This sample represents an uncultured Elusimicrobiaceae sp. MAG assembled and binned from ERR7738192.

collection_date

2014-06-16

assembly software

metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

sample derived from

ERS2586076

contamination screening input

reads

geographic location (longitude)

-34.58

geographic location (elevation)

1287

number of standard tRNAs extracted

45

CheckM strain heterogeneity

0

ENA-FIRST-PUBLIC

2022-04-01

ENA-LAST-UPDATE

2022-04-01

completeness software

CheckM;1.1.2;lineage_wf

nucleic acid extraction

https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

completeness approach

CheckM marker lineage: k__Bacteria (UID2495)

GTDB r202 classification

d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__CADBRU01;s__CADBRU01 sp900762815

binning software

MetaBAT2 v2.15; MAGpurify v2.1.0

inter-study species representative

ERR7738192_bin.26

5S rRNAs recovered

1

organism

uncultured Elusimicrobiales bacterium

sample collection device or method

https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

scientific_name

uncultured Elusimicrobiales bacterium

investigation type

metagenome-assembled genome

MAG coverage software

Reads (ERR7738192) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560556) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

metagenomic source

human gut metagenome

project name

Metagenome sequencing of Hadza gut microbiome

sequencing method

Illumina NovaSeq 6000

most complete 23S rRNA recovered

1

23S rRNAs recovered

1

most complete 5S rRNA recovered

0.5798319327731093

reassembly post binning

No

16S rRNAs recovered

1

intra-study species representative

ERR7738192_bin.26

environment (material)

feces

binning parameters

Reads from ERR7738192 were assembled into contigs (ERZ4560556). The following read sets from this study were the most similar to ERR7738192 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738192,ERR7738247,ERR7738190,ERR7738194,ERR7738550,ERR7738624,ERR7738604,ERR7738253,ERR7745951,ERR7746113. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4560556. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.

contamination score

0

tRNA extraction software

tRNAscan-SE;2.0.9;-B

reference for biomaterial

https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

taxonomic classification

GTDB-TK v1.7.0, r202 database, default parameters

16S recovery software

barrnap;0.9;--kingdom bac

environment (biome)

terrestrial biome

environment (feature)

human-associated habitat

geographic location (country and/or sea)

Tanzania

unique standard tRNAs extracted

20

ENA-CHECKLIST

ERC000011

16S recovered

TRUE

assembly quality

Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs.

taxonomic identity marker

multi-marker approach

MAG coverage depth

38.14

completeness score

96.56

geographic location (latitude)

-3.55

most complete 16S rRNA recovered

0.9843444227005871

contamination screening parameters

All reads in ERR7738192 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

isolation_source

human feces

Here, we examine the microbiome profile of 955 stool, hand, and environmental samples collected longitudinally for over a year from the Hadza hunter-gatherers of Tanzania. The data reveal annual cyclic reconfiguration of the microbiome, in which some taxa become undetectable only to reappear in a subsequent season.

host scientific name

Homo sapiens

host_taxid

9606

water_source

WELL

sample_type

feces

sample_type_expanded

FECES

bush_camp

GIDAMILANDA

collection_timestamp

2014-06-16

ENA-FIRST-PUBLIC

2018-08-13

empo_2

Animal-associated

ENA-LAST-UPDATE

2018-06-27

empo_3

Animal distal gut

empo_1

Host-asssociated

host_body_habitat

UBERON:feces

season

2014-ED

longitude

34.58

maize_observation

No

host_body_mass_index

not provided

env_feature

human-associated habitat

organism

human gut metagenome

physical_specimen_remaining

TRUE

host_body_site

UBERON:feces

host_weight

not provided

scientific_name

human gut metagenome

host_height

not provided

age_units

years

sample_source

HUMAN

host_life_stage

adult

env_package

human-gut

gender

FEMALE

latitude

-3.55

physical_specimen_location

Stanford University School of Medicine

host_body_product

UBERON:feces

height_units

not provided

host_subject_id

308

qiita_empo_2

Unknown

seasonality_unique_subjects

0

qiita_empo_1

Unknown

env_material

feces

qiita_empo_3

Unknown

env_biome

anthropogenic terrestrial biome

host_common_name

human

elevation

1287

ENA-CHECKLIST

ERC000011

dna_extracted

TRUE

sex

female

weight_units

not provided

host_age

22

sample_type_field_notes

HUMAN FECES

geo_loc_name

Tanzania

seasonality

0

story

not applicable

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX2689848" alias="qiita_ptid_4944:11358.1935" center_name="University of California San Diego Microbiome Initiative">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX2689848</PRIMARY_ID>
    <SUBMITTER_ID namespace="University of California San Diego Microbiome Initiative">qiita_ptid_4944:11358.1935</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>qiita_ptid_4944:11358.1935</TITLE>
  <STUDY_REF accession="ERP109605">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP109605</PRIMARY_ID>
      <SECONDARY_ID>PRJEB27517</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Here, we examine the microbiome profile of 955 stool, hand, and environmental samples collected longitudinally for over a year from the Hadza hunter-gatherers of Tanzania. The data reveal annual cyclic reconfiguration of the microbiome, in which some taxa become undetectable only to reappear in a subsequent season. Sequencing data is also deposited at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA392012/.</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="ERS2586076">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS2586076</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA4766113</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>11358.1935</LIBRARY_NAME>
      <LIBRARY_STRATEGY>AMPLICON</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>PCR</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <SINGLE/>
      </LIBRARY_LAYOUT>
      <LIBRARY_CONSTRUCTION_PROTOCOL>Illumina MiSeq EMP V4 515f,806rbc original protocol</LIBRARY_CONSTRUCTION_PROTOCOL>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina MiSeq</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS2586076</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA1528370</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX2689848&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX2689848&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
  <EXPERIMENT_ATTRIBUTES>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>barcode</TAG>
      <VALUE>GTGAGGGCAAGT</VALUE>
    </EXPERIMENT_ATTRIBUTE>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>center_name</TAG>
      <VALUE>Stanford University School of Medicine</VALUE>
    </EXPERIMENT_ATTRIBUTE>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>center_project_name</TAG>
      <VALUE>Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania</VALUE>
    </EXPERIMENT_ATTRIBUTE>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>in_house_identifier</TAG>
      <VALUE>95</VALUE>
    </EXPERIMENT_ATTRIBUTE>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>linker</TAG>
      <VALUE>GT</VALUE>
    </EXPERIMENT_ATTRIBUTE>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>original_barcode</TAG>
      <VALUE>not applicable</VALUE>
    </EXPERIMENT_ATTRIBUTE>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>pcr_primers</TAG>
      <VALUE>FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT</VALUE>
    </EXPERIMENT_ATTRIBUTE>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>primer</TAG>
      <VALUE>GTGTGCCAGCMGCCGCGGTAA</VALUE>
    </EXPERIMENT_ATTRIBUTE>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>run_center</TAG>
      <VALUE>Mayo Clinic Molecular Biology Core Facility</VALUE>
    </EXPERIMENT_ATTRIBUTE>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>run_date</TAG>
      <VALUE>5/26/15</VALUE>
    </EXPERIMENT_ATTRIBUTE>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>run_prefix</TAG>
      <VALUE>Hadza_16S_Run1</VALUE>
    </EXPERIMENT_ATTRIBUTE>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>sequencing_meth</TAG>
      <VALUE>Sequencing by synthesis</VALUE>
    </EXPERIMENT_ATTRIBUTE>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>target_gene</TAG>
      <VALUE>16S rRNA</VALUE>
    </EXPERIMENT_ATTRIBUTE>
    <EXPERIMENT_ATTRIBUTE>
      <TAG>target_subfragment</TAG>
      <VALUE>V4</VALUE>
    </EXPERIMENT_ATTRIBUTE>
  </EXPERIMENT_ATTRIBUTES>
</EXPERIMENT>
</EXPERIMENT_SET>

Metadata as EBI XML

<EXPERIMENT_SET>
<EXPERIMENT accession="ERX7306523" alias="webin-reads-Hadza_MoBio_hadza-E-H_O_22_1935" center_name="stanford university school of medicine">
  <IDENTIFIERS>
    <PRIMARY_ID>ERX7306523</PRIMARY_ID>
    <SUBMITTER_ID namespace="stanford university school of medicine">webin-reads-Hadza_MoBio_hadza-E-H_O_22_1935</SUBMITTER_ID>
  </IDENTIFIERS>
  <TITLE>Raw reads: Hadza_MoBio_hadza-E-H_O_22_1935</TITLE>
  <STUDY_REF accession="ERP133688">
    <IDENTIFIERS>
      <PRIMARY_ID>ERP133688</PRIMARY_ID>
      <SECONDARY_ID>PRJEB49206</SECONDARY_ID>
    </IDENTIFIERS>
  </STUDY_REF>
  <DESIGN>
    <DESIGN_DESCRIPTION>Shotgun metagenome sequencing of fecal sample 1935 from Hadza individual following powersoil DNA extraction (10.1126/science.aan4834). Reads are in non-random order due to clumpify.sh (BBTools).</DESIGN_DESCRIPTION>
    <SAMPLE_DESCRIPTOR accession="ERS2586076">
      <IDENTIFIERS>
        <PRIMARY_ID>ERS2586076</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioSample">SAMEA4766113</EXTERNAL_ID>
      </IDENTIFIERS>
    </SAMPLE_DESCRIPTOR>
    <LIBRARY_DESCRIPTOR>
      <LIBRARY_NAME>Hadza_MoBio_hadza-E-H_O_22_1935</LIBRARY_NAME>
      <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
      <LIBRARY_SOURCE>METAGENOMIC</LIBRARY_SOURCE>
      <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
      <LIBRARY_LAYOUT>
        <PAIRED/>
      </LIBRARY_LAYOUT>
    </LIBRARY_DESCRIPTOR>
  </DESIGN>
  <PLATFORM>
    <ILLUMINA>
      <INSTRUMENT_MODEL>Illumina NovaSeq 6000</INSTRUMENT_MODEL>
    </ILLUMINA>
  </PLATFORM>
  <EXPERIMENT_LINKS>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SAMPLE</DB>
        <ID>ERS2586076</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMISSION</DB>
        <ID>ERA7909145</ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-FASTQ-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX7306523&result=read_run&fields=run_accession,fastq_ftp,fastq_md5,fastq_bytes]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
    <EXPERIMENT_LINK>
      <XREF_LINK>
        <DB>ENA-SUBMITTED-FILES</DB>
        <ID><![CDATA[https://www.ebi.ac.uk/ena/portal/api/filereport?accession=ERX7306523&result=read_run&fields=run_accession,submitted_ftp,submitted_md5,submitted_bytes,submitted_format]]></ID>
      </XREF_LINK>
    </EXPERIMENT_LINK>
  </EXPERIMENT_LINKS>
</EXPERIMENT>
</EXPERIMENT_SET>