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Microbial taxonomy is increasingly influenced by genome-based computational methods. Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS, the Type (Strain) Genome Server, a user-friendly high-throughput web server for genome-based prokaryote taxonomy, connected to a large, continuously growing database of genomic, taxonomic and nomenclatural information. It infers genome-scale phylogenies and state-of-the-art estimates for species and subspecies boundaries from user-defined and automatically determined closest type genome sequences. TYGS also provides comprehensive access to nomenclature, synonymy and associated taxonomic literature. Clinically important examples demonstrate how TYGS can yield new insights into microbial classification, such as evidence for a species-level separation of previously proposed subspecies of Salmonella enterica . TYGS is an integrated approach for the classification of microbes that unlocks novel scientific approaches to microbiologists worldwide and is particularly helpful for the rapidly expanding field of genome-based taxonomic descriptions of new genera, species or subspecies. Information on type material is of fundamental importance in prokaryote taxonomy. Here, the authors develop TYGS, the Type (Strain) Genome Server, for genome-based prokaryote taxonomy and analysis using a comprehensive database of genomic and taxonomic data.

Interpretation of microbial genome data will be improved by a fully revised bacterial taxonomy. Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability to obtain most bacteria in pure culture and, to a lesser extent, by the historical use of phenotypes to guide classification. Culture-independent sequencing technologies have matured sufficiently that a comprehensive genome-based taxonomy is now possible. We used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence. Under this approach, 58% of the 94,759 genomes comprising the Genome Taxonomy Database had changes to their existing taxonomy. This result includes the description of 99 phyla, including six major monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into a single phylum. Our taxonomy should enable improved classification of uncultured bacteria and provide a sound basis for ecological and evolutionary studies.

The Genome Taxonomy Database is a phylogenetically consistent, genome-based taxonomy that provides rank-normalized classifications for ~150,000 bacterial and archaeal genomes from domain to genus. However, almost 40% of the genomes in the Genome Taxonomy Database lack a species name. We address this limitation by using commonly accepted average nucleotide identity criteria to set bounds on species and propose species clusters that encompass all publicly available bacterial and archaeal genomes. Unlike previous average nucleotide identity studies, we chose a single representative genome to serve as the effective nomenclatural ‘type’ defining each species. Of the 24,706 proposed species clusters, 8,792 are based on published names. We assigned placeholder names to the remaining 15,914 species clusters to provide names to the growing number of genomes from uncultivated species. This resource provides a complete domain-to-species taxonomic framework for bacterial and archaeal genomes, which will facilitate research on uncultivated species and improve communication of scientific results. A full species classification is built for all publicly available bacterial and archaeal genomes.

Studying and protecting each and every living species on Earth is a major challenge of the 21 st century. Yet, most species remain unknown or unstudied, while others attract most of the public, scientific and government attention. Although known to be detrimental, this taxonomic bias continues to be pervasive in the scientific literature, but is still poorly studied and understood. Here, we used 626 million occurrences from the Global Biodiversity Information Facility (GBIF), the biggest biodiversity data portal, to characterize the taxonomic bias in biodiversity data. We also investigated how societal preferences and taxonomic research relate to biodiversity data gathering. For each species belonging to 24 taxonomic classes, we used the number of publications from Web of Science and the number of web pages from Bing searches to approximate research activity and societal preferences. Our results show that societal preferences, rather than research activity, strongly correlate with taxonomic bias, which lead us to assert that scientists should advertise less charismatic species and develop societal initiatives (e.g. citizen science) that specifically target neglected organisms. Ensuring that biodiversity is representatively sampled while this is still possible is an urgent prerequisite for achieving efficient conservation plans and a global understanding of our surrounding environment.

Human papillomaviruses (HPVs) are an ancient and highly successful group of viruses that have co-evolved with their host to replicate in specific anatomical niches of the stratified epithelia. They replicate persistently in dividing cells, hijack key host cellular processes to manipulate the cellular environment and escape immune detection, and produce virions in terminally differentiated cells that are shed from the host. Some HPVs cause benign, proliferative lesions on the skin and mucosa, and others are associated with the development of cancer. However, most HPVs cause infections that are asymptomatic and inapparent unless the immune system becomes compromised. To date, the genomes of almost 450 distinct HPV types have been isolated and sequenced. In this Review, I explore the diversity, evolution, infectious cycle, host interactions and disease association of HPVs.Human papillomaviruses (HPVs) are a diverse group of viruses that replicate in specific anatomical niches of the stratified epithelia. Most HPVs cause asymptomatic infections, some cause benign, proliferative lesions on the skin and mucosa, and others are associated with the development of cancer. In this Review, McBride explores the diversity, evolution, infectious cycle, host interactions and disease association of HPVs.

Ammonia-oxidising archaea (AOA) are ubiquitous and abundant in nature and play a major role in nitrogen cycling. AOA have been studied intensively based on the amoA gene (encoding ammonia monooxygenase subunit A), making it the most sequenced functional marker gene. Here, based on extensive phylogenetic and meta-data analyses of 33,378 curated archaeal amoA sequences, we define a highly resolved taxonomy and uncover global environmental patterns that challenge many earlier generalisations. Particularly, we show: (i) the global frequency of AOA is extremely uneven, with few clades dominating AOA diversity in most ecosystems; (ii) characterised AOA do not represent most predominant clades in nature, including soils and oceans; (iii) the functional role of the most prevalent environmental AOA clade remains unclear; and (iv) AOA harbour molecular signatures that possibly reflect phenotypic traits. Our work synthesises information from a decade of research and provides the first integrative framework to study AOA in a global context. Ammonia-oxidising archaea (AOA) were only discovered a little over a decade ago and remain poorly characterized despite their ubiquity and importance for nitrogen cycling. Here, the authors define a taxonomy of AOA based on a resolved amoA phylogeny and describe emergent global patterns in AOA diversity.

The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV.

Key Points Biogeography is the study of the distribution of organisms and the ecological and evolutionary processes that shape those distributions. Over the past decade, microbiologists have established the existence of biogeographic patterns among a wide variety of microorganisms, and interest is now shifting towards identifying the mechanisms that shape these patterns. Traditionally, mechanisms that shape the composition and diversity within species are considered to be evolutionary processes, and those that shape the composition and diversity among species are considered to be ecological processes. However, microbial biogeography studies often characterize diversity along a continuous scale of taxonomic resolution using the nucleotide sequences of a single marker gene. In this case, the boundary between ecological and evolutionary processes is particularly blurry. Hence, we merge concepts from both fields to describe the processes that shape microbial biogeographic patterns. Here, we propose a theoretical framework that describes just four processes — selection, drift, dispersal and mutation — which interact to create and maintain microbial biogeographic patterns at all taxonomic scales. As an illustrative example, we show how these processes shape the most commonly studied biogeographic pattern: the distance–decay relationship. We carried out a literature review to assess the evidence for the relative importance of these processes in shaping microbial biogeographic patterns. Although selection imposed by current environmental factors had the strongest influence on microbial spatial distributions, historical processes driven by dispersal limitation also influenced the distribution of at least some microorganisms from all domains of life and from various habitat types, spatial scales and taxonomic resolutions. As different combinations of the same four processes can interact to create the same pattern, we conclude that it remains difficult to disentangle the relative importance of selection, drift, dispersal and mutation by analysing distance–decay patterns alone. We suggest that the field might advance by emphasizing process over pattern: tailoring studies to detect and evaluate specific processes through manipulative experiments, temporal data sets and the incorporation of theoretical models. Like larger organisms, microorganisms display distinct distributions in space and time. Martiny, Hanson and colleagues propose that four processes — selection, drift, dispersal and mutation — can shape such microbial biogeographic patterns, and analyse the literature to assess the evidence for their importance in shaping one pattern, the distance–decay relationship. Recently, microbiologists have established the existence of biogeographic patterns among a wide range of microorganisms. The focus of the field is now shifting to identifying the mechanisms that shape these patterns. Here, we propose that four processes — selection, drift, dispersal and mutation — create and maintain microbial biogeographic patterns on inseparable ecological and evolutionary scales. We consider how the interplay of these processes affects one biogeographic pattern, the distance–decay relationship, and review evidence from the published literature for the processes driving this pattern in microorganisms. Given the limitations of inferring processes from biogeographic patterns, we suggest that studies should focus on directly testing the underlying processes.

The field of plant genome sequencing has grown rapidly in the past 20 years, leading to increases in the quantity and quality of publicly available genomic resources. The growing wealth of genomic data from an increasingly diverse set of taxa provides unprecedented potential to better understand the genome biology and evolution of land plants. Here we provide a contemporary view of land plant genomics, including analyses on assembly quality, taxonomic distribution of sequenced species and national participation. We show that assembly quality has increased dramatically in recent years, that substantial taxonomic gaps exist and that the field has been dominated by affluent nations in the Global North and China, despite a wide geographic distribution of study species. We identify numerous disconnects between the native range of focal species and the national affiliation of the researchers studying them, which we argue are rooted in colonialism—both past and present. Luckily, falling sequencing costs, widening availability of analytical tools and an increasingly connected scientific community provide key opportunities to improve existing assemblies, fill sampling gaps and empower a more global plant genomics community. Analyses of plant genomes sequenced in the past 20 years, the species taxonomic distribution and national participation reveal that genome quality has increased but substantial taxonomic gaps exist, and that the field has been dominated by the Global North.

What a strain is and how many strains make up a natural bacterial population remain elusive concepts despite their apparent importance for assessing the role of intra-population diversity in disease emergence or response to environmental perturbations. To advance these concepts, we sequenced 138 randomly selected Salinibacter ruber isolates from two solar salterns and assessed these genomes against companion short-read metagenomes from the same samples. The distribution of genome-aggregate average nucleotide identity (ANI) values among these isolates revealed a bimodal distribution, with fourfold lower occurrence of values between 99.2% and 99.8% relative to ANI >99.8% or <99.2%, revealing a natural “gap” in the sequence space within species. Accordingly, we used this ANI gap to define genomovars and a higher ANI value of >99.99% and shared gene-content >99.0% to define strains. Using these thresholds and extrapolating from how many metagenomic reads each genomovar uniquely recruited, we estimated that –although our 138 isolates represented about 80% of the Sal. ruber population– the total population in one saltern pond is composed of 5,500 to 11,000 genomovars, the great majority of which appear to be rare in-situ. These data also revealed that the most frequently recovered isolate in lab media was often not the most abundant genomovar in-situ, suggesting that cultivation biases are significant, even in cases that cultivation procedures are thought to be robust. The methodology and ANI thresholds outlined here should represent a useful guide for future microdiversity surveys of additional microbial species.