Malassezia sympodialis
INSDC center name
EMG
Submitter Id
SMGC_7561_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
broad-scale environmental context
Human
broker name
EBI-EMG
collection date
2013-04-29
completeness score
97.58
completeness software
CheckM
contamination score
0.89
environmental medium
Human skin
geographic location (country and/or sea)
USA
geographic location (latitude)
38.984652
geographic location (longitude)
-77.094709
investigation type
metagenome-assembled genome
isolation_source
skin metagenome
local environmental context
Human skin
metagenomic 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 derived from
SAMN03025650,SAMN03025650,SAMN03025650,SAMN03025650,SAMN03025650,SAMN03025650,SAMN03025650,SAMN03025650,SAMN03025650,SAMN03025650,SAMN03025650,SAMN03025650,SAMN03025650,SAMN03025650,SAMN03025651,SAMN03025651,SAMN03025651,SAMN03025651,SAMN03025651,SAMN03025651,SAMN03025652,SAMN03025652,SAMN03025652,SAMN03025652,SAMN03025652,SAMN03025652,SAMN03025653,SAMN03025653,SAMN03025653,SAMN03025653,SAMN03025653,SAMN03025653,SAMN03025654,SAMN03025654,SAMN03025654,SAMN03025654,SAMN03025654,SAMN03025654,SAMN03025655,SAMN03025655,SAMN03025655,SAMN03025655,SAMN03025655,SAMN03025655,SAMN03025656,SAMN03025656,SAMN03025656,SAMN03025656,SAMN03025657,SAMN03025657,SAMN03025657,SAMN03025657,SAMN03025657,SAMN03025657,SAMN03025658,SAMN03025658,SAMN03025658,SAMN03025658,SAMN03025659,SAMN03025659,SAMN03025659,SAMN03025659,SAMN03025659,SAMN03025659,SAMN03025660,SAMN03025660,SAMN03025660,SAMN03025660,SAMN03025660,SAMN03025660,SAMN03025660,SAMN03025661,SAMN03025661,SAMN03025661,SAMN03025661,SAMN03025661,SAMN03025661,SAMN03025661,SAMN03025661,SAMN03025661,SAMN03025661,SAMN03025661,SAMN03025661,SAMN03025661,SAMN03025661,SAMN03025662,SAMN03025662,SAMN03025662,SAMN03025662,SAMN03025662,SAMN03025662,SAMN03025663,SAMN03025663,SAMN03025663,SAMN03025663,SAMN03025663,SAMN03025663,SAMN03025663,SAMN03025664,SAMN03025664,SAMN03025664,SAMN03025664,SAMN03025664,SAMN03025664,SAMN03025665,SAMN03025665,SAMN03025665,SAMN03025665,SAMN03025665,SAMN03025665,SAMN03025666,SAMN03025666,SAMN03025666,SAMN03025666,SAMN03025666,SAMN03025666,SAMN03025666
sample name
SMGC_7561_bin.1_MetaWRAP_v1.2.1_MAG
scientific_name
Malassezia sympodialis
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;5204;452284;1538075;162474;742845;55193;76777;1230383*
taxonomic identity marker
multi-marker approach