A complete domain-to-species taxonomy for Bacteria and Archaea

Parks, Donovan H.; Chuvochina, Maria; Chaumeil, Pierre-Alain; Rinke, Christian; Mussig, Aaron J.; Hugenholtz, Philip

doi:10.1038/s41587-020-0501-8

Cited by 1,034 publications

(1,139 citation statements)

References 60 publications

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“…Characterization of the high-quality MAGs GTDB-tk 1.3.0 [32] with GTDB taxonomy release 95 [33] were used to assess the novelty and the taxonomy of HQ MAGs. We used PROKKA 1.13.4 to annotate the MAGs [34].…”

Section: Metagenomics Assembly and Polishingmentioning

confidence: 99%

Long-Read Metagenomics to Retrieve High-Quality Metagenome-Assembled Genomes from Canine Feces

Cuscó¹,

Pérez²,

Viñes³

et al. 2020

Preprint

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Background. Metagenomics is a powerful and rapidly developing approach that provides new biological insights into the microbes inhabiting underexplored environments, such as canine fecal microbiome. We investigate long-read metagenomics with Nanopore sequencing to profile the fecal microbiome and to retrieve high-quality metagenome-assembled genomes (HQ MAGs) from a healthy dog.Results. More than 99% of total classified reads corresponded to Bacteria. The most abundant phylum was Bacteroidetes (~80% of total reads), followed by Firmicutes, Proteobacteria, and Fusobacteria. Prevotella (>50%) and Bacteroides (>20%) are the more abundant genera, followed by Fusobacterium, Megamonas, Sutterella, and other fecal-related genera, (each representing <5% of the total bacterial composition). We retrieved eight single-contig HQ MAGs and three medium-quality MAGs, after combining several metagenome dataset assemblies. The HQ MAGs corresponded to Succinivibrio, Sutterella, Prevotellamassilia, Phascolarctobacterium, Enterococcus, Blautia, and Catenibacterium genera. Succinivibrio HQ MAG represents a novel candidate bacterial species. Sutterella HQ MAG is potentially the first reported genome assembly for Sutterella stercoricanis, as assigned by 16S rRNA gene similarity. Prevotellamassilia, Phascolarctobacterium, Catenibacterium, and Blautia sp900541345 HQ MAGs improved the contiguity of previously reported genome assemblies in their respective genera, and the number of rRNA genes and tRNA genes. Finally, Enterococcus hirae and Blautia sp003287895 HQ MAGs represented species that already have a complete reference genome. At the technical level, we demonstrated that a high-molecular weight DNA extraction improved the taxonomic classification of the raw unassembled reads, the metagenomics assembly contiguity, and the retrieval of longer and circular contigs, which are potential HQ MAGs. Conclusions. Long-read metagenomics allowed us to recover HQ MAGs from canine feces of a healthy dog. The high-molecular weight DNA extraction to improve contiguity and the correction of the insertions and deletions to reduce frameshift errors ensure the retrieval of complete single-contig HQ MAGs.

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Section: Metagenomics Assembly and Polishingmentioning

confidence: 99%

Long-Read Metagenomics to Retrieve High-Quality Metagenome-Assembled Genomes from Canine Feces

Cuscó¹,

Pérez²,

Viñes³

et al. 2020

Preprint

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“…6, Additional File 5; Supplementary Table 3). Further analysis of the GTDB species designated Escherichia sp001660175 [88] con rmed that this species forms a monophyletic lineage that corresponds to the Clade II, among the cryptic environmental clades described by Whittam and his colleagues [89], which was subsequently documented in birds [90]. As Clade II is comparable in divergence to the other Escherichia spp.…”

Section: Taxonomic Diversity Of Cultured Bacterial Isolatesmentioning

confidence: 79%

“…pecorum of ocks of sheep, birds etc., as this species has also been isolated from sheep) A bacterial species cultured from chicken faeces and assigned to this genus and delineated as a species by analysis of its genome sequence. GTDB [88] has given this species the alphanumerical designation A bacterial species cultured from chicken faeces and assigned to this genus and delineated as a species by analysis of its genome sequence. GTDB [88] has given this species the alphanumerical designation sp002161565 The Type Strain is Sa1CVN1, which has been submitted for deposition in NCTC and DSMZ.…”

Section: Competing Interestsmentioning

confidence: 99%

A Genomic Blueprint of the Chicken Gut Microbiome

Gilroy¹,

Ray²,

Getino³

et al. 2020

Preprint

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Background: The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to deliver a genomic blueprint of this complex microbial community. Results: We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n=582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes This represents the most comprehensive view of the chicken gut associated microbiome to date, encompassing dozens of novel candidate bacterial genera and hundreds of novel candidate species. Keen to provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured bacterial isolates from faeces to deliver 282 whole genome sequences, incorporating thirty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii.Conclusions: Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provides a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.

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“…Therefore, we used in most analyses high-rank taxonomic annotations, but we also investigated main trends in the distribution of low rank taxa that may contribute genes to TeOM degradation in the Amazon River. Speci cally, we analysed genes associated to TeOM degradation that could be taxonomically assigned to genera or genomes from unknown genera present in the Genome Taxonomy Database (GTDB) database [89]. Only genera or genomes contributing functions in more than half of the samples in each of the river sections as well as in the plume and ocean samples were considered.…”

Section: Degradation Of Lignin-derived Aromatic Compoundsmentioning

confidence: 99%

“…Reference sequences with hits to poorly annotated sequences from other metagenomes were referred to as "Metagenomic". Approach 2: Low-rank taxonomic a liation was determined using MMseqs2 version 11-e1a1c [88] using default settings, based on the Genome Taxonomy Database (GTDB; publicly available in https://gtdb.ecogenomic.org/) [89].…”

Section: Gene Taxonomymentioning

confidence: 99%

Uncovering the Genomic Potential of the Amazon River Microbiome to Degrade Rainforest Organic Matter

Júnior

Sarmento

Miranda

et al. 2020

Preprint

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Background: The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analyzing 106 metagenomes from 30 sampling points distributed along the river.Results: We constructed the Amazon River basin Microbial non-redundant Gene Catalogue (AMnrGC) that includes ~3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant known environments (rivers and rainforest soil). Genes encoding for proteins potentially involved in lignin degradation pathways were correlated to tripartite tricarboxylates transporters and hemicellulose degradation machinery, pointing to a possible priming effect. Based on this, we propose a model on how the degradation of recalcitrant TeOM could be modulated by labile compounds in the Amazon River waters. Our results also suggest changes of the microbial community and its genomic potential along the river course.Conclusions: Our work contributes to expand significantly our comprehension of the world’s largest river microbiome and its potential metabolism related to TeOM degradation. Furthermore, the produced gene catalogue (AMnrGC) represents an important resource for future research in tropical rivers.

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A complete domain-to-species taxonomy for Bacteria and Archaea

Cited by 1,034 publications

References 60 publications

Long-Read Metagenomics to Retrieve High-Quality Metagenome-Assembled Genomes from Canine Feces

Long-Read Metagenomics to Retrieve High-Quality Metagenome-Assembled Genomes from Canine Feces

A Genomic Blueprint of the Chicken Gut Microbiome

Uncovering the Genomic Potential of the Amazon River Microbiome to Degrade Rainforest Organic Matter

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