Advanced continuous cultivation methods for systems microbiology

Abstract

Increasing the throughput of systems biology-based experimental characterization of in silicodesigned strains has great potential for accelerating the development of cell factories. For this, analysis of metabolism in the steady state is essential as only this enables the unequivocal definition of the physiological state of cells, which is needed for the complete description and in silico reconstruction of their phenotypes. In this review, we show that for a systems microbiology approach, high-resolution characterization of metabolism in the steady stategrowth space analysis (GSA) -can be achieved by using advanced continuous cultivation methods termed changestats. In changestats, an environmental parameter is continuously changed at a constant rate within one experiment whilst maintaining cells in the physiological steady state similar to chemostats. This increases the resolution and throughput of GSA compared with chemostats, and, moreover, enables following of the dynamics of metabolism and detection of metabolic switch-points and optimal growth conditions. We also describe the concept, challenge and necessary criteria of the systematic analysis of steady-state metabolism. Finally, we propose that such systematic characterization of the steady-state growth space of cells using changestats has value not only for fundamental studies of metabolism, but also for systems biology-based metabolic engineering of cell factories.

Selection of fast and slow growing bacteria from fecal microbiota using continuous culture with changing dilution rate

“…It should be emphasized that the main aim of using change-stat is not to obtain fully stabilized abundances of bacteria at a certain dilution rate, but rather to gain information about adaptive response of bacterial consortia to the changing dilution rate. Different change-stat and accelerostat techniques have been applied in pure culture studies earlier [16]. The De-stat culture has not been applied for studies of complex microbial consortia earlier, while chemostat gut models have been used by several groups.…”

“…Change-stat method is a modification of the classical chemostat or turbidostat cultures. The unifying concept behind different change-stats is the smooth continuous adjustment of an environmental parameter within a single experiment, while maintaining the physiological state of the culture practically stable [16]. …”

Use of Changestat for Growth Rate Studies of Gut Microbiota

“…Fecal samples were collected from seven healthy adult volunteers (19-37 years old, Caucasian, both male and female) and homogenized in four volumes of 5% DMSO-containing buffer, as described in Adamberg et al (2015). The exclusion criteria included the use of supplements of prebiotics and probiotics, laxatives and antibiotics for 4 weeks prior to donation.…”

“…An alternative continuous cultivation technology, changestat, in which all cultivation parameters are computer-controlled, has been developed in our lab. In changestat, the effect of a selected parameter is studied by the gradual change in this parameter within a certain range, while keeping all other conditions constant (Paalme et al, 1995;Kasemets et al, 2003;Adamberg et al, 2015). Our recent study highlighted the importance of dilution rate in determining the composition and diversity of fecal microbiota .…”

Energy Conservation and Carbon Flux Distribution During Fermentation of CO or H2/CO2 by Clostridium ljungdahlii

“…Clostridium ljungdahlii, a close relative of "Clostridium autoethanogenum, " is used as a model organism for studying the production of ethanol and acetate from syngas, which is a gas mixture mainly composed of carbon monoxide (CO), carbon dioxide (CO 2 ), and hydrogen (H 2 ) (Köpke et al, 2010(Köpke et al, , 2011aAdamberg et al, 2015;Dürre and Eikmanns, 2015;Liew et al, 2016a). Both CO and H 2 can act as energy sources for growth and metabolism of C. ljungdahlii during gas fermentation.…”