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Zulfiqar M, Singh V, Steinbeck C, Sorokina M. Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities. Crit Rev Microbiol 2024:1-40. [PMID: 38270170 DOI: 10.1080/1040841x.2024.2306465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Microbial communities thrive through interactions and communication, which are challenging to study as most microorganisms are not cultivable. To address this challenge, researchers focus on the extracellular space where communication events occur. Exometabolomics and interactome analysis provide insights into the molecules involved in communication and the dynamics of their interactions. Advances in sequencing technologies and computational methods enable the reconstruction of taxonomic and functional profiles of microbial communities using high-throughput multi-omics data. Network-based approaches, including community flux balance analysis, aim to model molecular interactions within and between communities. Despite these advances, challenges remain in computer-assisted biosynthetic capacities elucidation, requiring continued innovation and collaboration among diverse scientists. This review provides insights into the current state and future directions of computer-assisted biosynthetic capacities elucidation in studying microbial communities.
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Affiliation(s)
- Mahnoor Zulfiqar
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Vinay Singh
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Data Science and Artificial Intelligence, Research and Development, Pharmaceuticals, Bayer, Berlin, Germany
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2
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Beyond the Risk of Biofilms: An Up-and-Coming Battleground of Bacterial Life and Potential Antibiofilm Agents. Life (Basel) 2023; 13:life13020503. [PMID: 36836860 PMCID: PMC9959329 DOI: 10.3390/life13020503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/15/2023] Open
Abstract
Microbial pathogens and their virulence factors like biofilms are one of the major factors which influence the disease process and its outcomes. Biofilms are a complex microbial network that is produced by bacteria on any devices and/or biotic surfaces to escape harsh environmental conditions and antimicrobial effects. Due to the natural protective nature of biofilms and the associated multidrug resistance issues, researchers evaluated several natural anti-biofilm agents, including bacteriophages and their derivatives, honey, plant extracts, and surfactants for better destruction of biofilm and planktonic cells. This review discusses some of these natural agents that are being put into practice to prevent biofilm formation. In addition, we highlight bacterial biofilm formation and the mechanism of resistance to antibiotics.
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3
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Ba Q, Zhou J, Li J, Cheng S, Zhang X, Wang H. Mutagenic Characteristics of Six Heavy Metals in Escherichia coli: The Commonality and Specificity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13867-13877. [PMID: 36121417 PMCID: PMC9536316 DOI: 10.1021/acs.est.2c04785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/27/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
The history of long-term environmental exposure to heavy metals can be recorded in the genome as sporadic and specific mutations. Variable environments introduce diverse and adaptive mutations to organisms. To reveal the information hidden in genomes about environmental exposure to heavy metals, we performed long-term mutation accumulation (MA) experiments with Escherichia coli, analyzed genomes from 36 populations across 1650 generations with 6 heavy metal exposure regimes (arsenic, cadmium, chromium, copper, nickel, and lead), and inferred metal-specific evolution modes at the genomic level. All heavy metals induced genetic mutations with a mean rate of 3.459 × 10-9 per nucleotide per generation. The mutational spectrum exhibited distinct signatures; however, heavy metals also shared common mutation signatures prominently associated with all cancer types. The mutated genes showed an average similarity of 54.4% within the same exposure regime, whereas only 38.8% between exposure regimes. In terms of biological insights, mutated genes were enriched to fundamental cellular processes such as metabolism, motility, and transport. Our study elucidates the mutagenic commonality and specificity of environmental heavy metals, which are highly specific at mutational features and locus, but conserved at gene and functional levels, and may play crucial roles in the convergence of adaptation to heavy metals.
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Affiliation(s)
- Qian Ba
- State
Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell
Omics, School of Public Health, Shanghai
Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jingqi Zhou
- State
Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell
Omics, School of Public Health, Shanghai
Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jingquan Li
- State
Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell
Omics, School of Public Health, Shanghai
Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shujun Cheng
- State
Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell
Omics, School of Public Health, Shanghai
Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaokang Zhang
- School
of Public Health and Health Management, Gannan Medical University, Ganzhou 341000, China
| | - Hui Wang
- State
Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell
Omics, School of Public Health, Shanghai
Jiao Tong University School of Medicine, Shanghai 200025, China
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4
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Yan C, Li X, Zhang G, Bi J, Hao H, Hou H. Quorum Sensing (QS)-regulated target predictions of Hafnia alvei H4 based on the joint application of genome and STRING database. Food Res Int 2022; 157:111356. [DOI: 10.1016/j.foodres.2022.111356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/03/2022] [Accepted: 05/10/2022] [Indexed: 11/25/2022]
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5
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Arendse M, Khan S, Wani MY, Aqlan FM, Al-Bogami AS, Ahmad A. Quorum Sensing and Biofilm Disrupting Potential of Imidazole Derivatives in Chromobacterium violaceum Using Antimicrobial and Drug Discovery Approaches. Braz J Microbiol 2022; 53:565-582. [PMID: 35301694 PMCID: PMC9151946 DOI: 10.1007/s42770-022-00702-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 02/01/2022] [Indexed: 02/01/2023] Open
Abstract
Population of drug-resistant bacteria have increased at an alarming rate in the past few decades. The major reason for increasing drug resistance is the lack of new antibiotics and limited drug targets. It has therefore been a vital task to develop new antibiotics with different drug targets. Two such targets are biofilm formation and quorum sensing. Quorum sensing is cell to cell communication used by bacteria that initiates many important survival processes and aids in establishing pathogenesis. Both biofilm and quorum sensing are inter-related processes and play a major role in physiological and pathogenesis processes. In this study, five novel imidazole derivatives (IMA-1-IMA-5) were synthesised and tested for their antibacterial and anti-quorum sensing activities against Chromobacterium violaceum using different in silico and in vitro techniques following the standard protocols. In silico results revealed that all compounds were able to effectively bind to and interact sufficiently with the target protein CviR. CviR is a protein to which autoinducers bind to initiate the quorum sensing process. In silico results also revealed that the compounds generated favourable structural dynamics implying that the compounds would be able to effectively bind to CviR and inhibit quorum sensing. Susceptibility results revealed that IMA-1 is the most active of all the derivatives against both planktonic cells and biofilms. Qualitative and quantitative evaluation of anti-quorum sensing activity at sub-inhibitory concentrations of these compounds also revealed high activity for IMA-1. Down-regulation of most of the quorum sensing genes when cells were treated with the test compounds affirmed the high anti-quorum sensing activities of these compounds. The results from this study are promising and urges on the use of anti-quorum sensing and biofilm disrupting molecules to combat multi-drug resistance problem.
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Affiliation(s)
- Madison Arendse
- Clinical Microbiology and Infectious Diseases, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Shama Khan
- Clinical Microbiology and Infectious Diseases, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Mohmmad Younus Wani
- Department of Chemistry, College of Science, University of Jeddah, Jeddah, 21589, Kingdom of Saudi Arabia.
| | - Faisal Mohammed Aqlan
- Department of Chemistry, College of Science, University of Jeddah, Jeddah, 21589, Kingdom of Saudi Arabia
| | - Abdullah Saad Al-Bogami
- Department of Chemistry, College of Science, University of Jeddah, Jeddah, 21589, Kingdom of Saudi Arabia
| | - Aijaz Ahmad
- Clinical Microbiology and Infectious Diseases, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa.
- Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, 2193, South Africa.
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6
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Bacterial signal C10-HSL stimulates spore germination of Galactomyces geotrichum by transboundary interaction. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.06.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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7
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Zhou Y, Wang H, Xu S, Liu K, Qi H, Wang M, Chen X, Berg G, Ma Z, Cernava T, Chen Y. Bacterial-fungal interactions under agricultural settings: from physical to chemical interactions. STRESS BIOLOGY 2022; 2:22. [PMID: 37676347 PMCID: PMC10442017 DOI: 10.1007/s44154-022-00046-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/17/2022] [Indexed: 09/08/2023]
Abstract
Bacteria and fungi are dominant members of environmental microbiomes. Various bacterial-fungal interactions (BFIs) and their mutual regulation are important factors for ecosystem functioning and health. Such interactions can be highly dynamic, and often require spatiotemporally resolved assessments to understand the interplay which ranges from antagonism to mutualism. Many of these interactions are still poorly understood, especially in terms of the underlying chemical and molecular interplay, which is crucial for inter-kingdom communication and interference. BFIs are highly relevant under agricultural settings; they can be determinative for crop health. Advancing our knowledge related to mechanisms underpinning the interactions between bacteria and fungi will provide an extended basis for biological control of pests and pathogens in agriculture. Moreover, it will facilitate a better understanding of complex microbial community networks that commonly occur in nature. This will allow us to determine factors that are crucial for community assembly under different environmental conditions and pave the way for constructing synthetic communities for various biotechnological applications. Here, we summarize the current advances in the field of BFIs with an emphasis on agriculture.
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Affiliation(s)
- Yaqi Zhou
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Hongkai Wang
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Sunde Xu
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Kai Liu
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Hao Qi
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Mengcen Wang
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Xiaoyulong Chen
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, 8010, Graz, Austria
- Leibniz-Institute for Agricultural Engineering and Bioeconomy, Potsdam, Germany
- University of Potsdam, Potsdam, Germany
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, 8010, Graz, Austria.
| | - Yun Chen
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
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8
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Escobar-Muciño E, Arenas-Hernández MMP, Luna-Guevara ML. Mechanisms of Inhibition of Quorum Sensing as an Alternative for the Control of E. coli and Salmonella. Microorganisms 2022; 10:884. [PMID: 35630329 PMCID: PMC9143355 DOI: 10.3390/microorganisms10050884] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 02/05/2023] Open
Abstract
Quorum sensing (QS) is a process of cell-cell communication for bacteria such as E. coli and Salmonella that cause foodborne diseases, with the production, release, and detection of autoinducer (AI) molecules that participate in the regulation of virulence genes. All of these proteins are useful in coordinating collective behavior, the expression of virulence factors, and the pathogenicity of Gram-negative bacteria. In this work, we review the natural or synthetic inhibitor molecules of QS that inactivate the autoinducer and block QS regulatory proteins in E. coli and Salmonella. Furthermore, we describe mechanisms of QS inhibitors (QSIs) that act as competitive inhibitors, being a useful tool for preventing virulence gene expression through the downregulation of AI-2 production pathways and the disruption of signal uptake. In addition, we showed that QSIs have negative regulatory activity of genes related to bacterial biofilm formation on clinical artifacts, which confirms the therapeutic potential of QSIs in the control of infectious pathogens. Finally, we discuss resistance to QSIs, the design of next-generation QSIs, and how these molecules can be leveraged to provide a new antivirulence therapy to combat diseases caused by E. coli or Salmonella.
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Affiliation(s)
- Esmeralda Escobar-Muciño
- Posgrado en Microbiología, Centro de Investigación en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla C.P. 72570, Pue, Mexico;
| | - Margarita M. P. Arenas-Hernández
- Posgrado en Microbiología, Centro de Investigación en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla C.P. 72570, Pue, Mexico;
| | - M. Lorena Luna-Guevara
- Colegío de Ingeniería en Alimentos, Facultad de Ingeniería Química, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla C.P. 72570, Pue, Mexico
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9
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de Luis B, Morellá-Aucejo Á, Llopis-Lorente A, Martínez-Latorre J, Sancenón F, López C, Murguía JR, Martínez-Máñez R. Nanoprogrammed Cross-Kingdom Communication Between Living Microorganisms. NANO LETTERS 2022; 22:1836-1844. [PMID: 35171622 PMCID: PMC9940291 DOI: 10.1021/acs.nanolett.1c02435] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The engineering of chemical communication at the micro/nanoscale is a key emergent topic in micro/nanotechnology, synthetic biology, and related areas. However, the field is still in its infancy; previous advances, although scarce, have mainly focused on communication between abiotic micro/nanosystems or between microvesicles and living cells. Here, we have implemented a nanoprogrammed cross-kingdom communication involving two different microorganisms and tailor-made nanodevices acting as "nanotranslators". Information flows from the sender cells (bacteria) to the nanodevice and from the nanodevice to receiver cells (yeasts) in a hierarchical way, allowing communication between two microorganisms that otherwise would not interact.
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Affiliation(s)
- Beatriz de Luis
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), 28029 Madrid, Spain
| | - Ángela Morellá-Aucejo
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), 28029 Madrid, Spain
- Unidad
Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades
y Nanomedicina, Centro de Investigación Príncipe Felipe, Universitat Politècnica de València, 46012 Valencia, Spain
| | - Antoni Llopis-Lorente
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), 28029 Madrid, Spain
| | - Javier Martínez-Latorre
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), 28029 Madrid, Spain
| | - Félix Sancenón
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), 28029 Madrid, Spain
| | - Carmelo López
- Instituto
Universitario de Conservación y Mejora de la Agrodiversidad
Valenciana, Universitat Politècnica
de València (COMAV-UPV), 46022 Valencia, Spain
| | - José Ramón Murguía
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), 28029 Madrid, Spain
| | - Ramón Martínez-Máñez
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
- CIBER
de Bioingeniería, Biomateriales y
Nanomedicina (CIBER-BBN), 28029 Madrid, Spain
- Unidad
Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades
y Nanomedicina, Centro de Investigación Príncipe Felipe, Universitat Politècnica de València, 46012 Valencia, Spain
- Unidad
Mixta de Investigación en Nanomedicina y Sensores, Instituto
de Investigación Sanitaria La Fe, Universitat Politècnica de València, 46026 Valencia, Spain
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10
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Zhao X, Lian X, Liu Y, Zhou L, Wu B, Fu YV. A Peptide Derived from GAPDH Enhances Resistance to DNA Damage in Saccharomyces cerevisiae Cells. Appl Environ Microbiol 2022; 88:e0219421. [PMID: 34936834 PMCID: PMC8863060 DOI: 10.1128/aem.02194-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/16/2021] [Indexed: 11/20/2022] Open
Abstract
Social behaviors do not exist only in higher organisms but are also present in microbes that interact for the common good. Here, we report that budding yeast cells interact with their neighboring cells after exposure to DNA damage. Yeast cells irradiated with DNA-damaging UV light secrete signal peptides that can increase the survival of yeast cells exposed to DNA-damaging stress. The secreted peptide is derived from glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and it induced cell death of a fraction of yeast cells in the group. The data suggest that the GAPDH-derived peptide serves in budding yeast's social interaction in response to DNA-damaging stress. IMPORTANCE Many studies have shown that microorganisms, including bacteria and yeast, display increased tolerance to stress after exposure to the same stressor. However, the mechanism remains unknown. In this study, we report a striking finding that Saccharomyces cerevisiae cells respond to DNA damage by secreting a peptide that facilitates resistance to DNA-damaging stress. Although it has been shown that GAPDH possesses many key functions in cells aside from its well-established role in glycolysis, this study demonstrated that GAPDH is also involved in the social behaviors response to DNA-damaging stress. The study opens the gate to an interesting research field about microbial social activity for adaptation to a harsh environment.
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Affiliation(s)
- Xi Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Xianqiang Lian
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Liyan Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Bian Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yu V. Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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11
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The evolution of multicellularity and cancer: views and paradigms. Biochem Soc Trans 2021; 48:1505-1518. [PMID: 32677677 DOI: 10.1042/bst20190992] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 12/16/2022]
Abstract
Conceptually and mechanistically, the evolution of multicellularity required the integration of single cells into new functionally, reproductively and evolutionary stable multicellular individuals. As part of this process, a change in levels of selection occurred, with selection at the multicellular level overriding selection at the cell level. The stability of multicellular individuals is dependent on a combination of mechanisms that supress within-group evolution, by both reducing the occurrence of somatic mutations as well as supressing somatic selection. Nevertheless, mutations that, in a particular microenvironment, confer mutant lineages a fitness advantage relative to normal somatic cells do occur, and can result in cancer. This minireview highlights several views and paradigms that relate the evolution of multicellularity to cancer. As a phenomenon, cancer is generally understood as a failure of multicellular systems to suppress somatic evolution. However, as a disease, cancer is interpreted in different frameworks: (i) a breakdown of cooperative behaviors underlying the evolution of multicellularity, (ii) a disruption of molecular networks established during the emergence of multicellularity to impose constraints on single-celled units, or (iii) an atavistic state resulting from reactivating primitive programs that originated in the earliest unicellular species. A number of assumptions are common in all the views relating cancer as a disease to the evolution of multicellularity. For instance, cancer is considered a reversal to unicellularity, and cancer cells are thought to both resemble unicellular organisms and benefit from ancestral-like traits. Nevertheless, potential limitations of current paradigms should be acknowledged as different perspectives can provide novel insights with potential therapeutic implications.
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12
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Khalid S, Keller NP. Chemical signals driving bacterial-fungal interactions. Environ Microbiol 2021; 23:1334-1347. [PMID: 33511714 DOI: 10.1111/1462-2920.15410] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 12/19/2022]
Abstract
Microorganisms reside in diverse environmental communities where interactions become indispensable due to close physical associations. These interactions are driven by chemical communication among different microbial kingdoms, particularly between fungi and bacteria. Knowledge about these communication signals provides useful information about the nature of microbial interactions and allows predictions of community development in diverse environments. Here, we provide an update on the role of small signalling molecules in fungal-bacterial interactions with focus on agricultural and medicinal environments. This review highlights the range of - and response to - diverse biochemicals produced by both kingdoms with view to harnessing their properties towards drug discovery applications.
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Affiliation(s)
- Saima Khalid
- Department of Microbiology, Women University Mardan, Mardan, Pakistan
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin, Madison, WI, USA
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13
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Alkayyali T, Pope E, Wheatley SK, Cartmell C, Haltli B, Kerr RG, Ahmadi A. Development of a microbe domestication pod (MD Pod) for in situ cultivation of micro-encapsulated marine bacteria. Biotechnol Bioeng 2020; 118:1166-1176. [PMID: 33241862 DOI: 10.1002/bit.27633] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/01/2020] [Accepted: 11/20/2020] [Indexed: 11/10/2022]
Abstract
Microbial marine natural products hold significant potential for the discovery of new bioactive therapeutics such as antibiotics. Unfortunately, this discovery is hindered by the inability to culture the majority of microbes using traditional laboratory approaches. While many new methods have been developed to increase cultivability, a high-throughput in situ incubation chamber capable of simultaneously isolating individual microbes while allowing cellular communication has not previously been reported. Development of such a device would expedite the discovery of new microbial taxa and, thus, facilitate access to their associated natural products. In this study, this concept is achieved by the development of a new device termed by the authors as the microbe domestication (MD) Pod. The MD Pod enables single-cell cultivation by isolating marine bacterial cells in agarose microbeads produced using microfluidics, while allowing potential transmission of chemical signals between cells during in situ incubation in a chamber, or "Pod," that is deployed in the environment. The design of the MD Pod was optimized to ensure the use of biocompatible materials, allow for simple assembly in a field setting, and maintain sterility throughout incubation. The encapsulation process was designed to ensure that the viability of marine sediment bacteria was not adversely impacted by the encapsulation process. The process was validated using representative bacteria isolated from temperate marine sediment samples: Marinomonas polaris, Psychrobacter aquimaris, and Bacillus licheniformis. The overall process appeared to promote metabolic activity of most representative species. Thus, microfluidic encapsulation of marine bacteria and subsequent in situ incubation in the MD Pod is expected to accelerate marine natural products discovery by increasing the cultivability of marine bacteria.
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Affiliation(s)
- Tartela Alkayyali
- Faculty of Sustainable Design Engineering, University of Prince Edward Island, Prince Edward Island, Canada
| | - Emily Pope
- Departments of Biomedical Sciences, University of Prince Edward Island, Prince Edward Island, Canada
| | - Sydney K Wheatley
- Faculty of Sustainable Design Engineering, University of Prince Edward Island, Prince Edward Island, Canada
| | - Christopher Cartmell
- Departments of Chemistry, University of Prince Edward Island, Prince Edward Island, Canada
| | - Bradley Haltli
- Departments of Biomedical Sciences, University of Prince Edward Island, Prince Edward Island, Canada.,Nautilus Biosciences Croda, Prince Edward Island, Canada
| | - Russell G Kerr
- Departments of Biomedical Sciences, University of Prince Edward Island, Prince Edward Island, Canada.,Departments of Chemistry, University of Prince Edward Island, Prince Edward Island, Canada.,Nautilus Biosciences Croda, Prince Edward Island, Canada
| | - Ali Ahmadi
- Faculty of Sustainable Design Engineering, University of Prince Edward Island, Prince Edward Island, Canada
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14
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Markus V, Share O, Teralı K, Ozer N, Marks RS, Kushmaro A, Golberg K. Anti-Quorum Sensing Activity of Stevia Extract, Stevioside, Rebaudioside A and Their Aglycon Steviol. Molecules 2020; 25:E5480. [PMID: 33238612 PMCID: PMC7700441 DOI: 10.3390/molecules25225480] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/20/2020] [Accepted: 11/21/2020] [Indexed: 12/12/2022] Open
Abstract
Governments are creating regulations for consumers to reduce their sugar intake, prompting companies to increase the ratio of artificial sweeteners in their products. However, there is evidence of some deleterious effects ascribed to the aforementioned synthetic agents and therefore consumers and food manufacturers have turned their attention to natural dietary sweeteners, such as stevia, to meet their sweetening needs. Stevia is generally considered safe; however, emerging scientific evidence has implicated the agent in gut microbial imbalance. In general, regulation of microbial behavior is known to depend highly on signaling molecules via quorum sensing (QS) pathways. This is also true for the gut microbial community. We, therefore, evaluated the possible role of these stevia-based natural sweeteners on this bacterial communication pathway. The use of a commercial stevia herbal supplement resulted in an inhibitory effect on bacterial communication, with no observable bactericidal effect. Purified stevia extracts, including stevioside, rebaudioside A (Reb A), and steviol revealed a molecular interaction, and possible interruption of Gram-negative bacterial communication, via either the LasR or RhlR receptor. Our in-silico analyses suggest a competitive-type inhibitory role for steviol, while Reb A and stevioside are likely to inhibit LasR-mediated QS in a non-competitive manner. These results suggest the need for further safety studies on the agents.
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Affiliation(s)
- Victor Markus
- Department of Medical Biochemistry, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (V.M.); (K.T.)
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel; (O.S.); (R.S.M.)
| | - Orr Share
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel; (O.S.); (R.S.M.)
| | - Kerem Teralı
- Department of Medical Biochemistry, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (V.M.); (K.T.)
| | - Nazmi Ozer
- Department of Biochemistry, Faculty of Pharmacy, Girne American University, Kyrenia 99428, Cyprus;
| | - Robert S. Marks
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel; (O.S.); (R.S.M.)
- The Ilse Katz Center for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel; (O.S.); (R.S.M.)
- The Ilse Katz Center for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Karina Golberg
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel; (O.S.); (R.S.M.)
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15
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Liu Z, Zhang C, Wei Q, Zhang S, Quan Z, Li M. Temperature and salinity drive comammox community composition in mangrove ecosystems across southeastern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 742:140456. [PMID: 32629251 DOI: 10.1016/j.scitotenv.2020.140456] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/21/2020] [Accepted: 06/21/2020] [Indexed: 06/11/2023]
Abstract
Complete ammonia-oxidizing (comammox) microorganisms are newly recognized nitrifying bacteria found in natural and engineered ecosystems. Mangrove ecosystems are hotspots for nitrogen cycling, but the knowledge of comammox diversity and abundance, and particularly, driving factors, in these ecosystems is scarce. We here used deep sequencing to investigate comammox diversity in six mangrove ecosystems across southeastern China. Our results showed that comammox microorganisms in mangrove sediments were extremely diverse. Phylogenetic analysis revealed a novel comammox group within clade A that formed a distinct cluster for which no reference sequence existed, implying their potential uniqueness. Quantitative PCR demonstrated that comammox abundance was slightly higher than that of the canonical ammonia-oxidizing bacteria but significantly lower than that of ammonia-oxidizing archaea, indicating they are not the dominant ammonia oxidizers in mangrove ecosystems. Finally, variation partition analysis revealed a significant decrease in similarity of comammox communities along the geographical distance, and a pronounced effect of the geographic factors and sediment attributes on the composition of comammox microorganisms and the abundance variations of ammonia oxidizers. Temperature and salinity were the most important contributing factors that shaped the comammox community. Further, detection of diverse comammox microorganisms in extremely high-salinity sediments suggested that this community could adapt to high salinity environments, which indicates salinity may not be a critical factor resulting in the absence of comammox microorganisms in open-ocean environments. This study expanded the current understanding of the diversity and niche preference of comammox in mangrove ecosystems, and further enhanced our understanding of adaptation potential of comammox communities.
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Affiliation(s)
- Zongbao Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Cuijing Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Qiaoyan Wei
- School of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, Guangxi, PR China
| | - Siyu Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Zhexue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China.
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16
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Yu Z, Shi D, Liu W, Meng Y, Meng F. Metabolome responses of Enterococcus faecium to acid shock and nitrite stress. Biotechnol Bioeng 2020; 117:3559-3571. [PMID: 32662876 DOI: 10.1002/bit.27497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/26/2020] [Accepted: 07/08/2020] [Indexed: 01/21/2023]
Abstract
Enterococcus faecium is gaining increasing interest due to its virulence and tolerance to a range of stresses (e.g., acid shock and nitrite stress in human stomach). The chemical taxonomy and basic structural features of cellular metabolite can provide us a deeper understanding of bacterial tolerance at molecular level. Here, we used hierarchical classification and molecular composition analysis to investigate the metabolome responses of E. faecium to acid shock and nitrite stress. Our results showed that considerable high biodegradable compounds (e.g., dipeptides) were produced by E. faecium under acid shock, while nitrite stress induced the accumulations of some low biodegradable compounds (e.g., organoheterocyclic compounds and benzenoids). Complete genome analysis and metabolic pathway profiling suggested that E. faecium produced high biodegradable metabolites responsible for the proton-translocation and biofilm formation, which increase its tolerance to acid shock. Yet, the presence of low biodegradable metabolites due to the nitrite exposure could disturb the bacterial productions of surface proteins, and thus inhibiting biofilm formation. Our approach uncovered the hidden interactions between intracellular metabolites and exogenous stress, and will improve the understanding of host-microbe interactions.
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Affiliation(s)
- Zhong Yu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, China
| | - Dongchen Shi
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, China
| | - Wencong Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, China
| | - Yabing Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, China
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17
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Oleskin AV, Shenderov BA. Probiotics and Psychobiotics: the Role of Microbial Neurochemicals. Probiotics Antimicrob Proteins 2020; 11:1071-1085. [PMID: 31493127 DOI: 10.1007/s12602-019-09583-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In light of recent data, microorganisms should be construed as organisms that are capable of communication and collective behaviors. Microbial communication signals are involved both in interactions among microbial cells within microbial social systems, including the human body-inhabiting microconsortium, and the dialog between the microbiota and the host organism. The microbiota inhabits various niches of the host organism, especially the gastrointestinal (GI) tract. Microorganisms release diverse signal molecules and, in addition, specifically respond to host signals. This enables them to constantly interact with the nervous system including the brain and the immune system of the host organism. Evolutionarily conserved signals that are involved in the communication between microbiota and the host include neuroactive substances (neurochemicals) such as peptides, amino acids, biogenic amines, short-chain fatty acids, and gaseous substances. This ongoing dialog may either stabilize the host's physical and mental health state or, alternatively, cause serious health problems. Attempts are made to correct imbalances in the brain-gut-microbiota axis with probiotics including their subgroup called psychobiotics that release neuroactive substances directly influencing the human brain, psyche, and behavior. A number of recent review works address the microbiota-host system and its communication signals. Some of the publications focus on the involvement of neurochemicals in the bidirectional communication within the host-microbiota system. However, this work concentrates on the impact of bacterial cell components, metabolites, and signal molecules as promising alternatives to the currently widespread probiotics that have both advantages and disadvantages. Such biologically active agents of microbial origin are referred to as postbiotics or, alternatively, metabiotics (the term preferred in this work).
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Affiliation(s)
- Alexander V Oleskin
- General Ecology Department, School of Biology, Moscow State University, Vorobiev Hills, Moscow, Russia, 119991.
| | - Boris A Shenderov
- Laboratory of Bacteriology and Parasitology, Centre for Strategic Planning, Russian Ministry of Health; Moscow, Research Laboratory for Design & Implementation of Personalized Nutrition-Related Products & Diets, K. G. Razumovsky University of Technology & Management, Moscow, Russia
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18
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Winters M, Arneborg N, Appels R, Howell K. Can community-based signalling behaviour in Saccharomyces cerevisiae be called quorum sensing? A critical review of the literature. FEMS Yeast Res 2020; 19:5528315. [PMID: 31271429 DOI: 10.1093/femsyr/foz046] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/02/2019] [Indexed: 12/15/2022] Open
Abstract
Quorum sensing is a well-described mechanism of intercellular signalling among bacteria, which involves cell-density-dependent chemical signal molecules. The concentration of these quorum-sensing molecules increases in proportion to cell density until a threshold value is exceeded, which triggers a community-wide response. In this review, we propose that intercellular signalling mechanisms can be associated with a corresponding ecological interaction type based on similarities between how the interaction affects the signal receiver and producer. Thus, we do not confine quorum sensing, a specific form of intercellular signalling, to only cooperative behaviours. Instead, we define it as cell-density-dependent responses that occur at a critical concentration of signal molecules and through a specific signalling pathway. For fungal species, the medically important yeast Candida albicans has a well-described quorum sensing system, while this system is not well described in Saccharomyces cerevisiae, which is involved in food and beverage fermentations. The more precise definition for quorum sensing proposed in this review is based on the studies suggesting that S. cerevisiae may undergo intercellular signalling through quorum sensing. Through this lens, we conclude that there is a lack of evidence to support a specific signalling mechanism and a critical signal concentration of these behaviours in S. cerevisiae, and, thus, these features require further investigation.
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Affiliation(s)
- Michela Winters
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville 3010, Australia
| | - Nils Arneborg
- Department of Food Science, University of Copenhagen, Frederiksberg 1958, Denmark
| | - Rudi Appels
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville 3010, Australia
| | - Kate Howell
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville 3010, Australia
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19
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Pilařová V, Kočová Vlčková H, Jung O, Protti M, Buchta V, Mercolini L, Svec F, Nováková L. Unambiguous determination of farnesol and tyrosol in vaginal fluid using fast and sensitive UHPLC-MS/MS method. Anal Bioanal Chem 2020; 412:6529-6541. [PMID: 32468279 DOI: 10.1007/s00216-020-02699-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/28/2020] [Accepted: 05/08/2020] [Indexed: 11/26/2022]
Abstract
The new ultra-high performance liquid chromatography method with tandem mass spectrometry detection (UHPLC-MS/MS) has been optimized to allow fast, selective, and high-throughput analysis of two Candida albicans quorum sensing molecules (QSM), farnesol and tyrosol. The problem of the presence of the interference in the samples and system was successfully solved by careful optimization of chromatographic conditions. Charged hybrid stationary phase modified with pentafluorophenyl group and optimized gradient elution provided adequate separation selectivity and peak shapes. The impurity was identified as dibutyl phthalate and had the same m/z ions as farnesol leading to an important interference on selected reaction monitoring channel. Two different types of biological matrices originating from vaginal fluid, supernatant and sediment, were analysed. Micro-solid phase extraction in pipette tips was optimized for the selective isolation of QSM from the supernatant. The insufficient retention of farnesol on the extraction sorbent was improved when 1% of organic solvent was added prior to extraction, while the retention of tyrosol was only possible when using combined C8 and polymer sorbent type. Strong retention of farnesol had to be solved by increasing elution solvent strength and volume up to 600 μL. However, this approach did not allow the pretreatment of sediment samples due to the sorbent clogging. Therefore, our previously developed protein precipitation method was modified and validated to analyse the sediments. New developed UHPLC-MS/MS method provided suitable accuracy and precision for the determination of QSM in vaginal fluid while using only 50 μL sample volume and two different sample preparation methods.
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Affiliation(s)
- Veronika Pilařová
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203, 500 05, Hradec Králové, Czech Republic
| | - Hana Kočová Vlčková
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203, 500 05, Hradec Králové, Czech Republic
| | - Ondřej Jung
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203, 500 05, Hradec Králové, Czech Republic
| | - Michele Protti
- Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Vladimír Buchta
- Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Králové, Charles University, Sokolská 581, 500 05, Hradec Králové, Czech Republic
| | - Laura Mercolini
- Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Frantisek Svec
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203, 500 05, Hradec Králové, Czech Republic
| | - Lucie Nováková
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203, 500 05, Hradec Králové, Czech Republic.
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20
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Yaikhan T, Chuerboon M, Tippayatham N, Atimuttikul N, Nuidate T, Yingkajorn M, Tun AW, Buncherd H, Tansila N. Indole and Derivatives Modulate Biofilm Formation and Antibiotic Tolerance of Klebsiella pneumoniae. Indian J Microbiol 2019; 59:460-467. [PMID: 31762509 PMCID: PMC6842365 DOI: 10.1007/s12088-019-00830-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/30/2019] [Indexed: 12/16/2022] Open
Abstract
Intercellular communication is a crucial process for the multicellular community in both prokaryotes and eukaryotes. Indole has been recognized as a new member of the signal molecules which enables the regulated control of various bacterial phenotypes. To elucidate the inter-species relationship among enteric microorganisms via indole signaling, Klebsiella pneumoniae (KP) culture was treated with indole solution and examined for the pathogenicity by using various phenotypic tests. Both synthetic and naturally-produced indole preparations had no deteriorating effect on growth and autoaggregative capacity of KP. The results showed that biofilm formation of carbapenem-susceptible K. pneumoniae (KP-S) was clearly induced by indole exposure (≈ 2-10 folds), whereas no significant difference was observed in the resistant counterpart. In addition, the tolerance to β-lactam antibiotics of KP was altered upon exposure to indole and/or derivatives assessed by Kirby-Bauer disk diffusion test. Taken together, our finding indicates the functional role of indole in changing or modulating pathogenic behaviors of other bacteria.
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Affiliation(s)
- Thanachaporn Yaikhan
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, 90110 Thailand
| | - Manatsanan Chuerboon
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, 90110 Thailand
| | - Natchapol Tippayatham
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, 90110 Thailand
| | - Nateekarn Atimuttikul
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, 90110 Thailand
| | - Taiyeebah Nuidate
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Songkhla, 90110 Thailand
| | - Mingkwan Yingkajorn
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, 90110 Thailand
| | - Aung Win Tun
- Faculty of Graduate Studies, Mahidol University, Salaya, Nakhon Pathom 73170 Thailand
| | - Hansuk Buncherd
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, 90110 Thailand
| | - Natta Tansila
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, 90110 Thailand
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21
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Yu C, Hou L, Zheng Y, Liu M, Yin G, Gao J, Liu C, Chang Y, Han P. Evidence for complete nitrification in enrichment culture of tidal sediments and diversity analysis of clade a comammox Nitrospira in natural environments. Appl Microbiol Biotechnol 2018; 102:9363-9377. [PMID: 30094589 DOI: 10.1007/s00253-018-9274-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 06/26/2018] [Accepted: 07/25/2018] [Indexed: 11/27/2022]
Abstract
Complete ammonia oxidizers (comammox), as novel microbial communities, are predicted to play an important role in the nitrogen cycle. Here we reported the presence of complete nitrification in tidal sediments and examined the diversity and abundance of comammox in natural ecosystems. Metagenome and metatranscriptome of the enrichment culture from tidal sediments harbored the genes of comammox. Near-complete comammox AmoA/B/C- and Hao-like sequences showed close relationships to the known comammox (with sequence identity from 79 to 99%) rather than classical betaproteobacterial ammonia-oxidizing bacteria (β-AOB) (57 to 66%) and ammonia-oxidizing archaea (AOA) (24 to 38%). To analyze the diversity of comammox in natural environments, a new primer set targeting clade A comammox Nitrospira (COM-A) amoA genes was designed based on sequences obtained in this study and sequences from published database. In silico evaluation of the primers showed the high coverage of 89 and 100% in the COM-A amoA database. Application of the primers in six different ecosystems proved their strong availability. Community composition of COM-A suggested a relatively higher diversity than β-AOB in similar environments. Quantification results showed that COM-A amoA genes accounted for about 0.4-5.6% in total amoA genes. These results provide novel insight into our perception of the enigmatic comammox and have significant implications for profound understanding of complex nitrification process.
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Affiliation(s)
- Chendi Yu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China.
| | - Yanling Zheng
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China.
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China.
| | - Guoyu Yin
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China
| | - Juan Gao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Cheng Liu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Yongkai Chang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China
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22
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Nagy K, Ábrahám Á, Keymer JE, Galajda P. Application of Microfluidics in Experimental Ecology: The Importance of Being Spatial. Front Microbiol 2018; 9:496. [PMID: 29616009 PMCID: PMC5870036 DOI: 10.3389/fmicb.2018.00496] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/02/2018] [Indexed: 12/21/2022] Open
Abstract
Microfluidics is an emerging technology that is used more and more in biology experiments. Its capabilities of creating precisely controlled conditions in cellular dimensions make it ideal to explore cell-cell and cell-environment interactions. Thus, a wide spectrum of problems in microbial ecology can be studied using engineered microbial habitats. Moreover, artificial microfluidic ecosystems can serve as model systems to test ecology theories and principles that apply on a higher level in the hierarchy of biological organization. In this mini review we aim to demonstrate the versatility of microfluidics and the diversity of its applications that help the advance of microbiology, and in more general, experimental ecology.
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Affiliation(s)
- Krisztina Nagy
- Biological Research Centre, Institute of Biophysics, Hungarian Academy of Sciences, Szeged, Hungary
| | - Ágnes Ábrahám
- Biological Research Centre, Institute of Biophysics, Hungarian Academy of Sciences, Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged, Hungary
| | - Juan E. Keymer
- School of Biological Sciences and School of Physics, Pontifical Catholic University of Chile, Santiago, Chile
| | - Péter Galajda
- Biological Research Centre, Institute of Biophysics, Hungarian Academy of Sciences, Szeged, Hungary
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