Polymicrobial infections with specific Actinomyces and related organisms, using the current taxonomy

Actinomyces organisms reside on mucosal surfaces of the oropharynx and the genitourinary tract. Polymicrobial infections with Actinomyces organisms are increasingly being reported in the literature. Since these infections differ from classical actinomycosis, lacking of specific clinical and imaging findings, slow-growing Actinomyces organisms can be regarded as contaminants or insignificant findings. In addition, only limited knowledge is available about novel Actinomyces species and their clinical relevance. The recent reclassifications have resulted in the transfer of several Actinomyces species to novel genera Bowdeniella, Gleimia, Pauljensenia, Schaalia, or Winkia. The spectrum of diseases associated with specific members of Actinomyces and these related genera varies. In human infections, the most common species are Actinomyces israelii, Schaalia meyeri, and Schaalia odontolytica, which are typical inhabitants of the mouth, and Gleimia europaea, Schaalia turicensis, and Winkia neuii. In this narrative review, the purpose was to gather information on the emerging role of specific organisms within the Actinomyces and related genera in polymicrobial infections. These include Actinomyces graevenitzii in pulmonary infections, S. meyeri in brain abscesses and infections in the lower respiratory tract, S. turicensis in skin-related infections, G. europaea in necrotizing fasciitis and skin abscesses, and W. neuii in infected tissues around prostheses and devices. Increased understanding of the role of Actinomyces and related species in polymicrobial infections could provide improved outcomes for patient care. Key messages Due to the reclassification of the genus, many former Actinomyces species belong to novel genera Bowdeniella, Gleimia, Pauljensenia, Schaalia, or Winkia.Some of the species play emerging roles in specific infection types in humans.Increasing awareness of their clinical relevance as an established or a putative pathogen in polymicrobial infections brings about improved outcomes for patient care.

Trinickia violacea sp. nov. and Trinickia terrae sp. nov., isolated from forest soil

Two Gram-stain negative, aerobic and rod-shaped bacterial strains, DHOD12T and 7GSK02T, were isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Strain DHOD12T grew at 4-42 °C (optimum, 28-33 °C), pH 4.0-8.5 (optimum, pH 5.5-6.5) and in the presence of 0-1.5 % (w/v; optimum, 0-0.5 %)NaCl; while strain 7GSK02T grew at 12-42 °C (optimum, 28-33 °C), pH 4.0-8.5 (optimum, pH 5.0-6.0) and in the presence of 0-0.5 % (w/v; optimum, 0 %) NaCl. Strains DHOD12T and 7GSK02T had the highest 16S rRNA sequence similarities of 98.0 and 98.3 % with the same species Trinickia mobilis DHG64T, respectively, and 98.4 % between themselves. In the 16S rRNA phylogeny, they formed a clade that was sister to a major cluster consisting of all described Trinickia species. Phylogenomic analyses with the UBCG and PhyloPhlAn methods consistently showed that strains DHOD12T and 7GSK02T formed a clade with T. mobilis DHG64T that was a sister of a cluster containing the remainder of the Trinickia species. The DNA G+C contents of strains DHOD12T and 7GSK02T were 63.1 and 64.6 mol%, respectively. Digital DNA-DNA hybridization and average nucleotide identity values of strains DHOD12T, 7GSK02T and their closely related strains were in the ranges of 21.6-31.4 % and 77.1-86.9 %, respectively. These two strains had the same major respiratory quinone, ubiquinone-8, and both had C16 : 0, C17 : 0 cyclo and summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c) as their major fatty acids. Their major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Genomic analysis indicated that the two strains could have the potential to degrade aromatic compounds like other Trinickia species. On the basis of phenotypic and phylogenetic results, strains DHOD12T and 7GSK02T represent two novel species of the genus Trinickia, for which the names Trinickia violacea sp. nov. (type strain DHOD12T=LMG 30258T=CGMCC 1.15436T) and Trinickia terrae sp. nov. (type strain 7GSK02T=CGMCC 1.15432T=KCTC 62468T) are proposed.

Valid publication of four additional phylum names

The International Code of Nomenclature of Prokaryotes (ICNP) now includes the phylum category. For the purpose of the valid publication of their names under the ICNP, we consider here four phyla. Slightly modified descriptions of 'Abditibacteriota' Tahon et al. 2018 and 'Desulfobacterota' Waite et al. 2020 are provided to meet the requirements of the ICNP for phylum names. Methanobacteriota is proposed as a substitute for 'Euryarchaeota' Garrity and Holt 2021, while Nanobdellota is proposed to replace 'Nanoarchaeota' Huber et al. 2002, based on the genus Nanobdella Kato et al. 2022.

Equine brucellosis: current understanding and challenges

Brucellosis in equines, including horses, donkeys, and mules, is characterized by abscesses in tendons, bursae, and joints. Reproductive disorders, which are common in other animals, are rare in both males and females. Joint breeding of horses, cattle, and pigs was found as the main risk factor for equine brucellosis, with the transmission from equines to cattle or among equines possible, although unlikely. Hence, evaluation of the disease in equines can be considered an indirect indicator of the effectiveness of brucellosis control measures employed for other domestic species. Generally, the disease in equines reflects disease status in the sympatric domestic species, mainly cattle. It is important to note that in equines, the disease has no validated diagnostic test, which limits the interpretation of available data. Finally, it is important to mention that equines also represent significant Brucella spp. infection sources for humans. Considering the zoonotic aspect of brucellosis, the significant losses due to infection, and the representativeness of horses, mules, and donkeys in the society, as well as the continuous efforts to control and eradicate the disease in livestock, in this review, we covered the various aspects of brucellosis in equines and compile the sparse and diffuse information on the subject.

An Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Domestic Animals Described in 2018 to 2021

Novel bacterial taxonomy and nomenclature revisions can have significant impacts on clinical practice, disease epidemiology, and veterinary microbiology laboratory operations. Expansion of research on the microbiota of humans, animals, and insects has significant potential impacts on the taxonomy of organisms of clinical interest. Implications of taxonomic changes may be especially important when considering zoonotic diseases. Here, we address novel taxonomy and nomenclature revisions of veterinary significance. Noteworthy discussion centers around descriptions of novel mastitis pathogens in Streptococcaceae, Staphylococcaceae, and Actinomycetaceae; bovine reproductive tract pathogens in Corynebacteriaceae; novel members of Mannheimia spp., Leptospira spp., and Mycobacterium spp.; the transfer of Ochrobactrum spp. to Brucella spp.; and revisions to the genus Mycoplasma.

Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Nondomestic Animals Described in 2018 to 2021

Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.

An Update on Novel Taxa and Revised Taxonomic Status of Bacteria (Including Members of the Phylum Planctomycetota) Isolated from Aquatic Host Species Described in 2018 to 2021

Increased interest in farmed aquatic species, aquatic conservation measures, and microbial metabolic end-product utilization have translated into a need for awareness and recognition of novel microbial species and revisions to bacterial taxonomy. Because this need has largely been unmet, through a 4-year literature review, we present lists of novel and revised bacterial species (including members of the phylum Planctomycetota) derived from aquatic hosts that can serve as a baseline for future biennial summaries of taxonomic revisions in this field. Most new and revised taxa were noted within oxidase-positive and/or nonglucose fermentative Gram-negative bacilli, including members of the Tenacibaculum, Flavobacterium, and Vibrio genera. Valid and effectively published novel members of the Streptococcus, Erysipelothrix, and Photobacterium genera are additionally described from disease pathogenesis perspectives.

Detection and Identification of Mycoplasmopsis agassizii in Captive Tortoises with Different Clinical Signs in Italy

Mycoplasmopsis agassizii causes the Upper Respiratory Tract Disease (URTD) in tortoises. The severity of the disease usually ranges from mild to severe respiratory signs. Animals can recover, die, or become asymptomatic carriers and are source of infection for other tortoises. This study describes (i) the clinical history and the results obtained in ten years of diagnostic PCR activity for detecting M. agassizii in different species of captive tortoises in Italy, and (ii) the phylogenetic analysis of the 16S rRNA gene sequences of M. agassizii. A total of 26.0% out of 169 samples resulted positive by PCR and 32 out of 75 (42.7%) animals with symptoms were positive. Sequences ob-tained from the PCR products were conserved, differed from the sequence of the M. agassizii type strain PS6, and were identical to many M. agassizii sequences deposited in databases. In particular, the sequences were identical or very similar to sequences obtained previously from tortoises in It-aly. Since samples collected from different anatomical sites resulted positive, it is suggested that pools of conjunctival, nasal and oral swabs are tested for diagnostic purpose in both symptomatic and asymptomatic animals.

Profile of Aliarcobacter spp. from edible giblets: Genetic diversity, antibiotic resistance, biofilm formation

Aliarcobacter spp. are recognized as emerging foodborne pathogens and consumption of foods contaminated with them can be a hazard to human and animal health. This study was conducted to investigate the prevalence of Aliarcobacter spp. in edible internal organs of different animal species from retail markets and giblet sellers. Additionally, this study was focused on the antimicrobial resistance, virulence profiles, biofilm-forming capabilities, and phylogenetic relationships of obtained isolates. A total of 270 samples were analyzed from which, 28 (10.4 %) were isolated as Aliarcobacter spp. by conventional methods. Within the 28 Aliarcobacter spp. isolates, 17 (60.7 %) were identified as A. butzleri, 10 (35.7 %) were A. cryaerophilus and one (3.5 %) was A. skirrowii by PCR method. The disc diffusion method showed that the highest resistance rate of Aliarcobacter spp. was seen against oxacillin (78.5 %), and 20 (71.4 %) out of the 28 isolates exhibited multidrug resistance (MDR). Out of the 28 isolates, mviN, pldA, tlyA, and hecB virulence genes were detected in 85.7 %, 46.4 %, 46.4 %, and 3.5 %, respectively, but irgA, Cj1349, ciaB, cadF, and hecA genes were not detected. According to the microplate test, 27 (96.4 %) isolates had weak biofilm ability while one A. cryaerophilus isolate (3.6 %) exhibited strong biofilm formation. ERIC-PCR band patterns suggested that isolated Aliarcobacter spp. from giblets, have different contamination sources. The presence of pathogenic and multidrug-resistant Aliarcobacter spp. in food poses a potential risk to public health and control measures throughout the food chain are necessary to prevent the spread of these strains.

Schaalia (Formerly Actinomyces) turicensis Infection Following Open Rotator Cuff Repair

We report the case of a male in his early 70s who developed a deep infection after an open rotator cuff repair, with Schaalia turicensis as the only organism isolated from a surgical biopsy of the tendon remnants and phlegmatic/purulent material at the failed repair site. This species was originally within the genus Actinomyces. We report this case because it is the only one that we could locate where an infected open rotator cuff repair site grew S. turicensis. Our patient was not diabetic, did not smoke, and did not have other recent or concurrent infections. He had hypertension, hypothyroidism, depression, and a hyperactive bladder. Hence, he only had minor risk factors for infection. His postoperative shoulder infection was eradicated with surgical irrigation and debridement, and 6.5 weeks of primarily oral antibiotic treatment. We also review the literature on infections after any shoulder surgery where Schaalia or Actinomyces species were isolated.

Descriptions of Micromonospora grosourdyae nom. nov., Micromonospora sonchi comb. nov. and Micromonospora thawaii sp. nov. to resolve problems with the taxonomy and nomenclature of strains named Micromonospora endophytica

The name Micromonospora endophytica has been used for three different organisms. The first organism with this name is the species represented by strain DCWR9-8-2^T, a species published in 2015 but whose name was never validated. In 2019 the type species of the genus Jishengella was reclassified into the genus Micromonospora, while maintaining its original epithet, thus establishing the second group of organisms known as M. endophytica, but the first for which the name was validated. Additionally, in 2018 the reclassification of the genus Verrucosispora into the genus Micromonospora was proposed, but a new epithet has not been specified for the species named Verrucosispora endophytica, which remains an orphaned species. Therefore, it is necessary to propose new names that can unequivocally identify these taxa. We have analysed the taxonomic position of the strains, comparing them with the species with valid published names of the genus Micromonospora. We here propose Micromonospora thawaii sp. nov. for the species represented by strain DCWR9-8-2^T, and Micromonospora grosourdyae nom. nov. and Micromonospora sonchi comb. nov. for the two orphaned species of Verrucosispora, V. endophytica and Verrucosispora sonchi, respectively. Genomic analysis also showed that M. trujilloniae is a later heterotypic synonym of M. andamanensis.

Judicial Opinions 112–122

Opinion 112 denies the request to place Seliberia Aristovskaya and Parinkina 1963 (Approved Lists 1980) on the list of rejected names because the information provided is insufficient. For the same reason, Opinion 113 denies the request to reject Shewanella irciniae Lee et al. 2006 and Opinion 114 denies the request to reject the name Enterobacter siamensis Khunthongpan et al. 2014. Opinion 115 rejects the epithet of Moorella thermoautotrophica (Wiegel et al. 1981) Collins et al. 1994, which is regarded as a nomen confusum. To assess the consequences of Rule 8, Opinion 116 revisits names of taxa above the rank of genus which should comprise the stem of the name of a nomenclatural type and a category-specific ending but fail to do so. Such names should be orthographically corrected if the sole error is the inadvertent usage of an incorrect stem or be regarded as illegitimate if otherwise. The necessary corrections are made for a number of names. In Opinion 117, the request to designate Methylothermus subterraneus Hirayama et al. 2011 as the type species of the genus Methylothermus is denied because an equivalent action compatible with the Code was already conducted. In Opinion 118, the possible orthographical correction of the name Flaviaesturariibacter is treated, as are the analogous cases of Fredinandcohnia and Hydrogeniiclostidium . The genus names are corrected to Flaviaestuariibacter, Ferdinandcohnia and Hydrogeniiclostridium , respectively. Opinion 119 concludes that assigning Actinomycetales Buchanan 1917 (Approved Lists 1980) as nomenclatural type of the class Actinobacteria Stackebrandt et al. 1997 would not render that name legitimate if Rule 8 remained retroactive. The request is granted but Actinomycetales is also assigned as type of Actinomycetes Krassilnikov 1949 (Approved Lists 1980). In Opinion 120, the possible orthographical correction of the name Amycolatopsis albidoflavus is treated. It is grammatically corrected to Amycolatopsis albidoflava. Six names which could according to Rule 61 be grammatically corrected by anyone are also corrected. Opinion 121 denies the request to revise Opinion 69 and notes that Opinion 69 does not have the undesirable consequences emphasized in the request. In Opinion 122, the request to reject various taxon names of Mollicutes proposed in 2018 is denied because it is based on misinterpretations of the Code, which are clarified. Alternative ways to solve the perceived problems are outlined. These Opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.

An Unfavorable Outcome of M. chimaera Infection in Patient with Silicosis

Mycobacterium chimaera is a slow-growing, nontuberculous mycobacterium (NTM) belonging to the Mycobacterium avium complex (MAC). It was identified as a unique species in 2004. Since 2013 it has been reported as a cause of disseminated infection in patients after cardiac surgeries. Only a few cases associated with underlying lung diseases have been noted. M. chimaera infection is characterized by ambiguous symptoms. There is no treatment with proven effectiveness, and it has a poor prognosis. Silicosis is a disease that can predispose to mycobacterial infection. Silica damages pulmonary macrophages, inhibiting their ability to kill mycobacteria. We present a case of M. chimaera infection in a patient with silicosis and without other comorbidities. To our knowledge, it is the first case of silicosis associated with M. chimaera disease. A 45-year-old man presented with a persistent low-grade fever. Based on the clinical and radiological picture, positive cultures, and histological examination, the nontuberculous mycobacterial disease was diagnosed. First, multidrug therapy according to the treatment guidelines for MAC was implemented, then antibiotics were administrated, based on drug sensitivity. Despite the treatment, eradication was not achieved and the patient died. The analysis of M. chimaera infection cases could contribute to developing recommendations and thus improve the prognosis.

Common Features and Intra-Species Variation of Cutibacterium modestum Strains, and Emended Description of the Species

Cutibacterium modestum is a new species coined in 2020 as the fifth species of genus Cutibacterium, which includes Cutibacterium acnes. The species is predicted as a minor but common member of skin microbiome and includes a group tentatively named as “Propionibacterium humerusii”. The description of the species has been provided only with a single strain. To establish the characteristics of C. modestum and search for possible disease-related subtypes, we investigated the biochemical characteristics of eight live strains and performed in silico comparison of nine genomes. The common features, which included the morphology of Gram-stain positive short rods, the negativity of phenylalanine arylamidase, and several unique MALDI-TOF MS spectral peaks, were considered useful in laboratory identification. Pairwise comparisons of the genomes by in silico DNA–DNA hybridization showed similarity values of 98.1% or larger, which were far higher than the subspecies cutoff of 79–80%. The 16S rRNA gene sequences of thirteen isolates and genomes were identical. Their recA gene sequences were identical except for two strains, HM-510 (HL037PA2) and Marseille-P5998, which showed unique one-nucleotide polymorphisms. The biochemical features using API kits were slightly different among the isolates but far closer than those of the nearest other species, C. acnes and Cutibacterium namnetense. Spectra of MALDI-TOF mass spectrometry showed slight differences in the presence of m/z 10,512 (10 kD chaperonin GroS) and three other peaks, further clustering the eight isolates into three subtypes. These results indicated that these isolates did not separate to form subspecies-level clusters, but subtyping is possible by using recA gene sequences or MALDI-TOF mass spectrometry spectra. Moreover, this work has confirmed that a group “P. humerusii” is included in C. modestum.

Bacterial nomenclature in the era of genomics

The remarkable success of taxonomic discovery, powered by culturomics, genomics and metagenomics, creates a pressing need for new bacterial names while holding a mirror up to the slow pace of change in bacterial nomenclature. Here, I take a fresh look at bacterial nomenclature, exploring how we might create a system fit for the age of genomics, playing to the strengths of current practice while minimizing difficulties. Adoption of linguistic pragmatism-obeying the rules while treating recommendations as merely optional-will make it easier to create names derived from descriptions, from people or places or even arbitrarily. Simpler protologues and a relaxed approach to recommendations will also remove much of the need for expert linguistic quality control. Automated computer-based approaches will allow names to be created en masse before they are needed while also relieving microbiologists of the need for competence in Latin. The result will be a system that is accessible, inclusive and digital, while also fully capable of naming the unnamed millions of bacteria.

Taxonomic note on the family Pseudonocardiaceae based on phylogenomic analysis and descriptions of Allosaccharopolyspora gen. nov. and Halosaccharopolyspora gen. nov

The taxonomic positions of members within the family Pseudonocardiaceae were assessed based on phylogenomic trees reconstructed using core-proteome and genome blast distance phylogeny approaches. The closely clustered genome sequences from the type strains of validly published names within the family Pseudonocardiaceae were analysed using overall genome-related indices based on average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values. The family Pseudonocardiaceae consists of the type genus Pseudonocardia, as well as the genera Actinoalloteichus, Actinocrispum, Actinokineospora, Actinomycetospora, Actinophytocola, Actinopolyspora, Actinorectispora, Actinosynnema, Allokutzneria, Allosaccharopolyspora gen. nov., Amycolatopsis, Bounagaea, Crossiella, Gandjariella, Goodfellowiella, Haloactinomyces, Haloechinothrix, Halopolyspora, Halosaccharopolyspora gen. nov., Herbihabitans, Kibdelosporangium, Kutzneria, Labedaea, Lentzea, Longimycelium, Prauserella, Saccharomonospora, Saccharopolyspora, Saccharothrix, Salinifilum, Sciscionella, Streptoalloteichus, Tamaricihabitans, Thermocrispum, Thermotunica and Umezawaea. The G+C contents of the Pseudonocardiaceae genomes ranged from 66.2 to 74.6 mol% and genome sizes ranged from 3.69 to 12.28 Mbp. Based on the results of phylogenomic analysis, the names Allosaccharopolyspora coralli comb. nov., Halosaccharopolyspora lacisalsi comb. nov. and Actinoalloteichus caeruleus comb. nov. are proposed. This study revealed that Actinokineospora mzabensis is a heterotypic synonym of Actinokineospora spheciospongiae, Lentzea deserti is a heterotypic synonym of Lentzea atacamensis, Prauserella endophytica is a heterotypic synonym of Prauserella coralliicola, and Prauserella flava and Prauserella sediminis are heterotypic synonyms of Prauserella salsuginis. This study addresses the nomenclature conundrums of Actinoalloteichus cyanogriseus and Streptomyces caeruleus as well as Micropolyspora internatus and Saccharomonospora viridis.

Unravelling the eco-specificity and pathophysiological properties of Cutibacterium species in the light of recent taxonomic changes

In 2016, a new species name Cutibacterium acnes was coined for the well-documented species, Propionibacterium acnes, one of the most successful and clinically important skin commensals. The nomenclatural changes were brought about through creation of the genus Cutibacterium, when a group of propionibacteria isolates from the skin were transferred from the genus Propionibacterium and placed in the phylum Actinobacteria. Almost simultaneously, the discovery of two novel species of Cutibacterium occurred and the proposal of three subspecies of C. acnes were reported. These dramatic changes that occurred in a long-established taxon made it challenging for the non-specialist to correlate the huge volume of hitherto published work with current findings. In this review, we aim to correlate the eco-specificity and pathophysiological properties of these newly circumscribed taxa. We envisage that this information will shed light on the pathogenic potential of new isolates and enable better assessment of their clinical importance in the foreseeable future. Currently, five species are recognized within the genus: Cutibacterium acnes, Cutibacterium avidum, Cutibacterium granulosum, Cutibacterium modestum (previously, "Propionibacterium humerusii"), and Cutibacterium namnetense. These reside in different niches reflecting their uniqueness in their genetic makeup. Their pathogenicity includes acne inflammation, sarcoidosis, progressive macular hypomelanosis, prostate cancer, and infections (bone, lumbar disc, and heart). This is also the case for the three newly described subspecies of C. acnes, which are C. acnes subspecies acnes (C. acnes type I), subspecies defendens (C. acnes type II), and subspecies elongatum (C. acnes type III). C. acnes subspecies acnes is related to inflamed acne and sarcoidosis, while subspecies defendens to prostate cancer and subspecies elongatum to progressive macular hypomelanosis. Because the current nomenclature is based upon polyphasic analyses of the biochemical and pathogenic characteristics and comparative genomics, it provides a sound basis studying the pathophysiological roles of these species.

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.

Proposal of Bifidobacterium saeculare Biavati et al. 1992 as a later heterotypic synonym of Bifidobacterium gallinarum Watabe et al. 1983 and Bifidobacterium gallinarum subsp. saeculare subsp. nov

In 2018, Nouioui et al. transferred Bifidobacterium gallinarum and Bifidobacterium saeculare to Bifidobacterium pullorum as B. pullorum subsp. gallinarum and B. pullorum subsp. saeculare on the basis of digital DNA–DNA hybridization (dDDH) values. These two new subspecies were validated in the same year. However, we found that the genome (GenBank/ENA/DDBJ accession number JGZJ01000000) of B. pullorum used by Nouioui et al. in the dDDH analysis cannot represent B. pullorum . So, the taxonomic relationship between B. gallinarum , B. saeculare and B. pullorum should be re-examined. B. pullorum DSM 20433T had 88.7–89.0 % average nucleotide identity (ANI) values and 37.5–38.0 % dDDH values to the type strains of B. gallinarum and B. saeculare , respectively, less than the threshold for species demarcation, confirming that B. pullorum represents a different species from B. gallinarum and B. saeculare . The ANI values and dDDH values between the type strains of B. gallinarum and B. saeculare were 96.7–96.9 % and 73.0–73.3 %, respectively, greater than the threshold for species demarcation, confirming that they represent the same species. Relatively low dDDH values (less than the 79–80 % threshold for subspecies demarcation) between the type strains of B. gallinarum and B. saeculare indicated that B. saeculare can be considered as a subspecies of B. gallinarum . On the basis of the results presented here, (i) B. gallinarum and B. saeculare should not be transferred to B. pullorum ; (ii) we propose B. saeculare Biavati et al. 1992 as a later heterotypic synonym of B. gallinarum Watabe et al. 1983 and as a new subspecies of B. gallinarum , for which the name B. gallinarum subsp. saeculare subsp. nov. is proposed.

Cutibacterium modestum sp. nov., isolated from meibum of human meibomian glands, and emended descriptions of Cutibacterium granulosum and Cutibacterium namnetense

An anaerobic and aerotolerant bacterium, strain M12^T, was isolated from the meibum of inflamed human meibomian glands. Cells of the strain was Gram-stain-positive, non-spore-forming and non-motile rods. Growth on trypticase soy agar plates supplemented with 5 % sheep blood was fastest at 30-37 °C under anaerobic conditions. The 16S rRNA gene sequence of the strain revealed that it belongs to the genus Cutibacterium with a 98.0 % similarity value to the closest species, Cutibacterium acnes. Genome analysis of the strain with type strains of the other Cutibacterium species resulted in digital DNA-DNA hybridization values of 32.3-22.3% and average nucleotide identity (OrthoANI) values of 86.7-73.6 %. Biochemical and physiological analyses using API rapid ID 32A and API Coryne kits revealed relatively low reactivity of the strain compared with C. acnes and Cutibacterium namnetense. The most abundant major cellular fatty acid was iso-C_15 : 0. Fermentation end-products from glucose were propionate, lactate, succinate and acetate. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. Major menaquinones were MK-9(H₄), MK-9(H₂) and MK-9. The major peaks of the MALDI-TOF mass spectrometry spectrum were at 3493, 3712, 6986 and 7424 Da. The DNA G+C content was 59.9 mol%. Based on these findings, we propose a novel species, Cutibacterium modestum. The type strain of C. modestum is M12^T (=JCM 33380^T=DSM 109769^T). On the basis of further genomic analysis, we also provide emended descriptions of Cutibacterium granulosum (Prévot 1938) Scholz and Kilian 2016 and Cutibacterium namnetense (Aubin et al. 2016) Nouioui et al. 2018.

The Potato Yam Phyllosphere Ectosymbiont Paraburkholderia sp. Msb3 Is a Potent Growth Promotor in Tomato

The genus Paraburkholderia includes a variety of species with promising features for sustainable biotechnological solutions in agriculture through increasing crop productivity. Here, we present a novel Paraburkholderia isolate, a permanent and predominant member of the Dioscoreae bulbifera (yam family, Dioscoreaceae) phyllosphere, making up to 25% of the microbial community on leaf acumens. The 8.5 Mbp genome of isolate Msb3 encodes an unprecedented combination of features mediating a beneficial plant-associated lifestyle, including biological nitrogen fixation (BNF), plant hormone regulation, detoxification of various xenobiotics, degradation of aromatic compounds and multiple protein secretion systems including both T3SS and T6SS. The isolate exhibits significant growth promotion when applied to agriculturally important plants such as tomato, by increasing the total dry biomass by up to 40%. The open question about the “beneficial” nature of this strain led us to investigate ecological and generic boundaries in Burkholderia sensu lato. In a refined phylogeny including 279 Burkholderia sensu lato isolates strain Msb3 clusters within Clade I Paraburkholderia, which also includes few opportunistic strains that can potentially act as pathogens, as revealed by our ecological meta-data analysis. In fact, we demonstrate that all genera originating from the “plant beneficial and environmental” (PBE) Burkholderia species cluster include opportunists. This indicates that further functional examinations are needed before safe application of these strains in sustainable agricultural settings can be assured.

A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).

Classification of 'Streptomyces hyalinum' Hamada and Yokoyama as Embleya hyalina sp. nov., the second species in the genus Embleya, and emendation of the genus Embleya

The 16S rRNA gene sequence of 'Streptomyces hyalinum' NBRC 13850^T shows 99.7 % similarity to that of Embleya scabrispora DSM 41855^T; however, it shows <96.1 % similarity to any other type strains, including Streptomyces spp. Phylogenetic analysis based on 16S rRNA gene sequences clearly suggests that 'S. hyalinum' belongs to the genus Embleya rather than to Streptomyces. The strain possesses ll-diaminopimelic acid in the cell wall. The major menaquinone observed is MK-9(H₆), and MK-9(H₄) and MK-9(H₈) are minor components. The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. In this study, the whole genome of strain NBRC 13850^T was sequenced, and digital DNA-DNA hybridisation between 'S. hyalinum' NBRC 13850^T and E. scabrispora DSM 41855^T demonstrated 31.2 % of relatedness value between the two genomes. Morphological, chemotaxonomic, biochemical and physiological data also revealed that 'S. hyalinum' can be easily differentiated from E. scabrispora (the only the valid species of the genus Embleya) and that it merits separate species status. This phenotypic and genetic evidence reveals that 'S. hyalinum' represents a novel species of the genus Embleya; the name Embleya hyalina sp. nov. is proposed for this species. The type strain is NBRC 13850^T (=ATCC 29817^T=MB 891-A1^T). We also emended the description of the genus Embleya considering the feature of E. hyalina.

Transfer of Streptomyces catbensis Sakiyama et al. 2014 and Streptomyces seranimatus Wang et al. 2012 to Yinghuangia catbensis comb. nov. and Yinghuangia seranimata comb. nov

Phylogenetic analysis of Streptomyces catbensis VN07A0015^T and Streptomyces seranimatus YIM 45720^T based on 16S rRNA gene sequences suggested that these two strains are related to the genus Yinghuangia rather than Streptomyces. The strains form smooth spores in their spore chains and possessed ll-diaminopimelic acid in cell walls. Their main whole-cell sugars are arabinose, glucose, rhamnose and ribose, or ribose, mannose and galactose, respectively. The menaquinones are MK-9(H8), MK-9(H6) and MK-9(H4). The major polar lipids contain phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylinositol. These characteristics are consistent with the description of the genus Yinghuangia. Physiological, biochemical and chemotaxonomic data clarified that these two strains can be differentiated each other and also from Yinghuangia. aomiensis, only the valid species of the genus Yinghuangia. Therefore, S. catbensis Sakiyama et al. 2014 and S. seranimatus Wang et al. 2012 should be transferred to the genus Yinghuangia and be affiliated to different species, for which the names Yinghuangia catbensis comb. nov. (type strain VN07A0015^T=NBRC 107860^T=VTCC-A-1889^T=VTCC 41889^T) and Yinghuangia seranimata comb. nov. (type strain YIM 45720^T=CCTCC AA 206006^T=DSM 41883^T=BCRC 16903^T) are proposed.

Descriptions of Clavibacter insidiosus sp. nov. and Clavibacter tessellarius sp. nov

To complete the valid publication of the new species names resulting from reclassification of the genus Clavibacter, we here provide descriptions of Clavibacter insidiosus sp. nov. and Clavibacter tessellarius sp. nov.

Proposal of new combination, Cutibacterium acnes subsp. elongatum comb. nov., and emended descriptions of the genus Cutibacterium, Cutibacterium acnes subsp. acnes and Cutibacterium acnes subsp. defendens

In 2016, division of the genus Propionibacterium into four distinct genera was proposed. As a consequence, the species Propionibacterium acnes was transferred to Cutibacterium gen. nov. as Cutibacterium acnes comb. nov. The three recently proposed subspecies of P. acnes were not, however, accommodated in this proposal. Following a very recent validation of a new combination for C. acnes subsp. defendens and an automatically created C. acnes subsp. acnes , we now propose the new combination, C. acnes subsp. elongatum comb. nov. The type strain of Cutibacterium acnes subsp. elongatum is JCM 18919T (=NCTC 13655T). On the basis of further genomic and phenotypic (haemolysis and MALDI-TOF mass spectrometry) analyses of these subspecies, we also provide emended descriptions of the genus Cutibacterium Scholz and Kilian 2016, C. acnes subsp. acnes (Gilchrist 1900) Nouioui et al. 2018, and C. acnes subsp. defendens (McDowell et al. 2016) Nouioui et al. 2018.

Nontuberculous mycobacteria: Insights on taxonomy and evolution

Seventy years have passed since Ernest H. Runyon presented a phenotypic classification approach for nontuberculous mycobacteria (NTM), primarily as a starting point in trying to understand their clinical relevance. From numerical taxonomy (biochemical testing) to 16S rRNA gene sequencing to whole genome sequencing (WGS), our understanding of NTM has also evolved. Novel species are described at a rapid pace, while taxonomical relationships are re-defined in large part due to the accessibility of WGS. The evolutionary course of clonal complexes within species is better known for some NTM and less for others. In contrast with M. tuberculosis, much is left to learn about NTM as a whole.