Micro-Technologies for Assessing Microbial Dynamics in Controlled Environments

Davidson, Shanna-Leigh; Niepa, Tagbo H. R.

doi:10.3389/fmicb.2021.745835

Cited by 5 publications

(5 citation statements)

References 87 publications

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“…Co-culture systems to study contact independent interactions involving diffusible molecules using membrane-divided co-culture assay, conditioned media assay, or via microfluidics platform [ 48 ]. Membrane-divided co-cultures assay involves the physical separation of two microbial populations with semi-permeable membranes.…”

Section: Qualitative Methods To Study Microbial Interactionsmentioning

confidence: 99%

Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions

Srinivasan,

Jnana,

Murali

2024

Microb Ecol

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Microbial interactions function as a fundamental unit in complex ecosystems. By characterizing the type of interaction (positive, negative, neutral) occurring in these dynamic systems, one can begin to unravel the role played by the microbial species. Towards this, various methods have been developed to decipher the function of the microbial communities. The current review focuses on the various qualitative and quantitative methods that currently exist to study microbial interactions. Qualitative methods such as co-culturing experiments are visualized using microscopy-based techniques and are combined with data obtained from multi-omics technologies (metagenomics, metabolomics, metatranscriptomics). Quantitative methods include the construction of networks and network inference, computational models, and development of synthetic microbial consortia. These methods provide a valuable clue on various roles played by interacting partners, as well as possible solutions to overcome pathogenic microbes that can cause life-threatening infections in susceptible hosts. Studying the microbial interactions will further our understanding of complex less-studied ecosystems and enable design of effective frameworks for treatment of infectious diseases.

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Section: Qualitative Methods To Study Microbial Interactionsmentioning

confidence: 99%

Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions

Srinivasan,

Jnana,

Murali

2024

Microb Ecol

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“…They allow to improve of high-throughput screening, reducing the time and resources needed for experiments. Recently [ 69 ], three main microtechnology methods have appeared: Microarrays, microencapsulation [ 70 ] and micromechanical devices and microfluidics [ 71 ].…”

Section: Microbiologymentioning

confidence: 99%

“…T allow to improve of high-throughput screening, reducing the time and resources ne for experiments. Recently [69], three main microtechnology methods have appeared croarrays, microencapsulation [70] and micromechanical devices and microfluidics [ Microfluidics, a technique that has been rapidly developing in recent years, is w mentioning in more detail [72]. This droplet-based technique generates homogeneou crodroplets under precise control at the picoliter or nanoliter scale upon high-frequ vibration (~kHz) [73].…”

Section: Microtechnologymentioning

confidence: 99%

Modern Trends in Natural Antibiotic Discovery

Baranova

Alferova

Korshun

et al. 2023

Life

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Natural scaffolds remain an important basis for drug development. Therefore, approaches to natural bioactive compound discovery attract significant attention. In this account, we summarize modern and emerging trends in the screening and identification of natural antibiotics. The methods are divided into three large groups: approaches based on microbiology, chemistry, and molecular biology. The scientific potential of the methods is illustrated with the most prominent and recent results.

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“…Therefore, in this short and immediate time range, different and complex drivers determine the distribution and composition of microorganism populations in various hotspots (habitats). To characterize drivers operating on this time scale, the development of microfabrication offers the opportunity to design geometrically defined microdevices targeted for the analysis in situ of low volumes of microbial samples [9]. Precision environmental control typical of microfluidic circuits coupled to automated cell tracking and image analysis has already allowed quantification of microbial dynamics on a high spatial and temporal resolution scale guided by particular soil drivers, including soil or plant derivatives [10,11].…”

Section: Introductionmentioning

confidence: 99%

Automated high-content image-based characterization of microorganism behavioral diversity and distribution

Lupatelli,

Attard,

Kuhn

et al. 2023

Preprint

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Background Microorganisms evolved complex systems to respond to environmental signals. Gradients of particular molecules alter microbe behavior and distribution within their environment. Microdevice tools coupled to automated image-based methods are now employed to analyze instantaneous distribution and motion behaviors of microbial species in controlled environments at small temporal scales, mimicking to some extent macro conditions. Such technologies have already been adopted for investigations mainly on individual species. Similar versatile approaches must now be developed for the characterization of multiple and complex interactions between the microbial community and environment. Results Here, we provide a comprehensive step-by-step method for the characterization of species-specific behavior of a synthetic mixed microbial suspension in response to an environmental driver. By coupling accessible microfluidic devices with automated image analysis approaches, we evaluated the behavior response of three morphologically different telluric species (Phytophthora parasitica, Vorticella microstoma, Enterobacter aerogenes) to a potassium gradient driver. Using the TrackMate plug-in algorithms, we performed morphometric and then motion analysis to characterize each microbial species response to the driver. Such approach enabled us to confirm the different shape features of the three species, and to simultaneously characterize their particular motion adaptation to the driver, as well as their co-interaction dynamics. Conclusions The results obtained demonstrated the feasibility of the method to screen mixed-species suspension dynamics at high spatial and temporal scale. By increasing the complexity of suspensions, this approach could be integrated to support conventional omics methods, contributing to characterizing how the main drivers operate at the microbiota-host-environment interfaces. In its current advances, the method can integrate screening strategy, for example, for biocontrol agent evaluation, enlightening possible beneficial-pathogenic interactions based on co-colonization of micro habitats.

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Micro-Technologies for Assessing Microbial Dynamics in Controlled Environments

Cited by 5 publications

References 87 publications

Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions

Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions

Modern Trends in Natural Antibiotic Discovery

Automated high-content image-based characterization of microorganism behavioral diversity and distribution

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