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Modolon F, Schultz J, Duarte G, Vilela CLS, Thomas T, Peixoto RS. In situ devices can culture the microbial dark matter of corals. iScience 2023; 26:108374. [PMID: 38162026 PMCID: PMC10755713 DOI: 10.1016/j.isci.2023.108374] [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: 04/11/2023] [Revised: 09/16/2023] [Accepted: 10/27/2023] [Indexed: 01/03/2024] Open
Abstract
Most microorganisms found in environmental samples have never been cultured and can often only be explored through molecular or microscopic approaches. Here, we adapt the use of in situ diffusion-based devices to culture "yet-to-be-cultured" microorganisms associated with coral mucus and compare this with a traditional culturing method. The culturability of microorganisms associated with mucus of the coral Pocillopora damicornis increased by 420% and 570% with diffusion growth chambers and microwell chip devices, respectively, compared with the traditional method tested. The obtained cultures represent up to 64.4% of the total diversity of amplicon sequence variants (ASVs) found in the mucus of the coral P. damicornis. In addition, some previously uncultured microorganisms, such as members of the family Nitrosopumilaceae and halophilic/halotolerant bacteria were cultured. Our results validate alternative microbial culturing strategies to culture coral-associated microorganisms, while significantly increasing the culturability of previous microbial dark matter.
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Affiliation(s)
- Flúvio Modolon
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Júnia Schultz
- King Abdullah University of Science and Technology (KAUST), Marine Science and Bioscience Programs, Red Sea Research Center (RSRC) and Computational Biology Center (CBRC), Environmental and Engineering Sciences Division (BESE Thuwal, Makkah 23955, Saudi Arabia
| | - Gustavo Duarte
- King Abdullah University of Science and Technology (KAUST), Marine Science and Bioscience Programs, Red Sea Research Center (RSRC) and Computational Biology Center (CBRC), Environmental and Engineering Sciences Division (BESE Thuwal, Makkah 23955, Saudi Arabia
| | - Caren Leite Spindola Vilela
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Raquel Silva Peixoto
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- King Abdullah University of Science and Technology (KAUST), Marine Science and Bioscience Programs, Red Sea Research Center (RSRC) and Computational Biology Center (CBRC), Environmental and Engineering Sciences Division (BESE Thuwal, Makkah 23955, Saudi Arabia
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Khater A, Abdelrehim O, Mohammadi M, Azarmanesh M, Janmaleki M, Salahandish R, Mohamad A, Sanati-Nezhad A. Picoliter agar droplet breakup in microfluidics meets microbiology application: numerical and experimental approaches. LAB ON A CHIP 2020; 20:2175-2187. [PMID: 32420570 DOI: 10.1039/d0lc00300j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Droplet microfluidics has provided lab-on-a-chip platforms with the capability of bacteria encapsulation in biomaterials, controlled culture environments, and live monitoring of growth and proliferation. The droplets are mainly generated from biomaterials with temperature dependent gelation behavior which necessitates stable and size-controlled droplet formation within microfluidics. Here, the biomaterial is agar hydrogel with a non-Newtonian response at operating temperatures below 40 °C, the upper-temperature threshold for cells and pathogens. The size of the produced droplets and the formation regimes are examined when the agar is injected at a constant temperature of 37 °C with agar concentrations of 0.5%, 1%, and 2% and different flow rate ratios of the dispersed phase to the continuous phase (φ: 0.1 to 1). The numerical simulations show that φ and the capillary number (Ca) are the key parameters controlling the agar droplet size and formation regime, from dripping to jetting. Also, increasing the agar concentration produces smaller droplets. The simulation data were validated against experimental agar droplet generation and transport in microfluidics. This work helps to understand the physics of droplet generation in droplet microfluidic systems operating with non-Newtonian fluids. Pathogenic bacteria were successfully cultured and monitored in high resolution in agar droplets for further research in antibiotic susceptibility testing in bacteremia and urinary tract infection.
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Affiliation(s)
- Asmaa Khater
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
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Lawrence JR, Swerhone GDW, Kuhlicke U, Neu TR. In situevidence for metabolic and chemical microdomains in the structured polymer matrix of bacterial microcolonies. FEMS Microbiol Ecol 2016; 92:fiw183. [DOI: 10.1093/femsec/fiw183] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2016] [Indexed: 11/13/2022] Open
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Renner LD, Eswaramoorthy P, Ramamurthi KS, Weibel DB. Studying biomolecule localization by engineering bacterial cell wall curvature. PLoS One 2013; 8:e84143. [PMID: 24391905 PMCID: PMC3877235 DOI: 10.1371/journal.pone.0084143] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 11/12/2013] [Indexed: 11/22/2022] Open
Abstract
In this article we describe two techniques for exploring the relationship between bacterial cell shape and the intracellular organization of proteins. First, we created microchannels in a layer of agarose to reshape live bacterial cells and predictably control their mean cell wall curvature, and quantified the influence of curvature on the localization and distribution of proteins in vivo. Second, we used agarose microchambers to reshape bacteria whose cell wall had been chemically and enzymatically removed. By combining microstructures with different geometries and fluorescence microscopy, we determined the relationship between bacterial shape and the localization for two different membrane-associated proteins: i) the cell-shape related protein MreB of Escherichia coli, which is positioned along the long axis of the rod-shaped cell; and ii) the negative curvature-sensing cell division protein DivIVA of Bacillus subtilis, which is positioned primarily at cell division sites. Our studies of intracellular organization in live cells of E. coli and B. subtilis demonstrate that MreB is largely excluded from areas of high negative curvature, whereas DivIVA localizes preferentially to regions of high negative curvature. These studies highlight a unique approach for studying the relationship between cell shape and intracellular organization in intact, live bacteria.
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Affiliation(s)
- Lars D. Renner
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Technical University Dresden and the Max-Bergmann-Centre for Biomaterials, Dresden, Germany
| | - Prahathees Eswaramoorthy
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kumaran S. Ramamurthi
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Douglas B. Weibel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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Flores FC, de Lima JA, Ribeiro RF, Alves SH, Rolim CMB, Beck RCR, da Silva CB. Antifungal activity of nanocapsule suspensions containing tea tree oil on the growth of Trichophyton rubrum. Mycopathologia 2013; 175:281-6. [PMID: 23392821 DOI: 10.1007/s11046-013-9622-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 01/22/2013] [Indexed: 12/25/2022]
Abstract
The aim of this study was to evaluate, for the first time, the antifungal efficacy of nanocapsules and nanoemulsions containing Melaleuca alternifolia essential oil (tea tree oil) in an onychomycosis model. The antifungal activity of nanostructured formulations was evaluated against Trichophyton rubrum in two different in vitro models of dermatophyte nail infection. First, nail powder was infected with T. rubrum in a 96-well plate and then treated with the formulations. After 7 and 14 days, cell viability was verified. The plate counts for the samples were 2.37, 1.45 and 1.0 log CFU mL(-1) (emulsion, nanoemulsion containing tea tree oil and nanocapsules containing tea tree oil, respectively). A second model employed nails fragments which were infected with the microorganism and treated with the formulations. The diameter of fungal colony was measured. The areas obtained were 2.88 ± 2.08 mm(2), 14.59 ± 2.01 mm(2), 40.98 ± 2.76 mm(2) and 38.72 ± 1.22 mm(2) for the nanocapsules containing tea tree oil, nanoemulsion containing tea tree oil, emulsion and untreated nail, respectively. Nail infection models demonstrated the ability of the formulations to reduce T. rubrum growth, with the inclusion of oil in nanocapsules being most efficient.
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Affiliation(s)
- F C Flores
- Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
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Amna T, Hassan MS, Pandeya DR, Khil MS, Hwang IH. Classy non-wovens based on animate L. gasseri-inanimate poly(vinyl alcohol): upstream application in food engineering. Appl Microbiol Biotechnol 2013; 97:4523-31. [PMID: 23306644 DOI: 10.1007/s00253-012-4666-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 12/15/2012] [Accepted: 12/17/2012] [Indexed: 11/28/2022]
Abstract
We explored electrospinning as a feasible and practicable mode for encapsulation and stabilization of Lactobacillus gasseri. The utilized nanocomposite was prepared using sol-gel composed of animate L. gasseri and inanimate PVA. The objective was to examine the ability of electrospinning method to protect functional properties of probiotic L. gasseri. The PVA was used as an encapsulation matrix as it is biocompatible and hydrophilic in nature thus facilitate an easy revival of bacteria. The characterization of as-spun bioproduct was done by energy-dispersive X-ray spectrometer, SEM, and TEM, whereas thermal behavior was analyzed by thermogravimetry. The viability was confirmed by traditional pour plate method and fluorescence microscopy. Furthermore, to test whether the functionality of L. gasseri was affected, the encapsulated L. gasseri were fed to mouse for colonization. Our results pointed out that encapsulated bacteria were viable for months, and their metabolism was not affected by immobilization; thus, they could be used in food engineering and trade.
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Affiliation(s)
- Touseef Amna
- Department of Animal Science and Biotechnology, Chonbuk National University, Jeonju 561-756, Republic of Korea.
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Kumano I, Hosoda K, Suzuki H, Hirata K, Yomo T. Hydrodynamic trapping of Tetrahymena thermophila for the long-term monitoring of cell behaviors. LAB ON A CHIP 2012; 12:3451-3457. [PMID: 22825740 DOI: 10.1039/c2lc40367f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Microfluidic trapping technology has been widely applied for single-cell observation in order to reveal characteristic cell behaviors. However, this strategy has yet to be tested for monitoring highly motile cells, which are often biologically important. In this paper, we seek the conditions that enable effective and long-term trapping of a prominent model ciliate Tetrahymena thermophila within a hydrodynamic microfluidic device. Although motility and flexibility of T. thermophila make it difficult to avoid escaping from the trap, we show that tuning some key parameters in the hydrodynamic circuit was effective to achieve approximately 40 h cell retention, which is long enough to monitor cell behaviors over several generations. Here, we demonstrate the real-time observation of cell division and phagocytic digestion, revealing interesting phenomena such as a wide distribution in doubling time in a poor synthetic medium and heterogeneous time courses in digestion processes. Our results present a strategy for trapping highly motile ciliate cells in order to study the dynamic behaviors of single cells.
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Affiliation(s)
- Itsuka Kumano
- Graduate School of Information Science and Technology, Osaka University, Yamadaoka 1-5, Suita, Osaka 565-0871, Japan
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Gensheimer M, Brandis-Heep A, Agarwal S, Thauer RK, Greiner A. Polymer/Bacteria Composite Nanofiber Nonwovens by Electrospinning of Living Bacteria Protected by Hydrogel Microparticles. Macromol Biosci 2011; 11:333-7. [DOI: 10.1002/mabi.201000310] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2010] [Revised: 10/17/2010] [Indexed: 11/09/2022]
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