Madis Rumming
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View article: Additional file 1 of Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics
Additional file 1 of Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics Open
Additional file 1. Statistics of 16S rRNA gene sequence analysis.
View article: Additional file 2 of Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics
Additional file 2 of Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics Open
Additional file 2. Relative abundances of most abundant 16S rRNA gene sequences.
View article: Additional file 5 of Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics
Additional file 5 of Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics Open
Additional file 5. Analysis of the key enzymes of AD pathways in metagenome-assembled genomes (MAGs). The genetic determinants were categorized according to the four stages of the AD process, namely hydrolysis, acidogenesis, acetogenesis a…
View article: Additional file 4 of Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics
Additional file 4 of Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics Open
Additional file 4. Taxonomic affiliations of metagenome-assembled genomes (MAGs) of this study originating from HR biofilms.
View article: Additional file 3 of Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics
Additional file 3 of Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics Open
Additional file 3. Statistics of the obtained and processed metagenome and metatranscriptome sequences.
View article: Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors
Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors Open
For the members of Bathyarchaeota detected in the biofilm microbiomes, a hydrolytic lifestyle is proposed. This is the first study indicating that Bathyarchaeota members contribute presumably to hydrolysis and subsequent fermentation of or…
View article: MOESM4 of Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors
MOESM4 of Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors Open
Additional file 4. Compiled metagenome-assembled genomes that met the criteria of a minimum of 50% genome completeness and contamination rates of 10%.
View article: MOESM7 of Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors
MOESM7 of Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors Open
Additional file 7. Genomic loci of the analyzed Bathyarchaeota MAGs encoding those enzymatic functions, which are mentioned in the metabolic scheme (Fig. 3) as well as in the main text. n.d., not determined.
View article: MOESM3 of Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors
MOESM3 of Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors Open
Additional file 3. Sequencing and assembly statistics of the metagenome data for the microbial communities of the thermophilic and mesophilic biogas reactor systems. UASS, upflow anaerobic solid-state reactor; AF, anaerobic filter; n.d., n…
View article: Metadata-driven computational (meta)genomics. A practical machine learning approach
Metadata-driven computational (meta)genomics. A practical machine learning approach Open
A vast amount of bacterial and archaeal genomic sequences have been generated in the past decade through single cell sequencing and in particular binning of metagenomic sequences, but a detailed characterization of the functional features …
View article: MOESM2 of Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors
MOESM2 of Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors Open
Additional file 2. Previously published MAGs for the phylum Bathyarchaeota. The phylogenetic affiliation is shown in Fig. 2. *, completeness and contamination were estimated by CheckM [25].
View article: MOESM1 of Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants
MOESM1 of Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants Open
Additional file 1: BIOM-File S1. Final operational taxonomic unit (OTU) table in BIOM format, format specification 1.0.0. Contained are clustered OTUs with specific OTU IDs, their supporting 16S rRNA gene sequence counts per sample, and as…