Staff View: A three-dimensional (3D) printing approach to fabricate an isolation chip for high throughput in situ cultivation of environmental microbes

A three-dimensional (3D) printing approach to fabricate an isolation chip for high throughput in situ cultivation of environmental microbes

The full plethora of environmental bacteria is often poorly represented in vitro as the majority remain difficult, if not impossible, to culture under standard laboratory settings. These bacteria often require native conditions for the formation of cell masses that collectively have higher chances o...

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Main Authors:	Goh, Calvin Bok Sun, Goh, Clariss Hui Peng, Wong, Li Wen, Cheng, Wai Teng, Yule, Catherine Mary, Ong, Kuan Shion, Lee, Sui Mae, Pooria, Pasbakhsh *, Tan, Joash Ban Lee
Format:	Article
Published:	Royal Society of Chemistry 2022
Subjects:	QR Microbiology RC Internal medicine TS Manufactures
Online Access:	http://eprints.sunway.edu.my/3014/
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spelling	my.sunway.eprints.30142024-08-06T06:00:01Z http://eprints.sunway.edu.my/3014/ A three-dimensional (3D) printing approach to fabricate an isolation chip for high throughput in situ cultivation of environmental microbes Goh, Calvin Bok Sun Goh, Clariss Hui Peng Wong, Li Wen Cheng, Wai Teng Yule, Catherine Mary Ong, Kuan Shion Lee, Sui Mae Pooria, Pasbakhsh * Tan, Joash Ban Lee QR Microbiology RC Internal medicine TS Manufactures The full plethora of environmental bacteria is often poorly represented in vitro as the majority remain difficult, if not impossible, to culture under standard laboratory settings. These bacteria often require native conditions for the formation of cell masses that collectively have higher chances of survival. With that, a 3D-printed version of the isolation chip (iChip) was used to cultivate bacteria from a tropical peat swamp in situ prior to growth and maintenance in vitro. Briefly, plates made from either acrylonitrile butadiene styrene (ABS), polylactic acid (PLA), or epoxy resin were tested in terms of their usability and durability under acidic conditions similar to those of peat matter. The epoxy resin plates were then found to be most optimal for the sampling conditions. Peat soil samples were collected from the base of a Koompassia malaccensis tree and reconstituted in molten 10% (wt/vol) tryptone soy agar (TSA) prior to inoculation. The iChips were subsequently assembled and buried in the site of origin. As a comparison, bacteria from the same soil sample were cultivated directly on TSA and incubated at 28 °C for two weeks. Thereafter, agar plugs from the iChip were transferred to TSA plates to allow microcolonies within each plug to grow. Each pure isolate from both cultivation approaches that grew was then pooled and extracted for total DNA prior to 16S rRNA gene amplification and sequencing via Illumina MiSeq. Taxonomic abundance comparison revealed that the bacterial taxa at the level of order were significantly different between the two approaches, particularly in the orders, Burkholderiales, Xanthomonodales, Enterobacteriales, and Actinomycetales (differences of 12.0, 7.1, 8.0, and 4.2%, respectively). This indicated that the 3D-printed iChips present a possible low-cost tool for the isolation of bacterial genera that may not be able to grow on media directly in vitro. Royal Society of Chemistry 2022 Article PeerReviewed Goh, Calvin Bok Sun and Goh, Clariss Hui Peng and Wong, Li Wen and Cheng, Wai Teng and Yule, Catherine Mary and Ong, Kuan Shion and Lee, Sui Mae and Pooria, Pasbakhsh * and Tan, Joash Ban Lee (2022) A three-dimensional (3D) printing approach to fabricate an isolation chip for high throughput in situ cultivation of environmental microbes. Lab on a Chip, 22 (2). ISSN 1473-0197 DOI https://doi.org/10.1039/D1LC00723H 10.1039/D1LC00723H
institution	Sunway University
building	Sunway Campus Library
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Sunway University
content_source	Sunway Institutional Repository
url_provider	http://eprints.sunway.edu.my/
topic	QR Microbiology RC Internal medicine TS Manufactures
spellingShingle	QR Microbiology RC Internal medicine TS Manufactures Goh, Calvin Bok Sun Goh, Clariss Hui Peng Wong, Li Wen Cheng, Wai Teng Yule, Catherine Mary Ong, Kuan Shion Lee, Sui Mae Pooria, Pasbakhsh * Tan, Joash Ban Lee A three-dimensional (3D) printing approach to fabricate an isolation chip for high throughput in situ cultivation of environmental microbes
description	The full plethora of environmental bacteria is often poorly represented in vitro as the majority remain difficult, if not impossible, to culture under standard laboratory settings. These bacteria often require native conditions for the formation of cell masses that collectively have higher chances of survival. With that, a 3D-printed version of the isolation chip (iChip) was used to cultivate bacteria from a tropical peat swamp in situ prior to growth and maintenance in vitro. Briefly, plates made from either acrylonitrile butadiene styrene (ABS), polylactic acid (PLA), or epoxy resin were tested in terms of their usability and durability under acidic conditions similar to those of peat matter. The epoxy resin plates were then found to be most optimal for the sampling conditions. Peat soil samples were collected from the base of a Koompassia malaccensis tree and reconstituted in molten 10% (wt/vol) tryptone soy agar (TSA) prior to inoculation. The iChips were subsequently assembled and buried in the site of origin. As a comparison, bacteria from the same soil sample were cultivated directly on TSA and incubated at 28 °C for two weeks. Thereafter, agar plugs from the iChip were transferred to TSA plates to allow microcolonies within each plug to grow. Each pure isolate from both cultivation approaches that grew was then pooled and extracted for total DNA prior to 16S rRNA gene amplification and sequencing via Illumina MiSeq. Taxonomic abundance comparison revealed that the bacterial taxa at the level of order were significantly different between the two approaches, particularly in the orders, Burkholderiales, Xanthomonodales, Enterobacteriales, and Actinomycetales (differences of 12.0, 7.1, 8.0, and 4.2%, respectively). This indicated that the 3D-printed iChips present a possible low-cost tool for the isolation of bacterial genera that may not be able to grow on media directly in vitro.
format	Article
author	Goh, Calvin Bok Sun Goh, Clariss Hui Peng Wong, Li Wen Cheng, Wai Teng Yule, Catherine Mary Ong, Kuan Shion Lee, Sui Mae Pooria, Pasbakhsh * Tan, Joash Ban Lee
author_facet	Goh, Calvin Bok Sun Goh, Clariss Hui Peng Wong, Li Wen Cheng, Wai Teng Yule, Catherine Mary Ong, Kuan Shion Lee, Sui Mae Pooria, Pasbakhsh * Tan, Joash Ban Lee
author_sort	Goh, Calvin Bok Sun
title	A three-dimensional (3D) printing approach to fabricate an isolation chip for high throughput in situ cultivation of environmental microbes
title_short	A three-dimensional (3D) printing approach to fabricate an isolation chip for high throughput in situ cultivation of environmental microbes
title_full	A three-dimensional (3D) printing approach to fabricate an isolation chip for high throughput in situ cultivation of environmental microbes
title_fullStr	A three-dimensional (3D) printing approach to fabricate an isolation chip for high throughput in situ cultivation of environmental microbes
title_full_unstemmed	A three-dimensional (3D) printing approach to fabricate an isolation chip for high throughput in situ cultivation of environmental microbes
title_sort	three-dimensional (3d) printing approach to fabricate an isolation chip for high throughput in situ cultivation of environmental microbes
publisher	Royal Society of Chemistry
publishDate	2022
url	http://eprints.sunway.edu.my/3014/
_version_	1806692472812732416
score	13.211869

A three-dimensional (3D) printing approach to fabricate an isolation chip for high throughput in situ cultivation of environmental microbes

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