Project description:<p>A variety of anthropogenic organohalide contaminants generated from industry are released into the environment, and thus cause serious pollution that endangers human health. In the present study, we investigated the microbial community composition of industrial saponification wastewater using 16S rRNA sequencing, providing genomic insights of potential organohalide dehalogenation bacteria (OHDBs) by whole-metagenome sequencing. We also explored yet-to-culture OHDBs involved in the microbial community. Microbial diversity analysis reveals that Proteobacteria and Patescibacteria phyla dominate microbiome abundance of the wastewater. In addition, a total of six bacterial groups (Rhizobiales, Rhodobacteraceae, Rhodospirillales, Flavobạcteriales, Micrococcales, and Saccharimonadales) were found as biomarkers in the key organohalide removal module. Ninety-four metagenome-assembled genomes (MAGs) were reconstructed from the microbial community, and 105 hydrolytic dehalogenase genes within 42 MAGs were identified, suggesting that the potential for hydrolytic organohalide dehalogenation is present in the microbial community. Subsequently, we characterized the organohalide dehalogenation of an isolated OHDB, Microbacterium sp. J1-1, which shows the dehalogenation activities of chloropropanol, dichloropropanol, and epichlorohydrin. This study provides a community-integrated multi-omics approach to gain functional OHDBs for industrial organohalide dehalogenation.</p>

2022-11-21 | MTBLS3916 | MetaboLights

The proteome of extracellular vesicles secreted in vitro by porcine microbiota grown in complex β-mannan

Project description:The secretion of Extracellular Vesicles ((EVs) is a common process in both prokaryotic and eukaryotic cells for intercellular communication, survival, and pathogenesis. Previous studies have illustrated the presence of EVs in supernatants from pure cultures of bacteria, including Gram-positive and Gram-negative glycan-degrading gut commensals. However, the composition of vesicles formed in complex microbial communities has not been clearly defined. In a recent paper, we reported that wood-derived complex β-mannan, which shares structural similarity with conventional dietary fibers, can be used to modulate the porcine gut microbiota composition and activity. In this paper, we investigated the production, size, composition, and proteome of EVs secreted by the pig fecal microbiota after 24 h enrichment on complex β-mannan. Using transmission electron microscopy and nanoparticle tracking analysis, we identified EVs with an average size of 105 nm. We utilized mass spectrometry-based metaproteomic profiling of EV proteins against a database of 355 metagenome-assembled genomes (MAGs) from the porcine colon and thereby identified 303 proteins, of which 55% were only detected in the EVs isolated from the β-mannan culture. Most of the proteins extracted from the EVs isolated from the culture grown on β-mannan mapped to two MAGs, MAG53 and MAG272, belonging to the orders Clostridiales and Bacilli, respectively. Furthermore, the MAG with the third-most-detected proteins was MAG 343 belonging to the order Enterobacteriales. The most abundant proteins detected in the β-mannan proteome were involved in translation, energy production, amino acid and carbohydrate transport, as well as metabolism. Overall, our results demonstrate the release of EVs in a complex microbial community whereby the protein content of the EVs reflects the response of specific microbes to the available carbohydrate source.

2021-09-09 | PXD017420 | Pride

marine sediment metagenome

Project description:Metagenome assembled genomes (MAGs) from Gulf of Kutch pelagic sediments

| PRJNA598416 | ENA

marine sediment metagenome

Project description:Metagenome assembled genomes (MAGs) from Gulf of Khambhat pelagic sediments

| PRJNA598413 | ENA

Project description:Halichondria panicea draft genome and microbiome metagenome assembled genomes (MAGs)

| PRJNA753045 | ENA

gut metagenome

Project description:Metagenomic sequencing of yak faecal microbiota

| PRJNA624740 | ENA