The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum
but even so there remains a need to further clarify relationships ...within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
A genome-based polyphasic study was undertaken to establish the taxonomic status of an actinobacterium strain isolated from an actinorhizal root nodule. Strain ncl1
T
was found to have ...chemotaxonomic, cultural and morphological properties characteristic of members of the genus
Nocardia
. The strain was closely related to
Nocardia aurea
in the phylogenetic trees based on 16S rRNA gene and genome sequences. The draft genome of the strain is 8.9 Mbp in size, has a genomic DNA G + C content of 67.0% and was predicted to contain at least 19 biosynthetic gene clusters encoding for specialized metabolites. Strain ncl1
T
was distinguished from its closest neighbour,
N. aurea
DSM 103986
T
, by a broad range of phenotypic properties and by low average nucleotide identity and digital DNA-DNA hybridization scores. Consequently, the strain represents a novel
Nocardia
species for which the name
Nocardia noduli
sp. nov. is proposed. The type strain is ncl1
T
(CECT 30123
T
= DSM 110878
T
). The present study provides further evidence that actinorhizal nodules are a source of novel species of
Nocardia
.
Prokaryotic systematics is one of the most progressive disciplines that has embraced technological advances over the last century. The availability and affordability of new sequencing technologies ...and user-friendly software have revolutionised the discovery of novel prokaryotic taxa, including the identification and nomenclature of uncultivable microorganisms. These advances have enabled scientists to resolve the structure of complex heterogenous taxon and to rectify taxonomic status of misclassified strains due to errors associated with the sensitivity and/or reproducibility of phenotypic approaches. Time- and labour-intensive experimental characterisation of strains could be replaced with determining the presence or absence of genes or operons responsible for phenotypic and chemotaxonomic properties, such as the presence of mycolic acids and menaquinones. However, the quality of genomic data must be acceptable and phylogenomic threshold values for interspecies and supraspecies delineation should be carefully considered in combination of genome-based phylogeny for a reliable and robust classification. These technological developments have empowered prokaryotic systematists to reliably identify novel taxa with an understanding of community ecology and their biosynthetic and biodegradation potentials.
Recent studies highlighted the biosynthetic potential of nocardiae to produce diverse novel natural products comparable to that of Streptomyces, thereby making them an attractive source of new drug ...leads. Many of the 119 Nocardia validly named species were isolated from natural habitats but little is known about the diversity and the potential of the endophytic nocardiae of root nodule of actinorhizal plants.
The taxonomic status of an actinobacterium strain, designated ncl2
, was established in a genome-based polyphasic study. The strain was Gram-stain-positive, produced substrate and aerial hyphae that fragmented into coccoid and rod-like elements and showed chemotaxonomic properties that were also typical of the genus Nocardia. It formed a distinct branch in the Nocardia 16S rRNA gene tree and was most closely related to the type strains of Nocardia nova (98.6%), Nocardia jiangxiensis (98.4%), Nocardia miyuensis (97.8%) and Nocardia vaccinii (97.7%). A comparison of the draft genome sequence generated for the isolate with the whole genome sequences of its closest phylogenetic neighbours showed that it was most closely related to the N. jiangxiensis, N. miyuensis and N. vaccinii strains, a result underpinned by average nucleotide identity and digital DNA-DNA hybridization data. Corresponding taxogenomic data, including those from a pan-genome sequence analysis showed that strain ncl2
was most closely related to N. vaccinii DSM 43285
. A combination of genomic, genotypic and phenotypic data distinguished these strains from one another. Consequently, it is proposed that strain ncl2
(= DSM 110931
= CECT 30122
) represents a new species within the genus Nocardia, namely Nocardia alni sp. nov. The genomes of the N. alni and N. vaccinii strains contained 36 and 29 natural product-biosynthetic gene clusters, respectively, many of which were predicted to encode for a broad range of novel specialised products, notably antibiotics. Genome mining of the N. alni strain and the type strains of its closest phylogenetic neighbours revealed the presence of genes associated with direct and indirect mechanisms that promote plant growth. The core genomes of these strains mainly consisted of genes involved in amino acid transport and metabolism, energy production and conversion and transcription.
Our genome-based taxonomic study showed that isolate ncl2
formed a new centre of evolutionary variation within the genus Nocardia. This novel endophytic strain contained natural product biosynthetic gene clusters predicted to synthesize novel specialised products, notably antibiotics and genes associated with the expression of plant growth promoting compounds.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Over the last few decades, a wealth of evidence has formed the basis for “the Old Friends hypothesis” suggesting that, in contrast to the past, increasingly people are living in environments with ...limited and less diverse microbial exposure, with potential consequences for their health. Hence, including safe live or heat‐killed microbes in the diet may be beneficial in promoting and maintaining human health. In order to assess the safety of microbes beyond the current use of standardized cultures and probiotic supplements, new approaches are being developed. Here, we present evidence for the safety of heat‐killed Mycolicibacterium aurum Aogashima as a novel food, utilizing the decision tree approach developed by Pariza and colleagues (2015). We provide evidence that the genome of M. aurum Aogashima is free of (1) genetic elements associated with pathogenicity or toxigenicity, (2) transferable antibiotic resistance gene DNA, and (3) genes coding for antibiotics used in human or veterinary medicine. Moreover, a 90‐day oral toxicity study in rats showed that (4) the no observed adverse effect level (NOAEL) was the highest concentration tested, namely 2000 μg/kg BW/day. We conclude that oral consumption of heat‐killed M. aurum Aogashima is safe and warrants further evaluation as a novel food ingredient.
blurb for etocThere is growing realization of the health benefits of restoring human exposure to a more diverse range of microbes than we experience in increasingly urbanized lifestyles. In addition to probiotics, other environmental nonpathogenic organisms, such as environmental saprophytic nontuberculous (NTB) mycobacteria species, were once commonly present in the human diet. Here, we present evidence for the safety of heat‐killed Mycolicibacterium aurum Aogashima as a novel food, utilizing the decision tree approach developed by Pariza and colleagues (2015).
The taxonomic status, biotechnological and ecological potential of several Micromonospora strains isolated from an extreme hyper arid Atacama Desert soil were determined. Initially, a polyphasic ...study was undertaken to clarify the taxonomic status of five micromonosporae, strains LB4, LB19, LB32
, LB39
and LB41, isolated from an extreme hyper-arid soil collected from one of the driest regions of the Atacama Desert. All of the isolates were found to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus Micromonospora. Isolates LB32
and LB39
were distinguished from their nearest phylogenetic neighbours and proposed as new species, namely as Micromonospora arida sp. nov. and Micromonospora inaquosa sp. nov., respectively. Eluted methanol extracts of all of the isolates showed activity against a panel of bacterial and fungal indicator strains, notably against multi-drug resistant Klebsiella pneumoniae ATCC 700603 while isolates LB4 and LB41 showed pronounced anti-tumour activity against HepG2 cells. Draft genomes generated for the isolates revealed a rich source of novel biosynthetic gene clusters, some of which were unique to individual strains thereby opening up the prospect of selecting especially gifted micromonosporae for natural product discovery. Key stress-related genes detected in the genomes of all of the isolates provided an insight into how micromonosporae adapt to the harsh environmental conditions that prevail in extreme hyper-arid Atacama Desert soils.
This study was designed to determine the plant growth promoting (PGP) potential of members of the genus
. To this end, the genomes of 21 representative strains were examined for genes associated ...directly or indirectly with plant growth. All of the
genomes contained genes that encoded for products associated with the biosynthesis of auxins indole-3-glycerol phosphate synthases, anthranilate phosphoribosyltransferases (
D), anthranilate synthases, and aminases (
A and B), cytokinins (11 well-conserved genes within the predicted biosynthetic gene cluster), siderophores, and nitrogenases (
operon except for atypical
) as well as genes that modulate the effects of biotic and abiotic environmental stress (e.g., alkyl hydroperoxide reductases, aquaporin Z, heat shock proteins). In contrast, other genes were associated with strains assigned to one or more of four host-specific clusters. The genes encoding for phosphate solubilization (e.g., low-affinity inorganic phosphate transporters) and lytic enzymes (e.g., cellulases) were found in
cluster 1 genomes, while other genes were found only in cluster 3 genomes (e.g., alkaline phosphatases, extracellular endoglucanases, pectate lyases) or cluster 4 and subcluster 1c genomes (e.g., NAD(P) transhydrogenase genes). Genes encoding for chitinases were found only in the genomes of the type strains of
,
,
, and
. In short, these
genome analyses provide an insight into the PGP abilities of
strains of known taxonomic provenance. This is the first study designed to establish the underlying genetic basis of cytokinin production in
strains. Also, the discovery of additional genes in the biosynthetic gene cluster involved in cytokinin production opens up the prospect that
may have novel molecular mechanisms for cytokinin biosynthesis.
Advanced physicochemical and chemical absorption methods for chlorinated ethenes are feasible but incur high costs and leave traces of pollutants on the site. Biodegradation of such pollutants by ...anaerobic or aerobic bacteria is emerging as a potential alternative. Several mycobacteria including
L1,
NBB4,
JS60,
NBB3 and
JS623 have previously been described as assimilators of vinyl chloride (VC). In this study, we compared nucleotide sequence of VC cluster and performed a taxogenomic evaluation of these mycobacterial species. The results showed that the complete VC cluster was acquired by horizontal gene transfer and not intrinsic to the genus
. These results also revealed the presence of an additional
F1 gene that seems to be involved in Coenzyme M biosynthesis, which is ultimately used in the VC degradation pathway. Furthermore, we suggest for the first time that S/N-Oxide reductase encoding gene was involved in the dissociation of the SsuABC transporters from the organosulfur, which play a crucial role in the Coenzyme M biosynthesis. Based on genomic data,
L1,
NBB4
JS60,
NBB3 and
JS623 were misclassified and form a novel species within the genus
.
L1
(CECT 8761
= DSM 6695
) was the subject of polyphasic taxonomic studies and showed ANI and dDDH values of 84.7 and 28.5% with its close phylogenetic neighbour,
ATCC 33027
. Phenotypic, chemotaxonomic and genomic data considering strain L1
(CECT 8761
= DSM 6695
) as a type strain of novel species with the proposed name,
sp. nov.
A novel actinobacterial strain, designated NA12
T
, was isolated from coastal sediment sample of Nemrut Lake, a crater lake in eastern Anatolia, Turkey. The taxonomic position of the strain was ...established using a polyphasic approach. Cultural and chemotaxonomic characteristics of the strain were consistent with its classification within the family
Micromonosporaceae
. The 16S rRNA gene sequence analysis of strain NA12
T
showed that the strain closely related to
M. radicis
AZ1-13
T
,
M. zingiberis
PLAI 1-1
T
,
M. craniella
LHW63014
T
and
M. endophytica
202201
T
with pairwise sequence identity values ranging from 99.4 to 99.3%. Digital DNA–DNA hybridization values between strain NA12
T
and the closely related type strains were ranged from 41.0 to 18.3% while the average nucleotide identity values were between 87.3 and 86.5%, which are well below the designed cut-off points of 70 and 95%, respectively. The G + C content of genomic DNA was 71.5%. Whole-cell hydrolysates of strain NA12
T
contained 3-hydroxydiaminopimelic acid and
meso
-diaminopimelic acid. Cell-wall sugars were composed of arabinose, fucose, glucose, mannose, rhamnose and xylose. The polar lipid profile contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, glycophospholipid, amino-phospholipid and two unidentified phospholipids. The predominant menaquinones were MK-9(H
6
) and MK-9(H
4
). Major fatty acids were
iso
-C
16:0
and C
17:1
ω8c. Based upon the consensus of phenotypic and phylogenetic analyses as well as whole genome comparisons, strain NA12
T
(DSM 100982
T
= KCTC 39647
T
) is proposed to represent the type strain of a novel species,
Micromonospora craterilacus
sp. nov.
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