complete microbial genome sequence Search Results


mgieasy pathogen microbiome dna&rna extraction kit  (Complete Genomics Inc)
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assays mgieasy environmental microbiome dna extraction kit mgi tech  (Complete Genomics Inc)
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Complete Genomics Inc assays mgieasy environmental microbiome dna extraction kit mgi tech
Figure 1. Sampling and extraordinary nov- elty of the Deepest Ocean <t>microbiome</t> re- vealed by the MEER dataset (A) Sampling sites of hadal zones using the hu- man-occupied vehicle (HOV) Fendouzhe in this study, including the Philippine Basin (PB), the Yap Trench (YT), and the Mariana Trench (MT), as well as the bottom (Bt), northern slope (NS), and southern slope (SS) within the Mariana Trench. (B) Comparative analysis between the species- level representative genomes (SRGs) from the MEER dataset and the species-level genomes in the Ocean Microbiomics Database (OMD), the typical deep-sea and hadal sediment. The OMD included isolated reference genome (ISO) of Global Ocean Reference Genomes (GORG), sin- gle-cell amplified genome (SAG) of MAR Database (MARD), as well as seawater metagenomes of abyssopelagic layer (ABY, 4,500–6,000 m), bathypelagic layer (BAT, 1,000–4,500 m), meso- pelagic layer (MES, 200–1,000 m), and epipelagic layer (EPI, 0–200 m). Doughnut charts illustrate the sample habitat distribution in each habitat. Bar plots depict the distribution of MEER SRGs de- tected in reference habitats. (C) Taxonomic novelty of the MEER dataset against the Genome Taxonomy Database (GTDB, release 220). Light bars extending leftward indi- cate the finest taxonomic level to which SRGs or 16S rRNA gene amplicon sequence variants (ASVs) can be annotated. Solid bars extending rightward represent unreported taxa at each taxonomic level. (D) De novo phylogenetic tree of SRGs, color- coded by the 10 most abundant phyla in the MEER dataset. Purple shapes indicate the placement of three bacterial SRGs that could not be assigned to known phyla according to GTDB, with subtrees showing their neighboring clades and relative evolutionary divergence (RED) values. Note that the bacterial and archaeal trees were combined for visualization purpose but were not rooted together. (E) Distribution of novelty among SRGs and 16S rRNA gene ASVs across the 10 most abundant phyla. Stacked bar plots represent the number of unreported and known SRGs or ASVs, while or- ange lines and dots indicate the percentage of novelty. See also Figure S1 and Tables S1 and S2.
Assays Mgieasy Environmental Microbiome Dna Extraction Kit Mgi Tech, supplied by Complete Genomics Inc, used in various techniques. Bioz Stars score: 98/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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mgieasy stool microbiome dna extraction kit  (Complete Genomics Inc)
98
Complete Genomics Inc mgieasy stool microbiome dna extraction kit
Figure 1. Sampling and extraordinary nov- elty of the Deepest Ocean <t>microbiome</t> re- vealed by the MEER dataset (A) Sampling sites of hadal zones using the hu- man-occupied vehicle (HOV) Fendouzhe in this study, including the Philippine Basin (PB), the Yap Trench (YT), and the Mariana Trench (MT), as well as the bottom (Bt), northern slope (NS), and southern slope (SS) within the Mariana Trench. (B) Comparative analysis between the species- level representative genomes (SRGs) from the MEER dataset and the species-level genomes in the Ocean Microbiomics Database (OMD), the typical deep-sea and hadal sediment. The OMD included isolated reference genome (ISO) of Global Ocean Reference Genomes (GORG), sin- gle-cell amplified genome (SAG) of MAR Database (MARD), as well as seawater metagenomes of abyssopelagic layer (ABY, 4,500–6,000 m), bathypelagic layer (BAT, 1,000–4,500 m), meso- pelagic layer (MES, 200–1,000 m), and epipelagic layer (EPI, 0–200 m). Doughnut charts illustrate the sample habitat distribution in each habitat. Bar plots depict the distribution of MEER SRGs de- tected in reference habitats. (C) Taxonomic novelty of the MEER dataset against the Genome Taxonomy Database (GTDB, release 220). Light bars extending leftward indi- cate the finest taxonomic level to which SRGs or 16S rRNA gene amplicon sequence variants (ASVs) can be annotated. Solid bars extending rightward represent unreported taxa at each taxonomic level. (D) De novo phylogenetic tree of SRGs, color- coded by the 10 most abundant phyla in the MEER dataset. Purple shapes indicate the placement of three bacterial SRGs that could not be assigned to known phyla according to GTDB, with subtrees showing their neighboring clades and relative evolutionary divergence (RED) values. Note that the bacterial and archaeal trees were combined for visualization purpose but were not rooted together. (E) Distribution of novelty among SRGs and 16S rRNA gene ASVs across the 10 most abundant phyla. Stacked bar plots represent the number of unreported and known SRGs or ASVs, while or- ange lines and dots indicate the percentage of novelty. See also Figure S1 and Tables S1 and S2.
Mgieasy Stool Microbiome Dna Extraction Kit, supplied by Complete Genomics Inc, used in various techniques. Bioz Stars score: 98/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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microbial whole genome sequencing workflow  (Novogene)
86
Novogene microbial whole genome sequencing workflow
Figure 1. Sampling and extraordinary nov- elty of the Deepest Ocean <t>microbiome</t> re- vealed by the MEER dataset (A) Sampling sites of hadal zones using the hu- man-occupied vehicle (HOV) Fendouzhe in this study, including the Philippine Basin (PB), the Yap Trench (YT), and the Mariana Trench (MT), as well as the bottom (Bt), northern slope (NS), and southern slope (SS) within the Mariana Trench. (B) Comparative analysis between the species- level representative genomes (SRGs) from the MEER dataset and the species-level genomes in the Ocean Microbiomics Database (OMD), the typical deep-sea and hadal sediment. The OMD included isolated reference genome (ISO) of Global Ocean Reference Genomes (GORG), sin- gle-cell amplified genome (SAG) of MAR Database (MARD), as well as seawater metagenomes of abyssopelagic layer (ABY, 4,500–6,000 m), bathypelagic layer (BAT, 1,000–4,500 m), meso- pelagic layer (MES, 200–1,000 m), and epipelagic layer (EPI, 0–200 m). Doughnut charts illustrate the sample habitat distribution in each habitat. Bar plots depict the distribution of MEER SRGs de- tected in reference habitats. (C) Taxonomic novelty of the MEER dataset against the Genome Taxonomy Database (GTDB, release 220). Light bars extending leftward indi- cate the finest taxonomic level to which SRGs or 16S rRNA gene amplicon sequence variants (ASVs) can be annotated. Solid bars extending rightward represent unreported taxa at each taxonomic level. (D) De novo phylogenetic tree of SRGs, color- coded by the 10 most abundant phyla in the MEER dataset. Purple shapes indicate the placement of three bacterial SRGs that could not be assigned to known phyla according to GTDB, with subtrees showing their neighboring clades and relative evolutionary divergence (RED) values. Note that the bacterial and archaeal trees were combined for visualization purpose but were not rooted together. (E) Distribution of novelty among SRGs and 16S rRNA gene ASVs across the 10 most abundant phyla. Stacked bar plots represent the number of unreported and known SRGs or ASVs, while or- ange lines and dots indicate the percentage of novelty. See also Figure S1 and Tables S1 and S2.
Microbial Whole Genome Sequencing Workflow, supplied by Novogene, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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ingenious bioinformatics methods  (Schmid GmbH)
90
Schmid GmbH ingenious bioinformatics methods
Figure 1. Sampling and extraordinary nov- elty of the Deepest Ocean <t>microbiome</t> re- vealed by the MEER dataset (A) Sampling sites of hadal zones using the hu- man-occupied vehicle (HOV) Fendouzhe in this study, including the Philippine Basin (PB), the Yap Trench (YT), and the Mariana Trench (MT), as well as the bottom (Bt), northern slope (NS), and southern slope (SS) within the Mariana Trench. (B) Comparative analysis between the species- level representative genomes (SRGs) from the MEER dataset and the species-level genomes in the Ocean Microbiomics Database (OMD), the typical deep-sea and hadal sediment. The OMD included isolated reference genome (ISO) of Global Ocean Reference Genomes (GORG), sin- gle-cell amplified genome (SAG) of MAR Database (MARD), as well as seawater metagenomes of abyssopelagic layer (ABY, 4,500–6,000 m), bathypelagic layer (BAT, 1,000–4,500 m), meso- pelagic layer (MES, 200–1,000 m), and epipelagic layer (EPI, 0–200 m). Doughnut charts illustrate the sample habitat distribution in each habitat. Bar plots depict the distribution of MEER SRGs de- tected in reference habitats. (C) Taxonomic novelty of the MEER dataset against the Genome Taxonomy Database (GTDB, release 220). Light bars extending leftward indi- cate the finest taxonomic level to which SRGs or 16S rRNA gene amplicon sequence variants (ASVs) can be annotated. Solid bars extending rightward represent unreported taxa at each taxonomic level. (D) De novo phylogenetic tree of SRGs, color- coded by the 10 most abundant phyla in the MEER dataset. Purple shapes indicate the placement of three bacterial SRGs that could not be assigned to known phyla according to GTDB, with subtrees showing their neighboring clades and relative evolutionary divergence (RED) values. Note that the bacterial and archaeal trees were combined for visualization purpose but were not rooted together. (E) Distribution of novelty among SRGs and 16S rRNA gene ASVs across the 10 most abundant phyla. Stacked bar plots represent the number of unreported and known SRGs or ASVs, while or- ange lines and dots indicate the percentage of novelty. See also Figure S1 and Tables S1 and S2.
Ingenious Bioinformatics Methods, supplied by Schmid GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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complete bacterial genome sequences  (Monsanto Technology LLC)
90
Monsanto Technology LLC complete bacterial genome sequences
Figure 1. Sampling and extraordinary nov- elty of the Deepest Ocean <t>microbiome</t> re- vealed by the MEER dataset (A) Sampling sites of hadal zones using the hu- man-occupied vehicle (HOV) Fendouzhe in this study, including the Philippine Basin (PB), the Yap Trench (YT), and the Mariana Trench (MT), as well as the bottom (Bt), northern slope (NS), and southern slope (SS) within the Mariana Trench. (B) Comparative analysis between the species- level representative genomes (SRGs) from the MEER dataset and the species-level genomes in the Ocean Microbiomics Database (OMD), the typical deep-sea and hadal sediment. The OMD included isolated reference genome (ISO) of Global Ocean Reference Genomes (GORG), sin- gle-cell amplified genome (SAG) of MAR Database (MARD), as well as seawater metagenomes of abyssopelagic layer (ABY, 4,500–6,000 m), bathypelagic layer (BAT, 1,000–4,500 m), meso- pelagic layer (MES, 200–1,000 m), and epipelagic layer (EPI, 0–200 m). Doughnut charts illustrate the sample habitat distribution in each habitat. Bar plots depict the distribution of MEER SRGs de- tected in reference habitats. (C) Taxonomic novelty of the MEER dataset against the Genome Taxonomy Database (GTDB, release 220). Light bars extending leftward indi- cate the finest taxonomic level to which SRGs or 16S rRNA gene amplicon sequence variants (ASVs) can be annotated. Solid bars extending rightward represent unreported taxa at each taxonomic level. (D) De novo phylogenetic tree of SRGs, color- coded by the 10 most abundant phyla in the MEER dataset. Purple shapes indicate the placement of three bacterial SRGs that could not be assigned to known phyla according to GTDB, with subtrees showing their neighboring clades and relative evolutionary divergence (RED) values. Note that the bacterial and archaeal trees were combined for visualization purpose but were not rooted together. (E) Distribution of novelty among SRGs and 16S rRNA gene ASVs across the 10 most abundant phyla. Stacked bar plots represent the number of unreported and known SRGs or ASVs, while or- ange lines and dots indicate the percentage of novelty. See also Figure S1 and Tables S1 and S2.
Complete Bacterial Genome Sequences, supplied by Monsanto Technology LLC, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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complete microbial genomes  (Biotechnology Information)
86
Biotechnology Information complete microbial genomes
Figure 1. Sampling and extraordinary nov- elty of the Deepest Ocean <t>microbiome</t> re- vealed by the MEER dataset (A) Sampling sites of hadal zones using the hu- man-occupied vehicle (HOV) Fendouzhe in this study, including the Philippine Basin (PB), the Yap Trench (YT), and the Mariana Trench (MT), as well as the bottom (Bt), northern slope (NS), and southern slope (SS) within the Mariana Trench. (B) Comparative analysis between the species- level representative genomes (SRGs) from the MEER dataset and the species-level genomes in the Ocean Microbiomics Database (OMD), the typical deep-sea and hadal sediment. The OMD included isolated reference genome (ISO) of Global Ocean Reference Genomes (GORG), sin- gle-cell amplified genome (SAG) of MAR Database (MARD), as well as seawater metagenomes of abyssopelagic layer (ABY, 4,500–6,000 m), bathypelagic layer (BAT, 1,000–4,500 m), meso- pelagic layer (MES, 200–1,000 m), and epipelagic layer (EPI, 0–200 m). Doughnut charts illustrate the sample habitat distribution in each habitat. Bar plots depict the distribution of MEER SRGs de- tected in reference habitats. (C) Taxonomic novelty of the MEER dataset against the Genome Taxonomy Database (GTDB, release 220). Light bars extending leftward indi- cate the finest taxonomic level to which SRGs or 16S rRNA gene amplicon sequence variants (ASVs) can be annotated. Solid bars extending rightward represent unreported taxa at each taxonomic level. (D) De novo phylogenetic tree of SRGs, color- coded by the 10 most abundant phyla in the MEER dataset. Purple shapes indicate the placement of three bacterial SRGs that could not be assigned to known phyla according to GTDB, with subtrees showing their neighboring clades and relative evolutionary divergence (RED) values. Note that the bacterial and archaeal trees were combined for visualization purpose but were not rooted together. (E) Distribution of novelty among SRGs and 16S rRNA gene ASVs across the 10 most abundant phyla. Stacked bar plots represent the number of unreported and known SRGs or ASVs, while or- ange lines and dots indicate the percentage of novelty. See also Figure S1 and Tables S1 and S2.
Complete Microbial Genomes, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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nextgeneration sequencing microbial surveillance toolbox (ngs-mstb)  (AstraZeneca ltd)
90
AstraZeneca ltd nextgeneration sequencing microbial surveillance toolbox (ngs-mstb)
Figure 1. Sampling and extraordinary nov- elty of the Deepest Ocean <t>microbiome</t> re- vealed by the MEER dataset (A) Sampling sites of hadal zones using the hu- man-occupied vehicle (HOV) Fendouzhe in this study, including the Philippine Basin (PB), the Yap Trench (YT), and the Mariana Trench (MT), as well as the bottom (Bt), northern slope (NS), and southern slope (SS) within the Mariana Trench. (B) Comparative analysis between the species- level representative genomes (SRGs) from the MEER dataset and the species-level genomes in the Ocean Microbiomics Database (OMD), the typical deep-sea and hadal sediment. The OMD included isolated reference genome (ISO) of Global Ocean Reference Genomes (GORG), sin- gle-cell amplified genome (SAG) of MAR Database (MARD), as well as seawater metagenomes of abyssopelagic layer (ABY, 4,500–6,000 m), bathypelagic layer (BAT, 1,000–4,500 m), meso- pelagic layer (MES, 200–1,000 m), and epipelagic layer (EPI, 0–200 m). Doughnut charts illustrate the sample habitat distribution in each habitat. Bar plots depict the distribution of MEER SRGs de- tected in reference habitats. (C) Taxonomic novelty of the MEER dataset against the Genome Taxonomy Database (GTDB, release 220). Light bars extending leftward indi- cate the finest taxonomic level to which SRGs or 16S rRNA gene amplicon sequence variants (ASVs) can be annotated. Solid bars extending rightward represent unreported taxa at each taxonomic level. (D) De novo phylogenetic tree of SRGs, color- coded by the 10 most abundant phyla in the MEER dataset. Purple shapes indicate the placement of three bacterial SRGs that could not be assigned to known phyla according to GTDB, with subtrees showing their neighboring clades and relative evolutionary divergence (RED) values. Note that the bacterial and archaeal trees were combined for visualization purpose but were not rooted together. (E) Distribution of novelty among SRGs and 16S rRNA gene ASVs across the 10 most abundant phyla. Stacked bar plots represent the number of unreported and known SRGs or ASVs, while or- ange lines and dots indicate the percentage of novelty. See also Figure S1 and Tables S1 and S2.
Nextgeneration Sequencing Microbial Surveillance Toolbox (Ngs Mstb), supplied by AstraZeneca ltd, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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p acnes type ii reference strain atcc 11828  (ATCC)
96
ATCC p acnes type ii reference strain atcc 11828
Figure 1. Sampling and extraordinary nov- elty of the Deepest Ocean <t>microbiome</t> re- vealed by the MEER dataset (A) Sampling sites of hadal zones using the hu- man-occupied vehicle (HOV) Fendouzhe in this study, including the Philippine Basin (PB), the Yap Trench (YT), and the Mariana Trench (MT), as well as the bottom (Bt), northern slope (NS), and southern slope (SS) within the Mariana Trench. (B) Comparative analysis between the species- level representative genomes (SRGs) from the MEER dataset and the species-level genomes in the Ocean Microbiomics Database (OMD), the typical deep-sea and hadal sediment. The OMD included isolated reference genome (ISO) of Global Ocean Reference Genomes (GORG), sin- gle-cell amplified genome (SAG) of MAR Database (MARD), as well as seawater metagenomes of abyssopelagic layer (ABY, 4,500–6,000 m), bathypelagic layer (BAT, 1,000–4,500 m), meso- pelagic layer (MES, 200–1,000 m), and epipelagic layer (EPI, 0–200 m). Doughnut charts illustrate the sample habitat distribution in each habitat. Bar plots depict the distribution of MEER SRGs de- tected in reference habitats. (C) Taxonomic novelty of the MEER dataset against the Genome Taxonomy Database (GTDB, release 220). Light bars extending leftward indi- cate the finest taxonomic level to which SRGs or 16S rRNA gene amplicon sequence variants (ASVs) can be annotated. Solid bars extending rightward represent unreported taxa at each taxonomic level. (D) De novo phylogenetic tree of SRGs, color- coded by the 10 most abundant phyla in the MEER dataset. Purple shapes indicate the placement of three bacterial SRGs that could not be assigned to known phyla according to GTDB, with subtrees showing their neighboring clades and relative evolutionary divergence (RED) values. Note that the bacterial and archaeal trees were combined for visualization purpose but were not rooted together. (E) Distribution of novelty among SRGs and 16S rRNA gene ASVs across the 10 most abundant phyla. Stacked bar plots represent the number of unreported and known SRGs or ASVs, while or- ange lines and dots indicate the percentage of novelty. See also Figure S1 and Tables S1 and S2.
P Acnes Type Ii Reference Strain Atcc 11828, supplied by ATCC, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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microbial genomes  (Incyte corporation)
90
Incyte corporation microbial genomes
Figure 1. Sampling and extraordinary nov- elty of the Deepest Ocean <t>microbiome</t> re- vealed by the MEER dataset (A) Sampling sites of hadal zones using the hu- man-occupied vehicle (HOV) Fendouzhe in this study, including the Philippine Basin (PB), the Yap Trench (YT), and the Mariana Trench (MT), as well as the bottom (Bt), northern slope (NS), and southern slope (SS) within the Mariana Trench. (B) Comparative analysis between the species- level representative genomes (SRGs) from the MEER dataset and the species-level genomes in the Ocean Microbiomics Database (OMD), the typical deep-sea and hadal sediment. The OMD included isolated reference genome (ISO) of Global Ocean Reference Genomes (GORG), sin- gle-cell amplified genome (SAG) of MAR Database (MARD), as well as seawater metagenomes of abyssopelagic layer (ABY, 4,500–6,000 m), bathypelagic layer (BAT, 1,000–4,500 m), meso- pelagic layer (MES, 200–1,000 m), and epipelagic layer (EPI, 0–200 m). Doughnut charts illustrate the sample habitat distribution in each habitat. Bar plots depict the distribution of MEER SRGs de- tected in reference habitats. (C) Taxonomic novelty of the MEER dataset against the Genome Taxonomy Database (GTDB, release 220). Light bars extending leftward indi- cate the finest taxonomic level to which SRGs or 16S rRNA gene amplicon sequence variants (ASVs) can be annotated. Solid bars extending rightward represent unreported taxa at each taxonomic level. (D) De novo phylogenetic tree of SRGs, color- coded by the 10 most abundant phyla in the MEER dataset. Purple shapes indicate the placement of three bacterial SRGs that could not be assigned to known phyla according to GTDB, with subtrees showing their neighboring clades and relative evolutionary divergence (RED) values. Note that the bacterial and archaeal trees were combined for visualization purpose but were not rooted together. (E) Distribution of novelty among SRGs and 16S rRNA gene ASVs across the 10 most abundant phyla. Stacked bar plots represent the number of unreported and known SRGs or ASVs, while or- ange lines and dots indicate the percentage of novelty. See also Figure S1 and Tables S1 and S2.
Microbial Genomes, supplied by Incyte corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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mgieasy pathogen microbiome dna&rna extraction kit（96preps）  (Complete Genomics Inc)
N/A
Sample Prep
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Image Search Results


Figure 1. Sampling and extraordinary nov- elty of the Deepest Ocean microbiome re- vealed by the MEER dataset (A) Sampling sites of hadal zones using the hu- man-occupied vehicle (HOV) Fendouzhe in this study, including the Philippine Basin (PB), the Yap Trench (YT), and the Mariana Trench (MT), as well as the bottom (Bt), northern slope (NS), and southern slope (SS) within the Mariana Trench. (B) Comparative analysis between the species- level representative genomes (SRGs) from the MEER dataset and the species-level genomes in the Ocean Microbiomics Database (OMD), the typical deep-sea and hadal sediment. The OMD included isolated reference genome (ISO) of Global Ocean Reference Genomes (GORG), sin- gle-cell amplified genome (SAG) of MAR Database (MARD), as well as seawater metagenomes of abyssopelagic layer (ABY, 4,500–6,000 m), bathypelagic layer (BAT, 1,000–4,500 m), meso- pelagic layer (MES, 200–1,000 m), and epipelagic layer (EPI, 0–200 m). Doughnut charts illustrate the sample habitat distribution in each habitat. Bar plots depict the distribution of MEER SRGs de- tected in reference habitats. (C) Taxonomic novelty of the MEER dataset against the Genome Taxonomy Database (GTDB, release 220). Light bars extending leftward indi- cate the finest taxonomic level to which SRGs or 16S rRNA gene amplicon sequence variants (ASVs) can be annotated. Solid bars extending rightward represent unreported taxa at each taxonomic level. (D) De novo phylogenetic tree of SRGs, color- coded by the 10 most abundant phyla in the MEER dataset. Purple shapes indicate the placement of three bacterial SRGs that could not be assigned to known phyla according to GTDB, with subtrees showing their neighboring clades and relative evolutionary divergence (RED) values. Note that the bacterial and archaeal trees were combined for visualization purpose but were not rooted together. (E) Distribution of novelty among SRGs and 16S rRNA gene ASVs across the 10 most abundant phyla. Stacked bar plots represent the number of unreported and known SRGs or ASVs, while or- ange lines and dots indicate the percentage of novelty. See also Figure S1 and Tables S1 and S2.

Journal: Cell

Article Title: Microbial ecosystems and ecological driving forces in the deepest ocean sediments.

doi: 10.1016/j.cell.2024.12.036

Figure Lengend Snippet: Figure 1. Sampling and extraordinary nov- elty of the Deepest Ocean microbiome re- vealed by the MEER dataset (A) Sampling sites of hadal zones using the hu- man-occupied vehicle (HOV) Fendouzhe in this study, including the Philippine Basin (PB), the Yap Trench (YT), and the Mariana Trench (MT), as well as the bottom (Bt), northern slope (NS), and southern slope (SS) within the Mariana Trench. (B) Comparative analysis between the species- level representative genomes (SRGs) from the MEER dataset and the species-level genomes in the Ocean Microbiomics Database (OMD), the typical deep-sea and hadal sediment. The OMD included isolated reference genome (ISO) of Global Ocean Reference Genomes (GORG), sin- gle-cell amplified genome (SAG) of MAR Database (MARD), as well as seawater metagenomes of abyssopelagic layer (ABY, 4,500–6,000 m), bathypelagic layer (BAT, 1,000–4,500 m), meso- pelagic layer (MES, 200–1,000 m), and epipelagic layer (EPI, 0–200 m). Doughnut charts illustrate the sample habitat distribution in each habitat. Bar plots depict the distribution of MEER SRGs de- tected in reference habitats. (C) Taxonomic novelty of the MEER dataset against the Genome Taxonomy Database (GTDB, release 220). Light bars extending leftward indi- cate the finest taxonomic level to which SRGs or 16S rRNA gene amplicon sequence variants (ASVs) can be annotated. Solid bars extending rightward represent unreported taxa at each taxonomic level. (D) De novo phylogenetic tree of SRGs, color- coded by the 10 most abundant phyla in the MEER dataset. Purple shapes indicate the placement of three bacterial SRGs that could not be assigned to known phyla according to GTDB, with subtrees showing their neighboring clades and relative evolutionary divergence (RED) values. Note that the bacterial and archaeal trees were combined for visualization purpose but were not rooted together. (E) Distribution of novelty among SRGs and 16S rRNA gene ASVs across the 10 most abundant phyla. Stacked bar plots represent the number of unreported and known SRGs or ASVs, while or- ange lines and dots indicate the percentage of novelty. See also Figure S1 and Tables S1 and S2.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Sediment samples Collected from the Mariana Trench, the Yap Trench and the Philippine Basin MEER Critical commercial assays MGIEasy Environmental Microbiome DNA Extraction Kit MGI-Tech, China Cat#940-001731-00 MGIEasy Fast FS DNA Library Prep Set MGI-Tech, China Cat#940-000030-00 Deposited data Raw data This paper CNSA: CNP0004890 Raw data This paper NODE: OEP004067 Shotgun metagenome-derived specieslevel representative genomes This paper eLMSG: LMSG_G000037053.1 – LMSG_G000044616.1 Source code for quality control, assembly, binning, classification, and abundance profiling This paper https://github.com/meer-trench/genome_ catalogue Source code for ecological analyses This paper https://doi.org/10.5281/zenodo.13317475 Ocean Microbiomics Database Paoli et al.30 https://microbiomics.io/ocean/ GTDB database release 220 Parks et al.49 https://gtdb.ecogenomic.org/ SILVA database version 138 Pruesse et al.79 https://www.arb-silva.de/ Greengenes2 database release 2022.10 McDonald et al.52 https://ftp.microbio.me/greengenes_ release/2022.10/ Oligonucleotides 515F (Parada), Forward 5’-GTGYCAGCMGCCGCGGTAA-3’ N/A 806R (Apprill), Reverse 5’-GGACTACNVGGGTWTCTAAT-3’ N/A Software and algorithms QIMME2 Bolyen et al.80 https://github.com/qiime2 RESCRIPt (2024.10.0.dev0+7.g3c179ca) Robeson et al.81 https://github.com/bokulich-lab/RESCRIPt Cutadapt Martin et al.82 https://cutadapt.readthedocs.io/en/stable/ DADA2 Callahan et al.83 https://github.com/benjjneb/dada2 fastp (v0.23.2) Chen et al.84 https://github.com/OpenGene/fastp MEGAHIT (v1.2.9) Li et al.85 https://github.com/voutcn/megahit MetaBAT2 (v2.12.1) Kang et al.86 https://bitbucket.org/berkeleylab/metabat BWA (v0.7.17-r1188) Li et al.87 https://github.com/lh3/bwa dRep (v3.4.0) Olm et al.76 https://github.com/MrOlm/drep CoverM (v0.7.0) N/A https://github.com/wwood/CoverM GTDB-Tk (v2.4.0) Chaumeil et al.88 https://github.com/Ecogenomics/GTDBTk Prodigal Hyatt et al.89 https://github.com/hyattpd/Prodigal Mantis Queirós et al.90 https://github.com/PedroMTQ/mantis R (v4.1.0) R Project https://www.r-project.org/ R Studio Server v2023.12.1.402 Posit https://posit.co/products/open-source/ rstudio-server/ ggtree (v3.10.1) Yu et al.91 https://github.com/YuLab-SMU/ggtree ggtreeExtra (v1.12.0) Xu et al.92 https://github.com/YuLab-SMU/ ggtreeExtra vegan (v2.6-4) Oksanen et al.93 https://github.com/vegandevs/vegan (Continued on next page) e1 Cell 188, 1363–1377.e1–e3, March 6, 2025

Techniques: Sampling, Northern Blot, Isolation, Amplification, Sequencing