GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

Abstract The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy for prokaryotic genomes sourced from the NCBI Assembly database. GTDB R06-RS202 spans 254 090 bacterial and 4316 archaeal genomes, a 270% increase since the introduction of the GTDB in November, 2017. These genomes are organized into 45 555 bacterial and 2339 archaeal species clusters which is a 200% increase since the integration of species clusters into the GTDB in June, 2019. Here, we explore prokaryotic diversity from the perspective of the GTDB and highlight the importance of metagenome-assembled genomes in expanding available genomic representation. We also discuss improvements to the GTDB website which allow tracking of taxonomic changes, easy assessment of genome assembly quality, and identification of genomes assembled from type material or used as species representatives. Methodological updates and policy changes made since the inception of the GTDB are then described along with the procedure used to update species clusters in the GTDB. We conclude with a discussion on the use of average nucleotide identities as a pragmatic approach for delineating prokaryotic species.

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Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Nature Biotechnology ◽

10.1038/nbt.3893 ◽

2017 ◽

Vol 35 (8) ◽

pp. 725-731 ◽

Cited By ~ 409

Author(s):

Robert M Bowers ◽

◽

Nikos C Kyrpides ◽

Ramunas Stepanauskas ◽

Miranda Harmon-Smith ◽

...

Keyword(s):

Gene Sequence ◽

Marker Gene ◽

Comparative Genomic ◽

Archaeal Diversity ◽

Genome Sequences ◽

Assembly Quality ◽

Metagenomic Sequence ◽

Minimum Information ◽

A Genome ◽

Genomic Analyses

AbstractWe present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.

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Large-scale quality assessment of prokaryotic genomes with metashot/prok-quality

F1000Research ◽

10.12688/f1000research.54418.1 ◽

2021 ◽

Vol 10 ◽

pp. 822

Author(s):

Davide Albanese ◽

Claudio Donati

Keyword(s):

Quality Assessment ◽

Large Scale ◽

Metagenomic Sequencing ◽

Link Type ◽

Archaeal Species ◽

Prokaryotic Genomes ◽

Genomic Characterization ◽

Computational Workflow ◽

Quality Tool

Metagenomic sequencing allows large-scale identification and genomic characterization. Binning is the process of recovering genomes from complex mixtures of sequence fragments (metagenome contigs) of unknown bacteria and archaeal species. Assessing the quality of genomes recovered from metagenomes requires the use of complex pipelines involving many independent steps, often difficult to reproduce and maintain. A comprehensive, automated and easy-to-use computational workflow for the quality assessment of draft prokaryotic genomes, based on container technology, would greatly improve reproducibility and reusability of published results. We present metashot/prok-quality, a container-enabled Nextflow pipeline for quality assessment and genome dereplication. The metashot/prok-quality tool produces genome quality reports that are compliant with the Minimum Information about a Metagenome-Assembled Genome (MIMAG) standard, and can run out-of-the-box on any platform that supports Nextflow, Docker or Singularity, including computing clusters or batch infrastructures in the cloud. metashot/prok-quality is part of the metashot collection of analysis pipelines. Workflow and documentation are available under GPL3 licence on GitHub.

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Unexplored Archaeal Diversity in the Great Ape Gut Microbiome

mSphere ◽

10.1128/msphere.00026-17 ◽

2017 ◽

Vol 2 (1) ◽

Cited By ~ 41

Author(s):

Kasie Raymann ◽

Andrew H. Moeller ◽

Andrew L. Goodman ◽

Howard Ochman

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gut Microbiome ◽

Rrna Gene ◽

Great Ape ◽

Archaeal Diversity ◽

Full Diversity ◽

Archaeal Species ◽

Vital Component

ABSTRACT Our findings show that Archaea are a habitual and vital component of human and great ape gut microbiomes but are largely ignored on account of the failure of previous studies to realize their full diversity. Here we report unprecedented levels of archaeal diversity in great ape gut microbiomes, exceeding that detected by conventional 16S rRNA gene surveys. Paralleling what has been reported for bacteria, there is a vast reduction of archaeal diversity in humans. Our study demonstrates that archaeal diversity in the great ape gut microbiome greatly exceeds that reported previously and provides the basis for further studies on the role of archaea in the gut microbiome. Archaea are habitual residents of the human gut flora but are detected at substantially lower frequencies than bacteria. Previous studies have indicated that each human harbors very few archaeal species. However, the low diversity of human-associated archaea that has been detected could be due to the preponderance of bacteria in these communities, such that relatively few sequences are classified as Archaea even when microbiomes are sampled deeply. Moreover, the universal prokaryotic primer pair typically used to interrogate microbial diversity has low specificity to the archaeal domain, potentially leaving vast amounts of diversity unobserved. As a result, the prevalence, diversity, and distribution of archaea may be substantially underestimated. Here we evaluate archaeal diversity in gut microbiomes using an approach that targets virtually all known members of this domain. Comparing microbiomes across five great ape species allowed us to examine the dynamics of archaeal lineages over evolutionary time scales. These analyses revealed hundreds of gut-associated archaeal lineages, indicating that upwards of 90% of the archaeal diversity in the human and great ape gut microbiomes has been overlooked. Additionally, these results indicate a progressive reduction in archaeal diversity in the human lineage, paralleling the decline reported for bacteria. IMPORTANCE Our findings show that Archaea are a habitual and vital component of human and great ape gut microbiomes but are largely ignored on account of the failure of previous studies to realize their full diversity. Here we report unprecedented levels of archaeal diversity in great ape gut microbiomes, exceeding that detected by conventional 16S rRNA gene surveys. Paralleling what has been reported for bacteria, there is a vast reduction of archaeal diversity in humans. Our study demonstrates that archaeal diversity in the great ape gut microbiome greatly exceeds that reported previously and provides the basis for further studies on the role of archaea in the gut microbiome.

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Delimiting the genera of the Ficinia Clade (Cypereae, Cyperaceae) based on molecular phylogenetic data

PeerJ ◽

10.7717/peerj.10737 ◽

2021 ◽

Vol 9 ◽

pp. e10737

Author(s):

A. Muthama Muasya ◽

Isabel Larridon

Keyword(s):

Phylogenetic Position ◽

Pragmatic Approach ◽

Nuclear Markers ◽

Diagnostic Features ◽

The Core ◽

Molecular Phylogenetic ◽

Taxonomic Changes ◽

Plastid Markers ◽

Molecular Phylogenetic Data ◽

Level Identification

Generic delimitations in the Ficinia Clade of tribe Cypereae are revisited. In particular, we aim to establish the placement of annual species currently included in Isolepis of which the phylogenetic position is uncertain. Phylogenetic inference is based on two nuclear markers (ETS, ITS) and five plastid markers (the genes matK, ndhF, rbcL and rps16, the trnL intron and trnL-F spacer) data, analyzed using model based methods. Topologies based on nuclear and plastid data show incongruence at the backbone. Therefore, the results are presented separately. The monophyly of the smaller genera (Afroscirpoides, Dracoscirpoides, Erioscirpus, Hellmuthia, Scirpoides) is confirmed. However, Isolepis is paraphyletic as Ficinia is retrieved as one of its clades. Furthermore, Ficinia is paraphyletic if I. marginata and allies are excluded. We take a pragmatic approach based on the nuclear topology, driven by a desire to minimize taxonomic changes, to recircumscribe Ficinia to include the annual Isolepis species characterized by cartilaginous glumes and formally include all the Isolepis species inferred outside the core Isolepis clade. Consequently, the circumscription of Isolepis is narrowed to encompass only those species retrieved as part of the core Isolepis clade. Five new combinations are made (Ficinia neocapensis, Ficinia hemiuncialis, Ficinia incomtula, Ficinia leucoloma, Ficinia minuta). We present nomenclatural summary at genus level, identification keys and diagnostic features.

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Lengths of Orthologous Prokaryotic Proteins Are Affected by Evolutionary Factors

BioMed Research International ◽

10.1155/2015/786861 ◽

2015 ◽

Vol 2015 ◽

pp. 1-11 ◽

Cited By ~ 4

Author(s):

Tatiana Tatarinova ◽

Bilal Salih ◽

Jennifer Dien Bard ◽

Irit Cohen ◽

Alexander Bolshoy

Keyword(s):

Computational Efficiency ◽

Driving Factors ◽

Ranking Methods ◽

Factors Affecting ◽

The Third ◽

Archaeal Species ◽

Prokaryotic Genomes ◽

Reasonable Approach ◽

Open Question ◽

Long Genes

Proteins of the same functional family (for example, kinases) may have significantly different lengths. It is an open question whether such variation in length is random or it appears as a response to some unknown evolutionary driving factors. The main purpose of this paper is to demonstrate existence of factors affecting prokaryotic gene lengths. We believe that the ranking of genomes according to lengths of their genes, followed by the calculation of coefficients of association between genome rank and genome property, is a reasonable approach in revealing such evolutionary driving factors. As we demonstrated earlier, our chosen approach, Bubble-sort, combines stability, accuracy, and computational efficiency as compared to other ranking methods. Application of Bubble Sort to the set of 1390 prokaryotic genomes confirmed that genes of Archaeal species are generally shorter than Bacterial ones. We observed that gene lengths are affected by various factors: within each domain, different phyla have preferences for short or long genes; thermophiles tend to have shorter genes than the soil-dwellers; halophiles tend to have longer genes. We also found that species with overrepresentation of cytosines and guanines in the third position of the codon (GC3content) tend to have longer genes than species with low GC3content.

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Intragenomic Heterogeneity of 16S rRNA Genes Causes Overestimation of Prokaryotic Diversity

Applied and Environmental Microbiology ◽

10.1128/aem.01282-13 ◽

2013 ◽

Vol 79 (19) ◽

pp. 5962-5969 ◽

Cited By ~ 156

Author(s):

Dong-Lei Sun ◽

Xuan Jiang ◽

Qinglong L. Wu ◽

Ning-Yi Zhou

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Full Length ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Prokaryotic Diversity ◽

Prokaryotic Genomes ◽

General Guidance ◽

Different Levels

ABSTRACTEver since Carl Woese introduced the use of 16S rRNA genes for determining the phylogenetic relationships of prokaryotes, this method has been regarded as the “gold standard” in both microbial phylogeny and ecology studies. However, intragenomic heterogeneity within 16S rRNA genes has been reported in many investigations and is believed to bias the estimation of prokaryotic diversity. In the current study, 2,013 completely sequenced genomes of bacteria and archaea were analyzed and intragenomic heterogeneity was found in 952 genomes (585 species), with 87.5% of the divergence detected being below the 1% level. In particular, some extremophiles (thermophiles and halophiles) were found to harbor highly divergent 16S rRNA genes. Overestimation caused by 16S rRNA gene intragenomic heterogeneity was evaluated at different levels using the full-length and partial 16S rRNA genes usually chosen as targets for pyrosequencing. The result indicates that, at the unique level, full-length 16S rRNA genes can produce an overestimation of as much as 123.7%, while at the 3% level, an overestimation of 12.9% for the V6 region may be introduced. Further analysis showed that intragenomic heterogeneity tends to concentrate in specific positions, with the V1 and V6 regions suffering the most intragenomic heterogeneity and the V4 and V5 regions suffering the least intragenomic heterogeneity in bacteria. This is the most up-to-date overview of the diversity of 16S rRNA genes within prokaryotic genomes. It not only provides general guidance on how much overestimation can be introduced when applying 16S rRNA gene-based methods, due to its intragenomic heterogeneity, but also recommends that, for bacteria, this overestimation be minimized using primers targeting the V4 and V5 regions.

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