2024-12-11
ENA first public
ERC000047
ENA-CHECKLIST
CMR
INSDC center name
public
INSDC status
ERS22451911
SRA accession
binchicken_co68_306
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
metaSPAdes;3.15.4;default
assembly software
coverage and kmer
binning parameters
VAMB;3.0.2;default
binning software
engineered
broad-scale environmental context
2016-10-17
collection date
80.8
%
completeness score
CheckM2;1.0.2;default
completeness software
2.34
%
contamination score
This sample represents a Third Party Annotation (TPA) Metagenome-assembled genome assembled from the metagenomic runs ERR3173388,ERR3173389 of study ERP113854.
description
engineered
environmental medium
Denmark
geographic location (country and/or sea)
56.469698
DD
geographic location (latitude)
10.037277
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
anaerobic digester metagenome
isolation_source
anaerobic digester biome
local environmental context
anaerobic digester metagenome
metagenomic source
uncultured bacterium
organism
Short-chain fatty acid (SCFA) degradation is an essential step that occurs across methanogenic environments, and is usually catalyzed by SCFA-oxidizing bacteria in syntrophy with methanogens. Current knowledge of this functional guild is mainly based on isolated or enriched syntrophs due to past methodological limitations. However, it is unclear whether these reference organisms reflect the true ecological properties and in situ activities of the syntrophs that predominate in full-scale systems. Here we describe novel, metabolically versatile bacterial species playing key roles in SCFA oxidation which were ubiquitous in full-scale anaerobic sludge digesters. A genome-guided metatranscriptomic approach was employed, with 198 metagenome-assembled genomes (MAGs) generated from the microbiome of two digesters. The transcriptomic response of individual MAG was studied after stimulation with low concentration of acetate, propionate, or butyrate, to identify the positively responsive members. Such responding MAGs included one bacterium of the family Pelotomaculaceae, and two bacteria of the class Desulfomonilia, which encoded complete propionate or butyrate beta-oxidation pathways that were significantly upregulated under propionate or butyrate stimulation, respectively. These three SCFA oxidizers were detected in most of the 38 investigated digesters, and encoded unique genomic features compared with the well-characterized populations, including the metabolic pathways for phosphite oxidation, nitrite, or sulfate reduction.
project name
SAMEA5366189,SAMEA5366190
sample derived from
uncultured bacterium
scientific_name
Illumina HiSeq 2500
sequencing method
multi-marker approach
taxonomic identity marker
Metagenome-assembled genome: binchicken_co68_306
title