-dependent and independent technologies, this study revealed that the "common species" greatly contributed to the dynamic variation of bacterial community during straw decomposition. Twenty-three functional strains involved in straw decomposition were isolated, but only seven were detected in the high-throughput sequencing data. The straw decomposers, including the isolated strains and the agents determined by functional prediction, constituted only 0.024% (on average) of the total bacterial community. The ecological network showed that most of the identified decomposers were self-existent without associations with other species. These results showed that during straw composition, community assembly might be greatly determined by the majority, but straw decomposition functions might be largely determined by the minority and emphasized the importance of the rare species in community-specific functions.
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Affiliation(s)
- Ruibo Sun
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Research Centre of Phosphorus Efficient Utilization and Water Environment Protection Along the Yangtze River Economic Belt, College of Resources and Environment, Anhui Agricultural University, Hefei, China
- Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Ministry of Natural Resources, Hefei, China
| | - Xin Wang
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Research Centre of Phosphorus Efficient Utilization and Water Environment Protection Along the Yangtze River Economic Belt, College of Resources and Environment, Anhui Agricultural University, Hefei, China
- Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Ministry of Natural Resources, Hefei, China
| | | | - Mengxing Lu
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Research Centre of Phosphorus Efficient Utilization and Water Environment Protection Along the Yangtze River Economic Belt, College of Resources and Environment, Anhui Agricultural University, Hefei, China
- Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Ministry of Natural Resources, Hefei, China
| | - Hiba Shaghaleh
- College of Environment, Hohai University, Nanjing, China
| | - Wenjie Zhang
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Research Centre of Phosphorus Efficient Utilization and Water Environment Protection Along the Yangtze River Economic Belt, College of Resources and Environment, Anhui Agricultural University, Hefei, China
- Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Ministry of Natural Resources, Hefei, China
| | - Chaochun Zhang
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Research Centre of Phosphorus Efficient Utilization and Water Environment Protection Along the Yangtze River Economic Belt, College of Resources and Environment, Anhui Agricultural University, Hefei, China
- Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Ministry of Natural Resources, Hefei, China
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
- *Correspondence: Chaochun Zhang, ; Chao Ma,
| | - Chao Ma
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Research Centre of Phosphorus Efficient Utilization and Water Environment Protection Along the Yangtze River Economic Belt, College of Resources and Environment, Anhui Agricultural University, Hefei, China
- Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-restoration, Ministry of Natural Resources, Hefei, China
- *Correspondence: Chaochun Zhang, ; Chao Ma,
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23
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Borgonovi TF, Salgaço MK, Oliveira GLV, Carvalho LAL, Pinheiro DG, Todorov SD, Sivieri K, Casarotti SN, Penna ALB. Functional Fermented Milk with Fruit Pulp Modulates the In Vitro Intestinal Microbiota. Foods 2022; 11. [PMID: 36553855 DOI: 10.3390/foods11244113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The effect of putative probiotic fermented milk (FM) with buriti pulp (FMB) or passion fruit pulp (FMPF) or without fruit pulp (FMC) on the microbiota of healthy humans was evaluated. FM formulations were administered into a simulator of the human intestinal microbial ecosystem (SHIME®) to evaluate the viability of lactic acid bacteria (LAB), microbiota composition, presence of short-chain fatty acids (SCFA), and ammonium ions. The probiotic LAB viability in FM was affected by the addition of the fruit pulp. Phocaeicola was dominant in the FMPF and FMB samples; Bifidobacterium was related to FM formulations, while Alistipes was associated with FMPF and FMB, and Lactobacillus and Lacticaseibacillus were predominant in FMC. Trabulsiella was the central element in the FMC, while Mediterraneibacter was the central one in the FMPF and FMB networks. The FM formulations increased the acetic acid, and a remarkably high amount of propionic and butyric acids were detected in the FMB treatment. All FM formulations decreased the ammonium ions compared to the control; FMPF samples stood out for having lower amounts of ammonia. The probiotic FM with fruit pulp boosted the beneficial effects on the intestinal microbiota of healthy humans in addition to increasing SCFA in SHIME® and decreasing ammonium ions, which could be related to the presence of bioactive compounds.
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24
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Tan Y, Du H, Zhang H, Fang C, Jin G, Chen S, Wu Q, Zhang Y, Zhang M, Xu Y. Geographically Associated Fungus-Bacterium Interactions Contribute to the Formation of Geography-Dependent Flavor during High-Complexity Spontaneous Fermentation. Microbiol Spectr 2022; 10:e0184422. [PMID: 36135710 PMCID: PMC9603688 DOI: 10.1128/spectrum.01844-22] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 09/07/2022] [Indexed: 12/31/2022] Open
Abstract
Fermented foods often have attractive flavor characteristics to meet various human demands. An ever-challenging target is the production of fermented foods with equal flavor profiles outside the product's origin. However, the formation of geography-dependent flavor in high-complexity fermentations remains poorly understood. Here, taking Chinese liquor (baijiu) fermentation as an example, we collected 403 samples from 9 different locations in China across a latitude range of 27°N to 37°N. We revealed and validated the geography-dependent flavor formation patterns by using culture-independent (metabolomics, metagenomics, and metatranscriptomics) and culture-dependent tools. We found that the baijiu microbiomes along with their metabolites were flavor related and geography dependent. The geographical characteristics were determined mainly by 20 to 40 differentiated chemical markers in metabolites and the latitude-dependent fungal structure of the microbiome. About 48 to 156 core microbiota members out of 735 bacterial genera and 290 fungal genera contributed to the chemical markers. The contributions of both fungi and bacteria were greater than those from either bacteria or fungi alone. Representatively, we revealed that dynamic interdependent interactions between yeasts and Lactobacillus facilitated the metabolism of heterocyclic flavor chemicals such as 2-acetylpyrrole, 2,3,5-trimethylpyrazine, and 2-acetylfuran. Moreover, we found that the intraspecific genomic diversity and microbial structure were two biotic factors that contributed to dynamic microbiome assembly. Based on the assembly pattern, adjusting the composition and distribution of initial species was one option to regulate the formation of diverse flavor characteristics. Our study provided a rationale for developing a microbiome design to achieve a defined flavor goal. IMPORTANCE People consume many spontaneously fermented foods and beverages with different flavors on a daily basis. One crucial and hotly discussed question is how to reproduce fermented food flavor without geographical limitations to meet diverse human demands. The constantly enriched knowledge of the microbial contribution to fermented flavor offers valuable insights into flavor biotechnological development. However, we still have a poor understanding of what factors limit the reproduction of fermented flavor outside the product's origin in high-complexity spontaneous fermentations. Here, taking baijiu fermentation as an example, we revealed that geography-dependent flavor was contributed mainly by fungus-bacterium cooperative metabolism. The distinct initial microbial composition, distribution, and intraspecific genomic diversity limited reproducible microbial interactions and metabolism in different geographical areas. The abundant microbial resources and predicted fungus-bacterium interactions found in baijiu fermentation enable us to design a synthetic microbial community to reproduce desired flavor profiles in the future.
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Affiliation(s)
- Yuwei Tan
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
- Bioprocess Engineering, Wageningen University and Research, Wageningen, The Netherlands
| | - Hai Du
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Hongxia Zhang
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Chen Fang
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Guangyuan Jin
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Shuang Chen
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Qun Wu
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Menghui Zhang
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
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25
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Liu J, Huang TY, Liu G, Ye Y, Soteyome T, Seneviratne G, Xiao G, Xu Z, Kjellerup BV. Microbial Interaction between Lactiplantibacillus plantarum and Saccharomyces cerevisiae: Transcriptome Level Mechanism of Cell-Cell Antagonism. Microbiol Spectr 2022; 10:e0143322. [PMID: 35980205 PMCID: PMC9604076 DOI: 10.1128/spectrum.01433-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/27/2022] [Indexed: 02/05/2023] Open
Abstract
Lactiplantibacillus plantarum and Saccharomyces cerevisiae are frequently co-isolated in food, although playing different roles. This study aimed at investigating the microbial interaction between L. plantarum and S. cerevisiae, especially cell-cell direct interaction and their mechanism. Cell-cell and supernatant-cell coculture models were set up, with CFU counting, OD600 measurement, optical and atomic force microscopy performed to examine the growth and morphology of L. plantarum and S. cerevisiae cells. In cell-cell coculture model, L. plantarum cells inhibited S. cerevisiae growth (inhibition rate ~80%) with its own growth pattern unaffected. Cell-cell aggregation happened during coculture with surface roughness changed and partial S. cerevisiae cell lysis. Mature (24 h) L. plantarum cell-free culture supernatant showed inhibition (35%-75%) on S. cerevisiae growth independent of pH level, while supernatant from L. plantarum-S. cerevisiae coculture showed relatively stronger inhibition. Upon transcriptomics analysis, hypothesis on the mechanism of microbial interaction between L. plantarum and S. cerevisiae was demonstrated. When L. plantarum cell density reached threshold at 24 h, all genes in lamBDCA quorum sensing (QS) system was upregulated to potentially increase adhesion capability, leading to the aggregation to S. cerevisiae cell. The downregulation of whole basic physiological activity from DNA to RNA to protein, cell cycle, meiosis, and mitogen-activated protein kinase (MAPK) signaling pathways, as well as growth maintenance essential genes ari1, skg6, and kex2/gas1 might induce the decreased growth and proliferation rate and partial death of S. cerevisiae cells in coculture. IMPORTANCE L. plantarum and S. cerevisiae are frequently co-isolated in food, although playing different roles. The co-existence of L. plantarum and S. cerevisiae could result in variable effects, raising economic benefits and safety concerns in food industry. Previous research has reported the microbial interaction between L. plantarum and S. cerevisiae mainly rely on the signaling through extracellular metabolites. However, cell-cell aggregation has been observed with mechanism remain unknown. In the current study, the microbial interaction between L. plantarum and S. cerevisiae was investigated with emphasis on cell-cell direct interaction and further in-depth transcriptome level study showed the key role of lamBDCA quorum sensing system in L. plantarum. The results yield from this study demonstrated the antagonistic effect between L. plantarum and S. cerevisiae.
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Affiliation(s)
- Junyan Liu
- College of Light Industry and Food Science, Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, Academy of Contemporary Agricultural Engineering Innovations, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Key Laboratory of Green Processing and Intelligent Manufacturing of Lingnan Specialty Food, Ministry of Agriculture, Guangzhou, China
| | - Teng-Yi Huang
- Department of Laboratory Medicine, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Gongliang Liu
- College of Light Industry and Food Science, Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, Academy of Contemporary Agricultural Engineering Innovations, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Key Laboratory of Green Processing and Intelligent Manufacturing of Lingnan Specialty Food, Ministry of Agriculture, Guangzhou, China
| | - Yanrui Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Thanapop Soteyome
- Home Economics Technology, Rajamangala University of Technology Phra Nakhon, Bangkok, Thailand
| | | | - Gengsheng Xiao
- College of Light Industry and Food Science, Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, Academy of Contemporary Agricultural Engineering Innovations, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Key Laboratory of Green Processing and Intelligent Manufacturing of Lingnan Specialty Food, Ministry of Agriculture, Guangzhou, China
| | - Zhenbo Xu
- Home Economics Technology, Rajamangala University of Technology Phra Nakhon, Bangkok, Thailand
- National Institute of Fundamental Studies, Kandy, Sri Lanka
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou, China
- Research Institute for Food Nutrition and Human Health, Guangzhou, China
- Department of Civil and Environmental Engineering, University of Maryland, College Park, Maryland, USA
| | - Birthe V. Kjellerup
- Department of Civil and Environmental Engineering, University of Maryland, College Park, Maryland, USA
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26
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Xia M, Zhang X, Xiao Y, Sheng Q, Tu L, Chen F, Yan Y, Zheng Y, Wang M. Interaction of acetic acid bacteria and lactic acid bacteria in multispecies solid-state fermentation of traditional Chinese cereal vinegar. Front Microbiol 2022; 13:964855. [PMID: 36246224 PMCID: PMC9557190 DOI: 10.3389/fmicb.2022.964855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
The microbial community plays an important role on the solid-state fermentation (SSF) of Chinese cereal vinegar, where acetic acid bacteria (AAB) and lactic acid bacteria (LAB) are the dominant bacteria. In this study, the top-down (in situ) and bottom-up (in vitro) approaches were employed to reveal the interaction of AAB and LAB in SSF of Shanxi aged vinegar (SAV). The results of high-throughput sequencing indicates that Acetobacter pasteurianus and Lactobacillus helveticus are the predominant species of AAB and LAB, respectively, and they showed negative interrelationship during the fermentation. A. pasteurianus CGMCC 3089 and L. helveticus CGMCC 12062, both of which were isolated from fermentation of SAV, showed no nutritional competition when they were co-cultured in vitro. However, the growth and metabolism of L. helveticus CGMCC 12062 were inhibited during SSF due to the presence of A. pasteurianus CGMCC 3089, indicating an amensalism phenomenon between these two species. The transcriptomic results shows that there are 831 differentially expressed genes (|log2 (Fold Change)| > 1 and, p ≤ 0.05) in L. helveticus CGMCC 12062 under co-culture condition comparing to its mono-culture, which are mainly classified into Gene Ontology classification of molecular function, biological process, and cell composition. Of those 831 differentially expressed genes, 202 genes are up-regulated and 629 genes are down-regulated. The down-regulated genes were enriched in KEGG pathways of sugar, amino acid, purine, and pyrimidine metabolism. The transcriptomic results for A. pasteurianus CGMCC 3089 under co-culture condition reveals 529 differentially expressed genes with 393 up-regulated and 136 down-regulated, and the genes within KEGG pathways of sugar, amino acid, purine, and pyrimidine metabolism are up-regulated. Results indicate an amensalism relationship in co-culture of A. pasteurianus and L. helveticus. Therefore, this work gives a whole insight on the interaction between the predominant species in SSF of cereal vinegar from nutrient utilization, endogenous factors inhibition and the regulation of gene transcription.
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Affiliation(s)
- Menglei Xia
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xiaofeng Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yun Xiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Qing Sheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Linna Tu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Fusheng Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
| | - Yufeng Yan
- Shanxi Zilin Vinegar Industry Co., Ltd., Shanxi Province Key Laboratory of Vinegar Fermentation Science and Engineering, Taiyuan, China
| | - Yu Zheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China,*Correspondence: Yu Zheng, Min Wang,
| | - Min Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China,*Correspondence: Yu Zheng, Min Wang,
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27
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Kim D, Ito T, Hara A, Li Y, Kreth J, Koo H. Antagonistic interactions by a high H 2 O 2 -producing commensal streptococci modulate caries development by Streptococcus mutans. Mol Oral Microbiol 2022; 37:244-255. [PMID: 36156446 DOI: 10.1111/omi.12394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/06/2022] [Accepted: 09/18/2022] [Indexed: 11/29/2022]
Abstract
Dental caries (tooth-decay) is caused by biofilms harboring polymicrobial communities on teeth that leads to the onset of localized areas of enamel demineralization. Streptococcus mutans has been clinically associated with severe caries in childhood. Although commensal bacteria can combat S. mutans using self-generated antimicrobials such as hydrogen peroxide (H2 O2 ), constant sugar-rich diet consumption disrupts microbial homeostasis shifting towards cariogenic community. Recently, Streptococcus oralis subsp. tigurinus strain J22, an oral isolate, was identified as a uniquely potent H2 O2 producer. Here, we assess whether a high H2 O2 -producing commensal streptococci can modulate the spatial organization and virulence of S. mutans within biofilms. Using an experimental biofilm model, we find that the presence of S. oralis J22 can effectively inhibit the clustering, accumulation, and spatial organization of S. mutans on ex vivo human tooth surface, resulting in significant reduction of enamel demineralization. Notably, the generation of H2 O2 via pyruvate oxidase (SpxB) from S. oralis J22 is not repressed by sugars (a common repressor in other mitis group streptococci), resulting in enhanced inhibition of S. mutans growth (vs. S. gordonii). We further investigate its impact on biofilm virulence using an in vivo rodent caries model under sugar-rich diet. Co-infection of S. mutans with S. oralis results in reduced caries development compared to either species infected alone, whereas co-infection with S. gordonii has negligible effects, suggesting that the presence of an efficient, high H2 O2 -producer can disrupt S. mutans virulence. This work demonstrates that oral isolates with unusual high H2 O2 production may be capable of modulating biofilm cariogenicity in vivo. The findings also highlight the importance of bacterial antagonistic interactions within polymicrobial communities in health and in disease-causing state. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Dongyeop Kim
- Biofilm Research Laboratory, Department of Orthodontics, School of Dental Medicine, University of Pennsylvania.,Department of Preventive Dentistry, School of Dentistry, and Institute of Oral Bioscience, Jeonbuk National University
| | - Tatsuro Ito
- Biofilm Research Laboratory, Department of Orthodontics, School of Dental Medicine, University of Pennsylvania.,Department of Pediatric Dentistry, School of Dentistry at Matsudo, Nihon University
| | - Anderson Hara
- Department of Cariology, Operative Dentistry and Dental Public Health, Oral Health Research Institute, Indiana University School of Dentistry
| | - Yong Li
- Biofilm Research Laboratory, Department of Orthodontics, School of Dental Medicine, University of Pennsylvania
| | - Jens Kreth
- Departments of Restorative Dentistry and Molecular Microbiology & Immunology, Oregon Health & Science University
| | - Hyun Koo
- Biofilm Research Laboratory, Department of Orthodontics, School of Dental Medicine, University of Pennsylvania.,Divisions of Pediatric Dentistry & Community Oral Health, School of Dental Medicine, University of Pennsylvania.,Center for Innovation & Precision Dentistry, School of Dental Medicine, School of Engineering and Applied Sciences, University of Pennsylvania
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28
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Du S, Zhang Y, Shen JP, Hu HW, Zhang J, Shu C, He JZ. Alteration of Manure Antibiotic Resistance Genes via Soil Fauna Is Associated with the Intestinal Microbiome. mSystems 2022; 7:e0052922. [PMID: 35938729 DOI: 10.1128/msystems.00529-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Livestock wastes contain high levels of antibiotic resistance genes (ARGs) and a variety of human-related pathogens. Bioconversion of livestock manure using larvae of the beetle Protaetia brevitarsis is an effective technique for waste reduction and value creation; however, the fate of manure ARGs during gut passage and interaction with the gut microbiome of P. brevitarsis remains unclear. To investigate this, we fed P. brevitarsis with dry chicken manure for 6 days and measured bacterial community dynamics and ARG abundance and diversity along the P. brevitarsis gut tract using high-throughput quantitative PCR and metagenomics approaches. The diversity of ARGs was significantly lower in larval midgut, hindgut, and frass than in raw chicken manure, and around 80% of pathogenicity-related genes (PRGs) exhibited reduced abundance. Network analysis demonstrated that Bacteroidetes and Firmicutes were the key bacterial phyla associated with ARG reduction. Metagenomic analysis further indicated that ARGs, mobile genetic elements (MGEs), and PRGs were simultaneously attenuated in the hindgut, implicating a decreased likelihood for horizontal gene transfer (HGT) of ARGs among bacteria and pathogens during manure bioconversion. Our findings demonstrated that the attenuation of ARGs is strongly associated with the variation of the gut microbiome of P. brevitarsis, providing insights into mechanisms of risk mitigation of ARG dissemination during manure bioconversion. IMPORTANCE Saprophagous fauna like the oriental edible beetle (P. brevitarsis) plays a fundamental role in converting organic wastes into biofertilizer. Accumulating evidence has shown that soil fauna can reduce the abundance of ARGs, although the underlying mechanism of ARG reduction is still unclear. In our previous research, we found a large reduction of ARGs in vegetable roots and leaves from frass compared with raw manure, providing a promising biofertilizer for soil-vegetable systems. Therefore, in this study, temporal dynamic changes in the microbiomes of the donor (chicken manure) and host (P. brevitarsis) were investigated, and we found a close association between the gut microbiome and the alteration of ARGs. These results shed new light on how the insect gut microbiome can mitigate manure-borne ARGs and provide insights into the bioconversion process via a typical member of the saprophagous fauna, P. brevitarsis.
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Abstract
Chinese baijiu brewing is an open, complex, and synergetic functional microbiota fermentation process. Microbial interaction is pivotal for the regulation of microbial structure and function in the brewing microecosystem, consequently affecting the flavor and quality of baijiu. This article mainly summarizes the effect of microbial interactions among functional microbiota on the growth performance, flavor formation, and safe quality of baijiu fermentation process. In addition, the review specifically emphasizes on the microbial interactions for the regulation of “Ethyl Caproate-Increasing and Ethyl Lactate-Decreasing” in Chinese strong-flavor baijiu. Furthermore, the construction of synthetic microbiota by metabolic characteristics of the functional microbes and their interactions for regulating and controlling flavor quality of Chinese baijiu is also reviewed and prospected.
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Affiliation(s)
- Lei Gao
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Jian Zhou
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China.,Engineering Research Center of Biomass Materials, Ministry of Education, Southwest University of Science and Technology, Mianyang, China
| | - Guiqiang He
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China.,Engineering Research Center of Biomass Materials, Ministry of Education, Southwest University of Science and Technology, Mianyang, China
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Wang Y, Cheng X, Wang H, Zhou J, Liu X, Tuovinen OH. The Characterization of Microbiome and Interactions on Weathered Rocks in a Subsurface Karst Cave, Central China. Front Microbiol 2022; 13:909494. [PMID: 35847118 PMCID: PMC9277220 DOI: 10.3389/fmicb.2022.909494] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Karst caves are a natural oligotrophic subsurface biosphere widely distributed in southern China. Despite the progress in bacterial and fungal diversity, the knowledge about interactions between bacteria, fungi, and minerals is still limited in caves. Hence, for the first time, we investigated the interaction between bacteria and fungi living on weathered rocks in the Heshang Cave via high-throughput sequencing of 16S rRNA and ITS1 genes, and co-occurrence analysis. The mineral compositions of weathered rocks were analyzed by X-ray diffraction. Bacterial communities were dominated by Actinobacteria (33.68%), followed by Alphaproteobacteria (8.78%), and Planctomycetia (8.73%). In contrast, fungal communities were dominated by Sordariomycetes (21.08%) and Dothideomycetes (14.06%). Mineral substrata, particularly phosphorus-bearing minerals, significantly impacted bacterial (hydroxyapatite) and fungal (fluorapatite) communities as indicated by the redundancy analysis. In comparison with fungi, the development of bacterial communities was more controlled by the environmental selection indicated by the overwhelming contribution of deterministic processes. Co-occurrence network analysis showed that all nodes were positively linked, indicating ubiquitous cooperation within bacterial groups and fungal groups, as well as between bacteria and fungi under oligotrophic conditions in the subsurface biosphere. In total, 19 bacterial ASVs and 34 fungal OTUs were identified as keystone taxa, suggesting the fundamental role of fungi in maintaining the microbial ecosystem on weathered rocks. Ascomycota was most dominant in keystone taxa, accounting for 26.42%, followed by Actinobacteria in bacteria (24.53%). Collectively, our results confirmed the highly diverse bacterial and fungal communities on weathered rocks, and their close cooperation to sustain the subsurface ecosystem. Phosphorus-bearing minerals were of significance in shaping epipetreous bacterial and fungal communities. These observations provide new knowledge about microbial interactions between bacteria, fungi, and minerals in the subterranean biosphere.
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Affiliation(s)
- Yiheng Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaoyu Cheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Jianping Zhou
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaoyan Liu
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Olli H Tuovinen
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
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Sun H, Chai LJ, Fang GY, Lu ZM, Zhang XJ, Wang ST, Shen CH, Shi JS, Xu ZH. Metabolite-Based Mutualistic Interaction between Two Novel Clostridial Species from Pit Mud Enhances Butyrate and Caproate Production. Appl Environ Microbiol 2022; 88:e0048422. [PMID: 35695571 DOI: 10.1128/aem.00484-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Pit mud microbial consortia play crucial roles in the formation of Chinese strong-flavor baijiu's key flavor-active compounds, especially butyric and caproic acids. Clostridia, one of the abundant bacterial groups in pit mud, were recognized as important butyric and caproic acid producers. Research on the interactions of the pit mud microbial community mainly depends on correlation analysis at present. Interaction between Clostridium and other microorganisms and its involvement in short/medium-chain fatty acid (S/MCFA) metabolism are still unclear. We previously found coculture of two clostridial strains isolated from pit mud, Clostridium fermenticellae JN500901 (C.901) and Novisyntrophococcus fermenticellae JN500902 (N.902), could enhance S/MCFA accumulation. Here, we investigated their underlying interaction mechanism through the combined analysis of phenotype, genome, and transcriptome. Compared to monocultures, coculture of C.901 and N.902 obviously promoted their growth, including shortening the growth lag phase and increasing biomass, and the accumulation of butyric acid and caproic acid. The slight effects of inoculation ratio and continuous passage on the growth and metabolism of coculture indicated the relative stability of their interaction. Transwell coculture and transcriptome analysis showed the interaction between C.901 and N.902 was accomplished by metabolite exchange, i.e., formic acid produced by C.901 activated the Wood-Ljungdahl pathway of N.902, thereby enhancing its production of acetic acid, which was further converted to butyric acid and caproic acid by C.901 through reverse β-oxidation. This work demonstrates the potential roles of mutually beneficial interspecies interactions in the accumulation of key flavor compounds in pit mud. IMPORTANCE Microbial interactions played crucial roles in influencing the assembly, stability, and function of the microbial community. The metabolites of pit mud microbiota are the key to flavor formation of Chinese strong-flavor baijiu. So far, researches on the interactions of the pit mud microbial community have been mainly based on the correlation analysis of sequencing data, and more work needs to be performed to unveil the complicated interaction patterns. Here, we identified a material exchange-based mutualistic interaction system involving two fatty acid-producing clostridial strains (Clostridium fermenticellae JN500901 and Novisyntrophococcus fermenticellae JN500902) isolated from pit mud and systematically elucidated their interaction mechanism for promoting the production of butyric acid and caproic acid, the key flavor-active compounds of baijiu. Our findings provide a new perspective for understanding the complicated interactions of pit mud microorganisms.
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Yao S, Hao L, Zhou R, Jin Y, Huang J, Wu C. Multispecies biofilms in fermentation: Biofilm formation, microbial interactions, and communication. Compr Rev Food Sci Food Saf 2022; 21:3346-3375. [PMID: 35762651 DOI: 10.1111/1541-4337.12991] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 05/07/2022] [Accepted: 05/15/2022] [Indexed: 02/05/2023]
Abstract
Food fermentation is driven by microorganisms, which usually coexist as multispecies biofilms. The activities and interactions of functional microorganisms and pathogenic bacteria in biofilms have important implications for the quality and safety of fermented foods. It was verified that the biofilm lifestyle benefited the fitness of microorganisms in harsh environments and intensified the cooperation and competition between biofilm members. This review focuses on multispecies biofilm formation, microbial interactions and communication in biofilms, and the application of multispecies biofilms in food fermentation. Microbial aggregation and adhesion are important steps in the early stage of multispecies biofilm formation. Different biofilm-forming abilities and strategies among microorganisms lead to several types of multispecies biofilm formation. The spatial distribution of multispecies biofilms reflects microbial interactions and biofilm function. Then, we discuss the intrinsic factors and external manifestations of multispecies biofilm system succession. Several typical interspecies cooperation and competition modes and mechanisms of microbial communication were reviewed in this review. The main limitations of the studies included in this review are the relatively small number of studies of biofilms formed by functional microorganisms during fermentation and the lack of direct evidence for the formation process of multispecies biofilms and microbial interactions and communication within biofilms. This review aims to provide the food industry with a sufficient understanding of multispecies biofilms in food fermentation. Practical Application: Meanwhile, it offers a reference value for better controlling and utilizing biofilms during food fermentation process, and the improvement of the yield, quality, and safety of fermented products including Chinese Baijiu, cheeese,kefir, soy sauce, kombucha, and fermented olive.
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Affiliation(s)
- Shangjie Yao
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Liying Hao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Rongqing Zhou
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Yao Jin
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Jun Huang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Chongde Wu
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
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Wang P, Tong X, Zhang N, Miao T, Chan JPT, Huang H, Lee PKH, Li Y. Fomite Transmission Follows Invasion Ecology Principles. mSystems 2022;:e0021122. [PMID: 35502902 DOI: 10.1128/msystems.00211-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The invasion ecology principles illustrated in many ecosystems have not yet been explored in the context of fomite transmission. We hypothesized that invaders in fomite transmission are trackable, are neutrally distributed between hands and environmental surfaces, and exhibit a proximity effect. To test this hypothesis, a surrogate invader, Lactobacillus delbrueckii subsp. bulgaricus, was spread by a root carrier in an office housing more than 20 participants undertaking normal activities, and the microbiotas on skin and environmental surfaces were analyzed before and after invasion. First, we found that the invader was trackable. Its identity and emission source could be determined using microbial-interaction networks, and the root carrier could be identified using a rank analysis. Without prior information, L. bulgaricus could be identified as the invader emitted from a source that exclusively contained the invader, and the probable root carrier could be located. In addition to the single-taxon invasion by L. bulgaricus, multiple-taxon invasion was observed, as genera from sputum/saliva exhibited co-occurrence relationships on skin and environmental surfaces. Second, the invader had a below-neutral distribution in a neutral community model, suggesting that hands accrued heavier invader contamination than environmental surfaces. Third, a proximity effect was observed on a surface touch network. Invader contamination on surfaces decreased with increasing geodesic distance from the hands of the carrier, indicating that the carrier’s touching behaviors were the main driver of fomite transmission. Taken together, these results demonstrate the invasion ecology principles in fomite transmission and provide a general basis for the management of ecological fomite transmission. IMPORTANCE Fomite transmission contributes to the spread of many infectious diseases. However, pathogens in fomite transmission typically are either investigated individually without considering the context of native microbiotas or investigated in a nondiscriminatory way from the dispersal of microbiotas. In this study, we adopted an invasion ecology framework in which we considered pathogens as invaders, the surface environment as an ecosystem, and human behaviors as the driver of microbial dispersal. With this approach, we assessed the ability of quantitative ecological theories to track and forecast pathogen movements in fomite transmission. By uncovering the relationships between the invader and native microbiotas and between human behaviors and invader/microbiota dispersal, we demonstrated that fomite transmission follows idiosyncratic invasion ecology principles. Our findings suggest that attempts to manage fomite transmission for public health purposes should focus on the microbial communities and anthropogenic factors involved, in addition to the pathogens.
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Chen J, Song D, Liu D, Sun J, Wang X, Zhou W, Liang G. Soil Aggregation Shaped the Distribution and Interaction of Bacterial-Fungal Community Based on a 38-Year Fertilization Experiment in China. Front Microbiol 2022; 13:824681. [PMID: 35391728 PMCID: PMC8981921 DOI: 10.3389/fmicb.2022.824681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/14/2022] [Indexed: 12/13/2022] Open
Abstract
Soil aggregates provide different ecological niches for microorganisms, and in turn, the microbial interactions affect soil aggregation process. The response of the microbial community in bulk soil to different fertilization regimes has been well studied; however, the co-occurrence patterns of bacteria and fungi in different aggregates under various fertilization regimes remain unclear. Based on the long-term field experiment, we found that fertilization regimes contributed more to fungal than to bacterial community composition. Long-term fertilization decreased microbial interactions in large macroaggregates (LM), macroaggregates (MA) and silt and clay (SC) fractions, but increased in microaggregates (MI). The application of manure with inorganic fertilizers (NPKM) significantly increased the intensive cooperation between bacteria and fungi in LM and MA. Microbial communities in LM and MA were well separated and showed strong competition against microbes in MI and SC; hence, we concluded that the microbial habitat could be divided into two groups, large fractions (LM and MA) and small fractions (MI and SC). The bacterial genera Anaerolinea, Nocardioides, Ohtaekwangia, Geoalkalibacter, Lysobacter, Pedomicrobium, and Flavisolibacter were keystone taxa in inorganic fertilization, and Roseiflexus, Nitrospira, and Blastocatella were keystone taxa in NPKM, which were all sensitive to soil aggregation. In this study, we demonstrated that the NPKM decreased the microbial interactions within and between kingdoms in LM, MA, and SC, but enhanced nutrient availability and microbial interactions in MI, leading to the formation of biofilms and the strengthening of stress tolerance, which finally stimulated the formation and stabilization of soil aggregates. Thus, this study revealed how soil microbial competition or cooperation responded to different fertilization regimes at aggregate scales, and provided evidence for the stimulation of soil stability.
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Affiliation(s)
- Jie Chen
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilizer, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dali Song
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilizer, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Donghai Liu
- Institute of Plant Protection and Soil Fertility, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Jingwen Sun
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilizer, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiubin Wang
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilizer, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Zhou
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilizer, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guoqing Liang
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilizer, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
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35
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Glaser K, Albrecht M, Baumann K, Overmann J, Sikorski J. Biological Soil Crust From Mesic Forests Promote a Specific Bacteria Community. Front Microbiol 2022; 13:769767. [PMID: 35369523 PMCID: PMC8966483 DOI: 10.3389/fmicb.2022.769767] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/19/2022] [Indexed: 12/03/2022] Open
Abstract
Biological soil crusts (biocrusts) harbor a diverse community of various microorganisms with microalgae as primary producers and bacteria living in close association. In mesic regions, biocrusts emerge rapidly on disturbed surface soil in forest, typically after clear-cut or windfall. It is unclear whether the bacterial community in biocrusts is similar to the community of the surrounding soil or if biocrust formation promotes a specific bacterial community. Also, many of the interactions between bacteria and algae in biocrusts are largely unknown. Through high-throughput-sequencing analysis of the bacterial community composition, correlated drivers, and the interpretation of biological interactions in a biocrust of a forest ecosystem, we show that the bacterial community in the biocrust represents a subset of the community of the neighboring soil. Bacterial families connected with degradation of large carbon molecules, like cellulose and chitin, and the bacterivore Bdellovibrio were more abundant in the biocrust compared to bulk soil. This points to a closer interaction and nutrient recycling in the biocrust compared to bulk soil. Furthermore, the bacterial richness was positively correlated with the content of mucilage producing algae. The bacteria likely profit from the mucilage sheaths of the algae, either as a carbon source or protectant from grazing or desiccation. Comparative sequence analyses revealed pronounced differences between the biocrust bacterial microbiome. It seems that the bacterial community of the biocrust is recruited from the local soil, resulting in specific bacterial communities in different geographic regions.
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Affiliation(s)
- Karin Glaser
- Applied Ecology and Phycology, Institute for Biological Sciences, University of Rostock, Rostock, Germany
| | - Martin Albrecht
- Applied Ecology and Phycology, Institute for Biological Sciences, University of Rostock, Rostock, Germany
| | - Karen Baumann
- Department of Soil Science, Faculty of Agricultural and Environmental Science, University of Rostock, Rostock, Germany
| | - Jörg Overmann
- Department of Microbiology, Faculty of Life Sciences, Technische Universität Braunschweig, Braunschweig, Germany
| | - Johannes Sikorski
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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36
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Zhao Y, Chen L, Chen L, Huang J, Chen S, Yu Z. Exploration of the Potential Relationship Between Gut Microbiota Remodeling Under the Influence of High-Protein Diet and Crohn's Disease. Front Microbiol 2022; 13:831176. [PMID: 35308389 PMCID: PMC8927681 DOI: 10.3389/fmicb.2022.831176] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/07/2022] [Indexed: 12/20/2022] Open
Abstract
Diet and gut microbiota are both important factors in the pathogenesis of Crohn’s disease, and changes in diet can lead to alteration in gut microbiome. However, there is still insufficient exploration on interaction within the gut microbiota under high-protein diet (HPD) intervention. We analyzed the gut microbial network and marker taxa from patients with Crohn’s disease in public database (GMrepo, https://gmrepo.humangut.info) combined with investigation of the changes of composition and function of intestinal microbiome in mice fed on HPD by metagenomic sequencing. The results showed that there was an indirect negative correlation between Escherichia coli and Lachnospiraceae in patients with Crohn’s disease, and Escherichia coli was a marker for both Crohn’s disease and HPD intervention. Besides, enriched HH_1414 (one of the orthologs in eggNOG) related to tryptophan metabolism was from Helicobacter, whereas reduced orthologs (OGs) mainly contributed by Lachnospiraceae after HPD intervention. Our research indicates that some compositional changes in gut microbiota after HPD intervention are consistent with those in patients with Crohn’s disease, providing insights into potential impact of altered gut microbes under HPD on Crohn’s disease.
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Affiliation(s)
- Yiming Zhao
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Lulu Chen
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Liyu Chen
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Jing Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, China
| | - Shuijiao Chen
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zheng Yu
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
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Edgcomb VP, Teske AP, Mara P. Microbial Hydrocarbon Degradation in Guaymas Basin-Exploring the Roles and Potential Interactions of Fungi and Sulfate-Reducing Bacteria. Front Microbiol 2022; 13:831828. [PMID: 35356530 PMCID: PMC8959706 DOI: 10.3389/fmicb.2022.831828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
Hydrocarbons are degraded by specialized types of bacteria, archaea, and fungi. Their occurrence in marine hydrocarbon seeps and sediments prompted a study of their role and their potential interactions, using the hydrocarbon-rich hydrothermal sediments of Guaymas Basin in the Gulf of California as a model system. This sedimented vent site is characterized by localized hydrothermal circulation that introduces seawater sulfate into methane- and hydrocarbon-rich sediments, and thus selects for diverse hydrocarbon-degrading communities of which methane, alkane- and aromatics-oxidizing sulfate-reducing bacteria and archaea have been especially well-studied. Current molecular and cultivation surveys are detecting diverse fungi in Guaymas Basin hydrothermal sediments, and draw attention to possible fungal-bacterial interactions. In this Hypothesis and Theory article, we report on background, recent results and outcomes, and underlying hypotheses that guide current experiments on this topic in the Edgcomb and Teske labs in 2021, and that we will revisit during our ongoing investigations of bacterial, archaeal, and fungal communities in the deep sedimentary subsurface of Guaymas Basin.
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Affiliation(s)
| | - Andreas P. Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Paraskevi Mara
- Woods Hole Oceanographic Institution, Woods Hole, MA, United States
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38
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Ji M, Kong W, Jia H, Ding C, Anesio AM, Wang Y, Zhu YG. Similar heterotrophic communities but distinct interactions supported by red and green-snow algae in the Antarctic Peninsula. New Phytol 2022; 233:1358-1368. [PMID: 34606623 DOI: 10.1111/nph.17764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Snow algae are predicted to expand in polar regions due to climate warming, which can accelerate snowmelt by reducing albedo. Green snow frequently occurs near penguin colonies, and red snow distributes widely along ocean shores. However, the mechanisms underpinning the assemblage of algae and heterotrophs in colored snow remain poorly characterized. We investigated algal, bacterial, and fungal communities and their interactions in red and green snows in the Antarctic Peninsula using a high-throughput sequencing method. We found distinct algal community structure in red and green snows, and the relative abundance of dominant taxa varied, potentially due to nutrient status differences. Contrastingly, red and green snows exhibited similar heterotrophic communities (bacteria and fungi), whereas the relative abundance of fungal pathogens was substantially higher in red snow by 3.8-fold. Red snow exhibited a higher network complexity, indicated by a higher number of nodes and edges. Red snow exhibited a higher proportion of negative correlations among heterotrophs (62.2% vs 3.4%) and stronger network stability, suggesting the red-snow network is more resistant to external disturbance. Our study revealed that the red snow microbiome exhibits a more stable microbial network than the green snow microbiome.
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Affiliation(s)
- Mukan Ji
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Weidong Kong
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hongzeng Jia
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Chen Ding
- The Association of Science Education Promotion of China, Beijing, 100083, China
| | - Alexandre M Anesio
- Department of Environmental Science, Aarhus University, Roskilde, DK-4000, Denmark
| | - Yanfen Wang
- University of Chinese Academy of Sciences, Beijing, 100039, China
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Reginal Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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39
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Wang Y, Zhang C, Liu F, Jin Z, Xia X. Ecological succession and functional characteristics of lactic acid bacteria in traditional fermented foods. Crit Rev Food Sci Nutr 2022; 63:5841-5855. [PMID: 35014569 DOI: 10.1080/10408398.2021.2025035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fermented foods are important parts of traditional food culture with a long history worldwide. Abundant nutritional materials and open fermentation contribute to the diversity of microorganisms, resulting in unique product quality and flavor. Lactic acid bacteria (LAB), as important part of traditional fermented foods, play a decisive role in the quality and safety of fermented foods. Reproduction and metabolic of microorganisms drive the food fermentation, and microbial interaction plays a major role in the fermentation process. Nowadays, LAB have attracted considerable interest due to their potentialities to add functional properties to certain foods or as supplements along with the research of gut microbiome. This review focuses on the characteristics of diversity and variability of LAB in traditional fermented foods, and describes the principal mechanisms involved in the flavor formation dominated by LAB. Moreover, microbial interactions and their mechanisms in fermented foods are presented. They provide a theoretical basis for exploiting LAB in fermented foods and improving the quality of traditional fermented foods. The traditional fermented food industry should face the challenge of equipment automation, green manufacturing, and quality control and safety in the production.
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Affiliation(s)
- Yingyu Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, China
| | - Chenhao Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, China
| | | | - Zhengyu Jin
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, WuXi, China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, China
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40
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Khan I, Bai Y, Zha L, Ullah N, Ullah H, Shah SRH, Sun H, Zhang C. Mechanism of the Gut Microbiota Colonization Resistance and Enteric Pathogen Infection. Front Cell Infect Microbiol 2022; 11:716299. [PMID: 35004340 PMCID: PMC8733563 DOI: 10.3389/fcimb.2021.716299] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/26/2021] [Indexed: 12/26/2022] Open
Abstract
The mammalian gut microbial community, known as the gut microbiota, comprises trillions of bacteria, which co-evolved with the host and has an important role in a variety of host functions that include nutrient acquisition, metabolism, and immunity development, and more importantly, it plays a critical role in the protection of the host from enteric infections associated with exogenous pathogens or indigenous pathobiont outgrowth that may result from healthy gut microbial community disruption. Microbiota evolves complex mechanisms to restrain pathogen growth, which included nutrient competition, competitive metabolic interactions, niche exclusion, and induction of host immune response, which are collectively termed colonization resistance. On the other hand, pathogens have also developed counterstrategies to expand their population and enhance their virulence to cope with the gut microbiota colonization resistance and cause infection. This review summarizes the available literature on the complex relationship occurring between the intestinal microbiota and enteric pathogens, describing how the gut microbiota can mediate colonization resistance against bacterial enteric infections and how bacterial enteropathogens can overcome this resistance as well as how the understanding of this complex interaction can inform future therapies against infectious diseases.
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Affiliation(s)
- Israr Khan
- School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Functional Genomics and Molecular Diagnosis, Lanzhou University, Lanzhou, China.,Cuiying Biomedical Research Centre, Lanzhou University Second Hospital, Lanzhou, China
| | - Yanrui Bai
- School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Functional Genomics and Molecular Diagnosis, Lanzhou University, Lanzhou, China.,Cuiying Biomedical Research Centre, Lanzhou University Second Hospital, Lanzhou, China
| | - Lajia Zha
- School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Functional Genomics and Molecular Diagnosis, Lanzhou University, Lanzhou, China.,Cuiying Biomedical Research Centre, Lanzhou University Second Hospital, Lanzhou, China
| | - Naeem Ullah
- School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China
| | - Habib Ullah
- School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China.,Cuiying Biomedical Research Centre, Lanzhou University Second Hospital, Lanzhou, China
| | - Syed Rafiq Hussain Shah
- Department of Microecology, School of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Hui Sun
- Cuiying Biomedical Research Centre, Lanzhou University Second Hospital, Lanzhou, China
| | - Chunjiang Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China.,Gansu Key Laboratory of Functional Genomics and Molecular Diagnosis, Lanzhou University, Lanzhou, China
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Andrić S, Meyer T, Rigolet A, Prigent-Combaret C, Höfte M, Balleux G, Steels S, Hoff G, De Mot R, McCann A, De Pauw E, Argüelles Arias A, Ongena M. Lipopeptide Interplay Mediates Molecular Interactions between Soil Bacilli and Pseudomonads. Microbiol Spectr 2021; 9:e0203821. [PMID: 34878336 DOI: 10.1128/spectrum.02038-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Some Bacillus species, such as B. velezensis, are important members of the plant-associated microbiome, conferring protection against phytopathogens. However, our knowledge about multitrophic interactions determining the ecological fitness of these biocontrol bacteria in the competitive rhizosphere niche is still limited. Here, we investigated molecular mechanisms underlying interactions between B. velezensis and Pseudomonas as a soil-dwelling competitor. Upon their contact-independent in vitro confrontation, a multifaceted macroscopic outcome was observed and characterized by Bacillus growth inhibition, white line formation in the interaction zone, and enhanced motility. We correlated these phenotypes with the production of bioactive secondary metabolites and identified specific lipopeptides as key compounds involved in the interference interaction and motile response. Bacillus mobilizes its lipopeptide surfactin not only to enhance motility but also to act as a chemical trap to reduce the toxicity of lipopeptides formed by Pseudomonas. We demonstrated the relevance of these unsuspected roles of lipopeptides in the context of competitive tomato root colonization by the two bacterial genera. IMPORTANCE Plant-associated Bacillus velezensis and Pseudomonas spp. represent excellent model species as strong producers of bioactive metabolites involved in phytopathogen inhibition and the elicitation of plant immunity. However, the ecological role of these metabolites during microbial interspecies interactions and the way their expression may be modulated under naturally competitive soil conditions has been poorly investigated. Through this work, we report various phenotypic outcomes from the interactions between B. velezensis and 10 Pseudomonas strains used as competitors and correlate them with the production of specific metabolites called lipopeptides from both species. More precisely, Bacillus overproduces surfactin to enhance motility, which also, by acting as a chemical trap, reduces the toxicity of other lipopeptides formed by Pseudomonas. Based on data from interspecies competition on plant roots, we assume this would allow Bacillus to gain fitness and persistence in its natural rhizosphere niche. The discovery of new ecological functions for Bacillus and Pseudomonas secondary metabolites is crucial to rationally design compatible consortia, more efficient than single-species inoculants, to promote plant health and growth by fighting economically important pathogens in sustainable agriculture.
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Kosina SM, Rademacher P, Wetmore KM, de Raad M, Zemla M, Zane GM, Zulovich JJ, Chakraborty R, Bowen BP, Wall JD, Auer M, Arkin AP, Deutschbauer AM, Northen TR. Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms. Front Microbiol 2021; 12:757856. [PMID: 34956122 PMCID: PMC8696352 DOI: 10.3389/fmicb.2021.757856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing Pseudomonas stutzeri have been used for bioremediation, biocontrol, aquaculture management and wastewater denitrification. Furthermore, the use of P. stutzeri biofilms, in combination with consortia-based approaches, may offer advantages for these processes. Understanding the interspecific interaction within biofilm co-cultures or consortia provides a means for improvement of current technologies. However, the investigation of biofilm-based consortia has been limited. We present an adaptable and scalable method for the analysis of macroscopic interactions (colony morphology, inhibition, and invasion) between colony-forming bacterial strains using an automated printing method followed by analysis of the genes and metabolites involved in the interactions. Using Biofilm Interaction Mapping and Analysis (BIMA), these interactions were investigated between P. stutzeri strain RCH2, a denitrifier isolated from chromium (VI) contaminated soil, and 13 other species of pseudomonas isolated from non-contaminated soil. One interaction partner, Pseudomonas fluorescens N1B4 was selected for mutant fitness profiling of a DNA-barcoded mutant library; with this approach four genes of importance were identified and the effects on interactions were evaluated with deletion mutants and mass spectrometry based metabolomics.
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Affiliation(s)
- Suzanne M. Kosina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Peter Rademacher
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kelly M. Wetmore
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Markus de Raad
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcin Zemla
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | | | - Romy Chakraborty
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Benjamin P. Bowen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United States
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Manfred Auer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Trent R. Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United States
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Krespach MKC, Stroe MC, Flak M, Komor AJ, Nietzsche S, Sasso S, Hertweck C, Brakhage AA. Bacterial marginolactones trigger formation of algal gloeocapsoids, protective aggregates on the verge of multicellularity. Proc Natl Acad Sci U S A 2021; 118:e2100892118. [PMID: 34740967 DOI: 10.1073/pnas.2100892118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 12/17/2022] Open
Abstract
Photosynthetic microorganisms including the green alga Chlamydomonas reinhardtii are essential to terrestrial habitats as they start the carbon cycle by conversion of CO2 to energy-rich organic carbohydrates. Terrestrial habitats are densely populated, and hence, microbial interactions mediated by natural products are inevitable. We previously discovered such an interaction between Streptomyces iranensis releasing the marginolactone azalomycin F in the presence of C. reinhardtii Whether the alga senses and reacts to azalomycin F remained unknown. Here, we report that sublethal concentrations of azalomycin F trigger the formation of a protective multicellular structure by C. reinhardtii, which we named gloeocapsoid. Gloeocapsoids contain several cells which share multiple cell membranes and cell walls and are surrounded by a spacious matrix consisting of acidic polysaccharides. After azalomycin F removal, gloeocapsoid aggregates readily disassemble, and single cells are released. The presence of marginolactone biosynthesis gene clusters in numerous streptomycetes, their ubiquity in soil, and our observation that other marginolactones such as desertomycin A and monazomycin also trigger the formation of gloeocapsoids suggests a cross-kingdom competition with ecological relevance. Furthermore, gloeocapsoids allow for the survival of C. reinhardtii at alkaline pH and otherwise lethal concentrations of azalomycin F. Their structure and polysaccharide matrix may be ancestral to the complex mucilage formed by multicellular members of the Chlamydomonadales such as Eudorina and Volvox Our finding suggests that multicellularity may have evolved to endure the presence of harmful competing bacteria. Additionally, it underlines the importance of natural products as microbial cues, which initiate interesting ecological scenarios of attack and counter defense.
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Zhang Y, He Y, Sakowski EG, Preheim SP. Influence of Simplified Microbial Community Biofilms on Bacterial Retention in Porous Media under Conditions of Stormwater Biofiltration. Microbiol Spectr 2021; 9:e0110521. [PMID: 34704792 DOI: 10.1128/Spectrum.01105-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Porous media filters are used widely to remove bacteria from contaminated water, such as stormwater runoff. Biofilms that colonize filter media during normal function can significantly alter performance, but it is not clear how characteristics of individual populations colonizing porous media combine to affect bacterial retention. We assess how four bacterial strains isolated from stormwater and a laboratory strain, Pseudomonas aeruginosa PAO1, alter Escherichia coli retention in experimental sand columns under conditions of stormwater filtration relative to a clean-bed control. Our results demonstrate that these strains differentially affect E. coli retention, as was previously shown for a model colloid. To determine whether E. coli retention could be influenced by changes in relative abundance of strains within a microbial community, we selected two pairs of biofilm strains with the largest observed differences in E. coli retention and tested how changes in relative abundance of strain pairs in the biofilm affected E. coli retention. The results demonstrate that E. coli retention efficiency is influenced by the retention characteristics of the strains within biofilm microbial community, but individual strain characteristics influence retention in a manner that cannot be determined from changes in their relative abundance alone. This study demonstrates that changes in the relative abundance of specific members of a biofilm community can significantly alter filter performance, but these changes are not a simple function of strain-specific retention and the relative abundance. Our results suggest that the microbial community composition of biofilms should be considered when evaluating factors that influence filter performance. IMPORTANCE The retention efficiency of bacterial contaminants in biofilm-colonized biofilters is highly variable. Despite the increasing number of studies on the impact of biofilms in filters on bacterial retention, how individual bacterial strains within a biofilm community combine to influence bacterial retention is unknown. Here, we studied the retention of an E. coli K-12 strain, as a model bacterium, in columns colonized by four bacterial strains isolated from stormwater and P. aeruginosa, a model biofilm-forming strain. Simplified two-strain biofilm communities composed of combinations of the strains were used to determine how relative abundance of biofilm strains affects filter performance. Our results provide insight into how biofilm microbial composition influences bacterial retention in filters and whether it is possible to predict bacterial retention efficiency in biofilm-colonized filters from the relative abundance of individual members and the retention characteristics of cultured isolates.
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Abstract
While extremely prevalent, painful, and difficult to treat, vulvovaginal candidiasis remains largely understudied in the field of women's health. In a recent issue of mSystems, McKloud et al. (E. McKloud, C. Delaney, L. Sherry, R. Kean, et al., mSystems 6:e00622-21, 2021, https://doi.org/10.1128/mSystems.00622-21) shed light on a pivotal role of a complex Candida-Lactobacillus interplay that may regulate the pathophysiology of recurrent vulvovaginal candidiasis (RVVC). This advancement not only gives new insight into the molecular mechanisms governing interkingdom interactions modulating RVVC disease, but also provides evidence that probiotic Lactobacillus-based therapeutic approaches could be efficient for fighting these problematical fungal infections.
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46
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Sarkodee-Addo E, Tokiwa C, Bonney P, Aboagye DA, Yeboah A, Abebrese SO, Bam R, Nartey EK, Okazaki S, Yasuda M. Biofertilizer Activity of Azospirillum sp. B510 on the Rice Productivity in Ghana. Microorganisms 2021; 9:2000. [PMID: 34576895 DOI: 10.3390/microorganisms9092000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022] Open
Abstract
Rice production in Ghana has become unsustainable due to the extremely nutrient-poor soils. It is caused by inadequate soil fertility management, including the inefficient application of fertilizers. A practical solution could be the biofertilizers, Azospirillum sp. B510. We performed field trials in Ghana and Japan to compare the effects of B510 colonization on selected Ghanaian rice varieties grown. The B510 inoculation significantly enhanced the rice cultivars’ growth and yield. The phenotypic characteristics observed in rice varieties Exbaika, Ex-Boako, AgraRice, and Amankwatia were mainly short length and high tillering capacity. These features are attributed to the host plant (cv. Nipponbare), from which the strain B510 was isolated. Furthermore, Azospirillum species has been identified as the dominant colonizing bacterium of rice rhizosphere across a diverse range of agroecologies in all major rice-growing regions in Ghana. Our results suggest that the utilization of B510 as a bio-fertilizer presents a promising way to improve rice growth, enhance soil fertility, and sustain rice productivity in Ghana.
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Abstract
Bats are a key reservoir of coronaviruses (CoVs), including the agent of the severe acute respiratory syndrome, SARS-CoV-2, responsible for the recent deadly viral pneumonia pandemic. However, understanding how bats can harbor several microorganisms without developing illnesses is still a matter under discussion. Viruses and other pathogens are often studied as stand-alone entities, despite that, in nature, they mostly live in multispecies associations called biofilms—both externally and within the host. Microorganisms in biofilms are enclosed by an extracellular matrix that confers protection and improves survival. Previous studies have shown that viruses can secondarily colonize preexisting biofilms, and viral biofilms have also been described. In this review, we raise the perspective that CoVs can persistently infect bats due to their association with biofilm structures. This phenomenon potentially provides an optimal environment for nonpathogenic and well-adapted viruses to interact with the host, as well as for viral recombination. Biofilms can also enhance virion viability in extracellular environments, such as on fomites and in aquatic sediments, allowing viral persistence and dissemination. Moreover, understanding the biofilm lifestyle of CoVs in reservoirs might contribute to explaining several burning questions as to persistence and transmissibility of highly pathogenic emerging CoVs.
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48
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Lara EG, van der Windt I, Molenaar D, de Vos MGJ, Melkonian C. Using Functional Annotations to Study Pairwise Interactions in Urinary Tract Infection Communities. Genes (Basel) 2021; 12:genes12081221. [PMID: 34440394 PMCID: PMC8393552 DOI: 10.3390/genes12081221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 02/01/2023] Open
Abstract
The behaviour of microbial communities depends on environmental factors and on the interactions of the community members. This is also the case for urinary tract infection (UTI) microbial communities. Here, we devise a computational approach that uses indices of complementarity and competition based on metabolic gene annotation to rapidly predict putative interactions between pair of organisms with the aim to explain pairwise growth effects. We apply our method to 66 genomes selected from online databases, which belong to 6 genera representing members of UTI communities. This resulted in a selection of metabolic pathways with high correlation for each pairwise combination between a complementarity index and the experimentally derived growth data. Our results indicated that Enteroccus spp. were most complemented in its metabolism by the other members of the UTI community. This suggests that the growth of Enteroccus spp. can potentially be enhanced by complementary metabolites produced by other community members. We tested a few putative predicted interactions by experimental supplementation of the relevant predicted metabolites. As predicted by our method, folic acid supplementation led to the increase in the population density of UTI Enterococcus isolates. Overall, we believe our method is a rapid initial in silico screening for the prediction of metabolic interactions in microbial communities.
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Affiliation(s)
- Elena G. Lara
- Systems Biology Lab, AIMMS, Vrije Universiteit, 1081 HZ Amsterdam, The Netherlands; (E.G.L.); (D.M.)
| | | | - Douwe Molenaar
- Systems Biology Lab, AIMMS, Vrije Universiteit, 1081 HZ Amsterdam, The Netherlands; (E.G.L.); (D.M.)
| | - Marjon G. J. de Vos
- GELIFES, Universtity of Groningen, 9747 AG Groningen, The Netherlands;
- Correspondence: (M.G.J.d.V.); (C.M.)
| | - Chrats Melkonian
- Systems Biology Lab, AIMMS, Vrije Universiteit, 1081 HZ Amsterdam, The Netherlands; (E.G.L.); (D.M.)
- Correspondence: (M.G.J.d.V.); (C.M.)
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Wagner AO, Westerholm M, Stres B, Kopečný J. Editorial: Exploring the Role and Function of the Microbiota in Terrestrial Anaerobic Environments and Their Potential Biotechnological Application. Front Microbiol 2021; 12:722268. [PMID: 34385996 PMCID: PMC8353394 DOI: 10.3389/fmicb.2021.722268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Maria Westerholm
- Department of Molecular Sciences, BioCentre, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Blaz Stres
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jan Kopečný
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic (ASCR), Prague, Czechia
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50
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Figueroa CR, Jiang CZ, Torres CA, Fortes AM, Alkan N. Editorial: Regulation of Fruit Ripening and Senescence. Front Plant Sci 2021; 12:711458. [PMID: 34381486 PMCID: PMC8350513 DOI: 10.3389/fpls.2021.711458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/02/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Carlos R. Figueroa
- Institute of Biological Sciences, Campus Talca, Universidad de Talca, Talca, Chile
| | - Cai-Zhong Jiang
- Crops Pathology and Genetics Research Unit, USDA-ARS, Davis, CA, United States
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Carolina A. Torres
- Horticulture Department, Tree Fruit Research and Extension Center, Washington State University, Wenatchee, WA, United States
| | - Ana M. Fortes
- Faculty of Sciences, BioISI - Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
| | - Noam Alkan
- Department of Postharvest Science, Agricultural Research Organization (ARO), Rishon LeZion, Israel
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