Project description:The anaerobic digestion microbiomes has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods, i.e., amplicon sequencing, metaproteomics, metabolomics and phenotypics, in their ability to reflect the full-scale anaerobic digestion microbiome. The phenotypic fingerprinting reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting. Three different digester types, i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters reflected different operational parameters. The α-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, β-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method's features i.e., operational taxonomic units, metaproteins, metabolites, and phenotypic traits, yielded certain similar features yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, phenotypic fingerprinting is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.

2021-05-26 | PXD024788 | Pride

Stordalen Mire viromes (2014)

Project description:Stordalen Mire viromes (2014) Raw sequence reads

| PRJNA445426 | ENA

stream biofilm viromes

Project description:Benchmarking protocols for the generation of viromes from stream biofilms

| PRJEB33548 | ENA

NGS of virus derived small RNAs as a diagnostics method used to determine viromes of Hungarian vineyards

Project description:As virus diseases cannot be controlled by traditional plant protection methods the risk of their spread have to be minimized on vegetatively propagated plants, such as grapevine. Metagenomics approaches used for virus diagnostics, offer a unique opportunity to reveal the presence of all viral pathogens in the investigated plant, why their usage can reduce the risk of using infected material for a new plantation. Here we used a special field, deep sequencing of virus derived small RNAs, of this high throughput method for virus diagnostics and determined viromes of vineyards in Hungary. With NGS of virus derived small RNAs we could detect not only the viruses tested routinely, but also new ones, which have never been described in Hungary before. Virus presence didn’t correlated with the age of the plantation, moreover phylogenetic analysis of the identified virus isolates suggests that infections mostly caused by the usage of infected propagating material. Our results, validated by other molecular methods, highlighted further questions to be answered before these method can be introduced as a routine, reliable test for grapevine virus diagnostics.

2018-04-05 | GSE106240 | GEO

m5C RNA methylation modified or unmodified DNA:RNA hybrids pulldown

Project description:The biotin labeled DNA:RNA hybrids with or without RNA m5C modification were incubated with lysates of 293 cells treated with H2O2, and were pulled down by Streptavidin. The proteins pulled down by the empty beads control, unmodified or m5C-modified hybrids were analyzed by mass spectrometry

2022-04-29 | MSV000089337 | MassIVE

Viral Metagenomic Analysis of Bat Viromes

Project description:Viral Metagenomic Analysis of Bat Viromes

| PRJNA1068529 | ENA