Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing

The microbial biogas network is complex and intertwined, and therefore relatively stable in its overall functionality. However, if key functional groups of microorganisms are affected by biotic or abiotic factors, the entire efficacy may be impaired. Bacteriophages are hypothesized to alter the steering process of the microbial network. In this study, an enriched fraction of virus-like particles was extracted from a mesophilic biogas reactor and sequenced on the Illumina MiSeq and Nanopore GridION sequencing platforms. Metagenome data analysis resulted in identifying 375 metagenome-assembled viral genomes (MAVGs). Two-thirds of the classified sequences were only assigned to the superkingdom Viruses and the remaining third to the family Siphoviridae, followed by Myoviridae, Podoviridae, Tectiviridae, and Inoviridae. The metavirome showed a close relationship to the phage genomes that infect members of the classes Clostridia and Bacilli. Using publicly available biogas metagenomic data, a fragment recruitment approach showed the widespread distribution of the MAVGs studied in other biogas microbiomes. In particular, phage sequences from mesophilic microbiomes were highly similar to the phage sequences of this study. Accordingly, the virus particle enrichment approach and metavirome sequencing provided additional genome sequence information for novel virome members, thus expanding the current knowledge of viral genetic diversity in biogas reactors.BMBF, 031L0103, de.NBI - Partner - MetaProtServBMBF, 031A532B, de.NBI - Etablierungsphase - Koordinierungs- und Administrationseinheit - CAU - GeschäftsstelleBMBF, 031A533A, de.NBI - Etablierungsphase - Leistungszentrum - BiGi - Bioinformatisches Resourcenzentrum für mikrobielle Genomforschung in Biotechnologie und MedizinBMBF, 031A533B, de.NBI - Etablierungsphase - Leistungszentrum - BiGi - Bioinformatisches Resourcenzentrum für mikrobielle Genomforschung in Biotechnologie und MedizinBMBF, 031A534A, de.NBI - Etablierungsphase - Leistungszentrum - BioInfra.Prot - Bioinformatik der ProteomikBMBF, 031A535A, de.NBI - Etablierungsphase - Leistungszentrum CiBi - Zentrum für integrative BioinformatikBMBF, 031A537A, de.NBI - Etablierungsphase - Heidelberg Center for Human Bioinformatics - HD-HuB - Humane Genetik und Genomik, Humane Mikrobiomik, systematische Phänotypisierung humaner ZellenBMBF, 031A537B, de.NBI - Etablierungsphase-European Molecular Biology Laboratory-HD-HUBBMBF, 031A537C, de.NBI - Etablierungsphase - Heidelberg Center for Human Bioinformatics - HD-HuBBMBF, 031A537D, de.NBI - Etablierungsphase - Heidelberg Center for Human Bioinformatics - HD-HuB - Humane Genetik und Genomik, Humane Metagenomik, systematische Phänotypisierung humaner Zellen, Epigenetik und de.NBI Cloud Standort Heidelberg/BerlinBMBF, 031A538A, de.NBI - Etablierungsphase - Leistungszentrum: RBC - RNA Bioinformati

Recognition of valid open and online learning

Project ReOPEN has been funded with the support from the European Commission Erasmus+ KA2 Strategic partnership for VET project (N: 2016-1-LT01-KA202-023131)It has been a while since recognition of prior and non-formal learning was addressed by education providers and policy makers in Europe. Quite a number of universities in Europe established instruments and procedures properly addressing strategic goals to recognize prior and non-formal learning in the form of results in formal curricula. However, this practice has been challenged by two main factors and innovations in themselves. [...]Edukologijos tyrimų institutasInovatyvių studijų institutasVytauto Didžiojo universitetasŠvietimo akademij

Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing

Willenbücher K, Wibberg D, Huang L, et al. Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing. Microorganisms. 2022;10(2): 368.The microbial biogas network is complex and intertwined, and therefore relatively stable in its overall functionality. However, if key functional groups of microorganisms are affected by biotic or abiotic factors, the entire efficacy may be impaired. Bacteriophages are hypothesized to alter the steering process of the microbial network. In this study, an enriched fraction of virus-like particles was extracted from a mesophilic biogas reactor and sequenced on the Illumina MiSeq and Nanopore GridION sequencing platforms. Metagenome data analysis resulted in identifying 375 metagenome-assembled viral genomes (MAVGs). Two-thirds of the classified sequences were only assigned to the superkingdom Viruses and the remaining third to the family Siphoviridae, followed by Myoviridae, Podoviridae, Tectiviridae, and Inoviridae. The metavirome showed a close relationship to the phage genomes that infect members of the classes Clostridia and Bacilli. Using publicly available biogas metagenomic data, a fragment recruitment approach showed the widespread distribution of the MAVGs studied in other biogas microbiomes. In particular, phage sequences from mesophilic microbiomes were highly similar to the phage sequences of this study. Accordingly, the virus particle enrichment approach and metavirome sequencing provided additional genome sequence information for novel virome members, thus expanding the current knowledge of viral genetic diversity in biogas reactors

Parallelizable Microfluidic Platform to Model and Assess In Vitro Cellular Barriers: Technology and Application to Study the Interaction of 3D Tumor Spheroids with Cellular Barriers

Endothelial and epithelial cellular barriers play a vital role in the selective transport of solutes and other molecules. The properties and function of these barriers are often affected in case of inflammation and disease. Modelling cellular barriers in vitro can greatly facilitate studies of inflammation, disease mechanisms and progression, and in addition, can be exploited for drug screening and discovery. Here, we report on a parallelizable microfluidic platform in a multiwell plate format with ten independent cell culture chambers to support the modelling of cellular barriers co-cultured with 3D tumor spheroids. The microfluidic platform was fabricated by microinjection molding. Electrodes integrated into the chip in combination with a FT-impedance measurement system enabled transepithelial/transendothelial electrical resistance (TEER) measurements to rapidly assess real-time barrier tightness. The fluidic layout supports the tubeless and parallelized operation of up to ten distinct cultures under continuous unidirectional flow/perfusion. The capabilities of the system were demonstrated with a co-culture of 3D tumor spheroids and cellular barriers showing the growth and interaction of HT29 spheroids with a cellular barrier of MDCK cells