1
|
Al-Daghistani HI, Zein S, Abbas MA. Microbial communities in the Dead Sea and their potential biotechnological applications. Commun Integr Biol 2024; 17:2369782. [PMID: 38919836 PMCID: PMC11197920 DOI: 10.1080/19420889.2024.2369782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024] Open
Abstract
The Dead Sea is unique compared to other extreme halophilic habitats. Its salinity exceeds 34%, and it is getting saltier. The Dead Sea environment is characterized by a dominance of divalent cations, with magnesium chloride (MgCl2) levels approaching the predicted 2.3 M upper limit for life, an acidic pH of 6.0, and high levels of absorbed ultraviolet radiation. Consequently, only organisms adapted to such a polyextreme environment can survive in the surface, sinkholes, sediments, muds, and underwater springs of the Dead Sea. Metagenomic sequence analysis and amino acid profiling indicated that the Dead Sea is predominantly composed of halophiles that have various adaptation mechanisms and produce metabolites that can be utilized for biotechnological purposes. A variety of products have been obtained from halophilic microorganisms isolated from the Dead Sea, such as antimicrobials, bioplastics, biofuels, extremozymes, retinal proteins, colored pigments, exopolysaccharides, and compatible solutes. These resources find applications in agriculture, food, biofuel production, industry, and bioremediation for the detoxification of wastewater and soil. Utilizing halophiles as a bioprocessing platform offers advantages such as reduced energy consumption, decreased freshwater demand, minimized capital investment, and continuous production.
Collapse
Affiliation(s)
- Hala I. Al-Daghistani
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Sima Zein
- Department of Pharmaceutical Biotechnology, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Manal A. Abbas
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| |
Collapse
|
2
|
González A, Fullaondo A, Odriozola A. Techniques, procedures, and applications in microbiome analysis. ADVANCES IN GENETICS 2024; 111:81-115. [PMID: 38908906 DOI: 10.1016/bs.adgen.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Microbiota is a complex community of microorganisms living in a defined environment. Until the 20th century, knowledge of microbiota was partial, as the techniques available for their characterization were primarily based on bacteriological culture. In the last twenty years, the development of DNA sequencing technologies, multi-omics, and bioinformatics has expanded our understanding of microorganisms. We have moved from mainly considering them isolated disease-causing agents to recognizing the microbiota as an essential component of host biology. These techniques have shown that the microbiome plays essential roles in various host phenotypes, influencing development, physiology, reproduction, and evolution. This chapter provides researchers with a summary of the primary concepts, sample collection, experimental techniques, and bioinformatics analysis commonly used in microbiome research. The main features, applications in microbiome studies, and their advantages and limitations are included in each section.
Collapse
Affiliation(s)
- Adriana González
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.
| | - Asier Fullaondo
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Adrián Odriozola
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| |
Collapse
|
3
|
Rey-Velasco X, Deulofeu-Capo O, Sanz-Sáez I, Cardelús C, Ferrera I, Gasol JM, Sánchez O. Expanding success in the isolation of abundant marine bacteria after reduction in grazing and viral pressure and increase in nutrient availability. Microbiol Spectr 2023; 11:e0089023. [PMID: 37747249 PMCID: PMC10580928 DOI: 10.1128/spectrum.00890-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/03/2023] [Indexed: 09/26/2023] Open
Abstract
Isolation of microorganisms is a useful approach to gathering knowledge about their genomic properties, physiology, and ecology, in addition to allowing the characterization of novel taxa. We performed an extensive isolation effort on samples from seawater manipulation experiments that were carried out during the four astronomical seasons in a coastal site of the northwest Mediterranean to evaluate the impact of grazing, viral mortality, resource competition reduction, and light presence/absence on bacterioplankton growth. Isolates were retrieved using two growth media, and their full 16S rRNA gene was sequenced to assess their identity and calculate their culturability across seasons and experimental conditions. A total of 1,643 isolates were obtained, mainly affiliated to the classes Gammaproteobacteria (44%), Alphaproteobacteria (26%), and Bacteroidia (17%). Isolates pertaining to class Gammaproteobacteria were the most abundant in all experiments, while Bacteroidia were preferentially enriched in the treatments with reduced grazing. Sixty-one isolates had a similarity below 97% to cultured taxa and are thus putatively novel. Comparison of isolate sequences with 16S rRNA gene amplicon sequences from the same samples showed that the percentage of reads corresponding to isolates was 21.4% within the whole data set, with dramatic increases in the summer virus-reduced (71%) and diluted (47%) treatments. In fact, we were able to isolate the top 10 abundant taxa in several experiments and from the whole data set. We also show that top-down and bottom-up controls differentially affect taxa in terms of culturability. Our results indicate that culturing marine bacteria using agar plates can be successful in certain ecological situations. IMPORTANCE Bottom-up and top-down controls greatly influence marine microbial community composition and dynamics, which in turn have effects on their culturability. We isolated a high amount of heterotrophic bacterial strains from experiments where seawater environmental conditions had been manipulated and found that decreasing grazing and viral pressure as well as rising nutrient availability are key factors increasing the success in culturing marine bacteria. Our data hint at factors influencing culturability and underpin bacterial cultures as a powerful way to discover new taxa.
Collapse
Affiliation(s)
| | - Ona Deulofeu-Capo
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Isabel Sanz-Sáez
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
- Instituto de Diagnóstico Ambiental y Estudios del Agua (IDAEA-CSIC), Barcelona, Catalonia, Spain
| | - Clara Cardelús
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Isabel Ferrera
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, (IEO-CSIC), Fuengirola, Málaga, Spain
| | - Josep M. Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| |
Collapse
|
4
|
Sanz-Sáez I, Sánchez P, Salazar G, Sunagawa S, de Vargas C, Bowler C, Sullivan MB, Wincker P, Karsenti E, Pedrós-Alió C, Agustí S, Gojobori T, Duarte CM, Gasol JM, Sánchez O, Acinas SG. Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation. ISME COMMUNICATIONS 2023; 3:92. [PMID: 37660234 PMCID: PMC10475052 DOI: 10.1038/s43705-023-00290-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 09/04/2023]
Abstract
Traditional culture techniques usually retrieve a small fraction of the marine microbial diversity, which mainly belong to the so-called rare biosphere. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean. Here, we examined the fraction of heterotrophic bacterial communities in photic and deep ocean layers that could be recovered by culture-dependent techniques at a large scale. We compared 16S rRNA gene sequences from a collection of 2003 cultured heterotrophic marine bacteria with global 16S rRNA metabarcoding datasets (16S TAGs) covering surface, mesopelagic and bathypelagic ocean samples that included 16 of the 23 samples used for isolation. These global datasets represent 60 322 unique 16S amplicon sequence variants (ASVs). Our results reveal a significantly higher proportion of isolates identical to ASVs in deeper ocean layers reaching up to 28% of the 16S TAGs of the bathypelagic microbial communities, which included the isolation of 3 of the top 10 most abundant 16S ASVs in the global bathypelagic ocean, related to the genera Sulfitobacter, Halomonas and Erythrobacter. These isolates contributed differently to the prokaryotic communities across different plankton size fractions, recruiting between 38% in the free-living fraction (0.2-0.8 µm) and up to 45% in the largest particles (20-200 µm) in the bathypelagic ocean. Our findings support the hypothesis that sinking particles in the bathypelagic act as resource-rich habitats, suitable for the growth of heterotrophic bacteria with a copiotroph lifestyle that can be cultured, and that these cultivable bacteria can also thrive as free-living bacteria.
Collapse
Affiliation(s)
- Isabel Sanz-Sáez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain.
| | - Pablo Sánchez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, CH-8093, Zurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, CH-8093, Zurich, Switzerland
| | - Colomban de Vargas
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering; The Ohio State University, Columbus, OH, 43210, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France
| | - Eric Karsenti
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016, Paris, France
- Directors' Research European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Carlos Pedrós-Alió
- Department of Systems Biology, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Susana Agustí
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain.
| |
Collapse
|
5
|
Schultz J, Modolon F, Peixoto RS, Rosado AS. Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles. Front Microbiol 2023; 14:1167718. [PMID: 37333658 PMCID: PMC10272570 DOI: 10.3389/fmicb.2023.1167718] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/09/2023] [Indexed: 06/20/2023] Open
Abstract
More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth's microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed "microbial dark matter." Little is known regarding the ecological functions and biotechnological potential of these underexplored extremophiles, thus representing a vast untapped and uncharacterized biological resource. Advances in microbial cultivation approaches are key for a detailed and comprehensive characterization of the roles of these microbes in shaping the environment and, ultimately, for their biotechnological exploitation, such as for extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, and pigments, among others), astrobiology, and space exploration. Additional efforts to enhance culturable diversity are required due to the challenges imposed by extreme culturing and plating conditions. In this review, we summarize methods and technologies used to recover the microbial diversity of extreme environments, while discussing the advantages and disadvantages associated with each of these approaches. Additionally, this review describes alternative culturing strategies to retrieve novel taxa with their unknown genes, metabolisms, and ecological roles, with the ultimate goal of increasing the yields of more efficient bio-based products. This review thus summarizes the strategies used to unveil the hidden diversity of the microbiome of extreme environments and discusses the directions for future studies of microbial dark matter and its potential applications in biotechnology and astrobiology.
Collapse
Affiliation(s)
- Júnia Schultz
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Flúvio Modolon
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Silva Peixoto
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexandre Soares Rosado
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| |
Collapse
|
6
|
Ayon NJ. High-Throughput Screening of Natural Product and Synthetic Molecule Libraries for Antibacterial Drug Discovery. Metabolites 2023; 13:625. [PMID: 37233666 PMCID: PMC10220967 DOI: 10.3390/metabo13050625] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/27/2023] Open
Abstract
Due to the continued emergence of resistance and a lack of new and promising antibiotics, bacterial infection has become a major public threat. High-throughput screening (HTS) allows rapid screening of a large collection of molecules for bioactivity testing and holds promise in antibacterial drug discovery. More than 50% of the antibiotics that are currently available on the market are derived from natural products. However, with the easily discoverable antibiotics being found, finding new antibiotics from natural sources has seen limited success. Finding new natural sources for antibacterial activity testing has also proven to be challenging. In addition to exploring new sources of natural products and synthetic biology, omics technology helped to study the biosynthetic machinery of existing natural sources enabling the construction of unnatural synthesizers of bioactive molecules and the identification of molecular targets of antibacterial agents. On the other hand, newer and smarter strategies have been continuously pursued to screen synthetic molecule libraries for new antibiotics and new druggable targets. Biomimetic conditions are explored to mimic the real infection model to better study the ligand-target interaction to enable the designing of more effective antibacterial drugs. This narrative review describes various traditional and contemporaneous approaches of high-throughput screening of natural products and synthetic molecule libraries for antibacterial drug discovery. It further discusses critical factors for HTS assay design, makes a general recommendation, and discusses possible alternatives to traditional HTS of natural products and synthetic molecule libraries for antibacterial drug discovery.
Collapse
Affiliation(s)
- Navid J Ayon
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| |
Collapse
|
7
|
Gasparek M, Steel H, Papachristodoulou A. Deciphering mechanisms of production of natural compounds using inducer-producer microbial consortia. Biotechnol Adv 2023; 64:108117. [PMID: 36813010 DOI: 10.1016/j.biotechadv.2023.108117] [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: 07/21/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/22/2023]
Abstract
Living organisms produce a wide range of metabolites. Because of their potential antibacterial, antifungal, antiviral, or cytostatic properties, such natural molecules are of high interest to the pharmaceutical industry. In nature, these metabolites are often synthesized via secondary metabolic biosynthetic gene clusters that are silent under the typical culturing conditions. Among different techniques used to activate these silent gene clusters, co-culturing of "producer" species with specific "inducer" microbes is a particularly appealing approach due to its simplicity. Although several "inducer-producer" microbial consortia have been reported in the literature and hundreds of different secondary metabolites with attractive biopharmaceutical properties have been described as a result of co-cultivating inducer-producer consortia, less attention has been devoted to the understanding of the mechanisms and possible means of induction for production of secondary metabolites in co-cultures. This lack of understanding of fundamental biological functions and inter-species interactions significantly limits the diversity and yield of valuable compounds using biological engineering tools. In this review, we summarize and categorize the known physiological mechanisms of production of secondary metabolites in inducer-producer consortia, and then discuss approaches that could be exploited to optimize the discovery and production of secondary metabolites.
Collapse
Affiliation(s)
- Miroslav Gasparek
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom.
| | - Harrison Steel
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
| | | |
Collapse
|
8
|
Nguyen-Le TA, Zhao X, Bachmann M, Ruelens P, de Visser JAGM, Baraban L. High-Throughput Gel Microbeads as Incubators for Bacterial Competition Study. MICROMACHINES 2023; 14:645. [PMID: 36985052 PMCID: PMC10058504 DOI: 10.3390/mi14030645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Bacteria primarily live in structured environments, such as colonies and biofilms, attached to surfaces or growing within soft tissues. They are engaged in local competitive and cooperative interactions impacting our health and well-being, for example, by affecting population-level drug resistance. Our knowledge of bacterial competition and cooperation within soft matrices is incomplete, partly because we lack high-throughput tools to quantitatively study their interactions. Here, we introduce a method to generate a large amount of agarose microbeads that mimic the natural culture conditions experienced by bacteria to co-encapsulate two strains of fluorescence-labeled Escherichia coli. Focusing specifically on low bacterial inoculum (1-100 cells/capsule), we demonstrate a study on the formation of colonies of both strains within these 3D scaffolds and follow their growth kinetics and interaction using fluorescence microscopy in highly replicated experiments. We confirmed that the average final colony size is inversely proportional to the inoculum size in this semi-solid environment as a result of limited available resources. Furthermore, the colony shape and fluorescence intensity per colony are distinctly different in monoculture and co-culture. The experimental observations in mono- and co-culture are compared with predictions from a simple growth model. We suggest that our high throughput and small footprint microbead system is an excellent platform for future investigation of competitive and cooperative interactions in bacterial communities under diverse conditions, including antibiotics stress.
Collapse
Affiliation(s)
- Trang Anh Nguyen-Le
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), 01328 Dresden, Germany
| | - Xinne Zhao
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), 01328 Dresden, Germany
| | - Michael Bachmann
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), 01328 Dresden, Germany
- Tumor Immunology, University Cancer Center (UCC), University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 01309 Dresden, Germany
| | - Philip Ruelens
- Department of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - J. Arjan G. M. de Visser
- Department of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Larysa Baraban
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), 01328 Dresden, Germany
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01069 Dresden, Germany
| |
Collapse
|
9
|
Kapinusova G, Lopez Marin MA, Uhlik O. Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons. Front Microbiol 2023; 14:1089630. [PMID: 36960281 PMCID: PMC10027941 DOI: 10.3389/fmicb.2023.1089630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/10/2023] [Indexed: 03/09/2023] Open
Abstract
In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial "dark matter" hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.
Collapse
Affiliation(s)
| | | | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| |
Collapse
|
10
|
Duran C, Zhang S, Yang C, Falco ML, Cravo-Laureau C, Suzuki-Minakuchi C, Nojiri H, Duran R, Sassa F. Low-cost gel-filled microwell array device for screening marine microbial consortium. Front Microbiol 2022; 13:1031439. [PMID: 36590440 PMCID: PMC9800614 DOI: 10.3389/fmicb.2022.1031439] [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: 08/30/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
In order to exploit the microbes present in the environment for their beneficial resources, effective selection and isolation of microbes from environmental samples is essential. In this study, we fabricated a gel-filled microwell array device using resin for microbial culture. The device has an integrated sealing mechanism that enables high-density isolation based on the culture of microorganisms; the device is easily manageable, facilitating observation using bright-field microscopy. This low-cost device made from polymethyl methacrylate (PMMA)/polyethylene terephthalate (PET) has 900 microwells (600 μm × 600 μm × 700 μm) filled with a microbial culture gel medium in glass slide-sized plates. It also has grooves for maintaining the moisture content in the micro-gel. The partition wall between the wells has a highly hydrophobic coating to inhibit microbial migration to neighboring wells and to prevent exchange of liquid substances. After being hermetically sealed, the device can maintain moisture in the agarose gels for 7 days. In the bacterial culture experiment using this device, environmental bacteria were isolated and cultured in individual wells after 3 days. Moreover, the isolated bacteria were then picked up from wells and re-cultured. This device is effective for the first screening of microorganisms from marine environmental samples.
Collapse
Affiliation(s)
- Clelia Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Shiyi Zhang
- Graduate School of Information Science and Electrical Engineering, Kyushu University, Fukuoka, Japan
| | - Chongyang Yang
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Maria Lorena Falco
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Chiho Suzuki-Minakuchi
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Hideaki Nojiri
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France,*Correspondence: Robert Duran, ; Fumihiro Sassa,
| | - Fumihiro Sassa
- Graduate School of Information Science and Electrical Engineering, Kyushu University, Fukuoka, Japan,*Correspondence: Robert Duran, ; Fumihiro Sassa,
| |
Collapse
|
11
|
Lei W, Deckers A, Luchena C, Popova A, Reischl M, Jung N, Bräse S, Schwartz T, Krimmelbein IK, Tietze LF, Levkin PA. Droplet Microarray as a Powerful Platform for Seeking New Antibiotics Against Multidrug-Resistant Bacteria. Adv Biol (Weinh) 2022; 6:e2200166. [PMID: 35843867 DOI: 10.1002/adbi.202200166] [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: 06/17/2022] [Revised: 07/01/2022] [Indexed: 01/28/2023]
Abstract
Multidrug-resistant (MDR) bacteria is a severe threat to public health. Therefore, it is urgent to establish effective screening systems for identifying novel antibacterial compounds. In this study, a highly miniaturized droplet microarray (DMA) based high-throughput screening system is established to screen over 2000 compounds for their antimicrobial properties against carbapenem-resistant Klebsiella pneumoniae and methicillin resistant Staphylococcus aureus (MRSA). The DMA consists of an array of hydrophilic spots divided by superhydrophobic borders. Due to the differences in the surface wettability between the spots and the borders, arrays of hundreds of nanoliter-sized droplets containing bacteria and different drugs can be generated for screening applications. A simple colorimetric viability readout utilizing a conventional photo scanner is developed for fast single-step detection of the inhibitory effect of the compounds on bacterial growth on the whole array. Six hit compounds, including coumarins and structurally simplified estrogen analogs are identified in the primary screening and validated with minimum inhibition concentration assay for their antibacterial effect. This study demonstrates that the DMA-based high-throughput screening system enables the identification of potential antibiotics from novel synthetic compound libraries, offering opportunities for development of new treatments against multidrug-resistant bacteria.
Collapse
Affiliation(s)
- Wenxi Lei
- Institute of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Anke Deckers
- Institute of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Charlotte Luchena
- Institute of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Anna Popova
- Institute of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Markus Reischl
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Nicole Jung
- Institute of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.,Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Thomas Schwartz
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Ilga K Krimmelbein
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität, Tammannstr. 2, D-37077, Göttingen, Germany
| | - Lutz F Tietze
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität, Tammannstr. 2, D-37077, Göttingen, Germany
| | - Pavel A Levkin
- Institute of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.,Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| |
Collapse
|
12
|
Abstract
The vast majority of environmental microbes have not yet been cultured, and most of the knowledge on coral-associated microbes (CAMs) has been generated from amplicon sequencing and metagenomes. However, exploring cultured CAMs is key for a detailed and comprehensive characterization of the roles of these microbes in shaping coral health and, ultimately, for their biotechnological use as, for example, coral probiotics and other natural products. Here, the strategies and technologies that have been used to access cultured CAMs are presented, while advantages and disadvantages associated with each of these strategies are discussed. We highlight the existing gaps and potential improvements in culture-dependent methodologies, indicating several possible alternatives (including culturomics and in situ diffusion devices) that could be applied to retrieve the CAM "dark matter" (i.e., the currently undescribed CAMs). This study provides the most comprehensive synthesis of the methodologies used to recover the cultured coral microbiome to date and draws suggestions for the development of the next generation of CAM culturomics.
Collapse
|
13
|
Yu Y, Wen H, Li S, Cao H, Li X, Ma Z, She X, Zhou L, Huang S. Emerging microfluidic technologies for microbiome research. Front Microbiol 2022; 13:906979. [PMID: 36051769 PMCID: PMC9424851 DOI: 10.3389/fmicb.2022.906979] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
The importance of the microbiome is increasingly prominent. For example, the human microbiome has been proven to be strongly associated with health conditions, while the environmental microbiome is recognized to have a profound influence on agriculture and even the global climate. Furthermore, the microbiome can serve as a fascinating reservoir of genes that encode tremendously valuable compounds for industrial and medical applications. In the past decades, various technologies have been developed to better understand and exploit the microbiome. In particular, microfluidics has demonstrated its strength and prominence in the microbiome research. By taking advantage of microfluidic technologies, inherited shortcomings of traditional methods such as low throughput, labor-consuming, and high-cost are being compensated or bypassed. In this review, we will summarize a broad spectrum of microfluidic technologies that have addressed various needs in the field of microbiome research, as well as the achievements that were enabled by the microfluidics (or technological advances). Finally, how microfluidics overcomes the limitations of conventional methods by technology integration will also be discussed.
Collapse
Affiliation(s)
- Yue Yu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hui Wen
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Sihong Li
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Haojie Cao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xuefei Li
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhixin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaoyi She
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lei Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Shuqiang Huang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Shuqiang Huang,
| |
Collapse
|
14
|
Lloréns-Rico V, Simcock JA, Huys GR, Raes J. Single-cell approaches in human microbiome research. Cell 2022; 185:2725-2738. [DOI: 10.1016/j.cell.2022.06.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/20/2022] [Accepted: 06/20/2022] [Indexed: 10/17/2022]
|
15
|
Luo L, Xu Y, Chang Y, Sun B, Zhang L, Zhao Z, Liang L. Microbiota Comparison of Amur ide ( Leuciscus waleckii) Intestine and Waters at Alkaline Water and Freshwater as the Living Environment. Front Microbiol 2022; 13:881132. [PMID: 35602074 PMCID: PMC9114670 DOI: 10.3389/fmicb.2022.881132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
The intestinal microbiota of marine animals was influenced by the water and environment in which they live. The Amur ide (Leuciscus waleckii) adapts to extremely high alkalinity and is an ideal material for aquacultural studies of alkaline adaptation. In this study, we screened intestinal indicator flora and functional redundancy of intestinal colonies in alkaline-water species (AW) and freshwater species (FW) of Amur ide (L. waleckii) in these different aquatic environments. The available vs. community composition correlations were then predicted by contrasting each other with the flora contained in environmental water samples. Here, five microbial species and six genera were identified owing to the classifiable sequence. The intestinal microbiota that existed in AW and FW had approximately 1/3 of the operational taxonomic units in the respective living water environments, meaning gut microbes in the aqueous habitats will have an influential association with gut microbes in AW and FW. Compared to the bacterial composition of the FW intestine and that present in freshwater, Moraxella osloensis, Psychrobacter maritimus, and Psychrobacter faecalis were significantly enriched in the intestine of AW and alkaline water samples. In the FW intestine and freshwater samples, however, Cryptomonas curvata and Polynucleobacter asymbioticus were highly improved, which can be summarized as Enterobacter sp., the predominant population in the AW gut, while Aeromonas and Ralstonia being primarily present in FW intestines. Photosynthetic bacteria were most significant in both water samples. The results indicated that the intestinal microbiota composition, abundance, and diversity of AW and FW were quite different. In contrast, the microbial composition of the additional alkaline water and freshwater environments showed slight differences. This study expects to enhance our understanding of the alkalinity tolerance of L. waleckii, which will be provided for the breeding of fish living in alkaline water, and push the development of alkaline water resources with increased efficiency.
Collapse
Affiliation(s)
- Liang Luo
- Key Laboratory of Cold Water Fish Germplasm Resources and Multiplication and Cultivation of Heilongjiang Province, Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
| | - Yue Xu
- The Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Yumei Chang
- Key Laboratory of Cold Water Fish Germplasm Resources and Multiplication and Cultivation of Heilongjiang Province, Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
| | - Bo Sun
- Key Laboratory of Cold Water Fish Germplasm Resources and Multiplication and Cultivation of Heilongjiang Province, Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
| | - Limin Zhang
- Key Laboratory of Cold Water Fish Germplasm Resources and Multiplication and Cultivation of Heilongjiang Province, Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
| | - Zhigang Zhao
- Key Laboratory of Cold Water Fish Germplasm Resources and Multiplication and Cultivation of Heilongjiang Province, Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
| | - Liqun Liang
- Key Laboratory of Cold Water Fish Germplasm Resources and Multiplication and Cultivation of Heilongjiang Province, Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
| |
Collapse
|
16
|
Jin S, Wetzel D, Schirmer M. Deciphering mechanisms and implications of bacterial translocation in human health and disease. Curr Opin Microbiol 2022; 67:102147. [PMID: 35461008 DOI: 10.1016/j.mib.2022.102147] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 12/12/2022]
Abstract
Significant increases in potential microbial translocation, especially along the oral-gut axis, have been identified in many immune-related and inflammatory diseases, such as inflammatory bowel disease, colorectal cancer, rheumatoid arthritis, and liver cirrhosis, for which we currently have no cure or long-term treatment options. Recent advances in computational and experimental omics approaches now enable strain tracking, functional profiling, and strain isolation in unprecedented detail, which has the potential to elucidate the causes and consequences of microbial translocation. In this review, we discuss current evidence for the detection of bacterial translocation, examine different translocation axes with a primary focus on the oral-gut axis, and outline currently known translocation mechanisms and how they adversely affect the host in disease. Finally, we conclude with an overview of state-of-the-art computational and experimental tools for strain tracking and highlight the required next steps to elucidate the role of bacterial translocation in human health.
Collapse
Affiliation(s)
- Shen Jin
- ZIEL - Institute for Food and Health, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
| | - Daniela Wetzel
- ZIEL - Institute for Food and Health, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
| | - Melanie Schirmer
- ZIEL - Institute for Food and Health, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany.
| |
Collapse
|
17
|
Davidson SL, Niepa THR. Micro-Technologies for Assessing Microbial Dynamics in Controlled Environments. Front Microbiol 2022; 12:745835. [PMID: 35154021 PMCID: PMC8831547 DOI: 10.3389/fmicb.2021.745835] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
With recent advances in microfabrication technologies, the miniaturization of traditional culturing techniques has provided ideal methods for interrogating microbial communities in a confined and finely controlled environment. Micro-technologies offer high-throughput screening and analysis, reduced experimental time and resources, and have low footprint. More importantly, they provide access to culturing microbes in situ in their natural environments and similarly, offer optical access to real-time dynamics under a microscope. Utilizing micro-technologies for the discovery, isolation and cultivation of "unculturable" species will propel many fields forward; drug discovery, point-of-care diagnostics, and fundamental studies in microbial community behaviors rely on the exploration of novel metabolic pathways. However, micro-technologies are still largely proof-of-concept, and scalability and commercialization of micro-technologies will require increased accessibility to expensive equipment and resources, as well as simpler designs for usability. Here, we discuss three different miniaturized culturing practices; including microarrays, micromachined devices, and microfluidics; advancements to the field, and perceived challenges.
Collapse
Affiliation(s)
- Shanna-Leigh Davidson
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Tagbo H. R. Niepa
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA, United States
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, United States
- The McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| |
Collapse
|
18
|
Heuer C, Bahnemann J, Scheper T, Segal E. Paving the Way to Overcome Antifungal Drug Resistance: Current Practices and Novel Developments for Rapid and Reliable Antifungal Susceptibility Testing. SMALL METHODS 2021; 5:e2100713. [PMID: 34927979 DOI: 10.1002/smtd.202100713] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/05/2021] [Indexed: 06/14/2023]
Abstract
The past year has established the link between the COVID-19 pandemic and the global spread of severe fungal infections; thus, underscoring the critical need for rapid and realizable fungal disease diagnostics. While in recent years, health authorities, such as the Centers for Disease Control and Prevention, have reported the alarming emergence and spread of drug-resistant pathogenic fungi and warned against the devastating consequences, progress in the diagnosis and treatment of fungal infections is limited. Early diagnosis and patient-tailored therapy are established to be key in reducing morbidity and mortality associated with fungal (and cofungal) infections. As such, antifungal susceptibility testing (AFST) is crucial in revealing susceptibility or resistance of these pathogens and initiating correct antifungal therapy. Today, gold standard AFST methods require several days for completion, and thus this much delayed time for answer limits their clinical application. This review focuses on the advancements made in developing novel AFST techniques and discusses their implications in the context of the practiced clinical workflow. The aim of this work is to highlight the advantages and drawbacks of currently available methods and identify the main gaps hindering their progress toward clinical application.
Collapse
Affiliation(s)
- Christopher Heuer
- Institute of Technical Chemistry, Leibniz University Hannover, 30167, Hannover, Germany
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 320003, Israel
| | - Janina Bahnemann
- Institute of Technical Chemistry, Leibniz University Hannover, 30167, Hannover, Germany
| | - Thomas Scheper
- Institute of Technical Chemistry, Leibniz University Hannover, 30167, Hannover, Germany
| | - Ester Segal
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 320003, Israel
| |
Collapse
|
19
|
Rämä T, Quandt CA. Improving Fungal Cultivability for Natural Products Discovery. Front Microbiol 2021; 12:706044. [PMID: 34603232 PMCID: PMC8481835 DOI: 10.3389/fmicb.2021.706044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
The pool of fungal secondary metabolites can be extended by activating silent gene clusters of cultured strains or by using sensitive biological assays that detect metabolites missed by analytical methods. Alternatively, or in parallel with the first approach, one can increase the diversity of existing culture collections to improve the access to new natural products. This review focuses on the latter approach of screening previously uncultured fungi for chemodiversity. Both strategies have been practiced since the early days of fungal biodiscovery, yet relatively little has been done to overcome the challenge of cultivability of as-yet-uncultivated fungi. Whereas earlier cultivability studies using media formulations and biological assays to scrutinize fungal growth and associated factors were actively conducted, the application of modern omics methods remains limited to test how to culture the fungal dark matter and recalcitrant groups of described fungi. This review discusses the development of techniques to increase the cultivability of filamentous fungi that include culture media formulations and the utilization of known chemical growth factors, in situ culturing and current synthetic biology approaches that build upon knowledge from sequenced genomes. We list more than 100 growth factors, i.e., molecules, biological or physical factors that have been demonstrated to induce spore germination as well as tens of inducers of mycelial growth. We review culturing conditions that can be successfully manipulated for growth of fungi and visit recent information from omics methods to discuss the metabolic basis of cultivability. Earlier work has demonstrated the power of co-culturing fungi with their host, other microorganisms or their exudates to increase their cultivability. Co-culturing of two or more organisms is also a strategy used today for increasing cultivability. However, fungi possess an increased risk for cross-contaminations between isolates in existing in situ or microfluidics culturing devices. Technological improvements for culturing fungi are discussed in the review. We emphasize that improving the cultivability of fungi remains a relevant strategy in drug discovery and underline the importance of ecological and taxonomic knowledge in culture-dependent drug discovery. Combining traditional and omics techniques such as single cell or metagenome sequencing opens up a new era in the study of growth factors of hundreds of thousands of fungal species with high drug discovery potential.
Collapse
Affiliation(s)
- Teppo Rämä
- Marbio, Norwegian College of Fishery Science, University of Tromsø – The Arctic University of Norway, Tromsø, Norway
| | - C. Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| |
Collapse
|
20
|
Sung JY, Lee YJ, Cho YJ, Shin MN, Lee SJ, Lee HS, Koh H, Bae JW, Shin JH, Kim HJ, Lee DW. A large-scale metagenomic study for enzyme profiles using the focused identification of the NGS-based definitive enzyme research (FINDER) strategy. Biotechnol Bioeng 2021; 118:4360-4374. [PMID: 34309016 DOI: 10.1002/bit.27904] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/23/2021] [Accepted: 07/23/2021] [Indexed: 11/09/2022]
Abstract
Excavating the molecular details of many diverse enzymes from metagenomes remains challenging in agriculture, food, health, and environmental fields. We present a versatile method that accelerates metabolic enzyme discovery for highly selective gene capture in metagenomes using next-generation sequencing. Culture-independent enzyme mining of environmental DNA is based on a set of short identifying degenerate sequences specific for a wide range of enzyme superfamilies, followed by multiplexed DNA barcode sequencing. A strategy of 'focused identification of next-generation sequencing-based definitive enzyme research' enabled us to generate targeted enzyme datasets from metagenomes, resulting in minimal hands-on obtention of high-throughput biological diversity and potential function profiles, without being time-consuming. This method also provided a targeted inventory of predicted proteins and molecular features of metabolic activities from several metagenomic samples. We suggest that the efficiency and sensitivity of this method will accelerate the decryption of microbial diversity and the signature of proteins and their metabolism from environmental samples.
Collapse
Affiliation(s)
- Jae-Yoon Sung
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Yong-Jik Lee
- Department of Bio-Cosmetics, Seowon University, Chung-Ju, South Korea
| | - Yong-Joon Cho
- Department of Biological Sciences and Research Institute of Basic Sciences, Seoul National University, Seoul, South Korea
| | - Myeong-Na Shin
- Department of Central Area Crop Science, NICS, RDA, Suwon, South Korea
| | - Sang-Jae Lee
- Major in Food Biotechnology, Silla University, Busan, South Korea
| | - Han-Seung Lee
- Major in Food Biotechnology, Silla University, Busan, South Korea
| | - Hong Koh
- Department of Pediatrics, Yonsei University, Seoul, South Korea
| | - Jin-Woo Bae
- Department of Biology, Kyung Hee University, Seoul, South Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Hyun Jung Kim
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, USA
| | - Dong-Woo Lee
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| |
Collapse
|
21
|
Nemr RA, Patz S, Abdelwakeel SM, Khalil M, Ben Djadid A, Abdelfadeel MR, Morsi AT, Goda HA, Youssef HH, Hamza M, Abbas M, Fayez M, El-Sahhar KF, Becker M, Ruppel S, Hegazi NA. Culture Media Based on Leaf Strips/Root Segments Create Compatible Host/Organ Setup for in vitro Cultivation of Plant Microbiota. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.660790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Plant microbiota have co-evolved with their associated plants in the entire holobiont, and their assemblages support diversity and productivity on our planet. Of importance is in vitro cultivation and identification of their hub taxa for possible core microbiome modification. Recently, we introduced the in situ-similis culturing strategy, based on the use of plant leaves as a platform for in vitro growth of plant microbiota. Here, the strategy is further extended by exploring plant organ compatible cultivation of plant microbiota when grown on corresponding leaf/root-based culture media. Pooling the advantages of MPN enrichment methodology together with natural plant-only-based culture media, the introduced method efficiently constructed a nutritional milieu governed by vegan nutrients of plant origin, i.e., leaf strips/root segments, immersed in plain semi-solid water agar. MPN estimates exceeded log 7.0 and 4.0 g−1 of endo-rhizosphere and endo-phyllosphere, respectively, of maize and sunflower; being proportionate to those obtained for standard culture media. With sunflower, PCR-DGGE analyses indicated divergence in community composition of cultivable endophytes primarily attributed to culture media, signaling a certain degree of plant organ affinity/compatibility. Based on 16S rRNA gene sequencing of bacterial isolates, 20 genera comprising 32 potential species were enriched; belonged to Bacteroidetes, Firmicutes, and Alpha-/Gammaproteobacteria. The described cultivation strategy furnished diversified nutritive platform in terms of homologous/heterologous plant organ-based medium and ambient/limited oxygenic cultivation procedure. Duly, cultivability extended to > 8 genera: Bosea, Brevundimonas, Chitinophaga, Pseudoxanthomonas, Sphingobacterium Caulobacter, Scandinavium, and Starkeya; the latter three genera were not yet reported for Sunflower, and possible unknown species or even one new putative genus. Thus, both potential members of the major microbiome and rare isolates of satellite microbiomes can be isolated using the presented method. It is a feasible addition to traditional cultivation methods to explore new potential resources of PGPB for future biotechnological applications.
Collapse
|
22
|
A Pandemic Early Warning System Decision Analysis Concept Utilizing a Distributed Network of Air Samplers via Electrostatic Air Precipitation. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11115308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The COVID-19 pandemic has highlighted the need for improved airborne infectious disease monitoring capability. A key challenge is to develop a technology that captures pathogens for identification from ambient air. While pathogenic species vary significantly in size and shape, for effective airborne pathogen detection the target species must be selectively captured from aerosolized droplets. Captured pathogens must then be separated from the remaining aerosolized droplet content and characterized in real-time. While improvements have been made with clinical laboratory automated sorting in culture media based on morphological characteristics of cells, this application has not extended to aerosol samples containing bacteria, viruses, spores, or prions. This manuscript presents a strategy and a model for the development of an airborne pandemic early warning system using aerosol sampling.
Collapse
|
23
|
Zhang CJ, Chen YL, Sun YH, Pan J, Cai MW, Li M. Diversity, metabolism and cultivation of archaea in mangrove ecosystems. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:252-262. [PMID: 37073347 PMCID: PMC10077227 DOI: 10.1007/s42995-020-00081-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/19/2020] [Indexed: 05/03/2023]
Abstract
Mangroves comprise a globally significant intertidal ecosystem that contains a high diversity of microorganisms, including fungi, bacteria and archaea. Archaea is a major domain of life that plays important roles in biogeochemical cycles in these ecosystems. In this review, the potential roles of archaea in mangroves are briefly highlighted. Then, the diversity and metabolism of archaeal community of mangrove ecosystems across the world are summarized and Bathyarchaeota, Euryarchaeota, Thaumarchaeota, Woesearchaeota, and Lokiarchaeota are confirmed as the most abundant and ubiquitous archaeal groups. The metabolic potential of these archaeal groups indicates their important ecological function in carbon, nitrogen and sulfur cycling. Finally, some cultivation strategies that could be applied to uncultivated archaeal lineages from mangrove wetlands are suggested, including refinements to traditional cultivation methods based on genomic and transcriptomic information, and numerous innovative cultivation techniques such as single-cell isolation and high-throughput culturing (HTC). These cultivation strategies provide more opportunities to obtain previously uncultured archaea.
Collapse
Affiliation(s)
- Cui-Jing Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Yu-Lian Chen
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Yi-Hua Sun
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Ming-Wei Cai
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| |
Collapse
|
24
|
Mahler L, Niehs SP, Martin K, Weber T, Scherlach K, Hertweck C, Roth M, Rosenbaum MA. Highly parallelized droplet cultivation and prioritization of antibiotic producers from natural microbial communities. eLife 2021; 10:64774. [PMID: 33764297 PMCID: PMC8081529 DOI: 10.7554/elife.64774] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/19/2021] [Indexed: 11/13/2022] Open
Abstract
Antibiotics from few culturable microorganisms have saved millions of lives since the 20th century. But with resistance formation, these compounds become increasingly ineffective, while the majority of microbial and with that chemical compound diversity remains inaccessible for cultivation and exploration. Culturing recalcitrant bacteria is a stochastic process. But conventional methods are limited to low throughput. By increasing (i) throughput and (ii) sensitivity by miniaturization, we innovate microbiological cultivation to comply with biological stochasticity. Here, we introduce a droplet-based microscale cultivation system, which is directly coupled to a high-throughput screening for antimicrobial activity prior to strain isolation. We demonstrate that highly parallelized in-droplet cultivation starting from single cells results in the cultivation of yet uncultured species and a significantly higher bacterial diversity than standard agar plate cultivation. Strains able to inhibit intact reporter strains were isolated from the system. A variety of antimicrobial compounds were detected for a selected potent antibiotic producer.
Collapse
Affiliation(s)
- Lisa Mahler
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Sarah P Niehs
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Karin Martin
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Thomas Weber
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Kirstin Scherlach
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Christian Hertweck
- Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany.,Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Martin Roth
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| |
Collapse
|
25
|
Huang X, Li P, Zhou M, Li Y, Ou X, Chen P, Guggenberger G, Liu BF. A high-throughput ultrasonic spraying inoculation method promotes colony cultivation of rare microbial species. Environ Microbiol 2021; 23:1275-1285. [PMID: 33400374 DOI: 10.1111/1462-2920.15386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/28/2020] [Accepted: 01/03/2021] [Indexed: 11/30/2022]
Abstract
Current method for obtaining microbial colonies still relies on traditional dilution and spreading plate (DSP) procedures, which is labor-intensive, skill-dependent, low-throughput and inevitably causing dilution-to-extinction of rare microorganisms. Herein, we proposed a novel ultrasonic spraying inoculation (USI) method that disperses microbial suspensions into millions of aerosols containing single cells, which lately be deposited freely on a gel plate to achieve high-throughput culturing of colonies. Compared with DSP, USI significantly increased both distributing uniformity and throughput of the colonies on agar plates, improving the minimal colony-forming abundance of rare Escherichia coli mixed in a lake sample from 1% to 0.01%. Applying this novel USI to a lake sample, 16 cellulose-degrading colonies were screened out among 4766 colonies on an enlarged 150-mm-diameter LB plate. Meanwhile, they could only be occasionally observed when using commonly used DSP procedures. 16S rRNA sequencing further showed that USI increased colony-forming species from 11 (by DSP) to 23, including seven completely undetectable microorganisms in DSP-reared communities. In addition to avoidance of dilution-to-extinction, operation-friendly USI efficiently inoculated microbial samples on the agar plate in a high-throughput and single-cell form, which eliminated masking or out-competition from other species in associated groups, thereby improving rare species cultivability.
Collapse
Affiliation(s)
- Xizhi Huang
- Britton Chance Centre for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Pengjie Li
- Britton Chance Centre for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Mengfan Zhou
- Britton Chance Centre for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yiwei Li
- Britton Chance Centre for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaowen Ou
- Hubei Key Laboratory of Purification and Application of Plant Anti-Cancer Active Ingredients, Department of Chemistry and Life Science, Hubei University of Education, No. 129, Gaoxin 2nd Road, East Lake High-Tech Zone, Wuhan, 430205, China
| | - Peng Chen
- Britton Chance Centre for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Georg Guggenberger
- Institute of Soil Science, Leibniz University Hannover, Hannover, 30419, Germany
| | - Bi-Feng Liu
- Britton Chance Centre for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
26
|
Benítez X, Gonzalez EG, García J, Zúñiga P, de la Calle F, Cuevas C. Detection of a pederin-like compound using a dilution-to-extinction-based platform for the isolation of marine bacteria in drug discovery strategies. Microb Biotechnol 2021; 14:241-250. [PMID: 33094913 PMCID: PMC7888454 DOI: 10.1111/1751-7915.13679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 12/24/2022] Open
Abstract
The continued development of culturing technologies for the discovery of new molecules from marine microbes is of paramount importance for drug discovery. Coupled with this, the use of the high-throughput approach shows promise for increasing the number of Gram-negative and non-filamentous bacteria cultures that can be surveyed, since they show a lower potential of bioactivity. In this work, we propose a new strategy of high-throughput cultivation of bacteria inspired by a dilution-to-extinction (DTE) methodology for the isolation of, and screening for, new cytotoxic compound producing marine bacteria. A marine sponge tissue was directly used as inoculum and the results were compared with the data obtained through the direct plating isolation method. Enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) genomic fingerprinting indicated the isolation of four bioactive strains, three of them producers of a pederin-like compound, and the fourth one able to synthesize a different compound, still unidentified, rendered by the DTE approach, in comparison with one bioactive strain identified through the plating method. Analyses based on the 16S rRNA gene data showed the existence of two different species belonging to the genus Labrenzia. The efficiency and diversity ratio in the number of isolates and compounds are discussed. In view of the results, the proposed DTE approach proved to be efficient for the isolation of new cytotoxic compounds of marine origin and pave the way for future potential applications.
Collapse
Affiliation(s)
- Xulio Benítez
- Research and Development AreaPharmaMar S.A.Avda. De los Reyes, 1 P.I. La Mina‐NorteMadridColmenar Viejo28770Spain
| | - Elena G. Gonzalez
- Research and Development AreaPharmaMar S.A.Avda. De los Reyes, 1 P.I. La Mina‐NorteMadridColmenar Viejo28770Spain
| | - Jesus García
- Research and Development AreaPharmaMar S.A.Avda. De los Reyes, 1 P.I. La Mina‐NorteMadridColmenar Viejo28770Spain
| | - Paz Zúñiga
- Research and Development AreaPharmaMar S.A.Avda. De los Reyes, 1 P.I. La Mina‐NorteMadridColmenar Viejo28770Spain
| | - Fernando de la Calle
- Research and Development AreaPharmaMar S.A.Avda. De los Reyes, 1 P.I. La Mina‐NorteMadridColmenar Viejo28770Spain
| | - Carmen Cuevas
- Research and Development AreaPharmaMar S.A.Avda. De los Reyes, 1 P.I. La Mina‐NorteMadridColmenar Viejo28770Spain
| |
Collapse
|
27
|
Ha CWY, Devkota S. The new microbiology: cultivating the future of microbiome-directed medicine. Am J Physiol Gastrointest Liver Physiol 2020; 319:G639-G645. [PMID: 32996782 PMCID: PMC7792672 DOI: 10.1152/ajpgi.00093.2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The discovery of human-associated microscopic life forms has captivated the scientific community since their first documentation in the 17th century. Subsequent isolation and cultivation of microorganisms have spurred great leaps in medicine, including the discovery of antibiotics, identifying pathogens that cause infectious diseases, and vaccine development. The realization that there is a vast discrepancy between the number of microscopic cell counts and how many could thrive in the laboratory motivated the advent of sequencing-based approaches to characterize the uncultured fraction of the microbiota, leading to an unprecedented view into their composition and putative function on all bodily surfaces. It soon became apparent that specific members of the microbiota can be our commensal partners with new implications on various aspects of health, as well as a rich source of therapeutic compounds and tools for biotechnology. Harnessing the immense repertoire of microbial properties, however, inadvertently requires pure cultures for validation and manipulation of candidate genes, proteins, or metabolic pathways, just as mammalian cell culture has become an indispensable tool for mechanistic understanding of host biology. Yet, this renewed interest in growing microorganisms, individually or as a consortium, is stalled by the laborious nature of conventional cultivation methods. Addressing this unmet need through implementation of improved media design and new cultivation techniques is arguably instrumental to future milestones in translational microbiome research.
Collapse
Affiliation(s)
- Connie W. Y. Ha
- Division of Gastroenterology, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Suzanne Devkota
- Division of Gastroenterology, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| |
Collapse
|
28
|
|
29
|
Manzoor AA, Romita L, Hwang DK. A review on microwell and microfluidic geometric array fabrication techniques and its potential applications in cellular studies. CAN J CHEM ENG 2020. [DOI: 10.1002/cjce.23875] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ahmad Ali Manzoor
- Department of Chemical Engineering Ryerson University Toronto Ontario Canada
- Keenan Research Centre for Biomedical Science St. Michael's Hospital Toronto Ontario Canada
- Institute for Biomedical Engineering Science and Technology (iBEST) A partnership between Ryerson University and St. Michael's Hospital Toronto Ontario Canada
| | - Lauren Romita
- Department of Chemical Engineering Ryerson University Toronto Ontario Canada
- Keenan Research Centre for Biomedical Science St. Michael's Hospital Toronto Ontario Canada
- Institute for Biomedical Engineering Science and Technology (iBEST) A partnership between Ryerson University and St. Michael's Hospital Toronto Ontario Canada
| | - Dae Kun Hwang
- Department of Chemical Engineering Ryerson University Toronto Ontario Canada
- Keenan Research Centre for Biomedical Science St. Michael's Hospital Toronto Ontario Canada
- Institute for Biomedical Engineering Science and Technology (iBEST) A partnership between Ryerson University and St. Michael's Hospital Toronto Ontario Canada
| |
Collapse
|
30
|
Lei W, Demir K, Overhage J, Grunze M, Schwartz T, Levkin PA. Droplet-Microarray: Miniaturized Platform for High-Throughput Screening of Antimicrobial Compounds. ACTA ACUST UNITED AC 2020; 4:e2000073. [PMID: 32875737 DOI: 10.1002/adbi.202000073] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/20/2020] [Indexed: 01/12/2023]
Abstract
Currently, there are no time-saving and cost-effective high-throughput screening methods for the evaluation of bacterial drug-resistance. In this study, a droplet microarray (DMA) system is established as a miniaturized platform for high-throughput screening of antibacterial compounds using the emerging, opportunistic human pathogen Pseudomonas aeruginosa (P. aeruginosa) as a target. Based on the differences in wettability of DMA slides, a rapid method for generating microarrays of nanoliter-sized droplets containing bacteria is developed. The bacterial growth in droplets is evaluated using fluorescence. The new method enables immediate screening with libraries of antibiotics. A novel simple colorimetric readout method compatible with the nanoliter size of the droplets is established. Furthermore, the drug-resistance of P. aeruginosa 49, a multi-resistant strain from an environmental isolate, is investigated. This study demonstrates the potential of the DMA platform for the rapid formation of microarrays of bacteria for high-throughput drug screening.
Collapse
Affiliation(s)
- Wenxi Lei
- Institute of Biological and Chemical Systems-Functional Molecular Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen, 76344, Germany
| | - Konstantin Demir
- Institute of Biological and Chemical Systems-Functional Molecular Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen, 76344, Germany
| | - Joerg Overhage
- Department of Health Sciences, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Michael Grunze
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, Heidelberg, 69120, Germany
| | - Thomas Schwartz
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen, 76344, Germany
| | - Pavel A Levkin
- Institute of Biological and Chemical Systems-Functional Molecular Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen, 76344, Germany.,Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, 76131, Germany
| |
Collapse
|
31
|
The cell organization underlying structural colour is involved in Flavobacterium IR1 predation. ISME JOURNAL 2020; 14:2890-2900. [PMID: 32873891 PMCID: PMC7784876 DOI: 10.1038/s41396-020-00760-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 08/14/2020] [Accepted: 08/24/2020] [Indexed: 12/03/2022]
Abstract
Flavobacterium IR1 is a gliding bacterium with a high degree of colonial organization as a 2D photonic crystal, resulting in vivid structural coloration when illuminated. Enterobacter cloacae B12, an unrelated bacterium, was isolated from the brown macroalga Fucus vesiculosus from the same location as IR1. IR1 was found to be a predator of B12. A process of surrounding, infiltration, undercutting and killing of B12 supported improved growth of IR1. A combination of motility and capillarity facilitated the engulfment of B12 colonies by IR1. Predation was independent of illumination. Mutants of IR1 that formed photonic crystals less effectively than the wild type were reduced in predation. Conversely, formation of a photonic crystal was not advantageous in resisting predation by Rhodococcus spp. PIR4. These observations suggest that the organization required to create structural colour has a biological function (facilitating predation) but one that is not directly related to the photonic properties of the colony. This work is the first experimental evidence supporting a role for this widespread type of cell organization in the Flavobacteriia.
Collapse
|
32
|
Sanz-Sáez I, Salazar G, Sánchez P, Lara E, Royo-Llonch M, Sà EL, Lucena T, Pujalte MJ, Vaqué D, Duarte CM, Gasol JM, Pedrós-Alió C, Sánchez O, Acinas SG. Diversity and distribution of marine heterotrophic bacteria from a large culture collection. BMC Microbiol 2020; 20:207. [PMID: 32660423 PMCID: PMC7359222 DOI: 10.1186/s12866-020-01884-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/26/2020] [Indexed: 01/09/2023] Open
Abstract
Background Isolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. We have created a marine culture collection of heterotrophic bacteria (MARINHET) using a standard marine medium comprising a total of 1561 bacterial strains, and covering a variety of oceanographic regions from different seasons and years, from 2009 to 2015. Specifically, our marine collection contains isolates from both photic (817) and aphotic layers (744), including the mesopelagic (362) and the bathypelagic (382), from the North Western Mediterranean Sea, the North and South Atlantic Ocean, the Indian, the Pacific, and the Arctic Oceans. We described the taxonomy, the phylogenetic diversity and the biogeography of a fraction of the marine culturable microorganisms to enhance our knowledge about which heterotrophic marine isolates are recurrently retrieved across oceans and along different depths. Results The partial sequencing of the 16S rRNA gene of all isolates revealed that they mainly affiliate with the classes Alphaproteobacteria (35.9%), Gammaproteobacteria (38.6%), and phylum Bacteroidetes (16.5%). In addition, Alteromonas and Erythrobacter genera were found the most common heterotrophic bacteria in the ocean growing in solid agar medium. When comparing all photic, mesopelagic, and bathypelagic isolates sequences retrieved from different stations, 37% of them were 100% identical. This percentage increased up to 59% when mesopelagic and bathypelagic strains were grouped as the aphotic dataset and compared to the photic dataset of isolates, indicating the ubiquity of some bacterial isolates along different ocean depths. Finally, we isolated three strains that represent a new species, and the genome comparison and phenotypic characterization of two of these strains (ISS653 and ISS1889) concluded that they belong to a new species within the genus Mesonia. Conclusions Overall, this study highlights the relevance of culture-dependent studies, with focus on marine isolated bacteria from different oceanographic regions and depths, to provide a more comprehensive view of the culturable marine bacteria as part of the total marine microbial diversity.
Collapse
Affiliation(s)
- Isabel Sanz-Sáez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), 08003, Barcelona, Spain
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, CH-8093, Zurich, Switzerland
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), 08003, Barcelona, Spain
| | - Elena Lara
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), 08003, Barcelona, Spain.,Institute of Marine Sciences (CNR-ISMAR), National Research Council, Castello 2737/F Arsenale-Tesa 104, 30122, Venezia, Italy
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), 08003, Barcelona, Spain
| | - Elisabet L Sà
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), 08003, Barcelona, Spain
| | - Teresa Lucena
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - María J Pujalte
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), 08003, Barcelona, Spain
| | - Carlos M Duarte
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), 08003, Barcelona, Spain
| | - Carlos Pedrós-Alió
- Department of Systems Biology, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), 08003, Barcelona, Spain.
| |
Collapse
|
33
|
Davoodi E, Zhianmanesh M, Montazerian H, Milani AS, Hoorfar M. Nano-porous anodic alumina: fundamentals and applications in tissue engineering. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2020; 31:60. [PMID: 32642974 DOI: 10.1007/s10856-020-06398-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
Recently, nanomaterials have been widely utilized in tissue engineering applications due to their unique properties such as the high surface to volume ratio and diversity of morphology and structure. However, most methods used for the fabrication of nanomaterials are rather complicated and costly. Among different nanomaterials, anodic aluminum oxide (AAO) is a great example of nanoporous structures that can easily be engineered by changing the electrolyte type, anodizing potential, current density, temperature, acid concentration and anodizing time. Nanoporous anodic alumina has often been used for mammalian cell culture, biofunctionalization, drug delivery, and biosensing by coating its surface with biocompatible materials. Despite its wide application in tissue engineering, thorough in vivo and in vitro studies of AAO are still required to enhance its biocompatibility and thereby pave the way for its application in tissue replacements. Recognizing this gap, this review article aims to highlight the biomedical potentials of AAO for applications in tissue replacements along with the mechanism of porous structure formation and pore characteristics in terms of fabrication parameters.
Collapse
Affiliation(s)
- Elham Davoodi
- Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
| | - Masoud Zhianmanesh
- Department of Mechanical Engineering, Shahid Rajaee Teacher Training University, Shabanloo Street, Tehran, 16788, Iran
| | - Hossein Montazerian
- School of Engineering, University of British Columbia, Kelowna, BC, V1V 1V7, Canada
| | - Abbas S Milani
- School of Engineering, University of British Columbia, Kelowna, BC, V1V 1V7, Canada
| | - Mina Hoorfar
- School of Engineering, University of British Columbia, Kelowna, BC, V1V 1V7, Canada.
| |
Collapse
|
34
|
Abstract
Although not as ubiquitous as antibacterial susceptibility testing, antifungal susceptibility testing (AFST) is a tool of increasing importance in clinical microbiology laboratories. The goal of AFST is to reliably produce MIC values that may be used to guide patient therapy, inform epidemiological studies, and track rates of antifungal drug resistance. There are three methods that have been standardized by standards development organizations: broth dilution, disk diffusion, and azole agar screening for Aspergillus Other commonly used methods include gradient diffusion and the use of rapid automated instruments. Novel methodologies for susceptibility testing are in development. It is important for laboratories to consider not only the method of testing but also the interpretation (or lack thereof) of in vitro data.
Collapse
|
35
|
Nemr RA, Khalil M, Sarhan MS, Abbas M, Elsawey H, Youssef HH, Hamza MA, Morsi AT, El-Tahan M, Fayez M, Patz S, Witzel K, Ruppel S, El-Sahhar KF, Hegazi NA. " In situ similis" Culturing of Plant Microbiota: A Novel Simulated Environmental Method Based on Plant Leaf Blades as Nutritional Pads. Front Microbiol 2020; 11:454. [PMID: 32318031 PMCID: PMC7154060 DOI: 10.3389/fmicb.2020.00454] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 03/03/2020] [Indexed: 01/22/2023] Open
Abstract
High-throughput cultivation methods have recently been developed to accelerate the recovery of microorganisms reluctant to cultivation. They simulate in situ environmental conditions for the isolation of environmental microbiota through the exchange of growth substrates during cultivation. Here, we introduce leaf-based culture media adopting the concept of the plant being the master architect of the composition of its microbial community. Pre-physical treatments of sunflower plant leaves, namely punching, freezing, and/or autoclavation, allowed the diffusion of electrolytes and other nutrients to configure the leaf surface as a natural pad, i.e., creating an “in situ similis” environment suitable for the growth of rarely isolated microbiota. We used surface inoculation and membrane-filtration methods to assess the culturability of endophytic bacteria from the sunflower phyllosphere and rhizosphere. Both methods supported excellent colony-forming unit (CFU) development when compared to standard R2A medium, with a special affinity to support better growth of epiphytic and endophytic populations of the phyllosphere compared with the rhizosphere. A 16S rRNA gene analysis of >122 representative isolates indicated the cultivation of a diverse set of microorganisms by application of the new methods. It indicated the predominance of 13 genera of >30 potential species, belonging to Firmicutes, Proteobacteria, and Actinobacteria, and especially genera not commonly reported for sunflower, e.g., Rhizobium, Aureimonas, Sphingomonas, Paracoccus, Stenotrophomonas, Pantoea, Kosakonia, and Erwinia. The strategy successfully extended diversity and richness in the endophyllosphere compared to the endorhizosphere, while CFUs grown on the standard R2A medium mainly pertain to Firmicutes, especially Bacillus spp. MALDI-TOF MS analysis clustered the isolates according to their niche and potential functions, where the majority of isolates of the endorhizosphere were clustered away from those of the endophyllosphere. Isolates identified as Gammaproteobacteria and Alphaproteobacteria were distinguishably sub-clustered, which was in contrast to the heterogeneous isolates of Firmicutes (Bacillus spp.). In conclusion, leaf in situ similis cultivation is an effective strategy to support the future application of culturomics of plant microbiota. This is an effort to access novel isolates that are more adapted and competitive in their natural environments, especially those subjected to abiotic stresses like those prevailing in arid/semi-arid zones, and, consequently, to support the application of agro-biotechnologies, among other technologies, to improving agriculture in such zones.
Collapse
Affiliation(s)
- Rahma A Nemr
- Environmental Studies and Research Unit, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mohab Khalil
- Environmental Studies and Research Unit, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mohamed S Sarhan
- Environmental Studies and Research Unit, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mohamed Abbas
- Department of Microbiology, Faculty of Agriculture and Natural Resources, Aswan University, Aswan, Egypt
| | - Hend Elsawey
- Environmental Studies and Research Unit, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Hanan H Youssef
- Environmental Studies and Research Unit, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mervat A Hamza
- Environmental Studies and Research Unit, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Ahmed T Morsi
- Environmental Studies and Research Unit, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mahmoud El-Tahan
- Regional Center for Food and Feed, Agricultural Research Center, Giza, Egypt
| | - Mohamed Fayez
- Environmental Studies and Research Unit, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Sascha Patz
- Algorithms in Bioinformatics, Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Katja Witzel
- Department of Plant Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Silke Ruppel
- Department of Plant Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Kassem F El-Sahhar
- Department of Botany, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Nabil A Hegazi
- Environmental Studies and Research Unit, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| |
Collapse
|
36
|
Sun Y, Liu Y, Pan J, Wang F, Li M. Perspectives on Cultivation Strategies of Archaea. MICROBIAL ECOLOGY 2020; 79:770-784. [PMID: 31432245 DOI: 10.1007/s00248-019-01422-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
Archaea have been recognized as a major domain of life since the 1970s and occupy a key position in the tree of life. Recent advances in culture-independent approaches have greatly accelerated the research son Archaea. However, many hypotheses concerning the diversity, physiology, and evolution of archaea are waiting to be confirmed by culture-base experiments. Consequently, archaeal isolates are in great demand. On the other hand, traditional approaches of archaeal cultivation are rarely successful and require urgent improvement. Here, we review the current practices and applicable microbial cultivation techniques, to inform on potential strategies that could improve archaeal cultivation in the future. We first summarize the current knowledge on archaeal diversity, with an emphasis on cultivated and uncultivated lineages pertinent to future research. Possible causes for the low success rate of the current cultivation practices are then discussed to propose future improvements. Finally, innovative insights for archaeal cultivation are described, including (1) medium refinement for selective cultivation based on the genetic and transcriptional information; (2) consideration of the up-to-date archaeal culturing skills; and (3) application of multiple cultivation techniques, such as co-culture, direct interspecies electron transfer (DIET), single-cell isolation, high-throughput culturing (HTC), and simulation of the natural habitat. Improved cultivation efforts should allow successful isolation of as yet uncultured archaea, contributing to the much-needed physiological investigation of archaea.
Collapse
Affiliation(s)
- Yihua Sun
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China.
| |
Collapse
|
37
|
Markel U, Essani KD, Besirlioglu V, Schiffels J, Streit WR, Schwaneberg U. Advances in ultrahigh-throughput screening for directed enzyme evolution. Chem Soc Rev 2020; 49:233-262. [PMID: 31815263 DOI: 10.1039/c8cs00981c] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymes are versatile catalysts and their synthetic potential has been recognized for a long time. In order to exploit their full potential, enzymes often need to be re-engineered or optimized for a given application. (Semi-) rational design has emerged as a powerful means to engineer proteins, but requires detailed knowledge about structure function relationships. In turn, directed evolution methodologies, which consist of iterative rounds of diversity generation and screening, can improve an enzyme's properties with virtually no structural knowledge. Current diversity generation methods grant us access to a vast sequence space (libraries of >1012 enzyme variants) that may hide yet unexplored catalytic activities and selectivity. However, the time investment for conventional agar plate or microtiter plate-based screening assays represents a major bottleneck in directed evolution and limits the improvements that are obtainable in reasonable time. Ultrahigh-throughput screening (uHTS) methods dramatically increase the number of screening events per time, which is crucial to speed up biocatalyst design, and to widen our knowledge about sequence function relationships. In this review, we summarize recent advances in uHTS for directed enzyme evolution. We shed light on the importance of compartmentalization to preserve the essential link between genotype and phenotype and discuss how cells and biomimetic compartments can be applied to serve this function. Finally, we discuss how uHTS can inspire novel functional metagenomics approaches to identify natural biocatalysts for novel chemical transformations.
Collapse
Affiliation(s)
- Ulrich Markel
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany.
| | | | | | | | | | | |
Collapse
|
38
|
Iqbal KM, Bertino MF, Shah MR, Ehrhardt CJ, Yadavalli VK. Nanoscale Phenotypic Textures of Yersinia pestis Across Environmentally-Relevant Matrices. Microorganisms 2020; 8:microorganisms8020160. [PMID: 31979277 PMCID: PMC7074701 DOI: 10.3390/microorganisms8020160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 11/16/2022] Open
Abstract
The persistence of bacterial pathogens within environmental matrices plays an important role in the epidemiology of diseases, as well as impacts biosurveillance strategies. However, the adaptation potentials, mechanisms for survival, and ecological interactions of pathogenic bacteria such as Yersinia pestis are largely uncharacterized owing to the difficulty of profiling their phenotypic signatures. In this report, we describe studies on Y. pestis organisms cultured within soil matrices, which are among the most important reservoirs for their propagation. Morphological (nanoscale) and phenotypic analysis are presented at the single cell level conducted using Atomic Force Microscopy (AFM), coupled with biochemical profiles of bulk populations using Fatty Acid Methyl Ester Profiling (FAME). These studies are facilitated by a novel, customizable, 3D printed diffusion chamber that allows for control of the external environment and easy harvesting of cells. The results show that incubation within soil matrices lead to reduction of cell size and an increase in surface hydrophobicity. FAME profiles indicate shifts in unsaturated fatty acid compositions, while other fatty acid components of the phospholipid membrane or surface lipids remained consistent across culturing conditions, suggesting that phenotypic shifts may be driven by non-lipid components of Y. pestis.
Collapse
Affiliation(s)
- Kanwal M. Iqbal
- H.E.J. Research Institute, University of Karachi, Pakistan 75270; (K.M.I.); (M.R.S.)
| | - Massimo F. Bertino
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Muhammed R. Shah
- H.E.J. Research Institute, University of Karachi, Pakistan 75270; (K.M.I.); (M.R.S.)
| | | | - Vamsi K. Yadavalli
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA
- Correspondence: ; Tel.: +1-804-828-0587
| |
Collapse
|
39
|
Vaithiyanathan M, Safa N, Melvin AT. FluoroCellTrack: An algorithm for automated analysis of high-throughput droplet microfluidic data. PLoS One 2019; 14:e0215337. [PMID: 31042738 PMCID: PMC6493727 DOI: 10.1371/journal.pone.0215337] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 03/29/2019] [Indexed: 12/21/2022] Open
Abstract
High-throughput droplet microfluidic devices with fluorescence detection systems provide several advantages over conventional end-point cytometric techniques due to their ability to isolate single cells and investigate complex intracellular dynamics. While there have been significant advances in the field of experimental droplet microfluidics, the development of complementary software tools has lagged. Existing quantification tools have limitations including interdependent hardware platforms or challenges analyzing a wide range of high-throughput droplet microfluidic data using a single algorithm. To address these issues, an all-in-one Python algorithm called FluoroCellTrack was developed and its wide-range utility was tested on three different applications including quantification of cellular response to drugs, droplet tracking, and intracellular fluorescence. The algorithm imports all images collected using bright field and fluorescence microscopy and analyzes them to extract useful information. Two parallel steps are performed where droplets are detected using a mathematical Circular Hough Transform (CHT) while single cells (or other contours) are detected by a series of steps defining respective color boundaries involving edge detection, dilation, and erosion. These feature detection steps are strengthened by segmentation and radius/area thresholding for precise detection and removal of false positives. Individually detected droplet and contour center maps are overlaid to obtain encapsulation information for further analyses. FluoroCellTrack demonstrates an average of a ~92-99% similarity with manual analysis and exhibits a significant reduction in analysis time of 30 min to analyze an entire cohort compared to 20 h required for manual quantification.
Collapse
Affiliation(s)
- Manibarathi Vaithiyanathan
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Nora Safa
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Adam T Melvin
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana, United States of America
| |
Collapse
|
40
|
García C, Rendueles M, Díaz M. Liquid-phase food fermentations with microbial consortia involving lactic acid bacteria: A review. Food Res Int 2019; 119:207-220. [DOI: 10.1016/j.foodres.2019.01.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/16/2019] [Accepted: 01/20/2019] [Indexed: 12/27/2022]
|
41
|
Lee J, Park J, Kim T. Dynamic Culture and Selective Extraction of Target Microbial Cells in Self-Assembled Particle Membrane-Integrated Microfluidic Bioreactor Array. Anal Chem 2019; 91:6162-6171. [PMID: 30931565 DOI: 10.1021/acs.analchem.9b00762] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Various microfluidic devices have overcome many disadvantages common to conventional bioreactor systems by enabling active manipulation of cell-culture conditions, monitoring of cellular responses in high-throughput mode, and extraction of target cells in a relatively rapid and low-cost manner. However, existing microfluidic devices still have limitations, including the complexity of their operation and a lack of availability of dynamic control of the chemical environment. Here, we present a novel microfluidic bioreactor array device capable of not only the stable and dynamic programing of cell-culture environments but also the selective extraction of target cells. This device comprises 64 microchambers in a 16 × 4 array format, and each microchamber is integrated with a robust and nanoporous membrane on one side and an H-shaped entrance on the other. The membrane made of self-assembled particles allowed continuous and sequential delivery of various nutrients containing gene inducers to compartmentalized microbial cells, thereby enabling dynamic cell culturing. Additionally, the H-shaped entrance was used for local and selective blocking of the microchamber by employing UV-curable material, thereby enabling the retrieval of target cells from the device while sequestering nontarget cells in the microchambers. Our results demonstrated that the targeted rare cells could be isolated and separated from a mixture of cells by repeating the extraction procedure. Therefore, we anticipate that this microfluidic bioreactor array device will be widely used for not only screening/extraction but also off-chip postanalyses of various microorganisms.
Collapse
Affiliation(s)
- Jongwan Lee
- Department of Mechanical Engineering , Ulsan National Institute of Science and Technology (UNIST) , 50 UNIST-gil , Ulsan 44919 , Republic of Korea
| | - Jungyul Park
- Department of Mechanical Engineering , Sogang University , Sinsudong , Mapogu , Seoul 04107 , Republic of Korea
| | - Taesung Kim
- Department of Mechanical Engineering , Ulsan National Institute of Science and Technology (UNIST) , 50 UNIST-gil , Ulsan 44919 , Republic of Korea
| |
Collapse
|
42
|
Guo X, Silva KPT, Boedicker JQ. Single-cell variability of growth interactions within a two-species bacterial community. Phys Biol 2019; 16:036001. [DOI: 10.1088/1478-3975/ab005f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
43
|
Versluis D, de J. Bello González T, Zoetendal EG, van Passel MWJ, Smidt H. High throughput cultivation-based screening on porous aluminum oxide chips allows targeted isolation of antibiotic resistant human gut bacteria. PLoS One 2019; 14:e0210970. [PMID: 30653573 PMCID: PMC6336267 DOI: 10.1371/journal.pone.0210970] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 01/05/2019] [Indexed: 12/16/2022] Open
Abstract
The emergence of bacterial pathogens that are resistant to clinical antibiotics poses an increasing risk to human health. An important reservoir from which bacterial pathogens can acquire resistance is the human gut microbiota. However, thus far, a substantial fraction of the gut microbiota remains uncultivated and has been little-studied with respect to its resistance reservoir-function. Here, we aimed to isolate yet uncultivated resistant gut bacteria by a targeted approach. Therefore, faecal samples from 20 intensive care patients who had received the prophylactic antibiotic treatment selective digestive decontamination (SDD), i.e. tobramycin, polymyxin E, amphotericin B and cefotaxime, were inoculated anaerobically on porous aluminium oxide chips placed on top of poor and rich agar media, including media supplemented with the SDD antibiotics. Biomass growing on the chips was analysed by 16S rRNA gene amplicon sequencing, showing large inter-individual differences in bacterial cultivability, and enrichment of a range of taxonomically diverse operational taxonomic units (OTUs). Furthermore, growth of Ruminococcaceae (2 OTUs), Enterobacteriaceae (6 OTUs) and Lachnospiraceae (4 OTUs) was significantly inhibited by the SDD antibiotics. Strains belonging to 16 OTUs were candidates for cultivation to pure culture as they shared ≤95% sequence identity with the closest type strain and had a relative abundance of ≥2%. Six of these OTUs were detected on media containing SDD antibiotics, and as such were prime candidates to be studied regarding antibiotic resistance. One of these six OTUs was obtained in pure culture using targeted isolation. This novel strain was resistant to the antibiotics metrodinazole and imipenem. It was initially classified as member of the Ruminococcaceae, though later it was found to share 99% nucleotide identity with the recently published Sellimonas intestinalis BR72T. In conclusion, we show that high-throughput cultivation-based screening of microbial communities can guide targeted isolation of bacteria that serve as reservoirs of antibiotic resistance.
Collapse
Affiliation(s)
- Dennis Versluis
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Erwin G. Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Mark W. J. van Passel
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| |
Collapse
|
44
|
Agarose-based microwell array chip for high-throughput screening of functional microorganisms. Talanta 2019; 191:342-349. [DOI: 10.1016/j.talanta.2018.08.090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/27/2018] [Accepted: 08/31/2018] [Indexed: 11/23/2022]
|
45
|
Cheptsov VS, Tsypina SI, Minaev NV, Yusupov VI, Chichkov BN. New microorganism isolation techniques with emphasis on laser printing. Int J Bioprint 2018; 5:165. [PMID: 32596530 PMCID: PMC7294688 DOI: 10.18063/ijb.v5i1.165] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 10/16/2018] [Indexed: 01/05/2023] Open
Abstract
The study of biodiversity, growth, development, and metabolism of cultivated microorganisms is an integral part of modern microbiological, biotechnological, and medical research. Such studies require the development of new methods of isolation, cultivation, manipulation, and study of individual bacterial cells and their consortia. To this end, in recent years, there has been an active development of different isolation and three-dimensional cell positioning methods. In this review, the optical tweezers, surface heterogeneous functionalization, multiphoton lithography, microfluidic techniques, and laser printing are reviewed. Laser printing is considered as one of the most promising techniques and is discussed in detail.
Collapse
Affiliation(s)
- V S Cheptsov
- Department of Soil Science, Lomonosov Moscow State University, 11999 Moscow, Russia
| | - S I Tsypina
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia
| | - N V Minaev
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia
| | - V I Yusupov
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia
| | - B N Chichkov
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia.,Institut für Quantenoptik, Leibniz Universität Hannover, Welfengarten, 30167, Hannover
| |
Collapse
|
46
|
Abstract
BACKGROUND Miniaturization has not only driven microelectronics and generated new unforeseen options but has also dramatically changed sensors and analytics. DEVELOPMENTS The Lab on a Chip (LOC) technology enables laboratory processes to run fully automated in canals in the micrometre range. The biggest challenge for LOC is to keep production costs low despite miniaturization and application-specific design. If this is achieved medical laboratory analyses can usually be carried out faster and with less hands on time. This explains why LOCs are already integrated into many laboratory instruments and why point-of-care testing (POCT) can no longer be imagined without it. New markers, such as in liquid biopsies and measurement techniques, such as Raman spectroscopy and mass spectroscopy, create further potentials that will enable faster and more specific laboratory analyses to be made using LOC technology. CONCLUSION The LOC technology has the potential of changing the medical practice especially in cases when the central laboratory is not available or is unable to provide results fast enough.
Collapse
Affiliation(s)
- Klaus S Drese
- ISAT - Institut für Sensor- und Aktortechnik, Hochschule für angewandte Wissenschaften Coburg, Am Hofbräuhaus 1b, 96450, Coburg, Deutschland.
| |
Collapse
|
47
|
Feng XW, Ding WP, Xiong LY, Guo L, Sun JM, Xiao P. Recent Advancements in Intestinal Microbiota Analyses: A Review for Non-Microbiologists. Curr Med Sci 2018; 38:949-961. [PMID: 30536055 DOI: 10.1007/s11596-018-1969-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 06/12/2018] [Indexed: 02/06/2023]
Abstract
Microbial constituents naturally inhabiting the gastrointestinal tract may influence the homeostasis of the gut environment. The presence or overabundance of some bacterial taxa has been reported to be associated with complex diseases, and the metabolites of certain bacteria may contribute to diverse disorders by influencing signaling pathways. Therefore, the study of gut microbial population has emerged as a crucial field and a new potential area of clinical significance. Advances in the methods of microbiota analysis have shed light upon the details including species diversity, microfloral activities as well as the entire gut microbiota. Nevertheless, comprehensive reviews on this subject are still limited. For elucidating the appropriate selection strategy of the methods to address a particular research question, we comprehensively reviewed the continuously improving technologies, classical to newly developed, and dissected their relative advantages and drawbacks. In addition, aiming at the rapidly advancing next-generation sequencing, we enumerated the improvements in mainstream platforms and made the horizontal and vertical comparison among them. Additionally, we demonstrated the four main -omics methods, which may provide further mechanistic insights into the role of microbiota, to propel phylotyping analysis to functional analysis.
Collapse
Affiliation(s)
- Xiao-Wei Feng
- Department of Psychiatry, Wuhan Youfu Hospital, Wuhan, 430050, China
| | - Wen-Ping Ding
- Department of Ultrasound, Wuhan Women and Children's Health Care Center, Wuhan, 430016, China
| | - Ling-Yun Xiong
- Department of Plastic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Liang Guo
- Department of Plastic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jia-Ming Sun
- Department of Plastic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Peng Xiao
- Department of Plastic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| |
Collapse
|
48
|
Discovering novel hydrolases from hot environments. Biotechnol Adv 2018; 36:2077-2100. [PMID: 30266344 DOI: 10.1016/j.biotechadv.2018.09.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 12/12/2022]
Abstract
Novel hydrolases from hot and other extreme environments showing appropriate performance and/or novel functionalities and new approaches for their systematic screening are of great interest for developing new processes, for improving safety, health and environment issues. Existing processes could benefit as well from their properties. The workflow, based on the HotZyme project, describes a multitude of technologies and their integration from discovery to application, providing new tools for discovering, identifying and characterizing more novel thermostable hydrolases with desired functions from hot terrestrial and marine environments. To this end, hot springs worldwide were mined, resulting in hundreds of environmental samples and thousands of enrichment cultures growing on polymeric substrates of industrial interest. Using high-throughput sequencing and bioinformatics, 15 hot spring metagenomes, as well as several sequenced isolate genomes and transcriptomes were obtained. To facilitate the discovery of novel hydrolases, the annotation platform Anastasia and a whole-cell bioreporter-based functional screening method were developed. Sequence-based screening and functional screening together resulted in about 100 potentially new hydrolases of which more than a dozen have been characterized comprehensively from a biochemical and structural perspective. The characterized hydrolases include thermostable carboxylesterases, enol lactonases, quorum sensing lactonases, gluconolactonases, epoxide hydrolases, and cellulases. Apart from these novel thermostable hydrolases, the project generated an enormous amount of samples and data, thereby allowing the future discovery of even more novel enzymes.
Collapse
|
49
|
Palma Esposito F, Ingham CJ, Hurtado-Ortiz R, Bizet C, Tasdemir D, de Pascale D. Isolation by Miniaturized Culture Chip of an Antarctic bacterium Aequorivita sp. with antimicrobial and anthelmintic activity. ACTA ACUST UNITED AC 2018; 20:e00281. [PMID: 30225207 PMCID: PMC6139392 DOI: 10.1016/j.btre.2018.e00281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 09/04/2018] [Accepted: 09/04/2018] [Indexed: 01/28/2023]
Abstract
Novel microbial isolation approach allowed the identification of a Gram-negative Antarctic bacterium belonging to the genus Aequorivita. Aequorivita sp. showed antimicrobial and anthelmintic activity without toxic effect towards eukaryotic cells. The whole genome of Aequorivita sp. was sequenced and compared with other strains to identify biosynthetic gene clusters. This novel approach represents a promising strategy to isolate rare or novel strains useful for biotechnological applications.
Microbes are prolific sources of bioactive molecules; however, the cultivability issue has severely hampered access to microbial diversity. Novel secondary metabolites from as-yet-unknown or atypical microorganisms from extreme environments have realistic potential to lead to new drugs with benefits for human health. Here, we used a novel approach that mimics the natural environment by using a Miniaturized Culture Chip allowing the isolation of several bacterial strains from Antarctic shallow water sediments under near natural conditions. A Gram-negative Antarctic bacterium belonging to the genus Aequorivita was subjected to further analyses. The Aequorivita sp. genome was sequenced and a bioinformatic approach was applied to identify biosynthetic gene clusters. The extract of the Aequorivita sp. showed antimicrobial and anthelmintic activity towards Multidrug resistant bacteria and the nematode Caenorhabditis elegans. This is the first multi-approach study exploring the genomics and biotechnological potential of the genus Aequorivita that is a promising candidate for pharmaceutical applications.
Collapse
Affiliation(s)
- Fortunato Palma Esposito
- Institute of Protein Biochemistry, National Research Council, Naples, 80131, Italy.,Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
| | | | - Raquel Hurtado-Ortiz
- CIP-Collection of Institut Pasteur, Department of Microbiology, Institut Pasteur, Paris, 75015, France.,CRBIP-Biological Resource Centre, Department of Microbiology, Institut Pasteur, Paris, 75015, France
| | - Chantal Bizet
- CIP-Collection of Institut Pasteur, Department of Microbiology, Institut Pasteur, Paris, 75015, France.,CRBIP-Biological Resource Centre, Department of Microbiology, Institut Pasteur, Paris, 75015, France
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, 24106, Germany
| | - Donatella de Pascale
- Institute of Protein Biochemistry, National Research Council, Naples, 80131, Italy.,Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
| |
Collapse
|
50
|
Thøgersen MS, Melchiorsen J, Ingham C, Gram L. A Novel Microbial Culture Chamber Co-cultivation System to Study Algal-Bacteria Interactions Using Emiliania huxleyi and Phaeobacter inhibens as Model Organisms. Front Microbiol 2018; 9:1705. [PMID: 30105010 PMCID: PMC6077189 DOI: 10.3389/fmicb.2018.01705] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 07/09/2018] [Indexed: 02/03/2023] Open
Abstract
Our understanding of microbial natural environments combines in situ experimentation with studies of specific interactions in laboratory-based setups. The purpose of this work was to develop, build and demonstrate the use of a microbial culture chamber enabling both in situ and laboratory-based studies. The design uses an enclosed chamber surrounded by two porous membranes that enables the comparison of growth of two separate microbial populations but allowing free exchange of small molecules. Initially, we tested if the presence of the macroalga Fucus vesiculosus inside the chamber affected colonization of the outer membranes by marine bacteria. The alga did indeed enrich the total population of colonizing bacteria by more than a factor of four. These findings lead us to investigate the effect of the presence of the coccolithophoric alga Emiliania huxleyi on attachment and biofilm formation of the marine bacterium Phaeobacter inhibens DSM17395. These organisms co-exist in the marine environment and have a well-characterized interdependence on secondary metabolites. P. inhibens attached in significantly higher numbers when having access to E. huxleyi as compared to when exposed to sterile media. The experiment was carried out using a wild type (wt) strain as well as a TDA-deficient strain of P. inhibens. The ability of the bacterium to produce the antibacterial compound, tropodithietic acid (TDA) influenced its attachment since the P. inhibens DSM17395 wt strain attached in higher numbers to a surface within the first 48 h of incubation with E. huxleyi as compared to a TDA-negative mutant. Whilst the attachment of the bacterium to a surface was facilitated by presence of the alga, however, we cannot conclude if this was directly affected by the algae or whether biofilm formation was dependent on the production of TDA by P. inhibens, which has been implied by previous studies. In the light of these results, other applications of immersed culture chambers are suggested.
Collapse
Affiliation(s)
- Mariane S Thøgersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jette Melchiorsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| |
Collapse
|