The status Candidatus for uncultured taxa of Bacteria and Archaea: SWOT analysis

Cultivation of anaerobic bacteria: Foundations and principles

A brief history of techniques in anaerobic microbiology are presented leading up to the incorporation of several improvements we have used over the years to improve our culture of anaerobic microorganisms of environmental, industrial and clinical importance. Two overriding aspects from our combined 90 years of experience here are: the better one's control of anaerobic conditions and gas phases, the better results are obtained; techniques can and should be targeted for individual microorganisms and accompanying experiments. Continued improvements in anaerobic microbiology are expected and encouraged for the future.

Lyme borreliosis in Brazil: a critical review on the Baggio-Yoshinari syndrome (Brazilian Lyme-like disease)

SUMMARYLyme borreliosis or Lyme disease is the most frequently reported tick-borne disease in the Northern Hemisphere. In countries of the Southern Hemisphere, such as Brazil, since the early 1990s, some researchers have argued for the existence of an autochthonous Lyme-like borreliosis, known locally as the Baggio-Yoshinari syndrome (BYS), an alleged "Brazilian borreliosis" supposedly caused by a different strain of Borrelia burgdorferi and transmitted by hard ticks. Currently, the existence of BYS in Brazil is still accepted by a large part of the human health care workers, scientists, medical societies, and patients. In fact, this alleged "Brazilian borreliosis" has been the tick-borne zoonotic disease with the greatest number of reported cases and published studies in Brazil during this century, second only to Brazilian spotted fever. In this manuscript, we reviewed all manuscripts directly related to BYS that have been published in Brazil during the last 35 years. This analysis included 199 individual human cases that have been reported in Brazil since 1989, plus multiple studies on ticks, domestic, and wild animals. Our revision aimed to provide a critical opinion on whether the current published works allow healthcare workers, public health agencies, and patients to accept the existence of Lyme disease, BYS, or other Lyme borreliosis-related disease in Brazil. For this purpose, we evaluated the strengths and weaknesses of each published study, considering the diagnostic methods used, such as serological, microbiological, and molecular analyses. Based on these evaluations, we conclude that there is not enough evidence to support the occurrence of Lyme borreliosis in Brazil or that BYS (Brazilian Lyme-like disease) is caused by a bacterium of the genus Borrelia. This assumption is based on the inaccuracy, unreliability, and misinterpretation of the different diagnostic methods that have been used in Brazil. Recognizing the lack of technical evidence for the occurrence of Lyme borreliosis in Brazil has highly relevant implications. For example, it becomes imperative to raise awareness among the country's medical profession, as they have adopted unnecessary and extreme therapies recommended for patients with a supposed borrelial infection, including BYS, in Brazil. Finally, the technical analyses carried out in this study could be applied to other countries in the Southern Hemisphere (e.g., Argentina, South Africa, Australia), where cases classified and alleged as Lyme disease have been reported.

Options and considerations for validation of prokaryotic names under the SeqCode

Stable taxon names for Bacteria and Archaea are essential for capturing and documenting prokaryotic diversity. They are also crucial for scientific communication, effective accumulation of biological data related to the taxon names and for developing a comprehensive understanding of prokaryotic evolution. However, after more than a hundred years, taxonomists have succeeded in valid publication of only around 30 000 species names, based mostly on pure cultures under the International Code of Nomenclature of Prokaryotes (ICNP), out of the millions estimated to reside in the biosphere. The vast majority of prokaryotic species have not been cultured and are becoming increasingly known to us via culture-independent sequence-based approaches. Until recently, such taxa could only be addressed nomenclaturally via provisional names such as Candidatus or alphanumeric identifiers. Here, we present options and considerations to facilitate validation of names for these taxa using the recently established Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Community engagement and participation of relevant taxon specialists are critical and encouraged for the success of endeavours to formally name the uncultured majority.

Harmonious naming across nomenclature codes exemplified by the description of bacterial isolates from the mammalian gut

A dual system for naming prokaryotes is currently in place based on the well-established International Code of Nomenclature of Prokaryotes (ICNP) and the newly created Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Whilst recent creation of the SeqCode opened an avenue to accelerate the naming of uncultured taxa, the existence of two codes increases the risk of species being assigned multiple validly published names. In this work we present a workflow that aims to limit conflicts by firstly naming novel cultured taxa under the SeqCode, and secondly under the ICNP, enhancing the traceability of the taxa across the two codes. To exemplify this workflow, we describe four novel taxa isolated from the intestine of pigs: Intestinicryptomonas porci gen. nov., sp. nov. (strain CLA-KB-P66T, genome accession GCA_033971905.1TS) within a novel family, Intestinicryptomonaceae; Grylomicrobium aquisgranensis gen. nov., sp. nov. (CLA-KB-P133T, GCA_033971865.1TS); Absicoccus intestinalis sp. nov. (CLA-KB-P134T, GCA_033971885.1TS); and Mesosutterella porci sp. nov. (oilRF-744- wt-GAM-9T, GCF_022134585.1TS).

The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes

The naming of prokaryotes is governed by the International Code of Nomenclature of Prokaryotes (ICNP) and partially by the International Code of Nomenclature for Algae, Fungi and Plants (ICN). Such codes must be able to determine names of taxa in a universal and unambiguous manner, thus serving as a common language across different fields and activities. This unity is undermined when a new code of nomenclature emerges that overlaps in scope with an established, time-tested code and uses the same format of names but assigns different nomenclatural status values to the names. The resulting nomenclatural confusion is not beneficial to the wider scientific community. Such ambiguity is expected to result from the establishment of the 'Code of Nomenclature of Prokaryotes Described from DNA Sequence Data' ('SeqCode'), which is in general and specific conflict with the ICNP and the ICN. Shortcomings in the interpretation of the ICNP may have exacerbated the incompatibility between the codes. It is reiterated as to why proposals to accept sequences as nomenclatural types of species and subspecies with validly published names, now implemented in the SeqCode, have not been implemented by the International Committee on Systematics of Prokaryotes (ICSP), which oversees the ICNP. The absence of certain regulations from the ICNP for the naming of as yet uncultivated prokaryotes is an acceptable scientific argument, although it does not justify the establishment of a separate code. Moreover, the proposals rejected by the ICSP are unnecessary to adequately regulate the naming of uncultivated prokaryotes. To provide a better service to the wider scientific community, an alternative proposal to emend the ICNP is presented, which would result in Candidatus names being regulated analogously to validly published names. This proposal is fully consistent with previous ICSP decisions, preserves the essential unity of nomenclature and avoids the expected nomenclatural confusion.

How, not if, is the question mycologists should be asking about DNA-based typification

Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings challenge the present stance of some in the mycological community - that the current situation is satisfactory and that no change is needed to "the code" - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.

Naming new taxa of prokaryotes in the 21st century

The nomenclature of prokaryotes is regulated by the rules of the International Code of Nomenclature of Prokaryotes (ICNP) and is based on the Linnaean binomial system. The current rules of the Code only cover the nomenclature of the cultivated minority. Proposals to incorporate the uncultivated majority of bacteria and archaea under the rules of the Code were recently rejected by the International Committee on Systematics of Prokaryotes. The provisional rank of Candidatus can be used to name uncultivated prokaryotes whose names cannot be validly published under the rules of the ICNP, but their names can now be validated under the Code of Nomenclature of Prokaryotes Described from Sequence Data (the SeqCode), which was recently established to cover the nomenclature of the uncultivated majority. Metagenomics, single-cell genomics, and high-throughput cultivation techniques have led to a flood of new organisms currently waiting to be named. Automated programs such as GAN and Protologger can assist researchers in naming and describing newly discovered prokaryotes, cultivated as well as uncultivated. However, Latin and Greek skills remain indispensable for proper quality control of names that must meet the standards set by the codes of nomenclature.

Collection and curation of prokaryotic genome assemblies from type strains at NCBI

The public sequence databases are entrusted with the dual responsibility of providing an accessible archive to all submitters and supporting data reliability and its re-use to all users. Genomes from type materials can act as an unambiguous reference for a taxonomic name and play an important role in comparative genomics, especially for taxon verification or reclassification. The National Center for Biotechnology Information (NCBI) collects and curates information on prokaryotic type strains and genomes from type strains. The average nucleotide identity (ANI)-based quality control processes introduced at NCBI to verify the genomes from type strains and improve related sequence records are detailed here. Using the curated genomes from type strains as reference, the taxonomy of over 1.1 million GenBank genomes were verified and the taxonomy of over 7000 new submissions before acceptance to GenBank and over 1800 existing genomes in GenBank were reclassified.

Status of the SeqCode in the International Journal of Systematic and Evolutionary Microbiology

The recent publication of an alternative nomenclatural code that targets prokaryotes, the Code of Nomenclature of Prokaryotes Described from DNA Sequence Data (SeqCode), raises questions about how to treat names 'validly published' under that code in the International Journal of Systematic and Evolutionary Microbiology (IJSEM). Here, it is reiterated that the IJSEM must function in accordance with the International Code of Nomenclature of Prokaryotes (ICNP). It is also reiterated that the ICNP covers all prokaryotes and that it accordingly assigns a nomenclatural status to all names of prokaryotic taxa. This implies that the ICNP also assigns a status to names that are only 'validly published' under the SeqCode. It follows that the IJSEM must treat such names as not validly published, since 'validly published under the SeqCode' is not a nomenclatural status, under the ICNP. Such names should be marked accordingly as Candidatus names or printed in quotation marks. The same measures would need to be taken by other journals which intend to adhere to the ICNP.

Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type

Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.

Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database

Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.

It is time for a new type of type to facilitate naming the microbial world

Since January 1, 2001, the only acceptable nomenclatural type for species under the International Code of Nomenclature of Prokaryotes (ICNP) has been pure cultures. Here, we argue that this requirement is discordant with the more inclusive nature of nomenclatural types accepted under other codes of nomenclature and posit that the unique rigidity of the ICNP has failed to serve the broad research community and has stifled progress. This case is based on the axiom that many archaea and bacteria are interdependent in nature and therefore difficult, if not impossible, to grow, preserve, and distribute as pure cultures. As such, a large proportion of Earth's biodiversity cannot be named under the current system, which limits our ability to communicate about microbial diversity within and beyond the microbiology research community. Genome sequence data are now encouraged for valid publication of new taxa in microbial systematics journals, and metagenome-assembled genomes and single cell-amplified genomes are being generated rapidly from every biome on Earth. Thus, genome sequences are available for both cultivated and uncultivated microorganisms and can readily serve as a new category of nomenclatural type, allowing for a unified nomenclature for all archaea and bacteria, whether or not they are available as pure cultures. Ideally this would be under a single code of nomenclature but, as we review here, the newly established SeqCode will operate in parallel with the ICNP as a first step toward this goal.