Co-factor F430 monitoring as a manageable tool for methanogenic activity assessment in anaerobic (membrane) bioreactors

status: publishe

Dynamic constraint-based modelling of bioprocesses: a dynamic flux balance analysis model for recombinant Streptomyces lividans

status: publishe

Replication data for: "BIO-SPEC: an open-source bench-top parallel bioreactor system"

The replication data in this repository is a mirror of the Open Science Framework repository by the same authors: 10.17605/OSF.IO/39WSB. The BIO-SPEC is designed to address the need for an open-source, cost-effective, and flexible bench-top parallel bioreactor system. The purpose of the dataset is to allow replication of the hardware by providing all necessary design files and a detailed component list. It contains 3D models, schematics, and software to run on a Raspberry Pi. A discussion on the design, construction, and validation of the BIO-SPEC system is published elsewhere

BIO-SPEC: an open-source bench-top parallel bioreactor system

The BIO-SPEC is designed to address the need for an open-source, cost-effective, and flexible bench-top parallel bioreactor system. The system is suited for batch, sequencing batch, and chemostat cultivation. It features thermoelectric condensers on the off-gas to avoid the need for a chiller, while ensuring stable long-term operation. Its modular and customisable design allows for various configurations and applications in microbiology and bioprocessing. The hardware is controlled at the core by a Raspberry Pi, offering a cost-effective alternative to commercial systems, with flexibility in headplate design, gas supply, and feeding strategies. This paper details the design, construction, and validation of the BIO-SPEC system, demonstrating its capabilities and potential for diverse research applications. By bridging the gap between high-cost commercial systems and do-it-yourself alternatives, the BIO-SPEC provides an accessible and reliable solution for advancing microbiological and bioprocessing research

BIO-SPEC: an open-source bench-top parallel bioreactor system

The BIO-SPEC is designed to address the need for an open-source, cost-effective, and flexible bench-top parallel bioreactor system. The system is suited for batch, sequencing batch, and chemostat cultivation. It features thermoelectric condensers on the off-gas to avoid the need for a chiller, while ensuring stable long-term operation. Its modular and customisable design allows for various configurations and applications in microbiology and bioprocessing. The hardware is controlled at the core by a Raspberry Pi, offering a cost-effective alternative to commercial systems, with flexibility in headplate design, gas supply, and feeding strategies. This paper details the design, construction, and validation of the BIO-SPEC system, demonstrating its capabilities and potential for diverse research applications. By bridging the gap between high-cost commercial systems and do-it-yourself alternatives, the BIO-SPEC provides an accessible and reliable solution for advancing microbiological and bioprocessing research

BIO-SPEC: an open-source bench-top parallel bioreactor system

The BIO-SPEC is designed to address the need for an open-source, cost-effective, and flexible bench-top parallel bioreactor system. The system is suited for batch, sequencing batch, and chemostat cultivation. It features thermoelectric condensers on the off-gas to avoid the need for a chiller, while ensuring stable long-term operation. Its modular and customisable design allows for various configurations and applications in microbiology and bioprocessing. The hardware is controlled at the core by a Raspberry Pi, offering a cost-effective alternative to commercial systems, with flexibility in headplate design, gas supply, and feeding strategies. This paper details the design, construction, and validation of the BIO-SPEC system, demonstrating its capabilities and potential for diverse research applications. By bridging the gap between high-cost commercial systems and do-it-yourself alternatives, the BIO-SPEC provides an accessible and reliable solution for advancing microbiological and bioprocessing research

Spatiotemporal monitoring of a periodontal multispecies biofilm model : demonstration of prebiotic treatment responses

Biofilms are complex polymicrobial communities which are often associated with human infections such as the oral disease periodontitis. Studying these complex communities under controlled conditions requires in vitro biofilm model systems that mimic the natural environment as close as possible. This study established a multispecies periodontal model in the drip flow biofilm reactor in order to mimic the continuous flow of nutrients at the air-liquid interface in the oral cavity. The design is engineered to enable real-time characterization. A community of five bacteria, Streptococcus gordonii-GFPmut3*, Streptococcus oralis-GFPmut3*, Streptococcus sanguinis-pVMCherry, Fusobacterium nucleatum, and Porphyromonas gingivalis-SNAP26 is visualized using two distinct fluorescent proteins and the SNAP-tag. The biofilm in the reactor develops into a heterogeneous, spatially uniform, dense, and metabolically active biofilm with relative cell abundances similar to those in a healthy individual. Metabolic activity, structural features, and bacterial composition of the biofilm remain stable from 3 to 6 days. As a proof of concept for our periodontal model, the 3 days developed biofilm is exposed to a prebiotic treatment with L-arginine. Multifaceted effects of L-arginine on the oral biofilm were validated by this model setup. L-arginine showed to inhibit growth and incorporation of the pathogenic species and to reduce biofilm thickness and volume. Additionally, L-arginine is metabolized by Streptococcus gordonii-GFPmut3* and Streptococcus sanguinis-pVMCherry, producing high levels of ornithine and ammonium in the biofilm. In conclusion, our drip flow reactor setup is promising in studying spatiotemporal behavior of a multispecies periodontal community

Evaluation of Sample Preparation Methods for Inter-Laboratory Metabolomics Investigation of Streptomyces lividans TK24

In the past two decades, metabolomics has proved to be a valuable tool with many potential applications in different areas of science. However, there are still some challenges that need to be addressed, particularly for multicenter studies. These challenges are mainly attributed to various sources of fluctuation and unwanted variations that can be introduced at pre-analytical, analytical, and/or post-analytical steps of any metabolomics experiment. Thus, this study aimed at using Streptomyces lividans TK24 as the model organism in a cross-laboratory experiment in Manchester and Leuven to evaluate the reproducibility of a standard sample preparation method, and determine the optimal sample format (cell extract or quenched biomass) required to preserve the metabolic profile of the cells during cross-lab sample transportation and storage. Principal component analysis (PCA) scores plot of the gas chromatography-mass spectrometry (GC-MS) data from both laboratories displayed clear growth-dependent clustering patterns which was in agreement with the Procrustes analysis findings. In addition, the data generated in Manchester displayed tight clustering of cell pellets (quenched biomass) and metabolite extracts, confirming the stability of both sample formats during the transportation and storage period

Spatiotemporal monitoring demonstrates prebiotic treatment responses in a periodontal multispecies biofilm model

Abstract In vitro periodontal model systems are required for further elucidating phenomena behind periodontal pathogenesis and treatment applications. However, most oral biofilm models apply static conditions and are restricted to end-point measurements. This study established a multispecies periodontal model in the drip flow biofilm reactor in order to mimic shear flow in the oral cavity. The design is re-engineered to enable real-time characterization. A community of five bacteria, Streptococcus gordonii-GFPmut3*, Streptococcus oralis-GFPmut3*, Streptococcus sanguinis-pVMCherry, Fusobacterium nucleatum, and Porphyromonas gingivalis-SNAP26 is visualized using two distinct fluorescent proteins and the SNAP-tag. The biofilm in the reactor develops into a spatially uniform, dense and metabolically active biofilm with relative cell abundances similar to those in a healthy individual. Metabolic activity, structural features and bacterial composition of the biofilm remain stable from 3 up to 6 days. As a proof of concept for our periodontal model, the 3-day developed biofilm is exposed to a prebiotic treatment with L-arginine. Multifaceted effects of L-arginine on the oral biofilm were validated by this model setup. L-arginine showed to inhibit growth and co-aggregations of the pathogenic species, and to reduce biofilm thickness and volume. Additionally, L-arginine is metabolized by Streptococcus gordonii-GFPmut3* and Streptococcus sanguinis-pVMCherry, producing high levels of ornithine in the biofilm. In conclusion, our drip flow reactor setup is promising in studying spatiotemporal behavior of a multispecies periodontal community.</jats:p

Evaluation of Sample Preparation Methods for Inter-Laboratory Metabolomics Investigation of Streptomyces lividans TK24

In the past two decades, metabolomics has proved to be a valuable tool with many potential applications in different areas of science. However, there are still some challenges that need to be addressed, particularly for multicenter studies. These challenges are mainly attributed to various sources of fluctuation and unwanted variations that can be introduced at pre-analytical, analytical, and/or post-analytical steps of any metabolomics experiment. Thus, this study aimed at using Streptomyces lividans TK24 as the model organism in a cross-laboratory experiment in Manchester and Leuven to evaluate the reproducibility of a standard sample preparation method, and determine the optimal sample format (cell extract or quenched biomass) required to preserve the metabolic profile of the cells during cross-lab sample transportation and storage. Principal component analysis (PCA) scores plot of the gas chromatography-mass spectrometry (GC-MS) data from both laboratories displayed clear growth-dependent clustering patterns which was in agreement with the Procrustes analysis findings. In addition, the data generated in Manchester displayed tight clustering of cell pellets (quenched biomass) and metabolite extracts, confirming the stability of both sample formats during the transportation and storage period.</jats:p