Co-Culture of Gut Bacteria and Metabolite Extraction Using Fast Vacuum Filtration and Centrifugation

Journal article

Guraka, A., Duff, R., Waldron, J., Tripathi, G. and Kermanizadeh, A. 2024. Co-Culture of Gut Bacteria and Metabolite Extraction Using Fast Vacuum Filtration and Centrifugation. Methods and Protocols. 7 (74), pp. 1-13. https://doi.org/10.3390/mps7050074
AuthorsGuraka, A., Duff, R., Waldron, J., Tripathi, G. and Kermanizadeh, A.
Abstract

This protocol describes a robust method for the extraction of intra and extracellular metabolites of gut bacterial mono and co-cultures. In recent years, the co-culture techniques employed in the field of microbiology have demonstrated significant importance in regard to understanding cell–cell interactions, cross-feeding, and the metabolic interactions between different bacteria, fungi, and microbial consortia which enable the mimicking of complex co-habitant conditions. This protocol highlights a robust reproducible physiologically relevant culture and extraction protocol for the co-culture of gut bacterium. The novel extraction steps are conducted without using quenching and cell disruption through bead-cell methods, freeze–thaw cycles, and sonication, which tend to affect the physical and biochemical properties of intracellular metabolites and secretome. The extraction procedure of inoculated bacterial co-cultures and monocultures use fast vacuum filtration and centrifugation. The extraction methodology is fast, effective, and robust, requiring 4 h to complete.

Keywordsgut bacteria; co-culture; Bacteriodes thetaiotomicron; Limosilactobacillus fermentum; bacterial metabolites; short-chain fatty acids
Year2024
JournalMethods and Protocols
Journal citation7 (74), pp. 1-13
PublisherMPDI
ISSN2409-9279
Digital Object Identifier (DOI)https://doi.org/10.3390/mps7050074
Web address (URL)https://www.mdpi.com/2409-9279/7/5/74
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Online19 Sep 2024
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Deposited25 Sep 2024
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Nanomaterial-induced cell death in pulmonary and hepatic cells following exposure to three different metallic materials: The role of autophagy and apoptosis
Kermanizadeh, A., Jantzen, K., Ward, M.B., Durhuus, J.A., Juel Rasmussen, L., Loft, S. and Møller, P. 2017. Nanomaterial-induced cell death in pulmonary and hepatic cells following exposure to three different metallic materials: The role of autophagy and apoptosis. Nanotoxicology. Vol 11 (Issue 2), pp. 184-200. https://doi.org/10.1080/17435390.2017.1279359
A Flow Cytometry-based Method for the Screening of Nanomaterial-induced Reactive Oxygen Species Production in Leukocyte Sub-Populations in Whole Blood.
Kermanizadeh A, Jantzen K, Brown DM, Møller P and Loft S 2017. A Flow Cytometry-based Method for the Screening of Nanomaterial-induced Reactive Oxygen Species Production in Leukocyte Sub-Populations in Whole Blood. Basic & Clinical Pharmacology & Toxicology,. Vol 122 (Issue 1), pp. 149 - 156. https://doi.org/10.1111/bcpt.12845
Hepatic toxicity assessment of cationic liposome exposure in healthy and chronic alcohol fed mice.
Kermanizadeh A, Jacobsen NR, Roursgaard M, Loft S and Møller P 2017. Hepatic toxicity assessment of cationic liposome exposure in healthy and chronic alcohol fed mice. Heliyon. Vol 3 (Issue 11, Article: e00458). https://doi.org/10.1016/j.heliyon.2017.e00458
Overview of the Current Knowledge and Challenges Associated With Human Exposure to Nanomaterials
Kermanizadeh, A., Kim Jantzen, Astrid Skovmand, Ana C. D. Gouveia, Nicklas R. Jacobsen, Vicki Stone and Martin J. D. Clift 2017. Overview of the Current Knowledge and Challenges Associated With Human Exposure to Nanomaterials. in: Peter Grunwald (ed.) Biocatalysis and Nanotechnology New York Taylor & Francis. pp. 35
Nanotoxicology: Focus on nanomedicine
Johnston, H., Kermanizadeh, A. and Stone, V. Raj Bawa, Gerald F. Audette and Brian Reese (ed.) 2016. Nanotoxicology: Focus on nanomedicine. New York Routledge.
Inflammation and vascular effects after repeated intratracheal instillations of carbon black and lipopolysaccharide
Christophersen, D.V., Jacobsen, N.R., Jensen, D.M., Kermanizadeh, A., Sheykhzade, M., Loft, S., Voge, U., Wallin, H. and Møller, P. 2016. Inflammation and vascular effects after repeated intratracheal instillations of carbon black and lipopolysaccharide. PLos ONE. Vol 11 (Issue 8, Article: e0160731). https://doi.org/10.1371/journal.pone.0160731
Impact of serum as a dispersion agent for in vitro and in vivo toxicological assessments of TiO2 nanoparticles
Vranic, S., Gosens, I., Jacobsen, N.R., Jensen, K.A., Bokkers, B., Kermanizadeh, A., Stone, V., Baeza-Squiban, A., Cassee, F.R., Tran, L. and Boland, S. 2016. Impact of serum as a dispersion agent for in vitro and in vivo toxicological assessments of TiO2 nanoparticles. Archives of toxicology. Vol 91 (Issue 1), pp. 353 - 363. https://doi.org/10.1007/s00204-016-1673-3
Integrin Targeting and Toxicological Assessment of Peptide-Conjugated Liposome Delivery Systems to Activated Endothelial Cells
Kermanizadeh, A., Villadsen, K., Østrem, R.G., Jensen, K.J., Møller, P. and Loft, S. 2016. Integrin Targeting and Toxicological Assessment of Peptide-Conjugated Liposome Delivery Systems to Activated Endothelial Cells. Basic and Clinical Pharmacology and Toxicology. Vol 120 (Issue 4), pp. 380 - 389. https://doi.org/10.1111/bcpt.12692
Atherosclerosis and vasomotor dysfunction in arteries of animals after exposure to combustion-derived particulate matter or nanomaterials
Møller, P., Christophersen, D.V., Jacobsen, N.R., Skovmand, A., Gouveia, A.C.D., Andersen, M.H.G., Kermanizadeh, A., Jensen, D.M., Danielsen, P.H., Roursgaard, M., Jantzen, K. and Loft, S. 2016. Atherosclerosis and vasomotor dysfunction in arteries of animals after exposure to combustion-derived particulate matter or nanomaterials. Critical Reviews in Toxicology. Vol 46 (Issue 5), pp. 437-476. https://doi.org/10.3109/10408444.2016.1149451
A Multilaboratory Toxicological Assessment of a Panel of 10 Engineered Nanomaterials to Human Health - ENPRA Project - The Highlights, Limitations, and Current and Future Challenges
Kermanizadeh, A., Gosens, I., MacCalman, L., Johnston, H., Danielsen, P.H., Jacobsen, N.R., Lenz, A.-G., Fernandes, T., Schins, R.P.F., Cassee, F.R., Wallin, H., Kreyling, W., Stoeger, T., Loft, S., Møller, P., Tran, L. and Stone, V. 2016. A Multilaboratory Toxicological Assessment of a Panel of 10 Engineered Nanomaterials to Human Health - ENPRA Project - The Highlights, Limitations, and Current and Future Challenges. Journal of Toxicology and Environmental Health - Part B: Critical Reviews. Vol 19 (Issue 1), pp. 1-28. https://doi.org/10.1080/10937404.2015.1126210
An Overview of Nanoparticle Biocompatibility for Their Use in Nanomedicine
Matthew S.P. Boyles, Leagh G. Powell, Ali Kermanizadeh, Helinor J. Johnston, Barbara Rothen-Rutishauser, Vicki Stone and Martin J.D. Clift 2016. An Overview of Nanoparticle Biocompatibility for Their Use in Nanomedicine. in: Pharmaceutical Nanotechnology: Innovation and Production: Innovation and Production Wiley Online Library. pp. 443-468
Repair activity of oxidatively damaged DNA and telomere length in human lung epithelial cells after exposure to multi-walled carbon nanotubes.
Borghini A, Roursgaard M, Andreassi MG, Kermanizadeh A and Møller P 2016. Repair activity of oxidatively damaged DNA and telomere length in human lung epithelial cells after exposure to multi-walled carbon nanotubes. Mutagenesis. Vol 32 (Issue 1), p. 173–180. https://doi.org/10.1093/mutage/gew036
Hepatic oxidative stress, genotoxicity and vascular dysfunction in lean or obese Zucker rats
Løhr, M., Folkmann, J.K., Sheykhzade, M., Jensen, L.J., Kermanizadeh, A., Loft, S. and Møller, P. 2015. Hepatic oxidative stress, genotoxicity and vascular dysfunction in lean or obese Zucker rats. PLos ONE. Vol 10 (Issue 3, Article: e0118773). https://doi.org/10.1371/journal.pone.0118773
Nanomaterial translocation-the biokinetics, tissue accumulation, toxicity and fate of materials in secondary organs-A review
Kermanizadeh, A., Balharry, D., Wallin, H., Loft, S. and Møller, P. 2015. Nanomaterial translocation-the biokinetics, tissue accumulation, toxicity and fate of materials in secondary organs-A review. Critical Reviews in Toxicology. Vol 45 (Issue 10), pp. 837-872. https://doi.org/10.3109/10408444.2015.1058747
Acute and subacute pulmonary toxicity and mortality in mice after intratracheal instillation of ZnO nanoparticles in three laboratories
Jacobsen, N.R., Stoeger, T., van den Brule, S., Saber, A.T., Beyerle, A., Vietti, G., Mortensen, A., Szarek, J., Budtz, H.C., Kermanizadeh, A., Banerjee, A., Ercal, N., Vogel, U., Wallin, H. and Møller, P. 2015. Acute and subacute pulmonary toxicity and mortality in mice after intratracheal instillation of ZnO nanoparticles in three laboratories. Food and Chemical Toxicology. Vol 85 (Nov 2015), pp. 84 - 95. https://doi.org/10.1016/j.fct.2015.08.008
Comparative hazard identification by a single dose lung exposure of zinc oxide and silver nanomaterials in mice
Gosens, I., Kermanizadeh, A., Jacobsen, N.R., Lenz, A.-G., Bokkers, B., De Jong, W.H., Krystek, P., Tran, L., Stone, V., Wallin, H., Stoeger, T. and Cassee, F.R. 2015. Comparative hazard identification by a single dose lung exposure of zinc oxide and silver nanomaterials in mice. PLos ONE. Vol 10 (Issue 5, Article: 0126934). https://doi.org/10.1371/journal.pone.0126934
The global variability of diatomaceous earth toxicity: A physicochemical and in vitro investigation
Nattrass, C., Horwell, C.J., Damby, D.E., Kermanizadeh, A., Brown, D.M. and Stone, V. 2015. The global variability of diatomaceous earth toxicity: A physicochemical and in vitro investigation. Journal of Occupational Medicine and Toxicology. Vol 10 (Issue 1, Article: 23). https://doi.org/10.1186/s12995-015-0064-7
Nanotoxicology
Dominique Balharry, Eva Gubbins, Helinor Johnston, Kermanizadeh, A. and Vicki Stone 2015. Nanotoxicology. in: Nanoparticles in the Lung Boca Raton CRC Press.
The role of intracellular redox imbalance in nanomaterial induced cellular damage and genotoxicity: A review
Kermanizadeh, A., Chauché, C., Brown, D.M., Loft, S. and Møller, P. 2014. The role of intracellular redox imbalance in nanomaterial induced cellular damage and genotoxicity: A review. Environmental and Molecular Mutagenesis. Vol 56 (Issue 2), pp. 111 - 124. https://doi.org/10.1002/em.21926
Synergistic effects of zinc oxide nanoparticles and fatty acids on toxicity to caco-2 cells
Cao, Y., Roursgaard, M., Kermanizadeh, A., Loft, S. and Møller, P. 2014. Synergistic effects of zinc oxide nanoparticles and fatty acids on toxicity to caco-2 cells. International Journal of Toxicology. Vol 34 (Issue 1), pp. 67 - 76. https://doi.org/10.1177/1091581814560032
The role of p53 in lung macrophages following exposure to a panel of manufactured nanomaterials
Belade, E., Chrusciel, S., Armand, L., Simon-Deckers, A., Bussy, C., Caramelle, P., Gagliolo, J.-M., Boyer, L., Lanone, S., Pairon, J.-C., Kermanizadeh, A. and Boczkowski, J. 2014. The role of p53 in lung macrophages following exposure to a panel of manufactured nanomaterials. Archives of toxicology. Vol 89 (Issue 9), pp. 1543 - 1556. https://doi.org/10.1007/s00204-014-1324-5
Role of oxidative stress in carbon nanotube-generated health effects
Møller, P., Christophersen, D.V., Jensen, D.M., Kermanizadeh, A., Roursgaard, M., Jacobsen, N.R., Hemmingsen, J.G., Danielsen, P.H., Cao, Y., Jantzen, K., Klingberg, H., Hersoug, L.-G. and Loft, S. 2014. Role of oxidative stress in carbon nanotube-generated health effects. Archives of toxicology. Vol 88 (Issue 11), pp. 1939 - 1964. https://doi.org/10.1007/s00204-014-1356-x
Measurement of oxidative damage to DNA in nanomaterial exposed cells and animals
Møller, P., Jensen, D.M., Christophersen, D.V., Kermanizadeh, A., Jacobsen, N.R., Hemmingsen, J.G., Danielsen, P.H., Karottki, D.G., Roursgaard, M., Cao, Y., Jantzen, K., Klingberg, H., Hersoug, L.-G. and Loft, S. 2014. Measurement of oxidative damage to DNA in nanomaterial exposed cells and animals. Environmental and Molecular Mutagenesis. Vol 56 (Issue 2), pp. 97 - 110. https://doi.org/10.1002/em.21899
Applications of the comet assay in particle toxicology: Air pollution and engineered nanomaterials exposure
Møller, P., Hemmingsen, J.G., Jensen, D.M., Danielsen, P.H., Karottki, D.G., Jantzen, K., Roursgaard, M., Cao, Y., Kermanizadeh, A., Klingberg, H., Christophersen, D.V., Hersoug, L.-G. and Loft, S. 2014. Applications of the comet assay in particle toxicology: Air pollution and engineered nanomaterials exposure. Mutagenesis. Vol 30 (Issue 1), p. 67–83. https://doi.org/10.1093/mutage/geu035
Hepatic toxicology following single and multiple exposure of engineered nanomaterials utilising a novel primary human 3D liver microtissue model
Kermanizadeh, A., Løhr, M., Roursgaard, M., Messner, S., Gunness, P., Kelm, J.M., Møller, P., Stone, V. and Loft, S. 2014. Hepatic toxicology following single and multiple exposure of engineered nanomaterials utilising a novel primary human 3D liver microtissue model. Particle and Fibre Toxicology. Vol 11 (Issue 1, Article: 56). https://doi.org/10.1186/s12989-014-0056-2
The role of Kupffer cells in the hepatic response to silver nanoparticles.
Kermanizadeh, A., Chauché, C., Balharry, D., Brown, D. M., Kanase, N., Boczkowski, J., Lanone, S. and Stone, V. 2013. The role of Kupffer cells in the hepatic response to silver nanoparticles. Nanotoxicology. 1 (1), pp. 149-154. https://doi.org/10.3109/17435390.2013.866284