Bypassing Cultivation To Identify Bacterial Species

Rodriguez-R, Luis M.; Konstantinidis, Konstantinos T.

doi:10.1128/microbe.9.111.1

Cited by 553 publications

(506 citation statements)

References 7 publications

Supporting

Mentioning

463

Contrasting

Unclassified

Order By: Relevance

“…The three genomes exhibited a high average nucleotide identity (ANI)18 and average amino acid identity (AAI)19, which also support similar physiological patterns in both isolates: strains S5 and PM4 had 98.8% ANI, while ANI of both isolates with ‘G-plasma’ genome were about 98.7 and 98.4%, respectively, pointing at their similar evolutionary trajectories despite transcontinental localisation of their niches and highly complementary microbial structure and gene pools in AMD settings1 (also s. Fig. S1 for the AAI data).…”

Section: Resultsmentioning

confidence: 99%

Biology of archaea from a novel family Cuniculiplasmataceae (Thermoplasmata) ubiquitous in hyperacidic environments

Golyshina

Kublanov

Tran

et al. 2016

Sci Rep

View full text Add to dashboard Cite

The order Thermoplasmatales (Euryarchaeota) is represented by the most acidophilic organisms known so far that are poorly amenable to cultivation. Earlier culture-independent studies in Iron Mountain (California) pointed at an abundant archaeal group, dubbed ‘G-plasma’. We examined the genomes and physiology of two cultured representatives of a Family Cuniculiplasmataceae, recently isolated from acidic (pH 1–1.5) sites in Spain and UK that are 16S rRNA gene sequence-identical with ‘G-plasma’. Organisms had largest genomes among Thermoplasmatales (1.87–1.94 Mbp), that shared 98.7–98.8% average nucleotide identities between themselves and ‘G-plasma’ and exhibited a high genome conservation even within their genomic islands, despite their remote geographical localisations. Facultatively anaerobic heterotrophs, they possess an ancestral form of A-type terminal oxygen reductase from a distinct parental clade. The lack of complete pathways for biosynthesis of histidine, valine, leucine, isoleucine, lysine and proline pre-determines the reliance on external sources of amino acids and hence the lifestyle of these organisms as scavengers of proteinaceous compounds from surrounding microbial community members. In contrast to earlier metagenomics-based assumptions, isolates were S-layer-deficient, non-motile, non-methylotrophic and devoid of iron-oxidation despite the abundance of methylotrophy substrates and ferrous iron in situ, which underlines the essentiality of experimental validation of bioinformatic predictions.

show abstract

Section: Resultsmentioning

confidence: 99%

Biology of archaea from a novel family Cuniculiplasmataceae (Thermoplasmata) ubiquitous in hyperacidic environments

Golyshina

Kublanov

Tran

et al. 2016

Sci Rep

View full text Add to dashboard Cite

show abstract

“…It has been proposed that AAI derived from the conserved genes should be incorporated into prokaryotic taxonomy as AAI provides more robust resolution than ANI between divergent strains4748. The AAI thresholds from the 255 core genes are 87.8% and 98.41% for separating potential genera and species, respectively.…”

Section: Discussionmentioning

confidence: 99%

Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

Sangal

Goodfellow

Jones

et al. 2016

Sci Rep

108

View full text Add to dashboard Cite

Prokaryotic systematics provides the fundamental framework for microbiological research but remains a discipline that relies on a labour- and time-intensive polyphasic taxonomic approach, including DNA-DNA hybridization, variation in 16S rRNA gene sequence and phenotypic characteristics. These techniques suffer from poor resolution in distinguishing between closely related species and often result in misclassification and misidentification of strains. Moreover, guidelines are unclear for the delineation of bacterial genera. Here, we have applied an innovative phylogenetic and taxogenomic approach to a heterogeneous actinobacterial taxon, Rhodococcus, to identify boundaries for intrageneric and supraspecific classification. Seven species-groups were identified within the genus Rhodococcus that are as distantly related to one another as they are to representatives of other mycolic acid containing actinobacteria and can thus be equated with the rank of genus. It was also evident that strains assigned to rhodococcal species-groups are underspeciated with many misclassified using conventional taxonomic criteria. The phylogenetic and taxogenomic methods used in this study provide data of theoretical value for the circumscription of generic and species boundaries and are also of practical significance as they provide a robust basis for the classification and identification of rhodococci of agricultural, industrial and medical/veterinary significance.

show abstract

“…Predicted proteins were also re-analysed by both the BlastKOALA tool, to investigate the central and energy metabolic pathways 55 , and single DIAMOND searches on the nr database 56 , to refine the affiliations and functions of specific proteins belonging to sulfur and nitrogen metabolism. Analyses of average nucleotide identities and average amino acid identities were carried out using an online calculator provided by the Kostas Lab website 57 . Further confirmation of the phylogenetic assignment was carried out using the Kaiju webserver 58 , to assess the taxonomic affiliation of the contigs within the genome bin 11 against the complete set of bacterial and archaeal genomes.…”

Section: Phylogenomic Comparisonmentioning

confidence: 99%

A submarine volcanic eruption leads to a novel microbial habitat

et al. 2017

View full text Add to dashboard Cite

Submarine volcanic eruptions are major catastrophic events that allow investigation of the colonization mechanisms of newly formed seabed. We explored the seafloor after the eruption of the Tagoro submarine volcano off El Hierro Island, Canary Archipelago. Near the summit of the volcanic cone, at about 130 m depth, we found massive mats of long, white filaments that we named Venus's hair. Microscopic and molecular analyses revealed that these filaments are made of bacterial trichomes enveloped within a sheath and colonized by epibiotic bacteria. Metagenomic analyses of the filaments identified a new genus and species of the order Thiotrichales, Thiolava veneris. Venus's hair shows an unprecedented array of metabolic pathways, spanning from the exploitation of organic and inorganic carbon released by volcanic degassing to the uptake of sulfur and nitrogen compounds. This unique metabolic plasticity provides key competitive advantages for the colonization of the new habitat created by the submarine eruption. A specialized and highly diverse food web thrives on the complex three-dimensional habitat formed by these microorganisms, providing evidence that Venus's hair can drive the restart of biological systems after submarine volcanic eruptions.

show abstract

Bypassing Cultivation To Identify Bacterial Species

Abstract: Culture-independent genomic approaches identify credibly distinct clusters, avoid cultivation bias, and provide true insights into microbial species

Cited by 553 publications

References 7 publications

Biology of archaea from a novel family Cuniculiplasmataceae (Thermoplasmata) ubiquitous in hyperacidic environments

Biology of archaea from a novel family Cuniculiplasmataceae (Thermoplasmata) ubiquitous in hyperacidic environments

Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

A submarine volcanic eruption leads to a novel microbial habitat

Contact Info

Product

Resources

About