binned metagenome: spire_mag_01831283
Phocaeicola vulgatus
ENA first public
2024-09-20
INSDC center name
EMBL Heidelberg
INSDC status
public
Submitter Id
spire_mag_01831283
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software
megahit 1.2.9
binning parameters
default
binning software
metabat 2.12.1
broad-scale environmental context
human digestive system
broker name
EBI-EMG
collection date
2014-11-26
completeness score
99.98
completeness software
checkm2 0.1.3
contamination score
5.95
environmental medium
stool
geographic location (country and/or sea)
Switzerland
geographic location (latitude)
46.91670000
geographic location (longitude)
7.46670000
investigation type
metagenome-assembled genome
isolation_source
human gut metagenome
local environmental context
human gut
metagenomic source
human gut metagenome
project name
Age-dependent macular degeneration (AMD) is the most frequent cause of blindness in the elderly. There is evidence that nutrition, inflammation and genetic risk factors play an important role in the development of AMD. Recent studies suggest that the composition of the gut microbiome is associated with metabolic diseases through modulation of inflammation and host metabolism. To investigate whether compositional and functional alterations of the gut microbiome are associated with AMD, we sequenced the gut metagenomes of patients with AMD and controls. The genera Anaerotruncus and Oscillibacter as well as Ruminococcus torques and Eubacterium ventriosum were relatively enriched in patients with AMD, whereas Bacteroides eggerthii was enriched in controls. Patient's gut microbiomes were enriched in genes of the L-alanine fermentation, glutamate degradation and arginine biosynthesis pathways and decreased in genes of the fatty acid elongation pathway. These findings suggest that alterations in the gut microbiome are associated with AMD and that the interdependency between amino and fatty acid metabolism and AMD could be targeted by microbiome-altering interventions.
sample derived from
SAMEA3950616
sample name
spire_mag_01831283
scientific_name
Phocaeicola vulgatus
sequencing method
Illumina HiSeq 2000
taxonomic identity marker
multi-marker approach