Metagenome-Assembled Genome: SMGC_7562_bin.1_MetaW... - BioSample

Metagenome-Assembled Genome: SMGC_7562_bin.1_MetaWRAP_v1.2.1_MAG

Identifiers: BioSample: SAMEA114293886; SRA: ERS16282980

Organism: Clavispora lusitaniae
cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Pichiomycetes; Serinales; Metschnikowiaceae; Clavispora

Attributes

broad-scale environmental context	Human
collection date	2013-05-22
environmental medium	Human skin
geographic location	USA
investigation type	metagenome-assembled genome
isolation source	skin metagenome
project name	16S rRNA gene sequences amplified from subjects with eczema and age-matched healthy controls. <p> Microbes living in and on humans are ten times more numerous than human cells. Culture-based methods have been the primary techniques used to study microbes inhabiting humans however, many species are not successfully grown in culture. The NIH Roadmap for Medical Research Human Microbiome Project (HMP) aims to investigate the microbes in the gastrointestinal tract, oral cavity, skin, vagina, and nares. The goal of the HMP is to comprehensively characterize the human microbiota and analyze its role in human health and disease. <p> The skin serves not only as a barrier against invading pathogens and moisture loss, but also as a host to microbial communities. The skin of an adult is an approximately 2 square meter surface with a myriad of microenvironments. Atopic dermatitis (AD), more commonly known as eczema, is a common skin disorder that is exacerbated by Staphylococcus aureus colonization. This study aims to investigate the skin microbiota of AD patients at specific timepoints (quiescence, disease flares, and post-treatment) to examine how disease state correlates with changes in the skin microflora. <p> The 16S small subunit ribosomal (rRNA) gene is present in every bacterial cell, serving as a universal marker. The gene is sufficiently conserved to allow accurate alignment but adequately varied to enable phylogenetic analyses. Sequencing via 16S rRNA-based phylotyping has been used to survey the bacterial microbes on the skin. Initially, we will examine the bacterial diversity associated with AD using a 16S rRNA survey and later broadening to include fungi, viruses, archaea and mites. In addition, bacteria will be cultured on a wide variety of media and isolates representing both abundant and novel species will be selected for whole genome sequencing. <p> To characterize fungal diversity, we utilize two phylogenetic markers within the rDNA region: 18S rRNA and the Intervening Internal Transcribed Spacer (ITS) region. Full microbial diversity will be explored with shotgun metagenomic sequencing.
sample name	SMGC_7562_bin.1_MetaWRAP_v1.2.1_MAG
ENA-CHECKLIST	ERC000047
INSDC center name	EMG
Submitter Id	SMGC_7562_bin.1_MetaWRAP_v1.2.1_MAG
assembly quality	Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software	metaspades_v3.13.0
binning parameters	MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
binning software	MetaWRAP v1.2.1
broker name	EBI-EMG
completeness score	65.22
completeness software	CheckM
contamination score	4.35
geographic location (latitude)	38.984652
geographic location (longitude)	-77.094709
local environmental context	Human skin
metagenomic source	skin metagenome
sample derived from	SAMN03025667,SAMN03025667,SAMN03025667,SAMN03025667,SAMN03025667,SAMN03025667,SAMN03025667,SAMN03025667,SAMN03025667,SAMN03025667,SAMN03025667,SAMN03025667,SAMN03025667,SAMN03025667,SAMN03025668,SAMN03025668,SAMN03025668,SAMN03025668,SAMN03025668,SAMN03025668,SAMN03025669,SAMN03025669,SAMN03025669,SAMN03025669,SAMN03025669,SAMN03025669,SAMN03025670,SAMN03025670,SAMN03025670,SAMN03025670,SAMN03025670,SAMN03025670,SAMN03025671,SAMN03025671,SAMN03025671,SAMN03025671,SAMN03025671,SAMN03025671,SAMN03025672,SAMN03025672,SAMN03025672,SAMN03025672,SAMN03025672,SAMN03025672,SAMN03025673,SAMN03025673,SAMN03025673,SAMN03025673,SAMN03025674,SAMN03025674,SAMN03025674,SAMN03025674,SAMN03025674,SAMN03025674,SAMN03025675,SAMN03025675,SAMN03025675,SAMN03025675,SAMN03025676,SAMN03025676,SAMN03025676,SAMN03025676,SAMN03025676,SAMN03025676,SAMN03025677,SAMN03025677,SAMN03025677,SAMN03025677,SAMN03025677,SAMN03025677,SAMN03025677,SAMN03025678,SAMN03025678,SAMN03025678,SAMN03025678,SAMN03025678,SAMN03025678,SAMN03025678,SAMN03025678,SAMN03025678,SAMN03025678,SAMN03025678,SAMN03025678,SAMN03025678,SAMN03025678,SAMN03025679,SAMN03025679,SAMN03025679,SAMN03025679,SAMN03025679,SAMN03025679,SAMN03025680,SAMN03025680,SAMN03025680,SAMN03025680,SAMN03025680,SAMN03025680,SAMN03025681,SAMN03025681,SAMN03025681,SAMN03025681,SAMN03025681,SAMN03025681,SAMN03025681,SAMN03025682,SAMN03025682,SAMN03025682,SAMN03025682,SAMN03025682,SAMN03025682,SAMN03025683,SAMN03025683,SAMN03025683,SAMN03025683,SAMN03025683,SAMN03025683
scientific_name	Clavispora lusitaniae
sequencing method	Illumina HiSeq 2000
taxonomic classification	The taxonomy of this Metagenome-Assembled Genome was originally computed with BAT, which assigned the following NCBI taxonomicannotation: 1;131567;2759;33154;4751;451864;4890;716545;147537;4891;4892;27319;36910;36911
taxonomic identity marker	multi-marker approach

Description: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic runs SRR1632848,SRR1632849,SRR1632850,SRR1632851,SRR1632852,SRR1632853,SRR1632854,SRR1632855,SRR1632856,SRR1632857,SRR1632858,SRR1632859,SRR1632860,SRR1632861,SRR1632977,SRR1632978,SRR1632979,SRR1632980,SRR1632981,SRR1632982,SRR1632983,SRR1632984,SRR1632985,SRR1632986,SRR1632987,SRR1632988,SRR1632989,SRR1632990,SRR1632991,SRR1632992,SRR1632993,SRR1632994,SRR1632995,SRR1632996,SRR1632997,SRR1632998,SRR1632999,SRR1633000,SRR1633001,SRR1633002,SRR1633003,SRR1633004,SRR1633005,SRR1633006,SRR1633007,SRR1633008,SRR1633009,SRR1633010,SRR1633011,SRR1633012,SRR1633013,SRR1633014,SRR1633015,SRR1633016,SRR1633017,SRR1633018,SRR1633019,SRR1633020,SRR1633021,SRR1633022,SRR1633023,SRR1633024,SRR1633025,SRR1633026,SRR1633027,SRR1633028,SRR1633029,SRR1633030,SRR1633031,SRR1633032,SRR1633033,SRR1633133,SRR1633134,SRR1633135,SRR1633136,SRR1633137,SRR1633138,SRR1633139,SRR1633140,SRR1633141,SRR1633142,SRR1633143,SRR1633144,SRR1633145,SRR1633146,SRR1633147,SRR1633148,SRR1633149,SRR1633150,SRR1633151,SRR1633152,SRR1633153,SRR1633154,SRR1633155,SRR1633156,SRR1633157,SRR1633158,SRR1633159,SRR1633160,SRR1633161,SRR1633162,SRR1633163,SRR1633164,SRR1633165,SRR1633166,SRR1633167,SRR1633168,SRR1633169,SRR1633170,SRR1633171,SRR1633172,SRR1633173,SRR1633174,SRR1633175,SRR1633176,SRR1633177 of study SRP002480.

BioProject: PRJEB47281 Skin Microbial Genome Catalogue
Retrieve all samples from this project

Submission: EBI; 2023-08-23

Accession:: SAMEA114293886
ID:: 37122443

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Metagenome-Assembled Genome: SMGC_7562_bin.1_MetaWRAP_v1.2.1_MAG

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