The Next Million Names for Archaea and Bacteria

Pallen, Mark J.; Telatin, Andrea; Oren, Aharon

doi:10.1016/j.tim.2020.10.009

Cited by 52 publications

(43 citation statements)

References 25 publications

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“…Another example can be seen in our comparative analysis of LR-chr and HY-chr sequence, which used a subsequent version of GTDB than that used to originally classify the LR-chr sequences, and where both Defluviicoccus (LR-chr) genomes were reclassified as being from the closely related genus Azonexus, despite their previous consistency at genus level with 16S classification (see Supplementary Data 8). More broadly these differences reflect the rapidly changing landscape of microbial taxonomy and systematics, including the need to deal with the increasingly large numbers of draft genomes being obtained from metagenome surveys, the need for more flexible nomenclature systems 80,81 and the ongoing issue of how DNA sequence in general, and whole-genome sequence in particular, can be incorporated into the official procedures of prokaryotic systematics 82 . While we recognise that technical improvements in metagenome quality are only a small part of this landscape, it is worth highlighting that the kind of genomes recovered here would be virtually indistinguishable in quality from those obtained by the analysis of genomic DNA from cultured type material, and furthermore that both metagenome sequence data, and whole-genome sequence derived from them, are stable entities under any reasonable definition.…”

Section: Discussionmentioning

confidence: 99%

Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing

Arumugam

Bessarab

Haryono

et al. 2021

npj Biofilms Microbiomes

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New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes from complex microbial communities. Using long read data (ONT MinION) obtained from an ensemble of activated sludge enrichment bioreactors we recover 22 closed or complete genomes of community members, including several species known to play key functional roles in wastewater bioprocesses, specifically microbes known to exhibit the polyphosphate- and glycogen-accumulating organism phenotypes (namely Candidatus Accumulibacter and Dechloromonas, and Micropruina, Defluviicoccus and Candidatus Contendobacter, respectively), and filamentous bacteria (Thiothrix) associated with the formation and stability of activated sludge flocs. Additionally we demonstrate the recovery of close to 100 circularised plasmids, phages and small microbial genomes from these microbial communities using long read assembled sequence. We describe methods for validating long read assembled genomes using their counterpart short read metagenome-assembled genomes, and assess the influence of different correction procedures on genome quality and predicted gene quality. Our findings establish the feasibility of performing long read metagenome-assembled genome recovery for both chromosomal and non-chromosomal replicons, and demonstrate the value of parallel sampling of moderately complex enrichment communities to obtaining high quality reference genomes of key functional species relevant for wastewater bioprocesses.

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Section: Discussionmentioning

confidence: 99%

Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing

Arumugam

Bessarab

Haryono

et al. 2021

npj Biofilms Microbiomes

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“…We identified 12 MAGs that was previously named and/or cultured so the Latin binomial for these MAGs was updated (Supplementary table 7). For the rest of the MAGs, we used the approach described in Pallen et al [21] to provide novel Latin names to 56 MAG clusters. We have provided 12 new genus names and 51 novel species names (Table 1).…”

Section: Resultsmentioning

confidence: 99%

Linking carbohydrate structure with function in the human gut microbiome using hybrid metagenome assemblies

Ray

Troncoso‐Rey

Ahn‐Jarvis

et al. 2021

Preprint

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Complex carbohydrates that escape digestion in the small intestine, are broken down in the large intestine by enzymes encoded by the gut microbiome. This is a symbiotic relationship between particular microbes and the host, resulting in metabolic products that influence host gut health and are exploited by other microbes. However, the role of carbohydrate structure in directing microbiota community composition and the succession of carbohydrate-degrading microbes, is not fully understood. In this study we evaluate species-level compositional variation within a single microbiome in response to six structurally distinct carbohydrates in a controlled model gut using hybrid metagenome assemblies. We identified 509 high-quality metagenome-assembled genomes (MAGs) belonging to ten bacterial classes and 28 bacterial families. We found dynamic variations in the microbiome amongst carbohydrate treatments, and over time. Using these data, the MAGs were characterised as primary (0h to 6h) and secondary degraders (12h to 24h). Recent advances in sequencing technology allowed us to identify significant unexplored diversity amongst starch degrading species in the human gut microbiota including CAZyme profiles for novel MAGs.

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“…Such linguistic intricacies are intimidating to most microbiologists. We have therefore created over a million descriptive names before they are needed, using a computer program GAN that combines well-formed classical stems with relevant meanings (38). The simplest approach was to apply prefixes to existing names, which conserves their linguistic properties while supplying a semantic hint at their phylogeny.…”

Section: Bactoderma Albamentioning

confidence: 99%

“…Nonetheless, over recent decades, we have seen remarkable complexity layered on top of such simplicity in the creation of elaborate and stylized "protologues" (a word not used in the ICNP), stuffed full of long descriptions and arcane linguistic components, such as syllabifications and elaborate etymologies. Falling in line with such a tradition, we incorporated etymologies into our computer program GAN (38), while a subsequent program Protologger went even further in computerising the creation of extensive protologues (40).…”

Section: Minimal Protologuesmentioning

confidence: 99%

Bacterial Nomenclature in the Era of Genomics

Pallen

2021

Preprint

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The remarkable success of taxonomic discovery, powered by culturomics, genomics and metagenomics, creates a pressing need for new bacterial names, while holding a mirror up to the slow pace of change in bacterial nomenclature. Here, I take a fresh look at bacterial nomenclature, exploring how we might create a system fit for the age of genomics, playing to the strengths of current practice, while minimising difficulties. Adoption of linguistic pragmatism, obeying the rules while treating recommendations as merely optional will make it easier to create names derived from descriptions, from people or places or even arbitrarily. Simpler protologues and a relaxed approach to recommendations will also remove much of the need for expert linguistic quality control. Automated computer-based approaches will allow names to be created en masse before they are needed, while also relieving microbiologists of the need for competence in Latin. The result will be a system that is accessible, inclusive and digital, while also fully capable of naming the unnamed millions of bacteria.

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The Next Million Names for Archaea and Bacteria

Cited by 52 publications

References 25 publications

Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing

Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing

Linking carbohydrate structure with function in the human gut microbiome using hybrid metagenome assemblies

Bacterial Nomenclature in the Era of Genomics

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