Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons

Frontiers in Microbiology, Год журнала: 2023, Номер 14

Опубликована: Март 7, 2023

In terms of the number and diversity living units, prokaryotic empire is most represented form life on Earth, yet it still to a significant degree shrouded in darkness. This microbial “dark matter” hides great deal potential phylogenetically or metabolically diverse microorganisms, thus important acquire them pure culture. However, do we know what microorganisms really need for their growth, obstacles are cultivation previously unidentified taxa? Here review common sometimes unexpected requirements environmental especially soil-harbored bacteria, needed replication cultivation. These include resuscitation stimuli, physical chemical factors aiding cultivation, growth factors, co-cultivation laboratory natural neighborhood.

Язык: Английский

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Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification

Microbiology Resource Announcements, Год журнала: 2024, Номер 13(4)

Опубликована: Март 4, 2024

ABSTRACT The RDP Classifier is one of the most popular machine learning approaches for taxonomic classification due to its robustness and relatively high accuracy. Both taxonomy have been updated incorporate newly described taxa recent changes prokaryotic nomenclature.

Язык: Английский

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Global diversity of enterococci and description of 18 previously unknown species

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(10)

Опубликована: Фев. 28, 2024

Enterococci are gut microbes of most land animals. Likely appearing first in the guts arthropods as they moved onto land, diversified over hundreds millions years adapting to evolving hosts and host diets. Over 60 enterococcal species now known. Two species,

Язык: Английский

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

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Год журнала: 2024, Номер 74(1)

Опубликована: Янв. 5, 2024

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

Язык: Английский

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

Systematic and Applied Microbiology, Год журнала: 2022, Номер 45(5), С. 126305 - 126305

Опубликована: Июль 20, 2022

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 species, and phylogenomic methods are commonly classification higher taxonomic ranks. Additionally, environmental revealed a vast diversity as-yet-uncultivated taxa. In response to these developments, new code nomenclature, Code Nomenclature Prokaryotes Described from Sequence Data (SeqCode), developed over two years allow naming Archaea Bacteria using DNA sequences as nomenclatural types. SeqCode also allows cultured organisms, including fastidious prokaryotes that cannot be deposited culture collections. Several simplifications relative International (ICNP) implemented make nomenclature more accessible, easier apply readily communicated. By simplifying with goal unified classification, inclusive both uncultured taxa, will facilitate taxa in every biome on Earth, encourage isolation characterization promote synergies between ecological, environmental, physiological, biochemical, molecular biological disciplines describe prokaryotes.

Язык: Английский

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Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Июнь 1, 2023

Abstract Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts Endozoicomonadaceae family. The factors controlling their distribution functional diversity remain, however, poorly known. Here, we study ecology at an ocean basin-scale sampling specimens from three genera ( Pocillopora , Porites Millepora ) 99 reefs 32 islands across Pacific Ocean. analysis 2447 metabarcoding 270 metagenomic samples reveals that each genus harbored a distinct new species . These are composed nine lineages have biogeographic patterns. most common one, found in appears to be globally distributed symbiont with metabolic capabilities, including synthesis amino acids vitamins not produced host. other structured partly host genetic lineage mainly geographic location is more rarely associated Our results show different exhibit strategies host- associations defined bacteria level.

Язык: Английский

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Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes

FEMS Microbiology Letters, Год журнала: 2023, Номер 370

Опубликована: Янв. 1, 2023

Abstract The Genome Taxonomy Database (GTDB) is a taxonomic framework that defines prokaryotic taxa as monophyletic groups in concatenated protein reference trees according to systematic criteria. This has resulted substantial number of changes existing classifications (https://gtdb.ecogenomic.org). In the case union taxa, GTDB names were applied based on priority publication. division or change rank led formation new Latin above genus only made publicly available via website without associated published descriptions. sometimes confusion literature and databases. A provisional later other studies, while many still lack authorships. To reduce further confusion, here we propose descriptions for 329 GTDB-defined 223 which are suitable validation under International Code Nomenclature Prokaryotes (ICNP) 49 described from Sequence Data (SeqCode). For latter, designated 23 genomes type material. An additional 57 do not currently satisfy criteria either code proposed Candidatus.

Язык: Английский

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Cultivation strategies for prokaryotes from extreme environments

iMeta, Год журнала: 2023, Номер 2(3)

Опубликована: Июнь 12, 2023

Abstract The great majority of microorganisms are as‐yet‐uncultivated, mostly found in extreme environments. High‐throughput sequencing provides data‐rich genomes from single‐cell and metagenomic techniques, which has enabled researchers to obtain a glimpse the unexpected genetic diversity “microbial dark matter.” However, cultivating environments remains essential for dissecting utilizing functions extremophiles. Here, we provide straightforward protocol efficiently isolating prokaryotic different habitats (thermal, xeric, saline, alkaline, acidic, cryogenic environments), was established through previous successful work our long‐term experience extremophile resource mining. We propose common processes isolation at first then summarize multiple cultivation strategies recovering meanwhile specific tips that always overlooked but important. Furthermore, use multi‐omics‐guided microbial approaches culturing these as‐yet‐uncultivated two examples provided introduce how work. In summary, allows significantly improve efficiency pure cultures novel taxa, therefore paves way protection utilization resources

Язык: Английский

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First single-strain enrichments of Electrothrix cable bacteria, description of E. aestuarii sp. nov. and E. rattekaaiensis sp. nov., and proposal of a cable bacteria taxonomy following the rules of the SeqCode

Systematic and Applied Microbiology, Год журнала: 2024, Номер 47(1), С. 126487 - 126487

Опубликована: Янв. 1, 2024

Cable bacteria are electrically conductive, filamentous Desulfobulbaceae, which morphologically, functionally, and phylogenetically distinct from the other members of this family. have not been obtained in pure culture were therefore previously described as candidate genera, Candidatus Electrothrix Ca. Electronema; a representative latter is available single-strain sediment enrichment. Here we present an improved workflow to obtain first enrichments report their metagenome-assembled genomes (MAGs) morphology. Based on these results published high-quality MAGs morphological data cable both propose adopt genus names Electronema following rules Code Nomenclature Prokaryotes Described Sequence Data (SeqCode), with communis RBTS aureum GSTS, respectively, nomenclatural types genera. Furthermore, based average nucleotide identity (ANI) values <95% any species, two our three enrichment cultures novel species Electrothrix, E. aestuarii sp. nov. rattekaaiensis nov., according SeqCode.

Язык: Английский

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Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments

Nature Microbiology, Год журнала: 2024, Номер 9(4), С. 964 - 975

Опубликована: Март 22, 2024

Язык: Английский

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