cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10673724
title: MetaChick: characterization of the chicken caecal metagenome by deep shotgun sequencing

description: Data sources
DOI: 10.5281/zenodo.10699177
title: MetaChick: characterization of the chicken caecal metagenome by deep shotgun sequencing
DOI: 10.5281/zenodo.10719564
title: MetaChick: characterization of the chicken caecal metagenome by deep shotgun sequencing
DOI: 10.5281/zenodo.10784521
title: MetaChick: characterization of the chicken caecal metagenome by deep shotgun sequencing
DOI: 10.5281/zenodo.11491684
title: MetaChick: characterization of the chicken caecal metagenome by deep shotgun sequencing
DOI: 10.5281/zenodo.12820776
title: MetaChick: characterization of the chicken caecal metagenome by deep shotgun sequencing

description: Data sourcesThis dataset was constructed using the samples of the MetaChick project (phase 1) corresponding to the cecal content of 340 animals. Sequencing data and associated metadata have been submitted to INSDC (bioproject: PRJEB38174).
Sequencing data QC and metagenomic assemblyFirst, sequencing adapters removal and read trimming was performed with fastxtend. Reads mapped on the host genome (GRCg7b GCA_016699485.1) with bowtie2 were removed with samtools. Finally, metagenomic assembly was performed with metaSPAdes v3.14.1. Contigs of less than 1500 bp were removed.
MAGs recoveryMAGs were generated with MetaBAT 2 (multi-coverage mode) and MAGs quality was assessed with CheckM. MAGs with completeness < 70% or contamination > 5% or N50 < 8Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).
Non-redundant gene catalogGenes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.
MSPs recoveryA raw gene abundance table (13,6M genes quantified in 340 samples) was generated with meteorMeteor. Then, co-abundant genes were binned in Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer.
MAGs and MSPs taxonomic annotationDereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).
DOI: 10.5281/zenodo.13771776
title: MetaChick: characterization of the chicken caecal metagenome by deep shotgun sequencing

description: Data sourcesThis dataset was constructed using the samples of the MetaChick project (phase 1) corresponding to the cecal content of 340 animals. Sequencing data and associated metadata have been submitted to INSDC (bioproject: PRJEB38174).
Sequencing data QC and metagenomic assemblyFirst, sequencing adapters removal and read trimming was performed with fastxtend. Reads mapped on the host genome (GRCg7b GCA_016699485.1) with bowtie2 were removed with samtools. Finally, metagenomic assembly was performed with metaSPAdes v3.14.1. Contigs of less than 1500 bp were removed.
MAGs recoveryMAGs were generated with MetaBAT 2 (multi-coverage mode) and MAGs quality was assessed with CheckM. MAGs with completeness < 70% or contamination > 5% or N50 < 8Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).
Non-redundant gene catalogGenes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.
MSPs recoveryA raw gene abundance table (13,6M genes quantified in 340 samples) was generated with meteorMeteor. Then, co-abundant genes were binned in Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer.
MAGs and MSPs taxonomic annotationDereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).
DOI: 10.5281/zenodo.14181300
title: MetaChick: characterization of the chicken caecal metagenome by deep shotgun sequencing

description: Data sourcesThis dataset was constructed using the samples of the MetaChick project (phase 1) corresponding to the cecal content of 340 animals. Sequencing data and associated metadata have been submitted to INSDC (bioproject: PRJEB38174).
Sequencing data QC and metagenomic assemblyFirst, sequencing adapters removal and read trimming was performed with fastxtend. Reads mapped on the host genome (GRCg7b GCA_016699485.1) with bowtie2 were removed with samtools. Finally, metagenomic assembly was performed with metaSPAdes v3.14.1. Contigs of less than 1500 bp were removed.
MAGs recoveryMAGs were generated with MetaBAT 2 (multi-coverage mode) and MAGs quality was assessed with CheckM. MAGs with completeness < 70% or contamination > 5% or N50 < 8Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).
Non-redundant gene catalogGenes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.
MSPs recoveryA raw gene abundance table (13,6M genes quantified in 340 samples) was generated with meteorMeteor. Then, co-abundant genes were binned in Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer.
MAGs and MSPs taxonomic annotationDereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).
DOI: 10.5281/zenodo.10656835
title: A catalog of genes, genomes and species of the cat (Felis catus) intestinal microbiota

description: Data sourcesThis dataset was constructed using two different bioprojects:PRJNA758898 from Ma et al. 2022. 16 samples from 16 animals.PRJEB9357 from Deusch et al. 2015. 88 samples from 30 animals.PRJEB4391 from Deusch et al. 2014. 36 samples from 18 animals.PRJNA944553. 30 samples from 30 animals.PRJNA908260 from Bai et al. 2023. 8 samples from 8 animals.PRJNA923753 from Ho et al. 2023. 1 sample.Metagenomic assemblyDe novo metagenomic assembly was performed on samples listed above. First, sequencing adapters removal and read trimming was performed with fastp. Reads mapped on the host genome (GCF_018350175.1) with bowtie2 were removed with samtools. Finally, Metagenomic assembly was performed with metaSPAdes. Contigs of less than 1500 bp were removed.MAGs recoveryMAGs were generated with COMEBin (multi-coverage mode) and MAGs quality was assessed with CheckM2. MAGs with completeness < 70% or contamination > 5% or N50 < 5Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).Non-redundant gene catalogGenes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.MSPs recoverySamples from multiple cohorts (listed above + PRJNA906124 from Lee et al. 2022) were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (1,3M genes quantified in 212 samples). Then, co-abundant genes were binned in 344 Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer.MAGs and MSPs taxonomic annotationDereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).
DOI: 10.5281/zenodo.10699199
title: A catalog of genes, genomes and species of the cat (Felis catus) intestinal microbiota

description: Data sourcesThis dataset was constructed using two different bioprojects:PRJNA758898 from Ma et al. 2022. 16 samples from 16 animals.PRJEB9357 from Deusch et al. 2015. 88 samples from 30 animals.PRJEB4391 from Deusch et al. 2014. 36 samples from 18 animals.PRJNA944553. 30 samples from 30 animals.PRJNA908260 from Bai et al. 2023. 8 samples from 8 animals.PRJNA923753 from Ho et al. 2023. 1 sample.
Metagenomic assemblyDe novo metagenomic assembly was performed on samples listed above. First, sequencing adapters removal and read trimming was performed with fastp. Reads mapped on the host genome (GCF_018350175.1) with bowtie2 were removed with samtools. Finally, Metagenomic assembly was performed with metaSPAdes. Contigs of less than 1500 bp were removed.
MAGs recoveryMAGs were generated with COMEBin (multi-coverage mode) and MAGs quality was assessed with CheckM2. MAGs with completeness < 70% or contamination > 5% or N50 < 5Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).
Non-redundant gene catalogGenes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.
MSPs recoverySamples from multiple cohorts (listed above + PRJNA906124 from Lee et al. 2022) were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (1,3M genes quantified in 212 samples). Then, co-abundant genes were binned in 344 Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer.
MAGs and MSPs taxonomic annotationDereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).
DOI: 10.5281/zenodo.10719585
title: A catalog of genes, genomes and species of the cat (Felis catus) intestinal microbiota

description: Data sourcesThis dataset was constructed using two different bioprojects:PRJNA758898 from Ma et al. 2022. 16 samples from 16 animals.PRJEB9357 from Deusch et al. 2015. 88 samples from 30 animals.PRJEB4391 from Deusch et al. 2014. 36 samples from 18 animals.PRJNA944553. 30 samples from 30 animals.PRJNA908260 from Bai et al. 2023. 8 samples from 8 animals.PRJNA923753 from Ho et al. 2023. 1 sample.
Metagenomic assemblyDe novo metagenomic assembly was performed on samples listed above. First, sequencing adapters removal and read trimming was performed with fastp. Reads mapped on the host genome (GCF_018350175.1) with bowtie2 were removed with samtools. Finally, Metagenomic assembly was performed with metaSPAdes. Contigs of less than 1500 bp were removed.
MAGs recoveryMAGs were generated with COMEBin (multi-coverage mode) and MAGs quality was assessed with CheckM2. MAGs with completeness < 70% or contamination > 5% or N50 < 5Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).
Non-redundant gene catalogGenes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.
MSPs recoverySamples from multiple cohorts (listed above + PRJNA906124 from Lee et al. 2022) were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (1,3M genes quantified in 212 samples). Then, co-abundant genes were binned in 344 Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer.
MAGs and MSPs taxonomic annotationDereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).
DOI: 10.5281/zenodo.10784822
title: A catalog of genes, genomes and species of the cat (Felis catus) intestinal microbiota

description: Data sourcesThis dataset was constructed using two different bioprojects:PRJNA758898 from Ma et al. 2022. 16 samples from 16 animals.PRJEB9357 from Deusch et al. 2015. 88 samples from 30 animals.PRJEB4391 from Deusch et al. 2014. 36 samples from 18 animals.PRJNA944553. 30 samples from 30 animals.PRJNA908260 from Bai et al. 2023. 8 samples from 8 animals.PRJNA923753 from Ho et al. 2023. 1 sample.
Metagenomic assemblyDe novo metagenomic assembly was performed on samples listed above. First, sequencing adapters removal and read trimming was performed with fastp. Reads mapped on the host genome (GCF_018350175.1) with bowtie2 were removed with samtools. Finally, Metagenomic assembly was performed with metaSPAdes. Contigs of less than 1500 bp were removed.
MAGs recoveryMAGs were generated with COMEBin (multi-coverage mode) and MAGs quality was assessed with CheckM2. MAGs with completeness < 70% or contamination > 5% or N50 < 5Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).
Non-redundant gene catalogGenes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.
MSPs recoverySamples from multiple cohorts (listed above + PRJNA906124 from Lee et al. 2022) were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (1,3M genes quantified in 212 samples). Then, co-abundant genes were binned in 344 Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer.
MAGs and MSPs taxonomic annotationDereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).
DOI: 10.5281/zenodo.12820763
title: A catalog of genes, genomes and species of the cat (Felis catus) intestinal microbiota

description: Data sourcesThis dataset was constructed using two different bioprojects:PRJNA758898 from Ma et al. 2022. 16 samples from 16 animals.PRJEB9357 from Deusch et al. 2015. 88 samples from 30 animals.PRJEB4391 from Deusch et al. 2014. 36 samples from 18 animals.PRJNA944553. 30 samples from 30 animals.PRJNA908260 from Bai et al. 2023. 8 samples from 8 animals.PRJNA923753 from Ho et al. 2023. 1 sample.
Metagenomic assemblyDe novo metagenomic assembly was performed on samples listed above. First, sequencing adapters removal and read trimming was performed with fastp. Reads mapped on the host genome (GCF_018350175.1) with bowtie2 were removed with samtools. Finally, Metagenomic assembly was performed with metaSPAdes. Contigs of less than 1500 bp were removed.
MAGs recoveryMAGs were generated with COMEBin (multi-coverage mode) and MAGs quality was assessed with CheckM2. MAGs with completeness < 70% or contamination > 5% or N50 < 5Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).
Non-redundant gene catalogGenes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.
MSPs recoverySamples from multiple cohorts (listed above + PRJNA906124 from Lee et al. 2022) were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (1,3M genes quantified in 212 samples). Then, co-abundant genes were binned in 344 Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer.
MAGs and MSPs taxonomic annotationDereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).
DOI: 10.5281/zenodo.13771508
title: A catalog of genes, genomes and species of the cat (Felis catus) intestinal microbiota

description: Data sourcesThis dataset was constructed using two different bioprojects:PRJNA758898 from Ma et al. 2022. 16 samples from 16 animals.PRJEB9357 from Deusch et al. 2015. 88 samples from 30 animals.PRJEB4391 from Deusch et al. 2014. 36 samples from 18 animals.PRJNA944553. 30 samples from 30 animals.PRJNA908260 from Bai et al. 2023. 8 samples from 8 animals.PRJNA923753 from Ho et al. 2023. 1 sample.
Metagenomic assemblyDe novo metagenomic assembly was performed on samples listed above. First, sequencing adapters removal and read trimming was performed with fastp. Reads mapped on the host genome (GCF_018350175.1) with bowtie2 were removed with samtools. Finally, Metagenomic assembly was performed with metaSPAdes. Contigs of less than 1500 bp were removed.
MAGs recoveryMAGs were generated with COMEBin (multi-coverage mode) and MAGs quality was assessed with CheckM2. MAGs with completeness < 70% or contamination > 5% or N50 < 5Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).
Non-redundant gene catalogGenes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.
MSPs recoverySamples from multiple cohorts (listed above + PRJNA906124 from Lee et al. 2022) were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (1,3M genes quantified in 212 samples). Then, co-abundant genes were binned in 344 Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer.
MAGs and MSPs taxonomic annotationDereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).