Phylogeny Trumps Chemotaxonomy: A Case Study Involving Turicella otitidis

Genomic and Phenotypic Characterization of Streptomyces sirii sp. nov., Amicetin-Producing Actinobacteria Isolated from Bamboo Rhizospheric Soil

In our large-scale search for antimicrobial-producing bacteria, we isolated an actinomycete strain from rhizospheric soil of Bambusa vulgaris. The strain designated BP-8 showed noticeable antibacterial activity. BP-8 was subjected to a whole-genome analysis via a polyphasic taxonomy approach, and its antibacterial metabolite was identified by HRLS-MS. The results of the physiological and morphological analyses indicated that BP-8 is an aerobic, neutrophilic, mesophilic organism that is tolerant to 8% NaCl and can use a wide range of carbohydrates. It forms curly sporophores with a warty surface. The results of the phylogenetic and average nucleotide identity analyses and in silico DNA-DNA hybridization calculation indicated that BP-8 represents the type strain of a novel Streptomyces species. A comparative in silico analysis of the genome sequences of BP-8 and its closest related strains revealed the presence of genes encoding chemotaxonomic markers characteristic of Streptomyces. The antibacterial compound was identified as amicetin. Genomic mining also revealed more than 10 biosynthetic gene clusters that have not been described previously and may lead to the discovery of new valuable compounds. On the basis of these results, strain BP-8T (=VKM Ac-3066T = CCTCC AA 2024094T) is proposed as the type strain of the novel species Streptomyces sirii sp. nov.

Updating the Relationship Between the Threshold Value of Average Nucleotide Identity and Digital DNA-DNA Hybridization for Reliable Taxonomy of Corynebacterium

Currently, bacterial classification at the species level relies on the 95-96% average nucleotide identity (ANI) value that is known to be equivalent to a 70% digital DNA-DNA hybridization (dDDH) value. However, during the routine identification of bacteria in the uteri of camels with a history of conception failure, we found that four out of the seven strains (2298A, 2569A, 2652, 2571B, 1103A, 2571A, and 335C) could not be assigned to any valid Corynebacterium species. Furthermore, a 70% dDDH value did not correspond to a 95-96% ANI value in strain 2569A. Thus, we aimed to classify these strains and explain the mechanisms underlying gene repertoire diversity and the disagreement we found between the ANI and dDDH cutoff values. For this study, we extracted information from the genomes of 150 Corynebacterium-type species and seven sequenced genomes of uterine Corynebacterium isolates. We found that the 96.67% OrthoANI value should be used in place of the generally accepted 95-96% ANI threshold in order to obtain an equivalent 70% dDDH value. Phylogenomic analysis determined the evolutionary position of each uterine strain. Then, strains 2652 and 2571B were classified as C. camporealensis based on the ANI value (98.44% and 98.72%) and dDDH value (85.8% and 88.5%). Strain 2569A had a 96.58% ANI and a 69.4% dDDH value and was classified as C. urogenitale. The strains 335C, 1103A, 2571A, and 2298A were classified as novel Corynebacterium based on the ANI value (77.12, 94.01%, 94.26%, and 94.03%) and dDDH value (21.3%, 54.1%, 54.9%, and 51.3%), respectively. Genes for menaquinone biosynthesis and the saturation of chains were detected in uterine strains and their closely related type strains. Gene gain predominates as a source of variation in the gene repertoire. Most of these genes are gained by horizontal gene transfer, driven by genomic islands and prophage. In summary, we refined the ANI cutoff value for an accurate diagnosis of Corynebacterium. Moreover, we clarified the mechanism underlying the diversity of the gene repertoire and expanded the number of Corynebacterium species isolated from the camel uterus.

Amycolatopsis nalaikhensis sp. nov. and Amycolatopsis carbonis sp. nov., two novel actinobacteria with antimicrobial activity isolated from a coal mining site in Mongolia

Two-novel filamentous actinobacteria designated strains 2-2T and 2-15T were isolated from soil of a coal mining site in Mongolia, and their taxonomic positions were determined using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that each of the strains formed a distinct clade within the genus Amycolatopsis. The 16S rRNA gene sequence similarity analysis showed that both strains were mostly related to Amycolatopsis rhabdoformis NCIMB 14900T with 99.0 and 99.4% sequence similarity, respectively. The genome-based comparison indicated that strain 2-2T shared the highest digital DNA-DNA hybridization value of 35.6% and average nucleotide identity value of 86.9% with Amycolatopsis pretoriensis DSM 44654T, and strain 2-15T shared the corresponding values of 36.5 and 87.9% with A. rhabdoformis NCIMB 14900T, all of which being well below the thresholds for species delineation. The chemotaxonomic properties of both strains were typical of the genus Amycolatopsis. In silico prediction of chemotaxonomic markers was also carried out, and the results were consistent with the chemotaxonomic profiles of the genus. Genome mining for secondary metabolite production in strains 2-2T and 2-15T revealed the presence of 29 and 24 biosynthetic gene clusters involved in the production of polyketide synthase, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptides, lanthipeptide, terpenes, siderophore, and a number of other unknown type compounds. Both strains showed broad antifungal activity against several filamentous fungi and also antibacterial activity against methicillin-resistant Staphylococcus aureus and Acinetobacter baumannii. The phenotypic, biochemical, and chemotaxonomic properties indicated that both strains could be clearly distinguished from other species of Amycolatopsis, and thus the names Amycolatopsis nalaikhensis sp. nov. (type strain, 2-2T=KCTC 29695T=JCM 30462T) and Amycolatopsis carbonis (type strain, 2-15T=KCTC 39525T=JCM 30563T) are proposed accordingly.

Nitrospirillum viridazoti sp. nov., an Efficient Nitrogen-Fixing Species Isolated from Grasses

A group of Gram-negative plant-associated diazotrophic bacteria belonging to the genus Nitrospirillum was investigated, including both previously characterized and newly isolated strains from diverse regions and biomes, predominantly in Brazil. Phylogenetic analysis of 16S rRNA and recA genes revealed the formation of a distinct clade consisting of thirteen strains, separate from the formally recognized species N. amazonense (the closest species) and N. iridis. Comprehensive taxonomic analyses using the whole genomes of four strains (BR 11140T = AM 18T = Y-2T = DSM 2788T = ATCC 35120T, BR 11142T = AM 14T = Y-1T = DSM 2787T = ATCC 35119T, BR 11145 = CBAmC, and BR 12005) supported the division of these strains into two species: N. amazonense (BR 11142 T and BR 12005) and a newly proposed species (BR 11140 T and BR 11145), distinct from N. iridis. The phylogenomic analysis further confirmed the presence of the new Nitrospirillum species. Additionally, MALDI-TOF MS analysis of whole-cell mass spectra provided further evidence for the differentiation of the proposed Nitrospirillum species, separate from N. amazonense. Analysis of chemotaxonomy markers (i.e., genes involved in fatty acid synthesis, metabolism and elongation, phospholipid synthesis, and quinone synthesis) revealed that the new species highlights high similarity and evolutionary convergence with other Nitrospirillum species. This new species exhibited nitrogen fixation ability in vitro, it has similar NifHDK protein phylogeny position with the closest species, lacked denitrification capability, but possessed the nosZ gene, enabling N2O reduction, distinguishing it from the closest species. Despite being isolated from diverse geographic regions, soil types, and ecological niches, no significant phenotypic or physiological differences were observed between the proposed new species and N. amazonense. Based on these findings, a new species, Nitrospirillum viridazoti sp. nov., was classified, with the strain BR 11140T (DSM 2788T, ATCC 35120T) designated as the type strain.

(Pan)genomic analysis of two Rhodococcus isolates and their role in phenolic compound degradation

The genus Rhodococcus is recognized for its potential to degrade a large range of aromatic substances, including plant-derived phenolic compounds. We used comparative genomics in the context of the broader Rhodococcus pan-genome to study genomic traits of two newly described Rhodococcus strains (type-strain Rhodococcus pseudokoreensis R79T and Rhodococcus koreensis R85) isolated from apple rhizosphere. Of particular interest was their ability to degrade phenolic compounds as part of an integrated approach to treat apple replant disease (ARD) syndrome. The pan-genome of the genus Rhodococcus based on 109 high-quality genomes was open with a small core (1.3%) consisting of genes assigned to basic cell functioning. The range of genome sizes in Rhodococcus was high, from 3.7 to 10.9 Mbp. Genomes from host-associated strains were generally smaller compared to environmental isolates which were characterized by exceptionally large genome sizes. Due to large genomic differences, we propose the reclassification of distinct groups of rhodococci like the Rhodococcus equi cluster to new genera. Taxonomic species affiliation was the most important factor in predicting genetic content and clustering of the genomes. Additionally, we found genes that discriminated between the strains based on habitat. All members of the genus Rhodococcus had at least one gene involved in the pathway for the degradation of benzoate, while biphenyl degradation was mainly restricted to strains in close phylogenetic relationships with our isolates. The ~40% of genes still unclassified in larger Rhodococcus genomes, particularly those of environmental isolates, need more research to explore the metabolic potential of this genus.IMPORTANCERhodococcus is a diverse, metabolically powerful genus, with high potential to adapt to different habitats due to the linear plasmids and large genome sizes. The analysis of its pan-genome allowed us to separate host-associated from environmental strains, supporting taxonomic reclassification. It was shown which genes contribute to the differentiation of the genomes based on habitat, which can possibly be used for targeted isolation and screening for desired traits. With respect to apple replant disease (ARD), our isolates showed genome traits that suggest potential for application in reducing plant-derived phenolic substances in soil, which makes them good candidates for further testing against ARD.

Genomic Insights into the Symbiotic and Plant Growth-Promoting Traits of "Candidatus Phyllobacterium onerii" sp. nov. Isolated from Endemic Astragalus flavescens

A novel strain of Gram-negative, rod-shaped aerobic bacteria, identified as IY22, was isolated from the root nodules of Astragalus flavescens. The analysis of the 16S rDNA and recA (recombinase A) gene sequences indicated that the strain belongs to the genus Phyllobacterium. During the phylogenetic analysis, it was found that strain IY22 is closely related to P. trifolii strain PETP02T and P. bourgognense strain STM 201T. The genome of IY22 was determined to be 6,010,116 base pairs long with a DNA G+C ratio of 56.37 mol%. The average nucleotide identity (ANI) values showed a range from 91.7% to 93.6% when compared to its close relatives. Moreover, IY22 and related strains had digital DNA-DNA hybridization (dDDH) values ranging from 16.9% to 54.70%. Multiple genes (including nodACDSNZ, nifH/frxC, nifUS, fixABCJ, and sufABCDES) associated with symbiotic nitrogen fixation have been detected in strain IY22. Furthermore, this strain features genes that contribute to improving plant growth in various demanding environments. This study reports the first evidence of an association between A. flavescens and a rhizobial species. Native high-altitude legumes are a potential source of new rhizobia, and we believe that they act as a form of insurance for biodiversity against the threats of desertification and drought.

Amycolatopsis mongoliensis sp. nov., a novel actinobacterium with antifungal activity isolated from a coal mining site in Mongolia

A novel filamentous actinobacterium designated strain 4-36T showing broad-spectrum antifungal activity was isolated from a coal mining site in Mongolia, and its taxonomic position was determined using polyphasic approach. Optimum growth occurred at 30 °C, pH 7.5 and in the absence of NaCl. Aerial and substrate mycelia were abundantly formed on agar media. The colour of aerial mycelium was white and diffusible pigments were not formed. Phylogenetic analyses based on 16S rRNA gene sequence showed that strain 4-36T formed a distinct clade within the genus Amycolatopsis. The 16S rRNA gene sequence similarity showed that the strain was mostly related to Amycolatopsis lexingtonensis DSM 44544T and Amycolatopsis rifamycinica DSM 46095T with 99.3 % sequence similarity. However, the highest digital DNA-DNA hybridization value to closest species was 44.1 %, and the highest average nucleotide identity value was 90.2 %, both of which were well below the species delineation thresholds. Chemotaxonomic properties were typical of the genus Amycolatopsis, as the major fatty acids were C15 : 0, iso-C16 : 0 and C16 : 0, the cell-wall diamino acid was meso-diaminopimelic acid, the quinone was MK-9(H4), and the main polar lipids were diphosphatidylglycerol, phosphatidylmethanolamine and phosphatidylethanolamine. The in silico prediction of chemotaxonomic markers was also carried out by phylogenetic analysis. The genome mining for biosynthetic gene clusters of secondary metabolites in strain 4-36T revealed the presence of 34 gene clusters involved in the production of polyketide synthase, nonribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptide, lanthipeptide, terpenes, siderophore and many other unknown clusters. Strain 4-36T showed broad antifungal activity against several filamentous fungi. The phenotypic, biochemical and chemotaxonomic properties indicated that the strain could be clearly distinguished from other species of Amycolatopsis, and thus the name Amycolatopsis mongoliensis sp. nov. is proposed accordingly (type strain, 4-36T=KCTC 39526T=JCM 30565T).

Corynebacterium mendelii sp. nov., a novel bacterium isolated from Adélie penguin oral cavity

The taxonomic status of strain P5891T, isolated from an Adélie penguin beak swab, was investigated. Based on the 16S rRNA gene sequence, the strain was identified as a potentially novel Corynebacterium species, with the highest sequence similarities to Corynebacterium rouxii FRC0190T (96.7 %) and Corynebacterium epidermidicanis DSM 45586T (96.6 %). The average nucleotide identity values between strain P5891T and C. rouxii FRC0190T and C. epidermidicanis DSM 45586T were 68.2 and 69.2 %, respectively. The digital DNA-DNA hybridization values between strain P5891T and C. rouxii FRC0190T and C. epidermidicanis DSM 45586T were 23.7 and 21.4 %, respectively. Phylogenetic trees based on the 16S rRNA sequence placed strain P5891T in a separate branch with Corynebacterium canis 1170T and Corynebacterium freiburgense 1045T, while a phylogenomic tree based on the Corynebacterium species core genome placed the strain next to Corynebacterium choanae 200CHT. Extensive phenotyping and genomic analyses clearly confirmed that strain P5891T represents a novel species of the genus Corynebacterium, for which the name Corynebacterium mendelii sp. nov. is proposed, with the type strain P5891T (=CCM 8862T=LMG 31627T).

Metabolism and gene sequence variation in Turicella otitidis implies its adaptability and pathogenicity in extra-otic infection: a systematic review

Turicella otitidis belongs to the Corynebacteriaceae family and is a normal inhabitant of the ear and exists in a commensal relationship with its host. In children, T. otitidis is frequently associated with otitis media. The emergence of Turicella otitidis as a pathogen is concerning, particularly due to the limited availability of data on its pathogenic properties. The objective of this study is to conduct a systematic review of T. otitidis infections occurring in both the ear and other anatomical sites, and to summarize the differences in metabolism and genome sequences between isolates obtained from the ear and blood.

Prevalence of Gram positive bacteria in the affected individuals of Otitis media with effusion from the indigenous population of Southern Punjab, Pakistan: first report

Otitis media with effusion (OME) is a type of otitis media (OM) characterized by the presence of fluid behind intact tympanic membrane and is one of the most common diseases of early childhood. It is an infectious disease associated with the presence of many pathogenic bacteria in the middle ear of affected individuals. This study was aimed to determine the prevalence of Gram-positive bacteria from the middle ear of OME patients in the population of Southern Punjab, Pakistan. The incidence of OME under comprehensive healthcare setting was investigated in patients who consulted at the department of ear, throat and nose, Bahawal Victoria Hospital (BVH), Bahawalpur, from December, 2019 to May, 2021. Ear swabs were taken from affected and normal individuals. After culturing bacteria from the ear swabs, microscopic analysis and biochemical tests were performed to characterize the cultured Gram-positive bacteria. Out of 352 patients examined, 109 (30.9%) patients had OME. Age of the participants ranged from 14 to 50 years; individuals between the ages of 14 and 22 years had the highest infection rates, while individuals between 40 and 50 years had the lowest rate of infection. Tympanic membrane perforation, fever, cough, sore throat, ear pain and hearing problem showed association with symptoms of OME. Microscopic analysis and biochemical characterization showed the presence of streptococci and staphylococci in all the studied samples. The most frequently isolated bacteria were Streptococcus pneumoniae, Streptococcus pyogenes, and Staphylococcus aureus with percentage of 53.3%, 20% and 13.3% respectively. Enterococcus faecalis (6.6%) and Staphylococcus epidermidis (6.6%) were also identified in the studied samples. This study will help in the better medical administration of OME affected individuals.

Pan-genomic analysis of Corynebacterium amycolatum gives insights into molecular mechanisms underpinning the transition to a pathogenic phenotype

Corynebacterium amycolatum is a nonlipophilic coryneform which is increasingly being recognized as a relevant human and animal pathogen showing multidrug resistance to commonly used antibiotics. However, little is known about the molecular mechanisms involved in transition from colonization to the MDR invasive phenotype in clinical isolates. In this study, we performed a comprehensive pan-genomic analysis of C. amycolatum, including 26 isolates from different countries. We obtained the novel genome sequences of 8 of them, which are multidrug resistant clinical isolates from Spain and Tunisia. They were analyzed together with other 18 complete or draft C. amycolatum genomes retrieved from GenBank. The species C. amycolatum presented an open pan-genome (α = 0.854905), with 3,280 gene families, being 1,690 (51.52%) in the core genome, 1,121 related to accessory genes (34.17%), and 469 related to unique genes (14.29%). Although some classic corynebacterial virulence factors are absent in the species C. amycolatum, we did identify genes associated with immune evasion, toxin, and antiphagocytosis among the predicted putative virulence factors. Additionally, we found genomic evidence for extensive acquisition of antimicrobial resistance genes through genomic islands.

Genotype-phenotype correlations within the Geodermatophilaceae

The integration of genomic information into microbial systematics along with physiological and chemotaxonomic parameters provides for a reliable classification of prokaryotes. In silico analysis of chemotaxonomic traits is now being introduced to replace characteristics traditionally determined in the laboratory with the dual goal of both increasing the speed of the description of taxa and the accuracy and consistency of taxonomic reports. Genomics has already successfully been applied in the taxonomic rearrangement of Geodermatophilaceae (Actinomycetota) but in the light of new genomic data the taxonomy of the family needs to be revisited. In conjunction with the taxonomic characterisation of four strains phylogenetically located within the family, we conducted a phylogenetic analysis of the whole proteomes of the sequenced type strains and established genotype-phenotype correlations for traits related to chemotaxonomy, cell morphology and metabolism. Results indicated that the four isolates under study represent four novel species within the genus Blastococcus. Additionally, the genera Blastococcus, Geodermatophilus and Modestobacter were shown to be paraphyletic. Consequently, the new genera Trujillonella, Pleomorpha and Goekera were proposed within the Geodermatophilaceae and Blastococcus endophyticus was reclassified as Trujillonella endophytica comb. nov., Geodermatophilus daqingensis as Pleomorpha daqingensis comb. nov. and Modestobacter deserti as Goekera deserti comb. nov. Accordingly, we also proposed emended descriptions of Blastococcus aggregatus, Blastococcus jejuensis, Blastococcus saxobsidens and Blastococcus xanthilyniticus. In silico chemotaxonomic results were overall consistent with wet-lab results. Even though in silico discriminatory levels varied depending on the respective chemotaxonomic trait, this approach is promising for effectively replacing and/or complementing chemotaxonomic analyses at taxonomic ranks above the species level. Finally, interesting but previously overlooked insights regarding morphology and ecology were revealed by the presence of a repertoire of genes related to flagellum synthesis, chemotaxis, spore production and pilus assembly in all representatives of the family. A rich carbon metabolism including four different CO2 fixation pathways and a battery of enzymes able to degrade complex carbohydrates were also identified in Blastococcus genomes.

Description of Streptomyces griseiscabiei sp. nov. and reassignment of Streptomyces sp. strain NRRL B-16521 to Streptomyces acidiscabies

Streptomyces strain NRRL B-2795T (DSM 112329T=NRRL B-2795T) is described as the type strain of Streptomyces griseiscabiei sp. nov. using whole-genome average nucleotide identity and multilocus sequence analyses in addition to phenotypic characterization of carbon source utilization, spore chain morphology, melanin production, salt tolerance, pH tolerance, plant pathogenicity and antibiotic resistance. This strain was previously classified as Streptomyces scabiei but suggested as a potential novel species. A second Streptomyces strain, NRRL B-16521, previously named Streptomyces scabiei , and also previously suggested as a potential novel species, is assigned to Streptomyces acidiscabies based on whole-genome average nucleotide identity. Morphological and biochemical characterizations also support this designation for NRRL B-16521. Both Streptomyces sp. strain NRRL B-2795T and NRRL B-16521 cause common scab on multiple cultivars of potato.

Taxonomic revision of the genus Amphritea supported by genomic and in silico chemotaxonomic analyses, and the proposal of Aliamphritea gen. nov

A Gram-staining-negative, aerobic bacterium, designated strain PT3T was isolated from laboratory-reared larvae of the Japanese sea cucumber Apostichopus japonicus. Phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PT3T was closely related to Amphritea ceti RA1T (= KCTC 42154T = NBRC 110551T) and Amphritea spongicola MEBiC05461T (= KCCM 42943T = JCM 16668T) both with 98.3% sequence similarity, however, average nucleotide identity (ANI) and in silico DNA-DNA hybridization (in silico DDH) values among these three strains were below 95% and 70%, respectively, confirming the novelty of PT3T. Furthermore, the average amino acid identity (AAI) values of PT3T against other Amphritea species were on the reported genus delineation boundary (64-67%). Multilocus sequence analysis using four protein-coding genes (recA, mreB, rpoA, and topA) further demonstrated that PT3T, Amphritea ceti and Amphritea spongicola formed a monophyletic clade clearly separate from other members of the genus Amphritea. Three strains (PT3T, A. ceti　KCTC 42154T and A. spongicola JCM 16668T) also showed higher similarities in their core genomes compared to those of the other Amphritea spp. Based on the genome-based taxonomic approach, Aliamphritea gen. nov. was proposed together with the reclassification of the genus Amphritea and Aliamphritea ceti comb. nov. (type strain RA1T = KCTC 42154T = NBRC 110551T), Aliamphritea spongicola comb. nov. (type strain MEBiC05461T = KCCM 42943T = JCM 16668T), and Aliamphritea hakodatensis sp. nov. (type strain PT3T = JCM 34607T = KCTC 82591T) were suggested.

Streptomyces caniscabiei sp. nov., which causes potato common scab and is distributed across the world

Fourteen strains of Streptomyces isolated from scab lesions on potato are described as members of a novel species based on genetic distance, morphological observation and biochemical analyses. Morphological and biochemical characteristics of these strains are distinct from other described phytopathogenic species. Strain NE06-02DT has white aerial mycelium and grey, cylindrical, smooth spores on rectus-flexibilis spore chains. Members of this species group can utilize most of the International Streptomyces Project sugars, utilize melibiose and trehalose, produce melanin, grow on 6–7 % NaCl and pH 5–5.5 media, and are susceptible to oleandomycin (100 µg ml−1), streptomycin (20 µg ml−1) and penicillin G (30 µg ml−1). Though the 16S rRNA gene sequences from several members of this novel species are identical to the Streptomyces bottropensis 16S rRNA gene sequence, whole-genome average nucleotide identity and multi-locus sequence analysis confirm that the strains are members of a novel species. Strains belonging to this novel species have been isolated from the United States, Egypt and China with the earliest known members being isolated in 1961 from common scab lesions of potato in both California, USA, and Maine, USA. The name Streptomyces caniscabiei sp. nov. is proposed for strain NE06-02DT (=DSM111602T=ATCC TSD-236T) and the other members of this novel species group.

Phylogenomic Reappraisal of Fatty Acid Biosynthesis, Mycolic Acid Biosynthesis and Clinical Relevance Among Members of the Genus Corynebacterium

The genus Corynebacterium encompasses many species of biotechnological, medical or veterinary significance. An important characteristic of this genus is the presence of mycolic acids in their cell envelopes, which form the basis of a protective outer membrane (mycomembrane). Mycolic acids in the cell envelope of Mycobacterium tuberculosis have been associated with virulence. In this study, we have analysed the genomes of 140 corynebacterial strains, including representatives of 126 different species. More than 50% of these strains were isolated from clinical material from humans or animals, highlighting the true scale of pathogenic potential within the genus. Phylogenomically, these species are very diverse and have been organised into 19 groups and 30 singleton strains. We find that a substantial number of corynebacteria lack FAS-I, i.e., have no capability for de novo fatty acid biosynthesis and must obtain fatty acids from their habitat; this appears to explain the well-known lipophilic phenotype of some species. In most species, key genes associated with the condensation and maturation of mycolic acids are present, consistent with the reports of mycolic acids in their species descriptions. Conversely, species reported to lack mycolic acids lacked these key genes. Interestingly, Corynebacterium ciconiae, which is reported to lack mycolic acids, appears to possess all genes required for mycolic acid biosynthesis. We suggest that although a mycolic acid-based mycomembrane is widely considered to be the target for interventions by the immune system and chemotherapeutics, the structure is not essential in corynebacteria and is not a prerequisite for pathogenicity or colonisation of animal hosts.

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.

Addressing the sublime scale of the microbial world: reconciling an appreciation of microbial diversity with the need to describe species

There are fewer than 20,000 prokaryotic species with validly published names, meaning >99% of a reasonable estimate of microbial diversity remains formally unnamed. Here we explore the damaging consequences of the current practice in which each new species is described in a standardized publication, most typically a 'single strain species description'. This approach is both an impediment to scaling up progress in naming the microbial world and also a significant factor in the poor reputation of the discipline of microbial taxonomy. We conclude that significant changes in author habits are needed and make constructive suggestions as to how author practice should adapt.

Benchmarking DNA Extraction Methods for Phylogenomic Analysis of Sub-Antarctic Rhodococcus and Williamsia Species

Bacteria containing mycolic acids in their cell envelope are often recalcitrant to cell lysis, so extracting DNA of sufficient quality for third-generation sequencing and high-fidelity genome assembly requires optimization, even when using commercial kits with protocols for hard-to-lyse bacteria. We benchmarked three spin-column-based kits against a classical DNA extraction method employing lysozyme, proteinase K and SDS for six lysozyme-resistant, sub-Antarctic strains of Corynebaceriales. Prior cultivation in broths containing glycine at highly growth-inhibitory concentrations (4.0–4.5%) improved cell lysis using both classical and kit methods. The classical method produced DNA with average fragment sizes of 27–59 Kbp and tight fragment size ranges, meeting quality standards for genome sequencing, assembly and phylogenomic analyses. By 16S rRNA gene sequencing, we classified two strains as Williamsia and four strains as Rhodococcus species. Pairwise comparison of average nucleotide identity (ANI) and alignment fraction (AF), plus genome clustering analysis, confirmed Rhodococcus sp. 1163 and 1168 and Williamsia sp. 1135 and 1138 as novel species. Phylogenetic, lipidomic and biochemical analyses classified psychrotrophic strains 1139 and 1159 as R. qingshengii and R. erythropolis, respectively, using ANI similarity of >98% and AF >60% for species delineation. On this basis, some members of the R. erythropolis genome cluster groups, including strains currently named as R. enclensis, R. baikonurensis, R. opacus and R. rhodochrous, would be reclassified either as R. erythropolis or R. qingshengii.

Case-Control Microbiome Study of Chronic Otitis Media with Effusion in Children Points at Streptococcus salivarius as a Pathobiont-Inhibiting Species

Chronic otitis media with effusion (OME) has been associated with a shift in microbiome composition and microbial interaction in the upper respiratory tract (URT). While most studies have focused on potential pathogens, this study aimed to find bacteria that could be protective against OME through a case-control microbiome study and characterization of isolates from healthy subjects. The URT and ear microbiome profiles of 70 chronic OME patients and 53 controls were compared by 16S rRNA amplicon sequencing. Haemophilus influenzae was the most frequent classic middle ear pathobiont. However, other taxa, especially Alloiococcus otitis, were also frequently detected in the ear canal of OME patients. Streptococci of the salivarius group and Acinetobacter lwoffii were more abundant in the nasopharynx of healthy controls than in OME patients. In addition to the microbiome analysis, 142 taxa were isolated from healthy individuals, and 79 isolates of 13 different Streptococcus species were tested for their pathobiont-inhibiting potential. Of these, Streptococcus salivarius isolates showed a superior capacity to inhibit the growth of H. influenzae, Moraxella catarrhalis, Streptococcus pneumoniae, Streptococcus pyogenes, Staphylococcus aureus, A. otitis, and Corynebacterium otitidis. S. salivarius strains thus show potential as a probiotic for prevention or treatment of OME based on their overrepresentation in the healthy nasopharynx and their ability to inhibit the growth of respiratory pathobionts. (This study has been registered at ClinicalTrials.gov under registration no. NCT03109496.)

IMPORTANCE The majority of probiotics marketed today target gastrointestinal health. This study searched for bacteria native to the human upper respiratory tract, with a beneficial potential for respiratory and middle ear health. Comparison of the microbiomes of children with chronic otitis media with effusion (OME) and of healthy controls identified Streptococcus salivarius as a health-associated and prevalent inhabitant of the human nasopharynx. However, beneficial potential should be assessed at strain level. Here, we also isolated specific S. salivarius strains from the healthy individuals in our study. These isolates showed a beneficial safety profile and efficacy potential to inhibit OME pathogens in vitro. These properties will now have to be evaluated and confirmed in human clinical studies.

Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019

Knowledge of novel prokaryotic taxon discovery and nomenclature revisions is of importance to clinical microbiology laboratory practice, infectious disease epidemiology, and studies of microbial pathogenesis. Relative to bacterial isolates derived from human clinical specimens, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2018 and 2019. Included are several changes pertinent to former designations of or within Propionibacterium spp., Corynebacterium spp., Clostridium spp., Mycoplasma spp., Methylobacterium spp., and Enterobacteriaceae Future efforts to ascertain clinical relevance for many of these changes may be augmented by a document development committee that has been appointed by the Clinical and Laboratory Standards Institute.

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Corynebacterium godavarianum Jani et al. 2018 and Corynebacterium hadale Wei et al. 2018 are both later heterotypic synonyms of Corynebacterium gottingense Atasayar et al. 2017, proposal of an emended description of Corynebacterium gottingense Atasayar et al. 2017

Seven strains of an unidentifiable Corynebacterium species recovered from blood cultures, urine or cerebrospinal fluid over 26 years, closest to but differentiated from Corynebacterium imitans by 16S rRNA gene and partial rpoB gene sequencing, were studied. In November 2017, Atasayar et al. described a blood culture isolate as Corynebacterium gottingense sp. nov., which had >99 % similarity by 16S rRNA gene sequencing to the Canadian strains. In January 2018, Jani et al. described Corynebacterium godavarianum sp. nov., recovered from the Godavari River, India, which also had >99 % similarity by 16S/rpoB sequencing to the Canadian strains and C. gottingense. In May 2018, Wei et al. described Corynebacterium hadale recovered from hadopelagic water; this too had >99 % similarity by 16S rRNA gene sequencing to C. gottingense, C. godavarianum and the Canadian strains. C. gottingense DSM 103494^T and C. godavarianum LMG 29598^T were acquired and whole genome sequencing was performed (not previously done). Results were compared with genomes from C. hadale (GenBank accession NQMQ01) and the Canadian isolates. We found that these ten genomes formed a single taxon when compared using digital DNA-DNAhybridization, average nucleotide identity using blastn and average amino acid identity criteria but exhibited some subtle biochemical and chemotaxonomic differences. Heuristically, we propose that C. godavarianum and C. hadale are later heterotypic synonyms of, and the Canadian isolates are identifiable as, C. gottingense. We provide an emended description of Corynebacterium gottingense Atasayar et al. 2017; genomes ranged from 2.48 to 2.69 Mb (C. gottingense DSM 103494^T, 2.62 Mb) with G+C content of 65.1-65.6 mol% (WGS), recovered from clinical and environmental sites.

Reconstructing the Phylogeny of Corynebacteriales while Accounting for Horizontal Gene Transfer

Horizontal gene transfer is a common mechanism in Bacteria that has contributed to the genomic content of existing organisms. Traditional methods for estimating bacterial phylogeny, however, assume only vertical inheritance in the evolution of homologous genes, which may result in errors in the estimated phylogenies. We present a new method for estimating bacterial phylogeny that accounts for the presence of genes acquired by horizontal gene transfer between genomes. The method identifies and corrects putative transferred genes in gene families, before applying a gene tree-based summary method to estimate bacterial species trees. The method was applied to estimate the phylogeny of the order Corynebacteriales, which is the largest clade in the phylum Actinobacteria. We report a collection of 14 phylogenetic trees on 360 Corynebacteriales genomes. All estimated trees display each genus as a monophyletic clade. The trees also display several relationships proposed by past studies, as well as new relevant relationships between and within the main genera of Corynebacteriales: Corynebacterium, Mycobacterium, Nocardia, Rhodococcus, and Gordonia. An implementation of the method in Python is available on GitHub at https://github.com/UdeS-CoBIUS/EXECT (last accessed April 2, 2020).

Update on the classification of higher ranks in the phylum Actinobacteria

Genome analysis is one of the main criteria for description of new taxa. Availability of genome sequences for all the actinobacteria with a valid nomenclature will, however, require another decade's works of sequencing. This paper describes the rearrangement of the higher taxonomic ranks of the members of the phylum 'Actinobacteria', using the phylogeny of 16S rRNA gene sequences and supported by the phylogeny of the available genome sequences. Based on the refined phylogeny of the 16S rRNA gene sequences, we could arrange all the members of the 425 genera of the phylum 'Actinobacteria' with validly published names currently in use into six classes, 46 orders and 79 families, including 16 new orders and 10 new families. The order Micrococcales Prévot 1940 (Approved Lists 1980) emend. Nouioui et al. 2018 is now split into 11 monophyletic orders: the emended order Micrococcales and ten proposed new orders Aquipuribacterales, Beutenbergiales, Bogoriellales, Brevibacteriales, Cellulomonadales, Demequinales, Dermabacterales, Dermatophilales, Microbacteriales and Ruaniales. Further, the class 'Actinobacteria' Stackebrandt et al. 1997 emend. Nouioui et al. 2018 was described without any nomenclature type, and therefore the name 'Actinobacteria' is deemed illegitimate. In accordance to Rule 8 of the International Code of Nomenclature of Prokaryotes, Parker et al. 2019, we proposed the name Actinomycetia which is formed by using the stem of the name Actinomycetales Buchanan 1917 (Approved Lists 1980) emend. Zhi et al. 2009, to replace the name 'Actinobacteria'. The nomenclature type of the proposed new class Actinomycetia is the order Actinomycetales Buchanan 1917 (Approved Lists 1980) emend. Zhi et al. 2009.

Panel 7 - Pathogenesis of otitis media - a review of the literature between 2015 and 2019

OBJECTIVE

To perform a comprehensive review of the literature from July 2015 to June 2019 on the pathogenesis of otitis media. Bacteria, viruses and the role of the microbiome as well as the host response are discussed. Directions for future research are also suggested.

DATA SOURCES

PubMed database of the National Library of Medicine.

REVIEW METHODS

PubMed was searched for any papers pertaining to OM pathogenesis between July 2015 and June 2019. If in English, abstracts were assessed individually for their relevance and included in the report. Members of the panel drafted the report based on these searches and on new data presented at the 20th International Symposium on Recent Advances in Otitis Media.

CONCLUSIONS

The main themes that arose in OM pathogenesis were around the need for symptomatic viral infections to develop disease. Different populations potentially having different mechanisms of pathogenesis. Novel bacterial otopathogens are emerging and need to be monitored. Animal models need to continue to be developed and used to understand disease pathogenesis.

IMPLICATIONS FOR PRACTICE

The findings in the pathogenesis panel have several implications for both research and clinical practice. The most urgent areas appear to be to continue monitoring the emergence of novel otopathogens, and the need to develop prevention and preventative therapies that do not rely on antibiotics and protect against the development of the initial OM episode.

Reviewing the Pathogenic Potential of the Otitis-Associated Bacteria Alloiococcus otitidis and Turicella otitidis

Alloiococcus otitidis and Turicella otitidis are common bacteria of the human ear. They have frequently been isolated from the middle ear of children with otitis media (OM), though their potential role in this disease remains unclear and confounded due to their presence as commensal inhabitants of the external auditory canal. In this review, we summarize the current literature on these organisms with an emphasis on their role in OM. Much of the literature focuses on the presence and abundance of these organisms, and little work has been done to explore their activity in the middle ear. We find there is currently insufficient evidence available to determine whether these organisms are pathogens, commensals or contribute indirectly to the pathogenesis of OM. However, building on the knowledge currently available, we suggest future approaches aimed at providing stronger evidence to determine whether A. otitidis and T. otitidis are involved in the pathogenesis of OM. Such evidence will increase our understanding of the microbial risk factors contributing to OM and may lead to novel treatment approaches for severe and recurrent disease.

The Mycobacterial Cell Envelope: A Relict From the Past or the Result of Recent Evolution?

Mycobacteria are well known for their taxonomic diversity, their impact on global health, and for their atypical cell wall and envelope. In addition to a cytoplasmic membrane and a peptidoglycan layer, the cell envelope of members of the order Corynebacteriales, which include Mycobacterium tuberculosis, also have an arabinogalactan layer connecting the peptidoglycan to an outer membrane, the so-called “mycomembrane.” This unusual cell envelope composition of mycobacteria is of prime importance for several physiological processes such as protection from external stresses and for virulence. Although there have been recent breakthroughs in the elucidation of the composition and organization of this cell envelope, its evolutionary origin remains a mystery. In this perspectives article, the characteristics of the cell envelope of mycobacteria with respect to other actinobacteria will be dissected through a molecular evolution framework in order to provide a panoramic view of the evolutionary pathways that appear to be at the origin of this unique cell envelope. In combination with a robust molecular phylogeny, we have assembled a gene matrix based on the presence or absence of key determinants of cell envelope biogenesis in the Actinobacteria phylum. We present several evolutionary scenarios regarding the origin of the mycomembrane. In light of the data presented here, we also propose a novel alternative hypothesis whereby the stepwise acquisition of core enzymatic functions may have allowed the sequential remodeling of the external cell membrane during the evolution of Actinobacteria and has led to the unique mycomembrane of slow-growing mycobacteria as we know it today.

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria 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.