cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12702035
title: Updated Files from the revision 1 (986 cMAGs and prokka annotations, all supplemental files)

description: Included are the following files1) Assembly files (47) in the form of .fasta for each of the 47 different samples (8 participants x 5 or 6 time points). This is the results of the assembly from hybrid long read data (all Pacbio Revio + ONT Promethion > Q20). Assemblies performed using metaMDBG. This file includes all contigs from the pipeline described in the manuscript and will include both high-quality and complete MAGs. "hybrid_assemblies.tar.gz"2) Assembly files (40) in the form of .fasta for the short read metaspades and tell-seq assembly methods"SR_tellseq_assemblies.tar.gz""SR_metaspades_assemblies.tar.gz"

3) Assembly files from sub-sampling experiment: 3 samples (A6, D5, and H6) were deep sequenced with both PB Revio and ONT Promethion lsk114 R10.4.1 SUP400. Data was randomly subsampled to various depths (1, 5, 10, 20, 30, 40 Gbp, and all) and then assembled with both metaMDBG and metaFlye. -A6: total of 26 files (PB was less than 40 Gbp thus no 40 Gbp subsampling depth)-D5: total of 28 files-H6: total of 28 files-total: 82 files"LR_ONTPB_sub_assemblies.tar.gz"

4) Tar file of all circular contigs from assemblies. This will include 47 separate fasta files (1 for each participant and time point). This data was used for the viral and plasmid analyses. "Hsap_circ_contigs_47_assemblies.tar.gz"5) File containing all of the 985 cMAGs with annotations generated using prokka

"985cMAGs_prokkaannotation.tar.gz

6) Deep taxonomic profiling feature table: Pacbio samples (45) with features classified using the GTDB and 985 cMAGs custom database"PB_985cMAG-sourmash_45s_2162f" #feature table"mapping-file_PB45s_2162f_deID.txt" #mapping file, deidentified7) tar file containing all genomes in the updated quality 'c986 cMAGs' (>90% completeness, <5% contamination, contig=18) tar file containing all prokka annotation files associated with the 986 cMAGs9) All supplemental tables or data files used in the revision
DOI: 10.5281/zenodo.12702036
title: Data from long read metagenomics dataset

description: Included are the following files1) Assembly files (47) in the form of .fasta for each of the 47 different samples (8 participants x 5 or 6 time points). This is the results of the assembly from hybrid long read data (all Pacbio Revio + ONT Promethion > Q20). Assemblies performed using metaMDBG. This file includes all contigs from the pipeline described in the manuscript and will include both high-quality and complete MAGs. "hybrid_assemblies.tar.gz"2) Assembly files (40) in the form of .fasta for the short read metaspades and tell-seq assembly methods"SR_tellseq_assemblies.tar.gz""SR_metaspades_assemblies.tar.gz"

3) Assembly files from sub-sampling experiment: 3 samples (A6, D5, and H6) were deep sequenced with both PB Revio and ONT Promethion lsk114 R10.4.1 SUP400. Data was randomly subsampled to various depths (1, 5, 10, 20, 30, 40 Gbp, and all) and then assembled with both metaMDBG and metaFlye. -A6: total of 26 files (PB was less than 40 Gbp thus no 40 Gbp subsampling depth)-D5: total of 28 files-H6: total of 28 files-total: 82 files"LR_ONTPB_sub_assemblies.tar.gz"

4) Tar file of all circular contigs from assemblies. This will include 47 separate fasta files (1 for each participant and time point). This data was used for the viral and plasmid analyses. "Hsap_circ_contigs_47_assemblies.tar.gz"5) File containing all of the 985 cMAGs with annotations generated using prokka

"985cMAGs_prokkaannotation.tar.gz

6) Deep taxonomic profiling feature table: Pacbio samples (45) with features classified using the GTDB and 985 cMAGs custom database"PB_985cMAG-sourmash_45s_2162f" #feature table"mapping-file_PB45s_2162f_deID.txt" #mapping file, deidentified
DOI: 10.5281/zenodo.15327299
title: Updated Files from the revision 1 (986 cMAGs and prokka annotations, all supplemental files)

description: Included are the following files1) Assembly files (47) in the form of .fasta for each of the 47 different samples (8 participants x 5 or 6 time points). This is the results of the assembly from hybrid long read data (all Pacbio Revio + ONT Promethion > Q20). Assemblies performed using metaMDBG. This file includes all contigs from the pipeline described in the manuscript and will include both high-quality and complete MAGs. "hybrid_assemblies.tar.gz"2) Assembly files (40) in the form of .fasta for the short read metaspades and tell-seq assembly methods"SR_tellseq_assemblies.tar.gz""SR_metaspades_assemblies.tar.gz"

3) Assembly files from sub-sampling experiment: 3 samples (A6, D5, and H6) were deep sequenced with both PB Revio and ONT Promethion lsk114 R10.4.1 SUP400. Data was randomly subsampled to various depths (1, 5, 10, 20, 30, 40 Gbp, and all) and then assembled with both metaMDBG and metaFlye. -A6: total of 26 files (PB was less than 40 Gbp thus no 40 Gbp subsampling depth)-D5: total of 28 files-H6: total of 28 files-total: 82 files"LR_ONTPB_sub_assemblies.tar.gz"

4) Tar file of all circular contigs from assemblies. This will include 47 separate fasta files (1 for each participant and time point). This data was used for the viral and plasmid analyses. "Hsap_circ_contigs_47_assemblies.tar.gz"5) File containing all of the 985 cMAGs with annotations generated using prokka

"985cMAGs_prokkaannotation.tar.gz

6) Deep taxonomic profiling feature table: Pacbio samples (45) with features classified using the GTDB and 985 cMAGs custom database"PB_985cMAG-sourmash_45s_2162f" #feature table"mapping-file_PB45s_2162f_deID.txt" #mapping file, deidentified7) tar file containing all genomes in the updated quality 'c986 cMAGs' (>90% completeness, <5% contamination, contig=18) tar file containing all prokka annotation files associated with the 986 cMAGs9) All supplemental tables or data files used in the revision
DOI: 10.15468/dl.fuqw2b
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rosa moyesii",
 "Country is Norway",
 "HasCoordinate is true"
 ]
}

 The dataset includes 49 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010571-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/gtt-yd3-492
title: †Diplobathrida Moore & Laudon, 1943

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/v66-yz7-l2a
title: Raja

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1k3-10h-y88
title: Equus (Equus) caballus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ct4-77t-4s0
title: †Palorbitolina lenticularis (Blumenbach, 1805)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/67x-qy1-4e3
title: Hexanchidae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wcx-cq3-w9e
title: Chondrichthyes

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wk5-g4j-jgj
title: †Palorbitolina lenticularis (Blumenbach, 1805)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/q7p-m8q-038
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vyf-aw2-pgh
title: Bos taurus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7zn-h09-8xy
title: Elephantidae Gray, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wxr-jp5-rbz
title: Bos taurus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/e93-lc8-07l
title: Cibicides Montfort, 1808

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/18l-sd1-x8v
title: †Palorbitolina lenticularis (Blumenbach, 1805)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ct1-6c0-ak8
title: Carcharhinidae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5ch-zld-ye3
title: Paradoxides

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/glx-hk5-39p
title: †Palorbitolina lenticularis (Blumenbach, 1805)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/40a-p5d-e90
title: †Palorbitolina lenticularis (Blumenbach, 1805)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xr7-hhm-sxq
title: Sus scrofa Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/79h-26b-bf7
title: Bryozoa

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/n4d-q6e-nd7
title: †Megistaspis (Megistaspis) limbata (Boeck, 1838)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rdf-2lg-bl5
title: Equus (Equus) caballus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/m49-e8m-k5f
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pk0-xn9-l86
title: †Schizophoria King, 1850

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/f5e-gpt-bff
title: †Petalotrypa compressa Ulrich, 1890

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tc0-xd1-l85
title: Squalus acanthias Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5xq-rkb-3m3
title: Porifera Grant, 1836

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/a46-w3b-sj4
title: Melanogrammus aeglefinus (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/bxv-3s1-094
title: †Dictyaraea micrantha Reuss, 1866

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kmb-pc0-sev
title: †Productus Sowerby, 1814

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/19r-25r-ktv
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/w1g-9za-lw9
title: Bos taurus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2ce-ytm-g04
title: †Palorbitolina lenticularis (Blumenbach, 1805)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xme-yqk-y78
title: †Cyrtospirifer Nalivkin in Fredericks, 1924

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.syyhan
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pterocuma rostratum",
 "Country is Ukraine",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021773-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/2h8-2cw-tyd
title: †Palorbitolina lenticularis (Blumenbach, 1805)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jg3-z9k-74q
title: Sus scrofa Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.29939312
title: Supplementary Material for: The Causal Role of Gut Microbiota and Immune Cell Mediation in Gastroenteropancreatic Neuroendocrine Neoplasms: A Mendelian Randomization Study

description: Background: Gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs) are a diverse group of tumors arising from neuroendocrine cells, often characterized by slow growth and subtle symptoms, leading to advanced-stage diagnoses. The gut microbiota (GM) has been implicated in various gastrointestinal malignancies, but its relationship with GEP-NENs remains unclear.
Objective: This study aimed to elucidate the causal relationship between specific GM traits and GEP-NENs using Mendelian Randomization (MR) analysis, and to explore the potential mediating role of immune cells in this relationship.
Methods: A two-sample MR analysis was employed using genome-wide association study (GWAS) data to explore causal associations between GM and GEP-NENs. Genetic variants significantly associated with GM traits were selected as instrumental variables (IVs). Forward MR analysis identified significant GM traits associated with GEP-NENs, followed by reverse analysis to exclude reverse causation. Bayesian weighted Mendelian randomization (BWMR) was employed for verification. Mediation analysis was conducted using a two-step approach to evaluate the mediating role of immune cell traits in these causal relationships. Sensitivity analyses, including heterogeneity and pleiotropy tests, were conducted to ensure the robustness of the findings.
Results: Our analysis identified significant causal associations between 45 GM traits and GEP-NENs, involving 25 bacterial taxa and 20 metabolic pathways. Specifically, s_Paraprevotella_xylaniphila showed the strongest association with pancreatic NEN (P-NEN, OR: 0.473, P: 0.005); metabolic pathway PWY.6588 (pyruvate fermentation to acetone) exhibited the strongest association with gastric NEN (G-NEN, OR: 2.706, P: 0.003); pathway PWY0.845 (superpathway of pyridoxal 5'-phosphate biosynthesis and salvage) had the strongest association with small intestine NEN (SI-NEN, OR: 1.898, P: 0.001); and g_Roseburia displayed the strongest association with colorectal NEN (C-NEN, OR: 0.504, P: 0.007). Furthermore, mediation analyses revealed that specific immune cell traits significantly mediated these associations, with CD3⁻ lymphocyte absolute count showing a notable mediation effect (12.187%, P: 0.019) between g_Clostridium and G-NEN, highlighting the crucial role of immune modulation in GEP-NEN pathogenesis.
Conclusions: In conclusion, our MR analysis provides robust causal evidence that specific GM taxa significantly influence the risk of GEP-NENs, and that this effect is partially mediated through discrete subsets of circulating immune cells. These findings underscore the GM–immune axis as a novel preventive and therapeutic target in GEP-NENs.
DOI: 10.6084/m9.figshare.29939312.v1
title: Supplementary Material for: The Causal Role of Gut Microbiota and Immune Cell Mediation in Gastroenteropancreatic Neuroendocrine Neoplasms: A Mendelian Randomization Study

description: Background: Gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs) are a diverse group of tumors arising from neuroendocrine cells, often characterized by slow growth and subtle symptoms, leading to advanced-stage diagnoses. The gut microbiota (GM) has been implicated in various gastrointestinal malignancies, but its relationship with GEP-NENs remains unclear.
Objective: This study aimed to elucidate the causal relationship between specific GM traits and GEP-NENs using Mendelian Randomization (MR) analysis, and to explore the potential mediating role of immune cells in this relationship.
Methods: A two-sample MR analysis was employed using genome-wide association study (GWAS) data to explore causal associations between GM and GEP-NENs. Genetic variants significantly associated with GM traits were selected as instrumental variables (IVs). Forward MR analysis identified significant GM traits associated with GEP-NENs, followed by reverse analysis to exclude reverse causation. Bayesian weighted Mendelian randomization (BWMR) was employed for verification. Mediation analysis was conducted using a two-step approach to evaluate the mediating role of immune cell traits in these causal relationships. Sensitivity analyses, including heterogeneity and pleiotropy tests, were conducted to ensure the robustness of the findings.
Results: Our analysis identified significant causal associations between 45 GM traits and GEP-NENs, involving 25 bacterial taxa and 20 metabolic pathways. Specifically, s_Paraprevotella_xylaniphila showed the strongest association with pancreatic NEN (P-NEN, OR: 0.473, P: 0.005); metabolic pathway PWY.6588 (pyruvate fermentation to acetone) exhibited the strongest association with gastric NEN (G-NEN, OR: 2.706, P: 0.003); pathway PWY0.845 (superpathway of pyridoxal 5'-phosphate biosynthesis and salvage) had the strongest association with small intestine NEN (SI-NEN, OR: 1.898, P: 0.001); and g_Roseburia displayed the strongest association with colorectal NEN (C-NEN, OR: 0.504, P: 0.007). Furthermore, mediation analyses revealed that specific immune cell traits significantly mediated these associations, with CD3⁻ lymphocyte absolute count showing a notable mediation effect (12.187%, P: 0.019) between g_Clostridium and G-NEN, highlighting the crucial role of immune modulation in GEP-NEN pathogenesis.
Conclusions: In conclusion, our MR analysis provides robust causal evidence that specific GM taxa significantly influence the risk of GEP-NENs, and that this effect is partially mediated through discrete subsets of circulating immune cells. These findings underscore the GM–immune axis as a novel preventive and therapeutic target in GEP-NENs.
DOI: 10.3535/b7m-7dg-0mb
title: †Palorbitolina lenticularis (Blumenbach, 1805)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/nc4-62p-e9d
title: Cidaris Leske, 1778

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/s8m-1bw-cv5
title: †Oolopygus d'Orbigny, 1857

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/snm-68a-1hf
title: †Palorbitolina lenticularis (Blumenbach, 1805)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/khh-0cv-h2z
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/w3z-4e4-rc2
title: †Palorbitolina lenticularis (Blumenbach, 1805)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.48510/fk2/rlwgbc
title: Antimicrobial Susceptibility Testing (AST) Data for Klebsiella pneumoniae Isolates in Latvia

description: This dataset summarizes antimicrobial susceptibility testing (AST) results for Klebsiella pneumoniae isolates obtained from clinical samples and wastewater sources.
Antimicrobial susceptibility interpretations were performed in accordance with the European Committee on Antimicrobial Susceptibility Testing (EUCAST) Clinical Breakpoint Tables, version 15.0. Interpretation was based on measured inhibition zone diameters and minimum inhibitory concentrations (MICs), as applicable for each antimicrobial agent tested.
Susceptibility categories were assigned using EUCAST-defined interpretive criteria. Results are reported using standardized abbreviations to ensure consistency and comparability across isolates and antimicrobial classes. Antimicrobial agents were categorized by route of administration when relevant (oral or intravenous).
Where applicable, phenotypic resistance mechanisms were recorded, including extended-spectrum β-lactamase (ESBL) production, AmpC β-lactamase activity, and the presence of carbapenemase enzymes.
Carbapenemase types documented in the dataset include NDM (New Delhi metallo-β-lactamase), OXA-48 (oxacillinase-48), and KPC (Klebsiella pneumoniae carbapenemase).
DOI: 10.15468/dl.99j8r4
title: Occurrence Download

description: A dataset containing 416 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Jumellea rossii Senghas",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 416 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003576-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vj9ftb
title: Occurrence Download

description: A dataset containing 1176 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Kandelia obovata Sheue, H.Y.Liu & J.W.H.Yong",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1176 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003664-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.64ahcf
title: Occurrence Download

description: A dataset containing 6210 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Kalopanax septemlobus (Thunb.) Koidz.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6210 records from 144 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003663-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kzrntt
title: Occurrence Download

description: A dataset containing 1722 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Kennedia coccinea (Curtis) Vent.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1722 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003666-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.er7vp7
title: Occurrence Download

description: A dataset containing 8910 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Khaya senegalensis (Desv.) A.Juss.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 8910 records from 161 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003668-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wt65g7
title: Occurrence Download

description: A dataset containing 7592 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Kelletia kelletii (Forbes, 1852)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 7592 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003665-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.