Customizable 3D printed diffusion chambers for studies of bacterial pathogen phenotypes in complex environments

Wilson, Lyddia; Iqbal, Kanwal M; Simmons-Ehrhardt, Terrie; Bertino, Massimo F.; Shah, Mohammad Raza; Yadavalli, Vamsi K.; Ehrhardt, Christopher J.

doi:10.1016/j.mimet.2019.05.002

Cited by 7 publications

(6 citation statements)

References 39 publications

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“…Elsewhere, an SLA-printed incubation/diffusion chamber was designed for culturing bacteria from soil samples to study their interaction dynamics. The chamber facilitated diffusion of soil components with target cells and also allowed single-cell and ensemble bacterial phenotypic analyses[ 61 ].…”

Section: 3d-printed Bioreactor For Biological Applicationsmentioning

confidence: 99%

3D-printed Bioreactors for In Vitro Modeling and Analysis

Priyadarshini¹,

Dikshit²,

Zhang³

2024

IJB

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In recent years, three-dimensional (3D) printing has markedly enhanced the functionality of bioreactors by offering the capability of manufacturing intricate architectures, which changes the way of conducting in vitro biomodeling and bioanalysis. As 3D-printing technologies become increasingly mature, the architecture of 3D-printed bioreactors can be tailored to specific applications using different printing approaches to create an optimal environment for bioreactions. Multiple functional components have been combined into a single bioreactor fabricated by 3D-printing, and this fully functional integrated bioreactor outperforms traditional methods. Notably, several 3D-printed bioreactors systems have demonstrated improved performance in tissue engineering and drug screening due to their 3D cell culture microenvironment with precise spatial control and biological compatibility. Moreover, many microbial bioreactors have also been proposed to address the problems concerning pathogen detection, biofouling, and diagnosis of infectious diseases. This review offers a reasonably comprehensive review of 3D-printed bioreactors for in vitro biological applications. We compare the functions of bioreactors fabricated by various 3D-printing modalities and highlight the benefit of 3D-printed bioreactors compared to traditional methods.

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Section: 3d-printed Bioreactor For Biological Applicationsmentioning

confidence: 99%

3D-printed Bioreactors for In Vitro Modeling and Analysis

Priyadarshini¹,

Dikshit²,

Zhang³

2024

IJB

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“…There are multiple manufactured modifications of the diffusion chamber principle and you can even build these devices yourself ( Epstein et al, 2010 ). The original construction of the microbial chamber has been modified using different materials and 3D printing ( Wilson et al, 2019 ). Other diffusion-based techniques build upon porous and semi-permeable membranes as well, such as the soil substrate membrane system that Svenning et al (2003) used to culture methanotrophs or the hollow-fiber membrane chamber ( Aoi et al, 2009 ).…”

Section: Ways Of Increasing Cultivability Using Top-down and Bottom-up Approachesmentioning

confidence: 99%

Improving Fungal Cultivability for Natural Products Discovery

Rämä

Quandt

2021

Front. Microbiol.

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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.

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“…The chamber is designed to hold three small agar plugs (40 mm diameter) as the substrate for bacterial inoculation (Figure 1). The chamber was configured and fabricated as previously reported by our group [22]. Briefly, the agar plugs are held in place by two identical lid pieces with gridded meshes.…”

Section: Fabrication Of 3d Printed Cell-culture Chambermentioning

confidence: 99%

“…Towards this objective, we designed a customizable and cost-effective device to expose target organisms to the complex abiotic and biotic components of soil matrix without (a) the risk of contamination from endemic soil bacteria, or (b) the difficulty in directly harvesting target bacteria for phenotypic analysis. In order to grow Y. pestis in a soil environment, custom-engineered 3-D printed growth chambers were prepared (Figure 1) [22]. Initially, it is useful to compare these devices with previously reported chambers designed to expose cells to external environments.…”

Section: Chamber Design and Cell Culturementioning

confidence: 99%

Nanoscale Phenotypic Textures of Yersinia pestis Across Environmentally-Relevant Matrices

et al. 2020

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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.

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Customizable 3D printed diffusion chambers for studies of bacterial pathogen phenotypes in complex environments

Cited by 7 publications

References 39 publications

3D-printed Bioreactors for In Vitro Modeling and Analysis

3D-printed Bioreactors for In Vitro Modeling and Analysis

Improving Fungal Cultivability for Natural Products Discovery

Nanoscale Phenotypic Textures of Yersinia pestis Across Environmentally-Relevant Matrices

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