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Metagenome-assembled genome: ERR318683_bin.75_CONCOCT_v1.1_MAG

Identifiers
BioSample: SAMEA14080599; SRA: ERS11683855
Organism
Campylobacter upsaliensis
cellular organisms; Bacteria; Pseudomonadati; Campylobacterota; Epsilonproteobacteria; Campylobacterales; Campylobacteraceae; Campylobacter
Attributes
collection date2006-05-01
broad-scale environmental contextHost-associated
local-scale environmental contextMammals
environmental mediumDigestive system
geographic locationUSA
investigation typemetagenome-assembled genome
isolation sourcegut metagenome
project nameDespite being obligate carnivores, cats are fed a wide range of dietary macronutrients within commercial diets. Little is known regarding the feline gastrointestinal microbiome and how it is impacted by diet. Using 16S RNA analysis, changes in diet (protein:carbohydrate ratio) do affect fecal microbiota of growing kittens. However, to investigate potential functional differences deep Illumina shotgun sequencing is required and a study of microbial structure and function in these animals is reported here. This is the largest and most comprehensive analysis of the feline gastrointestinal microbiome to date. It provides an overview of the taxa and gene functions present and how they are impacted by the dietary protein: carbohydrate ratio. The more diverse structure of the high-protein diet might reflect a more specialized microbiome. As anticipated, our permutation approach reduced the number of pathways to a more manageable set. The reduced data set identified six pathways readily interpretable to the study design.
sample nameERR318683_bin.75_CONCOCT_v1.1_MAG
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2023-01-03
ENA-LAST-UPDATE2023-01-03
External IdSAMEA14080599
INSDC center aliasEBI
INSDC center nameEuropean Bioinformatics Institute
INSDC first public2023-01-03T00:32:55Z
INSDC last update2023-01-03T00:32:55Z
INSDC statuspublic
Submitter IdERR318683_bin.75_CONCOCT_v1.1_MAG
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwaremetaSPAdes v3.12.0
binning parametersDefault
binning softwareCONCOCT v1.1
broker nameEMG broker account, EMBL-EBI
completeness score99.88
completeness softwareCheckM
contamination score0.0
geographic location (latitude)40.103878
geographic location (longitude)-88.2252
metagenomic sourcegut metagenome
sample derived fromSAMEA2145937
scientific_nameCampylobacter upsaliensis
sequencing methodIllumina HiSeq 2000
taxonomic identity markermulti-marker approach
Description

This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR318683 of study ERP003671.

BioProject
PRJEB51895 Large-scale analysis of novel cellular microbes from the mammal gut biome
Retrieve all samples from this project

Submission
EBI; 2023-01-04
Accession:
SAMEA14080599
ID:
32558287

BioProject Nucleotide

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