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text: Samples prepared at Lighthouse Lab in Glasgow by Harper VanSteenhouse, Yumi Kasai, David Gray, Carol Clugston, Anna Dominiczak and Alex Alderton, Roberto Amato, Jeffrey Barrett, Sonia Goncalves, Ewan Harrison, David K. Jackson, Ian Johnston, Dominic Kwiatkowski, Cordelia Langford, John Sillitoe on behalf of the Wellcome Sanger Institute COVID-19 Surveillance Team (https://www.sanger.ac.uk/covid-team)

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text: not provided

characteristic: collector name

text: Samples prepared at Lighthouse Laboratory Plymouth by Lighthouse Laboratory Plymouth and Alex Alderton, Roberto Amato, Jeffrey Barrett, Sonia Goncalves, Ewan Harrison, David K. Jackson, Ian Johnston, Dominic Kwiatkowski, Cordelia Langford, John Sillitoe on behalf of the Wellcome Sanger Institute COVID-19 Surveillance Team (https://www.sanger.ac.uk/covid-team)

characteristic: description

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Scotland

characteristic: geographic location (region and locality)

text: Human

text: not provided

text: Human

text: not provided

text: not provided

text: not provided


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: SC

text: Lighthouse Laboratory Plymouth

text: not provided

text: United Kingdom

text: Wales

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: organism

text: active surveillance in response to outbreak

characteristic: title


characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: SC

characteristic: broker name

text: Lighthouse Laboratory Plymouth

characteristic: collecting institution

characteristic: collection date

text: not provided

text: United Kingdom

text: Northern Ireland

text: Human

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: sample capture status


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: SC

text: Lighthouse Laboratory Plymouth

text: not provided

characteristic: collector name

characteristic: description

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

text: not provided

text: not provided

text: not provided


E-MTAB-10589:Sample 1

characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-10589:Sample 1

tag: Namespace:Wellcome Sanger Institute, Cambridge, UK

unit: week

characteristic: age

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: All tissue samples used for this study were obtained with written informed consent from all participants in accordance with the guidelines in The Declaration of Helsinki 2000. Human embryo and fetal samples were obtained from the MRC and Wellcome-funded Human Developmental Biology Resource (HDBR43, http:// www.hdbr.org), with appropriate maternal written consent and approval from the Newcastle and North Tyneside NHS Health Authority Joint Ethics Committee (08/H0906/21+5). The HDBR is regulated by the UK Human Tissue Authority (HTA; www.hta.gov.uk) and operates in accordance with the relevant HTA Codes of Practice. All tissues for sequencing and spatial work were collected in saline (HypoThermosol biopreservation media) and stored 4°C until processing. Tissue dissociation was conducted within 24 hours of tissue retrieval with the exception of tissues that were cryopreserved and stored in -80°C Ten micron cryosections were cut and placed in duplicate on Visium slides (beta product version). These were processed according to the manufacturer’s instructions. Briefly, sections were fixed with cold methanol, stained with haematoxylin and eosin and imaged on a Hamamatsu NanoZoomer S60 before permeabilisation, reverse transcription and cDNA synthesis using a template-switching protocol. Second-strand cDNA was liberated from the slide and single-indexed libraries prepared using a 10x Genomics PCR-based protocol.

text: late embryonic stage

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: gonad

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

text: Sample 1

characteristic: title


E-MTAB-10589:Sample 10

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute, Cambridge, UK

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-10589:Sample 10

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: late embryonic stage

text: normal

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: gonad

text: Homo sapiens

text: male

text: Sample 10


E-MTAB-10589:Sample 2

characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-10589:Sample 2

characteristic: age

text: ArrayExpress

text: human

characteristic: common name

text: late embryonic stage

text: normal

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: gonad

text: Homo sapiens

text: female

text: Sample 2


E-MTAB-10589:Sample 3

text: public

text: E-MTAB-10589:Sample 3

text: ArrayExpress

text: human

text: late embryonic stage

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: gonad

characteristic: organism part

text: Homo sapiens

text: female

text: Sample 3


E-MTAB-10589:Sample 4

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-10589:Sample 4

text: ArrayExpress

text: human

text: late embryonic stage

text: normal

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: gonad

text: Homo sapiens

text: female

characteristic: sex

text: Sample 4

characteristic: title


E-MTAB-10589:Sample 5

characteristic: ENA-CHECKLIST

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-10589:Sample 5

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: late embryonic stage

text: normal

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: gonad

text: Homo sapiens

text: female

text: Sample 5


E-MTAB-10589:Sample 6

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-10589:Sample 6

characteristic: age

text: ArrayExpress

text: human

characteristic: common name

text: late embryonic stage

characteristic: developmental stage

text: normal

characteristic: disease

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: gonad

text: Homo sapiens

text: female

text: Sample 6


E-MTAB-10589:Sample 7

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-10589:Sample 7

text: ArrayExpress

text: human

text: late embryonic stage

text: normal

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: gonad

characteristic: organism part

text: Homo sapiens

text: male

text: Sample 7


E-MTAB-10589:Sample 8

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10589:Sample 8

text: ArrayExpress

text: human

text: late embryonic stage

text: normal

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: gonad

text: Homo sapiens

text: male

characteristic: sex

text: Sample 8

characteristic: title


E-MTAB-10589:Sample 9

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10589:Sample 9

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: late embryonic stage

text: normal

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: gonad

text: Homo sapiens

text: female

text: Sample 9


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: INSTITUT PASTEUR

text: public

tag: Namespace:INSTITUT PASTEUR

text: Shigella sonnei

text: Shigella sonnei


E-MTAB-11984:Sample 1_WT_control

text: public

text: E-MTAB-11984:Sample 1_WT_control

tag: Namespace:Institute of Environmental Medicine, Karolinska Institutet

unit: day

characteristic: age

text: ArrayExpress

text: zebrafish

characteristic: common name

text: Protocols: The generation of germ-free zebrafish (wild-type AB) followed previously established protocols [1]. In brief, 2 hpf embryos were transferred to petri dishes with sterile E3 medium, supplemented with ampicillin (100 μg/mL), kanamycin (5 μg/mL) and amphotericin B (250 ng/mL) and incubated at 28°C. At 50% epiboly up to shield stage (6 hpf), the embryos were surface disinfected with 0.1% of polyvinylpyrroidone-iodine (PVP-I) for exactly 2 min, followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium, transferred to flasks and incubated at 28°C. The viability was monitored, and sterile medium was refreshed daily. At day 4, the hatched embryos were used for the sterility validation. A day 5, germ-free zebrafish were exposed to the combination of GO (30 µg/mL) and butyrate (2.5 mM) for 24 h. GO and BA were pre-incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate, four replicates, i.e. eighty larvae in total, were used for each condition. After the exposure, zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly, zebrafish larvae were euthanized with 0.01% of tricaine for 5 min, collected in 1.5 mL tube, and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre-warmed enzyme mix containing 460 μL of 0.25% trypsin-EDTA (Gibco) and 40 μL of collagenase (Sigma-Aldrich) at the concentration of 100 mg/mL, followed by mechanical dissociation using P1000 and then P200 pipette tips in heat-block at 30 °C until the tissue was no longer visible (about 10 min). The dissociation was then stopped by adding 800 μL DMEM (Corning Cat# 10-013-CV) with 10% FBS (Fisher Scientific). The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT, followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh, with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non-viable cells (Invitrogen Cat# D15106) at the dose of 3 μM for 10 min at room temperature before the fluorescence-activated cell sorting (BD FACSAria III, BD Biosciences, NJ, USA). The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately after the sorting. The cells were then proceeded with the single-cell RNA sequencing analysis. 1. Pham LN, Kanther M, Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3, 1862-1875 (2008). 2. Bresciani E, Broadbridge E, Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae, MethodsX. 5, 1287-1290 (2018). Single-cell RNA sequencing (scRNA-seq) was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab, Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single-Cell Instrument (10x Genomics, Pleasanton, USA) to generate single-cell gel beads in emulsion (GEMs) using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics) following the manufacture’s protocol. Briefly, GEMs were generated by combining barcoded Single Cell 3’ v3.1 Gel Beads, a Master Mix containing cells, and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation, the Gel Bead was dissolved, primers containing an Illumina TruSeq Read 1(read 1 sequencing primer), 16 nt 10x Barcode, 12 nt unique molecular identifier (UMI) and 30 nt poly(dT) sequence were released, and the co-partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, 16 rxns PN-1000268) following the manufacture’s protocol. After GEMs generation, primers were mixed with the cell lysate and a Master Mix containing reverse transcription (RT) reagents to produce barcoded, full-length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first-strand cDNA from the post GEM-RT reaction mixture, which included leftover biochemical reagents and primers. Barcoded, full-length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 (read 2 primer sequence) were added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.

text: embryo

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: pool of 80 individuals

characteristic: individual

text: not applicable

characteristic: isolate

text: Danio rerio

text: Danio rerio

text: whole organism

text: Danio rerio

text: not available

characteristic: stimulus

text: AB

characteristic: strain

text: Sample 1_WT_control


E-MTAB-11984:Sample 2_WT_GO+BA

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Institute of Environmental Medicine, Karolinska Institutet

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-11984:Sample 2_WT_GO+BA

text: ArrayExpress

text: zebrafish

text: embryo

text: wild type genotype

text: pool of 80 individuals

text: not applicable

text: Danio rerio

characteristic: organism

text: Danio rerio

text: whole organism

characteristic: organism part

text: Danio rerio

text: not available

characteristic: sex

text: graphene oxide (30 ug/mL) and butyrate (2.5 mM)

text: AB

text: Sample 2_WT_GO+BA

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR1855535 of study ERP021695.

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: uncultured Bacteroidales bacterium

text: We studied the intestinal microbiome in feces from sows, five days after farrowing, their piglets during suckling and two weeks after weaning, 5-day old artificially reared and formula-fed siblings, and FP infected with Clostridium difficile.

characteristic: project name

characteristic: sample derived from

text: uncultured Bacteroidales bacterium

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855535_bin.1_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Clostridium sp.

characteristic: organism

text: uncultured Clostridium sp.

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855535_bin.12_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: metaSPAdes v3.15.3

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: uncultured Clostridia bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Clostridia bacterium

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855535_bin.13_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Lachnospiraceae bacterium

characteristic: organism

text: uncultured Lachnospiraceae bacterium

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855535_bin.14_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: metaSPAdes v3.15.3

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: uncultured Firmicutes bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Firmicutes bacterium

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__;o__;f__;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855535_bin.15_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Clostridia bacterium

characteristic: organism

text: uncultured Clostridia bacterium

text: NextSeq 500

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855535_bin.16_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: metaSPAdes v3.15.3

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: uncultured Clostridia bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Clostridia bacterium

text: NextSeq 500

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855535_bin.17_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Ruminococcus sp.

characteristic: organism

text: uncultured Ruminococcus sp.

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Ruminococcus;s__

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855535_bin.20_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: metaSPAdes v3.15.3

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: uncultured Parabacteroides sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Parabacteroides sp.

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855535_bin.22_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR1855535 of study ERP021695.

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Bacteroidales bacterium

characteristic: organism

text: We studied the intestinal microbiome in feces from sows, five days after farrowing, their piglets during suckling and two weeks after weaning, 5-day old artificially reared and formula-fed siblings, and FP infected with Clostridium difficile.

text: uncultured Bacteroidales bacterium

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__;g__;s__

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855535_bin.23_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: metaSPAdes v3.15.3

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: uncultured Clostridia bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Clostridia bacterium

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__;f__;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855535_bin.25_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Clostridia bacterium

characteristic: organism

text: uncultured Clostridia bacterium

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__;s__

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855535_bin.27_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: metaSPAdes v3.15.3

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: uncultured Lachnospiraceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Lachnospiraceae bacterium

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855535_bin.3_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Bacteroidales bacterium

characteristic: organism

text: uncultured Bacteroidales bacterium

text: NextSeq 500

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855535_bin.30_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: metaSPAdes v3.15.3

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: uncultured Bacteroidales bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Bacteroidales bacterium

text: NextSeq 500

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855535_bin.31_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Clostridia bacterium

characteristic: organism

text: uncultured Clostridia bacterium

text: NextSeq 500

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855535_bin.35_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: metaSPAdes v3.15.3

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: uncultured Lachnospiraceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Lachnospiraceae bacterium

text: NextSeq 500

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855535_bin.36_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Clostridia bacterium

characteristic: organism

text: uncultured Clostridia bacterium

text: NextSeq 500

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855535_bin.38_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: metaSPAdes v3.15.3

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR1855535 of study ERP021695.

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: uncultured Clostridia bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Clostridia bacterium

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855535_bin.39_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Bacteroidales bacterium

characteristic: organism

text: We studied the intestinal microbiome in feces from sows, five days after farrowing, their piglets during suckling and two weeks after weaning, 5-day old artificially reared and formula-fed siblings, and FP infected with Clostridium difficile.

text: uncultured Bacteroidales bacterium

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__;g__;s__

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855535_bin.41_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: metaSPAdes v3.15.3

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: uncultured Ruminococcus sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Ruminococcus sp.

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Ruminococcus;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855535_bin.42_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Bacteroidales bacterium

characteristic: organism

text: uncultured Bacteroidales bacterium

text: NextSeq 500

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855535_bin.5_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: metaSPAdes v3.15.3

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: uncultured Anaerosporobacter sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Anaerosporobacter sp.

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Anaerosporobacter;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855535_bin.8_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR1855536 of study ERP021695.

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Clostridia bacterium

characteristic: organism

text: uncultured Clostridia bacterium

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__;s__

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855536_bin.1_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: metaSPAdes v3.15.3

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: uncultured Clostridia bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Clostridia bacterium

text: NextSeq 500

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855536_bin.10_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Clostridia bacterium

characteristic: organism

text: uncultured Clostridia bacterium

text: NextSeq 500

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855536_bin.12_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: metaSPAdes v3.15.3

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: uncultured Clostridia bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Clostridia bacterium

text: NextSeq 500

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855536_bin.15_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Clostridia bacterium

characteristic: organism

text: uncultured Clostridia bacterium

text: NextSeq 500

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855536_bin.17_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: metaSPAdes v3.15.3

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: Turicibacter sanguinis

text: We studied the intestinal microbiome in feces from sows, five days after farrowing, their piglets during suckling and two weeks after weaning, 5-day old artificially reared and formula-fed siblings, and FP infected with Clostridium difficile.

characteristic: project name

characteristic: sample derived from

text: Turicibacter sanguinis

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Erysipelotrichia;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Turicibacter;s__Turicibacter sanguinis

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855536_bin.18_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Clostridium sp.

characteristic: organism

text: uncultured Clostridium sp.

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855536_bin.19_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: metaSPAdes v3.15.3

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: uncultured Lachnospiraceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Lachnospiraceae bacterium

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855536_bin.26_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Prevotellaceae bacterium

characteristic: organism

text: uncultured Prevotellaceae bacterium

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__;s__

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855536_bin.28_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: metaSPAdes v3.15.3

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR1855536 of study ERP021695.

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: uncultured bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured bacterium

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855536_bin.31_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Bacteroidales bacterium

characteristic: organism

text: uncultured Bacteroidales bacterium

text: NextSeq 500

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__;g__;s__

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855536_bin.33_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: metaSPAdes v3.15.3

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: uncultured Clostridia bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Clostridia bacterium

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855536_bin.35_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Clostridia bacterium

characteristic: organism

text: We studied the intestinal microbiome in feces from sows, five days after farrowing, their piglets during suckling and two weeks after weaning, 5-day old artificially reared and formula-fed siblings, and FP infected with Clostridium difficile.

text: uncultured Clostridia bacterium

text: NextSeq 500

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855536_bin.36_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: metaSPAdes v3.15.3

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: uncultured Clostridia bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Clostridia bacterium

text: NextSeq 500

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855536_bin.38_metaWRAP_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.3

characteristic: binning software

text: Pig digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: common name

characteristic: completeness score

text: CheckM

text: Feces

text: Germany

text: metagenome-assembled genome

text: pig gut metagenome

text: Intestine

text: pig gut metagenome

text: uncultured Clostridia bacterium

characteristic: organism

text: uncultured Clostridia bacterium

text: NextSeq 500

text: multi-marker approach

text: Metagenome-assembled genome: ERR1855536_bin.40_metaWRAP_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

text: public

text: metaSPAdes v3.15.3

text: metaWRAP v1.3

text: Pig digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Feces

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: pig gut metagenome

characteristic: isolation source

text: Intestine

characteristic: local environmental context

text: pig gut metagenome

characteristic: metagenomic source

text: Methanobrevibacter gottschalkii

characteristic: project name

characteristic: sample derived from

text: Methanobrevibacter gottschalkii

text: NextSeq 500

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__Methanobrevibacter gottschalkii

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: ERR1855536_bin.5_metaWRAP_v1.3_MAG