Genomic and phylogenomic insights into the family Streptomycetaceae lead to the proposal of six novel genera

The family Streptomycetaceae is a large and diverse family within the phylum Actinomycetota . The members of the family are known for their ability to produce medically important secondary metabolites, notably antibiotics. In this study, 19 type strains showing low 16S rRNA gene similarity (<97.3 %) to other members of the family Streptomycetaceae were identified and their high genetic diversity was reflected in a phylogenomic analysis using conserved universal proteins. This analysis resulted in the identification of six distinct genus-level clades, with two separated from the genus Streptacidiphilus and four separated from the genus Streptomyces . Compared with members of the genera Streptacidiphilus and Streptomyces , average amino acid identity (AAI) analysis of the novel genera identified gave values within the range of 63.9–71.3 %, as has been previously observed for comparisons of related but distinct bacterial genera. The whole-genome phylogeny was reconstructed using PhyloPhlAn 3.0 based on an optimized subset of conserved universal proteins, the results of AAI and percentage of conserved proteins (POCP) analyses indicated that these phylogenetically distinct taxa may be assigned to six novel genera, namely Actinacidiphila gen. nov., Mangrovactinospora gen. nov., Peterkaempfera gen. nov., Phaeacidiphilus gen. nov., Streptantibioticus gen. nov. and Wenjunlia gen. nov.

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.

Out with the old and in with the new: time to rethink twentieth century chemotaxonomic practices in bacterial taxonomy

Chemotaxonomic methods played an important role in the development of the polyphasic approach to classification of Archaea and Bacteria. However, we here argue that routine application of these methods is unnecessary in an era when genomic data are available and sufficient for species delineation. Thus, authors who choose not to utilize such methods should not be forced to do so during the peer review and editorial handling of manuscripts describing novel species. Instead, we argue that chemotaxonomy will thrive if improved analytical methods are introduced and deployed, primarily by specialist laboratories, in studies at taxonomic levels above the characterisation of novel species.

Opinion: Response to concerns about the use of DNA sequences as types in the nomenclature of prokaryotes

In the current Opinion we respond to the major concerns by Bisgaard et al. (2019) and Overmann et al. (2019) and conclude that the adoption of sequences as types for the names of prokaryotes will allow for improvements of the taxonomic framework, increased stability of names derived from robust phylogenomic methods, and enable a full circumscription of the microbial world rather than just the cultivated minority.

Proposal of the suffix -ota to denote phyla. Addendum to 'Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes'

As an addendum to the earlier proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes (Oren et al., Int J Syst Evol Microbiol 2015;65:4284-4287) we propose the suffix -ota to denote phyla, replacing the somewhat awkward -aeota. We therefore present a new draft modified version of Rule 8 of the International Code of Nomenclature of Prokaryotes and a corrected list of names of phyla to be considered for validation after approval of the proposal to include the rank of phylum in the Code.

Two novel species of rapidly growing mycobacteria: Mycobacterium lehmannii sp. nov. and Mycobacterium neumannii sp. nov

Two rapidly growing mycobacteria with identical 16S rRNA gene sequences were the subject of a polyphasic taxonomic study. The strains formed a well-supported subclade in the mycobacterial 16S rRNA gene tree and were most closely associated with the type strain of Mycobacterium novocastrense. Single and multilocus sequence analyses based on hsp65, rpoB and 16S rRNA gene sequences showed that strains SN 1900^T and SN 1904^T are phylogenetically distinct but share several chemotaxonomic and phenotypic features that are are consistent with their classification in the genus Mycobacterium. The two strains were distinguished by their different fatty acid and mycolic acid profiles, and by a combination of phenotypic features. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values for strains SN 1900^T and SN 1904^T were 61.0 % and 94.7 %, respectively; in turn, the corresponding dDDH and ANI values with M. novocastrense DSM 44203^T were 41.4 % and 42.8 % and 89.3 % and 89.5 %, respectively. These results show that strains SN1900^T and SN 1904^T form new centres of taxonomic variation within the genus Mycobacterium. Consequently, strains SN 1900^T (40^T=CECT 8763^T=DSM 43219^T) and SN 1904^T (2409^T=CECT 8766^T=DSM 43532^T) are considered to represent novel species, for which the names Mycobacteriumlehmannii sp. nov. and Mycobacteriumneumannii sp. nov. are proposed. A strain designated as 'Mycobacteriumacapulsensis' was shown to be a bona fide member of the putative novel species, M. lehmannii.

Mycobacterium eburneum sp. nov., a non-chromogenic, fast-growing strain isolated from sputum

A polyphasic study was undertaken to establish the taxonomic position of a non-chromogenic, rapidly growing Mycobacterium strain that had been isolated from sputum. The strain, CECT 8775T, has chemotaxonomic and cultural properties consistent with its classification in the genus Mycobacterium and was distinguished from the type strains of closely related mycobacterial species, notably from Mycobacterium paraense DSM 46749T, its nearest phylogenetic neighbour, based on 16S rRNA, hsp65 and rpoB gene sequence data. These organisms were also distinguished by a broad range of chemotaxonomic and phenotypic features and by a digital DNA-DNA relatedness value of 22.8 %. Consequently, the strain is considered to represent a novel species of Mycobacterium for which the name Mycobacterium eburneum sp. nov is proposed; the type strain is X82T (CECT 8775T=DSM 44358T).

Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes

The International Code of Nomenclature of Prokaryotes covers the nomenclature of prokaryotes up to the rank of class. We propose here modifying the Code to include the rank of phylum so that names of phyla that fulfil the rules of the Code will obtain standing in the nomenclature.

Gram-positive bacterial lipoglycans based on a glycosylated diacylglycerol lipid anchor are microbe-associated molecular patterns recognized by TLR2

Innate immune recognition is the first line of host defense against invading microorganisms. It is a based on the detection, by pattern recognition receptors (PRRs), of invariant molecular signatures that are unique to microorganisms. TLR2 is a PRR that plays a major role in the detection of Gram-positive bacteria by recognizing cell envelope lipid-linked polymers, also called macroamphiphiles, such as lipoproteins, lipoteichoic acids and mycobacterial lipoglycans. These microbe-associated molecular patterns (MAMPs) display a structure based on a lipid anchor, being either an acylated cysteine, a glycosylated diacylglycerol or a mannosyl-phosphatidylinositol respectively, and having in common a diacylglyceryl moiety. A fourth class of macroamphiphile, namely lipoglycans, whose lipid anchor is made, as for lipoteichoic acids, of a glycosylated diacylglycerol unit rather than a mannosyl-phosphatidylinositol, is found in Gram-positive bacteria and produced by certain Actinobacteria, including Micrococcus luteus, Stomatococcus mucilaginosus and Corynebacterium glutamicum. We report here that these alternative lipoglycans are also recognized by TLR2 and that they stimulate TLR2-dependant cytokine production, including IL-8, TNF-α and IL-6, and cell surface co-stimulatory molecule CD40 expression by a human macrophage cell line. However, they differ by their co-receptor requirement and the magnitude of the innate immune response they elicit. M. luteus and S. mucilaginosus lipoglycans require TLR1 for recognition by TLR2 and induce stronger responses than C. glutamicum lipoglycan, sensing of which by TLR2 is dependent on TLR6. These results expand the repertoire of MAMPs recognized by TLR2 to lipoglycans based on a glycosylated diacylglycerol lipid anchor and reinforce the paradigm that macroamphiphiles based on such an anchor, including lipoteichoic acids and alternative lipoglycans, induce TLR2-dependant innate immune responses.

Mannan chain length controls lipoglycans signaling via and binding to TLR2

TLR2 is a pattern-recognition receptor that is activated by a large variety of conserved microbial components, including lipoproteins, lipoteichoic acids, and peptidoglycan. Lipoglycans are TLR2 agonists found in some genera of the phylogenetic order Actinomycetales, including Mycobacterium. They are built from a mannosyl-phosphatidyl-myo-inositol anchor attached to a (alpha1-->6)-linked d-mannopyranosyl chain whose units can be substituted by d-mannopyranosyl and/or d-arabinofuranosyl units. At this time, little is known about the molecular bases underlying their ability to induce signaling via this receptor. We have recently shown that the anchor must be at least triacylated, including a diacylglyceryl moiety, whereas the contribution of the glycosidic moiety is not yet clearly defined. We show herein that lipoglycan activity is directly determined by mannan chain length. Indeed, activity increases with the number of units constituting the (alpha1-->6)-mannopyranosyl backbone but is also critically dependent on the substitution type of the 2-hydroxyl of these units. We thus provide evidence for the definition of a new pattern that includes the nonlipidic moiety of the molecules, most probably as a result of the (alpha1-->6)-mannopyranosyl backbone being a highly conserved structural feature among lipoglycans. Moreover, we demonstrate that lipoglycans can bind cell surface-expressed TLR2 and that their ability to induce signaling might be, at least in part, dictated by their avidity for the receptor. Finally, our data suggest that lipoglycans and lipoproteins have a common binding site. The present results are thus discussed in the light of the recently published crystal structure of a TLR1-TLR2-lipopeptide complex.

Tuberculosis: an under-diagnosed aetiological agent in uveitis with an effective treatment

PURPOSE

To highlight the diversity of clinical presentations with tubercular uveitis in a nonendemic setting, and discuss the diagnostic approach and an effective treatment.

METHOD

Descriptive case series.

RESULTS

A total of 12 cases of varied presentations of tubercular uveitis diagnosed over a period of 1 year of which six cases are described in detail. Presentations included choroidal tuberculomas, multifocal choroiditis, recurrent granulomatous uveitis, panuveitis with cystoid macular oedema, and serpiginous choroiditis. All cases had a chronic or recurrent course and responded very well to antitubercular treatment. Diagnosis was mainly assisted by positive tuberculin testing.

CONCLUSION

A high index of suspicion helps diagnose ocular tuberculosis in areas of low prevalence of the disease. It forms part of the differential diagnosis of any chronic or recurrent uveitis, especially in an at-risk patient. Antitubercular treatment seems highly effective.

Prevotella marshii sp. nov. and Prevotella baroniae sp. nov., isolated from the human oral cavity

Eleven strains of anaerobic Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise two homogeneous groups, designated E2 and E4. 16S rRNA gene sequence analysis revealed that members of both groups belonged to the genus Prevotella but were distinct from any species with validly published names. This distinction was confirmed by DNA–DNA hybridization and phenotypic tests. Two novel species are therefore proposed: Prevotella marshii sp. nov. (group E2) and Prevotella baroniae (group E4). Both species are saccharolytic; the end-products of fermentation for P. marshii are acetic, propionic and succinic acids, while P. baroniae produces acetic and succinic acids with minor amounts of isovaleric and isobutyric acids. The G+C content of the DNA of the type strain of Prevotella marshii is 51 mol% and that of Prevotella baroniae is 52 mol%. The type strain for P. marshii is E9.34T (=DSM 16973T=CCUG 50419T) and that for P. baroniae is E9.33T (=DSM 16972T=CCUG 50418T).

The cell wall of the pathogenic bacterium Rhodococcus equi contains two channel-forming proteins with different properties

We have identified in organic solvent extracts of whole cells of the gram-positive pathogen Rhodococcus equi two channel-forming proteins with different and complementary properties. The isolated proteins were able to increase the specific conductance of artificial lipid bilayer membranes made from phosphatidylcholine-phosphatidylserine mixtures by the formation of channels able to be permeated by ions. The channel-forming protein PorA(Req) (R. equi pore A) is characterized by the formation of cation-selective channels, which are voltage gated. PorA(Req) has a single-channel conductance of 4 nS in 1 M KCl and shows high permeability for positively charged solutes because of the presence of negative point charges. According to the results of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), the protein has an apparent molecular mass of about 67 kDa. The analysis (using the effect of negative charges on channel conductance) of the concentration dependence of the single-channel conductance suggested that the diameter of the cell wall channel is about 2.0 nm. The second channel (formed by PorB(Req) [R. equi pore B]) shows a preferred movement of anions through the channel and is not voltage gated. This channel shows a single-channel conductance of 300 pS in 1 M KCl and is characterized by the presence of positive point charges in or near the channel mouth. Based on SDS-PAGE, the apparent molecular mass of the channel-forming protein is about 11 kDa. Channel-forming properties of the investigated cell wall porins were compared with those of others isolated from mycolic acid-containing actinomycetes. We present here the first report of a fully characterized anion-selective cell wall channel from a member of the order Actinomycetales.

Satisfaction with communication, medical knowledge, and coping style in patients with metastatic cancer

Interviews were conducted with 77 patients aged 19-84, admitted to a medical oncology ward for assessment and modification of treatment. Satisfaction with information provided about tests, symptoms and treatment was assessed, together with satisfaction with care in general, factual knowledge concerning cancer and other medical conditions, and anxiety. Habitual style of coping with stress by information-seeking vs avoidance was measured using the Miller Behavioral Style Scale. Satisfaction levels were generally high. Patients reporting the highest level of satisfaction with information were more avoidant in their coping style than the remainder, and were also less anxious. Factual knowledge about cancer was in contrast greater among patients who were less satisfied with communication. These patterns were not dependent on age or education. It is argued that satisfaction with communication in medical settings is not a simple function of communication skills and the provision of adequately structured information, but that patients' tendencies to cope with stress by seeking out or avoiding information need to be taken into account.