High-Pressure Microfluidics for Ultra-Fast Microbial Phenotyping

Abstract

Here, we present a novel methodology based on high-pressure microfluidics to rapidly perform temperature-based phenotyping of microbial strains from deep-sea environments. The main advantage concerns the multiple on-chip temperature conditions that can be achieved in a single experiment at pressures representative of the deep-sea, overcoming the conventional limitations of large-scale batch metal reactors to conduct fast screening investigations. We monitored the growth of the model strain Thermococcus barophilus over 40 temperature and pressure conditions, without any decompression, in only 1 week, whereas it takes weeks or months with conventional approaches. The results are later compared with data from the literature. An additional example is also shown for a hydrogenotrophic methanogen strain (Methanothermococcus thermolithotrophicus), demonstrating the robustness of the methodology. These microfluidic tools can be used in laboratories to accelerate characterizations of new isolated species, changing the widely accepted paradigm that high-pressure microbiology experiments are time-consuming.

Microbial membrane lipid adaptations to high hydrostatic pressure in the marine environment

“…Frontiers in Molecular Biosciences frontiersin.org membranes do not change upon decompression of the cultures or enrichments prior to analysis. Previous studies have assessed the effect of decompression on microbial growth, cell mobility and morphology, but the effect on membrane composition has yet to be examined (Cario et al, 2022a). Similar caveats have been faced when studying changes in microbial gene expression upon HHP, and a solution to it has been to fix samples while they are under HHP (Feike et al, 2012).…”

Multi-Attribute Subset Selection enables prediction of representative phenotypes across microbial populations

“…A lot of work has been done to characterize the phenotypes of microbes for applications ranging from drug discovery to industrial fermentation 29 , 30 . Numerous technologies have been developed to facilitate the generation of phenotypic data in microbes and other biological systems 31 , including Biolog Phenotype MicroArrays 12 , 32 , robotic screening tools 33 , microfluidics devices 34 – 36 , imaging 20 , 37 , 38 and multiplexed bioreactors, such as the eVOLVER 39 . However, compared to the rapid decrease in sequencing cost, measuring phenotypes is still relatively cost and labor-intensive; thus, prioritizing which conditions and organisms to measure is a crucial component of experimental design.…”

Prediction of representative phenotypes using Multi-Attribute Subset Selection

“…A lot of work has been done to characterize the phenotypes of microbes for applications ranging from drug discovery to industrial fermentation (Demain and Sanchez 2009;Schmidt 2005). Numerous technologies have been developed to facilitate the generation of phenotypic data, in microbes and other biological systems (Yeung, Sahin, and Andrews 2022), including Biolog Phenotype MicroArrays (Hosmer et al 2022;Bochner 2009), robotic screening tools (Barton et al 2018), microfluidics devices (Cario et al 2022;Behrendt et al 2020;Kehe et al 2021), imaging (Ohya et al 2005;Kritikos et al 2017;D'Orazio et al 2022) and multiplexed bioreactors, such as the eVOLVER (Wong et al 2018). However, compared to the rapid decrease in sequencing cost, measuring 3 phenotypes is still relatively cost and labor intensive; thus, prioritizing which conditions and organisms to measure is a crucial component of experimental design.…”