Whole-genome sequencing analysis of Cutibacterium spp. recovered from health care-associated endodontic infections

OBJECTIVE

Cutibacterium acnes (C. acnes) has been detected in culture and molecular studies of endodontic microbiota, indicating its potential as a neglected pathogen in endodontic infections. This study aimed to conduct a complete genomic analysis of three Cutibacterium spp. isolates obtained from persistent endodontic infections in patients from Chile.

DESIGN

Whole genome sequencing and comprehensive genomic analysis using diverse bioinformatics platforms and databases were carried out.

RESULTS

In-silico analysis confirmed that strains A1 and E3 correspond to C. acnes species, while strain B1 corresponds to C. namnetense. Additionally, C. acnes strain A1 belongs to the phylotype IA1, sequence type (ST) 4 and belongs to the clonal complex (CC) 4, whereas C. acnes strain E3 belongs to a novel ST. No antibiotic resistance, however, a variable distribution and identity of the VF was found.

CONCLUSIONS

Detailed analysis of genes associated with virulence factors shed light on the intrinsic pathogenic capacity of these strains, which may indicate differential adaptation to their specific niches or diversity in pathogenicity within the species.

Whole genome sequencing distinguishes skin colonizing from infection-associated Cutibacterium acnes isolates

Introduction

Cutibacterium acnes can both be a helpful colonizer of the human skin as well as the causative agent of acne and purulent infections. Until today, it is a moot point whether there are C. acnes strains exclusively devoted to be part of the skin microbiome and others, that carry special features enabling them to cause disease. So far, the search for the molecular background of such diverse behavior has led to inconsistent results.

Methods

In the present study, we prospectively collected C. acnes strains from 27 infected persons and 18 healthy controls employing rigid selection criteria to ensure their role as infectious agent or colonizer. The genome sequences from these strains were obtained and carefully controlled for quality.

Results

Deduced traditional phylotyping assigned almost all superficial isolates to type IA1, while the clinical strains were evenly distributed between types IA1, IB, and II. Single locus sequence typing (SLST) showed a predominance of A1 type for the control strains, whereas 56% of the clinical isolates belonged to types A1, H1 and K8. Pangenome analysis from all the present strains and 30 published genomes indicated the presence of an open pangenome. Except for three isolates, the colonizing strains clustered in clades separate from the majority of clinical strains, while 4 clinical strains clustered with the control strains. Identical results were obtained by a single nucleotide polymorphism (SNP) analysis. However, there were no significant differences in virulence gene contents in both groups.

Discussion

Genome-wide association studies (GWAS) from both the pangenome and SNP data consistently showed genomic differences between both groups located in metabolic pathway and DNA repair genes. Thus, the different behavior of colonizing and infectious C. acnes strains could be due to special metabolic capacities or flexibilities rather than specific virulence traits.

Cutibacterium adaptation to life on humans provides a novel biomarker of C. acnes infections

The domestication of cattle provided Propionibacteriaceae the opportunity to adapt to human skin. These bacteria constitute a distinct genus ( Cutibacterium ), and a single species within that genus ( C. acnes ) dominates 25% of human skin. C. acnes protects humans from pathogen colonization, but it can also infect indwelling medical devices inserted through human skin. Proteins that help Cutibacteria live on our skin may also act as virulence factors during an opportunistic infection, like a shoulder periprosthetic joint infection (PJI). To better understand the evolution of this commensal and opportunistic pathogen, we sought to extensively characterize one of these proteins, RoxP. This secreted protein is only found in the Cutibacterium genus, helps C. acnes grow in oxic environments, and is required for C. acnes to colonize human skin. Structure-based sequence analysis of twenty-one RoxP orthologs (71-100% identity to C. acnes strain KPA171202 RoxP_1) revealed a high-degree of molecular surface conservation and helped identify a potential heme-binding interface. Biophysical evaluation of a subset of seven RoxP orthologs (71-100% identity) demonstrated that heme-binding is conserved. Computational modeling of these orthologs suggests that RoxP heme-binding is mediated by an invariant molecular surface composed of a surface-exposed tryptophan (W66), adjacent cationic pocket, and nearby potential heme axial ligands. Further, these orthologs were found to undergo heme-dependent oligomerization. To further probe the role of this protein in C. acnes biology, we developed four monoclonal anti-RoxP antibodies, assessed the binding of those antibodies to a subset of ten RoxP orthologs (71-100% identity), developed an anti-RoxP sandwich ELISA (sELISA) with sub-nanogram sensitivity, and adapted that sELISA to quantitate RoxP in human biofluids that can be infected by C. acnes (serum, synovial fluid, cerebrospinal fluid). This study expands our understanding of how an environmental bacterium evolved to live on humans, and the assays developed in this work can now be used to identify this organism when it gains access to sterile sites to cause opportunistic infections.

Author Summary

The longer humans live, the more they require internal "replacement parts," like prosthetic joints. Increased placement of these and other medical devices has increased their complications, which frequently are infections caused by microbes that live on humans. One of these microbes is Cutibacterium acnes , which dominates 25% of human skin. It appears that when humans domesticated cattle, a C. acnes ancestor adapted from living in cows to living on people. One of these adaptations was RoxP, a protein only found in Cutibacterium and carried by all C. acnes . Here, we describe our extensive characterization of RoxP. We found that distantly related RoxP conserve high stability at the low pH found on human skin. They also conserve the ability to bind heme, a source of iron used by microbes when they infect humans. As a part of this work, we developed tests that measure RoxP to identify C. acnes growth. In a clinic or hospital, these tests could allow a doctor to rapidly identify C. acnes infections, which would improve patient outcomes and lower healthcare costs. This work has helped us better understand how C. acnes adapted to live on humans and to identify C. acnes infections of medical devices.

Oily fish reduces the risk of acne by lowering fasting insulin levels: A Mendelian randomization study

Meat intake, particularly from oily fish, has been associated with various chronic diseases. However, its relationship with acne has always been controversial. Therefore, we have adopted Mendelian randomization (MR) analysis to investigate the causal relationship between different types of meat intake and acne. The exposure and outcome datasets for this study were obtained from the Integrative Epidemiology Unit (IEU) Open GWAS project. Seven datasets on meat intake were included, which consisted of non-oily fish, oily fish, lamb/mutton, poultry, pork, beef, and processed meat. The main methods used for MR analysis were inverse variance weighted, weighted median, and MR-egger. To ensure the accuracy of the results, heterogeneity, pleiotropy, and Mendelian randomization pleiotropy residual sum and outlier (MR-PRESSO) analyses were conducted. Additionally, an analysis of four risk factors (fasting insulin, insulin resistance, total testosterone level, and estradiol level) was performed to investigate the underlying mechanisms linking statistically significant meat intake to acne. Oily fish intake was found to be a protective factor for acne (OR: 0.22, 95% CI: 0.10-0.49, p < .001), and it was also observed that oily fish intake can reduce the level of fasting insulin by the IVW method (OR: 0.89, 95% CI: 0.81-0.98, p = .02). No causal relationship was identified between other types of meat intake and acne. The intake of oily fish reduces the risk of acne by lowering fasting insulin levels.

Comprehensive lipidomic analysis of the genus Cutibacterium

Cutibacterium are part of the human skin microbiota and are opportunistic microorganisms that become pathogenic in immunodeficient states. These lipophilic bacteria willingly inhabit areas of the skin where sebaceous glands are abundant; hence, there is a need to thoroughly understand their metabolism. Lipids are no longer considered only structural elements but also serve as signaling molecules and may have antigenic properties. Lipidomics remains a major research challenge, mainly due to the diverse physicochemical properties of lipids. Therefore, this study aimed to perform a large comparative lipidomic analysis of eight representatives of the Cutibacterium genus, including four phylotypes of C. acnes and two strains of C. granulosum, C. avidum, and C. namnetense. Lipidomic analysis was performed by liquid chromatography‒mass spectrometry (LC-MS) in both positive and negative ion modes, allowing the detection of the widest range of metabolites. Fatty acid analysis by gas chromatography‒mass spectrometry (GC-MS) corroborated the lipidomic data. As a result, 128 lipids were identified, among which it was possible to select marker compounds, some of which were characteristic even of individual C. acnes phylotypes. These include phosphatidylcholine PC 30:0, sphingomyelins (SM 33:1, SM 35:1), and phosphatidylglycerol with an alkyl ether substituent PG O-32:0. Moreover, cardiolipins and fatty acid amides were identified in Cutibacterium spp. for the first time. This comparative characterization of the cutibacterial lipidome with the search for specific molecular markers reveals its diagnostic potential for clinical microbiology.

IMPORTANCE

Cutibacterium (previously Propionibacterium) represents an important part of the human skin microbiota, and its role in clinical microbiology is growing due to opportunistic infections. Lipidomics, apart from protein profiling, has the potential to prove to be a useful tool for defining the cellular fingerprint, allowing for precise differentiation of microorganisms. In this work, we presented a comparative analysis of lipids found in eight strains of the genus Cutibacterium, including a few C. acnes phylotypes. Our results are one of the first large-scale comprehensive studies regarding the bacterial lipidome, which also enabled the selection of C. acnes phylotype-specific lipid markers. The increased role of lipids not only as structural components but also as diagnostic markers or potential antigens has led to new lipid markers that can be used as diagnostic tools for clinical microbiology. We believe that the findings in our paper will appeal to a wide range of researchers.

The Microbiome and Acne: Perspectives for Treatment

The skin microbiome consists of the microorganisms populating the human skin. Cutibacterium acnes (C. acnes, formerly named Propionibacterium acnes) is recognized as a key factor in acne development, regulating inflammatory and immune pathways. Dysbiosis has been described as the imbalance in skin microbiome homeostasis and may play a role in acne pathogenesis. Microbial interference has been shown to be a contributor to healthy skin homeostasis and staphylococcal strains may exclude acne-associated C. acnes phylotypes. In this review we present an update on the skin microbiome in acne and discuss how current acne treatments such as benzoyl peroxide, orally administered isotretinoin, and antibiotics may affect the skin microbiome homeostasis. We highlight the collateral damage of acne antibiotics on the skin microbiome, including the risk of antimicrobial resistance and the dysregulation of the microbiome equilibrium that may occur even with short-term antibiotic courses. Consequently, the interest is shifting towards new non-antibiotic pharmacological acne treatments. Orally administered spironolactone is an emerging off-label treatment for adult female patients and topical peroxisome proliferator-activated receptor gamma (PPARγ) modulation is being studied for patients with acne. The potential application of topical or oral probiotics, bacteriotherapy, and phage therapy for acne are further promising areas of future research.

"Are we barking up the wrong tree? Too much emphasis on Cutibacterium acnes and ignoring other pathogens"- a study based on next-generation sequencing of normal and diseased discs

BACKGROUND

The majority of literature on bacterial flora in the disc stands disadvantaged in utilizing traditional culture methods and targeting a single bacterium, Cutibacterium acnes.

PURPOSE

Our objective was to document the diversity in the bacterial flora between normal and degenerated discs for shortlisting potential pathogens using next-generation genomic tools.

STUDY DESIGN

Experimental case-control study.

METHODS

Researchers employed 16S metagenome sequencing to profile bacterial diversity in magnetic resonance imaging normal healthy discs from brain-dead organ voluntary donors (n=20) and 40 degenerated disc samples harvested during surgery (Modic [MC]=20 and non-Modic [NMC]=20). The V3-V4 region was amplified using universal bacterial primers 341F and 806R, and the libraries were sequenced using Illumina NovoSeq 6000 platform. Statistical significance was set at bacteria with a minimum of 100 operational taxonomic unit (OTU) and present in at least 70% of the samples. The quality check-filtered reads were processed using the QIIME-2 pipeline. The OTU clustering and taxonomic classification were carried out for the merged reads using the Greengenes/SILVA reference database. Validation was done by identification of bacterial metabolites in samples using the liquid chromatography-mass spectrometry approach.

RESULTS

Abundant bacteria differing widely in diversity, as evidenced by Alfa and Beta diversity analysis, were present in all control and degenerative samples. The number of bacterial genera was 27 (14-gram-positive: 13-gram-negative) in the control group, 23 (10-gram-positive: 11-gram-negative) in the Modic group, and 16 (11-gram-positive: 5-gram-negative) in the non-Modic group. In the Modic group, gram-negative bacteria OTUs were found to be predominant (more than 50% of the total bacteria identified), whereas in control and non-Modic groups the OTUs of gram-positive bacteria were predominant. Species-level analysis revealed an abundance of opportunistic gram-negative pathogens like Pseudomonas aeruginosa, Sphingomonos paucibacillus, and Ochrobactrum quorumnocens in the discs with Modic changes, more than in non-Modic discs. The presence of bacterial metabolites and quorum-sensing molecules like N-decanoyl-L-homoserine lactone, 6-hydroxynicotinic acid, 2-aminoacetophenone, 4-hydroxy-3-polyprenylbenzoate, PE (16:1(9Z)/18:0) and phthalic acid validated the colonization and cell-cell communication of bacteria in disc ruling out contamination theory. Cutibacterium acnes was not the predominant bacteria in any of the three groups of discs and in fact was in the 16th position in the order of abundance in the control discs (0.72%), seventh position in the Modic discs (1.41%), and 12th position (0.53%) in the non-Modic discs.

CONCLUSION

This study identified a predominance of gram-negative bacteria in degenerated discs and highlights that Cutibacterium acnes may not be the only degeneration-causing bacteria. This may be attributed to the environment, diet, and lifestyle habits of the sample population. Though the study does not reveal the exact pathogen, it may pave the way for future studies on the subject.

CLINICAL SIGNIFICANCE

These findings invite further investigation into causal relationships of bacterial profile with disc degeneration phenotypes as well as phenotype-driven clinical treatment protocols.

CUTIS-SEQ, a flexible bilocus sequence typing scheme that provides high resolution of Cutibacterium acnes strains across all subspecies

OBJECTIVES

A 'high resolution' Single Locus Sequence Typing (SLST) scheme has been described for the anaerobic skin bacterium Cutibacterium acnes that seemingly discriminates sequence types (STs) to a level commensurate with previously described Multilocus Sequence Typing (MLST) methods (MLST₄; MLST₈; MLST₉). However, no quantifiable evaluation of SLST versus MLST for differentiation of C. acnes strains, especially in relation to the subspecies of the bacterium, known as C. acnes subsp. acnes (type I), C. acnes subsp. defendens (type II) and C. acnes subsp. elongatum (type III), has been performed which is vital given its increasing use. To address this, we examined the discriminatory power of SLST versus MLST with a large group of isolates representative of all subspecies.

METHODS

Simpson's index of diversity (D) was used for quantitative comparison of the resolving power of the SLST and MLST schemes for 186 isolates of C. acnes covering all three subspecies.

RESULTS

When strains were considered collectively, SLST and all three MLST approaches had similar D values > 90%. However, at the subspecies level there were significant differences between the methods, most strikingly a reduced discrimination of type II and type III strains (D <80%) by SLST versus MLST₈, and to a lesser extent MLST₄. The MLST₉ method also performed poorly for type II strains (D <70%), but did display the best results for type I (D = 90%). By combining the SLST locus with the camp2 gene sequence to create a novel and flexible high-resolution Bilocus Sequence Typing (BLST) scheme, known as CUTIS-SEQ typing (CUTIbacterium acneS BilocuS sEQuence Typing), we achieved improved resolution at both species and, critically, subspp. levels.

CONCLUSIONS

CUTIS-SEQ provides an opportunity to improve differentiation of C. acnes isolates by SLST without significantly impacting laboratory workload, or compromising application to complex biological communities. A CUTIS-SEQ isolate database is now available as part of the C. acnes PubMLST database at https://pubmlst.org.

Nutritional Interactions between Bacterial Species Colonising the Human Nasal Cavity: Current Knowledge and Future Prospects

The human nasal microbiome can be a reservoir for several pathogens, including Staphylococcus aureus. However, certain harmless nasal commensals can interfere with pathogen colonisation, an ability that could be exploited to prevent infection. Although attractive as a prophylactic strategy, manipulation of nasal microbiomes to prevent pathogen colonisation requires a better understanding of the molecular mechanisms of interaction that occur between nasal commensals as well as between commensals and pathogens. Our knowledge concerning the mechanisms of pathogen exclusion and how stable community structures are established is patchy and incomplete. Nutrients are scarce in nasal cavities, which makes competitive or mutualistic traits in nutrient acquisition very likely. In this review, we focus on nutritional interactions that have been shown to or might occur between nasal microbiome members. We summarise concepts of nutrient release from complex host molecules and host cells as well as of intracommunity exchange of energy-rich fermentation products and siderophores. Finally, we discuss the potential of genome-based metabolic models to predict complex nutritional interactions between members of the nasal microbiome.

Different Cutibacterium acnes Phylotypes Release Distinct Extracellular Vesicles

Bacterial extracellular vesicles (EVs) perform various biological functions, including those that are critical to microbes. Determination of EVs composition allows for a deep understanding of their role in the bacterial community and communication among them. Cutibacterium acnes, formerly Propionibacterium acnes, are commensal bacteria responsible for various infections, e.g., prosthesis, sarcoidosis, soft-tissue infections, and the most known but still controversial—acnes lesion. In C. acnes, three major phylotypes represented variable disease associations. Herein, for the first time, we present a comparative analysis of EVs obtained from three C. acnes phylotypes (IA1, IB, and II) to demonstrate the existence of differences in their protein and lipid composition. In the following work, the morphological analysis of EVs was performed, and the SDS-PAGE protein profile and the lipid profile were presented using the TLC and MALDI-TOF MS methods. This study allowed us to show major differences between the protein and lipid composition of C. acnes EVs. This is a clear indication that EVs released by different phylotypes of the one species are not identical to each other in terms of composition and should be separately analyzed each time to obtain reliable results.

A case report of native vertebral osteomyelitis caused by Cutibacterium modestum

Background

Cutibacterium modestum was named in 2020. C. modestum was previously called Propionibacterium humerusii. Several implant-associated infections caused by Cutibacterium species have been previously reported, but native vertebral osteomyelitis due to these bacteria has rarely been reported.

Case presentation

A 72-year-old man, who had previously received several nerve block injections for low back pain, was referred to our hospital for deterioration in back pain in the last 1 month. MRI findings were suggestive of L5-S1 vertebral osteomyelitis. Blood cultures and bone biopsy culture revealed the presence of Gram-positive bacilli. The isolate was identified as C. modestum by 16SrRNA gene sequencing. A diagnosis of vertebral osteomyelitis caused by C. modestum was made. Minocycline followed by oral amoxicillin was administered for 3 months. His symptom improved and did not recur after treatment completion.

Conclusion

A case of vertebral osteomyelitis caused by C. modestum was encountered. Although C. modestum is very similar to C. acnes, it could be accurately identified by 16SrRNA gene sequencing. This case represents the first documented C. modestum infection in humans.

Vertebral osteomyelitis caused by the novel pathogen Cutibacterium modestum: a case report

Background

Cutibacterium modestum is one of the five species of the genus Cutibacterium. While C. acnes has been reported as an important pathogen in bone and joint infections, the clinical characteristics of C. modestum infections remain unclear. Moreover, thus far, there has been no clinical case report regarding C. modestum infections.

Case presentation

An 82-year-old man with a history of repeated trigger point injections for lumbago at the L4 level presented with fever and an exacerbation of lumbago. Physical examination indicated knocking pain at the L4–L5 levels; magnetic resonance imaging showed irregular bone destruction of the L4 vertebral body, and low T1 and high T2 intensity lesions at the L4–L5 intervertebral disc. Two sets of blood cultures (two aerobic and two anaerobic) were performed. Intravenous cefazolin was administered, considering the common pathogens of vertebral osteomyelitis, such as Staphylococcus aureus. The patient’s condition did not improve; thereafter, anaerobic culture bottles revealed Gram-positive rods on day 11 of incubation. There was no evidence of infective endocarditis upon transthoracic echocardiography. Needle aspiration from the L4–L5 intervertebral disc was performed on day 13 that also showed the presence of Gram-positive rods. The patient was diagnosed with vertebral osteomyelitis caused by C. modestum using a combination of characteristic peak analysis with matrix-assisted laser desorption ionization (MALDI), microbial biochemistry examinations, and 16S rRNA gene sequencing from the blood and pus cultures. He was successfully treated with alternative intravenous ampicillin, followed by oral amoxicillin for 10 weeks, according to the tests for ampicillin susceptibility, with a minimum inhibitory concentration of 0.016 μg/mL using E-test® under aerobic conditions.

Conclusions

Cutibacterium modestum is a microorganism that is difficult to identify. A combination of characteristic peaks with MALDI, appropriate microbial biochemical examinations, and 16S rRNA gene sequencing may serve as an efficient guide for the identification of C. modestum.

Microbiome and Probiotics in Acne Vulgaris—A Narrative Review

Acne vulgaris is a chronic disease characterised by the appearance of eruptions such as whiteheads, blackheads, pustules, papules, and cysts. Among factors that cause acne vulgaris are the abnormal keratinisation of the sebaceous canal, bacterial colonisation (Cutibacterium acnes), increased sebum production, genotypic factors, and hormonal disorders. Treatment is often long and tedious, and can lead to a reduction in quality of life and social isolation. The intestinal microbiota is greatly important in the formation of acne lesions. It is also responsible for the proper immunity of the organism. Acne is a disease that can be related to the condition of the digestive tract and its microbiome. Research shows that the use of probiotics may reduce skin eruptions. The probiotic supplementation and cosmetics markets are very dynamically developing. The use of internal supplementation and probiotic-containing cosmetics gives hope for the improvement of the skin condition of people with acne.

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.

Comparative Genomic Analyses and CRISPR-Cas Characterization of Cutibacterium acnes Provide Insights Into Genetic Diversity and Typing Applications

Cutibacterium acnes is an important member of the human skin microbiome and plays a critical role in skin health and disease. C. acnes encompasses different phylotypes that have been found to be associated with different skin phenotypes, suggesting a genetic basis for their impact on skin health. Here, we present a comprehensive comparative analysis of 255 C. acnes genomes to provide insights into the species genetic diversity and identify unique features that define various phylotypes. Results revealed a relatively small and open pan genome (6,240 genes) with a large core genome (1,194 genes), and three distinct phylogenetic clades, with multiple robust sub-clades. Furthermore, we identified several unique gene families driving differences between distinct C. acnes clades. Carbohydrate transporters, stress response mechanisms and potential virulence factors, potentially involved in competitive growth and host colonization, were detected in type I strains, which are presumably responsible for acne. Diverse type I-E CRISPR-Cas systems and prophage sequences were detected in select clades, providing insights into strain divergence and adaptive differentiation. Collectively, these results enable to elucidate the fundamental differences among C. acnes phylotypes, characterize genetic elements that potentially contribute to type I-associated dominance and disease, and other key factors that drive the differentiation among clades and sub-clades. These results enable the use of comparative genomics analyses as a robust method to differentiate among the C. acnes genotypes present in the skin microbiome, opening new avenues for the development of biotherapeutics to manipulate the skin microbiota.

Trichococcus shcherbakoviae subsp. psychrophilus subsp. nov., a psychrotolerant facultative anaerobe isolated from a cold spring

A psychrotolerant facultative anaerobe, strain SKBG^T, was isolated from the bottom sediments of the cold mineral spring Buxichen (Buryatia, Russia). Gram-positive non-motile cocci with a diameter of 1.75-2.5 µm were observed singly or in long chains. Cells grew in the temperature range from ̶ 5-35 °C. Growth was observed within the pH range of 7.0-9.5, with the optimum growth at pH 7.6 and at a NaCl concentration from 0-1.0 % (optimum 0.1 % (w/v)). Strain SKBG^T was a chemoorganoheterotroph that used sugars and some organic acids as substrates. The predominant fatty acids in cell walls were С_16:1ω9, С_18:1ω9, and С_16 : 0. The 16S rRNA gene sequence of strain SKBG^T shared high similarity (>99 %) with those of the type strains of the genus Trichococcus. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain SKBG^T and Trichococcus shcherbakoviae Art^T (=DSM 107162^T=VKM B-3260^T) were 70.1 and 95.4 %, respectively. The genomic DNA G+C content of strain SKBG^T was 47.1 mol%. Compared with the type strain of T. shcherbakoviae, the new strain was characterized by a temperature optimum for growth (10 °C) significantly lower than that of T. shcherbakoviae DSM 107162^T (20-30 °C). Based on phenotypic and genomic characteristics, the isolate SKBG^T was classified as T. shcherbakoviae subsp. psychrophilus subsp. nov. The type strain is SKBG^T (=VKM B-3241^Т=JCM 33326^T).

Cutibacterium acnes phylogenetic type IC and II isolated from patients with non-acne diseases exhibit high-level biofilm formation

Cutibacterium (formerly Propionibacterium) acnes is an important for not only exacerbating factor of acne vulgaris but also pathogen of surgical site infections (SSIs) in orthopedics and plastic surgery. Although biofilm-forming (BF) C. acnes are associated with intractable SSI, characteristics of these strains were still unknown. Here, we explored detailed molecular epidemiological features of BF C. acnes isolated as causative pathogen of infectious diseases. Phylogenetic types of 205 C. acnes strains isolated between 2013 and 2018 from 18 clinical departments of a university hospital in Japan were determined by single-locus sequence type (SLST). Clade H (traditional type IC) and K (type II) which are less relevant with healthy skin and acne vulgaris, were detected in 26.8% (55/205) and 16.1% (33/205) of the strains, respectively. The incidence of them was significantly higher than that of acne patients (H and K, each 2.9%, P < 0.05). In addition, SLST distribution of C. acnes strains differed by each department and isolation site. When biofilm formation was quantified, 51 strains (24.9%) were defined as high-BF strains. Notably, most high-BF strains were classified into the strains of clade H (56.4%, 31/55) and clade K (54.4%, 18/33), and these strains were frequently found in the strains isolated from patients of medical emergency center and plastic surgery. Similarly, high-BF strains were frequently found among the isolates from blood (35.7%) and catheters (30.0%), with a high proportion belonging to clades H and K. Compared to C. acnes strains isolated from acne patients, antimicrobial-resistant strains were less identified in non-acne patients. Our findings showed that pathogenicity of C. acnes strains differs by their phylogenetic types. Furthermore, we showed clade H and K have the ability of high biofilm formation and suggest that these strains have potential to become a risk factor for SSI.

Wastewater from the Edible Oil Industry as a Potential Source of Lipase- and Surfactant-Producing Actinobacteria

Wastewaters generated from various stages of edible oil production in a canola processing facility were collected with the aim of determining the presence of lipase-producing actinobacteria of potential industrial significance. The high chemical oxygen demand (COD) readings (up to 86,700 mg L⁻¹ in some samples) indicated that the wastewater exhibited the nutritional potential to support bacterial growth. A novel approach was developed for the isolation of metagenomic DNA from the oil-rich wastewater samples. Microbiota analysis of the buffer tank and refinery condensate tank wastewater samples showed a dominance of Cutibacterium acnes subsp. defendens, followed by a limited number of other actinobacterial genera, indicating the presence of a highly specialized actinobacterial population. Cultured isolates with typical actinobacterial morphology were analyzed for their ability to produce lipases and biosurfactants. Two strains, designated as BT3 and BT4, exhibited the highest lipase production levels when grown in the presence of tributyrin and olive oil (1.39 U mg⁻¹ crude protein and 0.8 U mg⁻¹ crude protein, respectively) and were subsequently definitively identified by genome sequencing to be related to Streptomyces albidoflavus. Cultivation of the strains in media containing different types of oils did not markedly increase the level of enzyme production, with the exception of strain BT4 (1.0 U mg⁻¹ crude protein in the presence of peanut oil). Genome sequencing of the two strains, BT3 and BT4, revealed the presence of a range of lipase and esterase genes that may be involved in the production of the enzymes detected in this study. The presence of gene clusters involved in the production of biosurfactants were also detected, notably moreso in strain BT3 than BT4.

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.

What Do We See in Spectra?: Assignment of High-Intensity Peaks of Cutibacterium and Staphylococcus Spectra of MALDI-TOF Mass Spectrometry by Interspecies Comparative Proteogenomics

Matrix-assisted laser-desorption/ionization time-of-flight (MALDI–TOF) mass spectrometry is a widely used and reliable technology to identify microbial species and subspecies. The current methodology is based on spectral fingerprinting, analyzing protein peaks, most of which are yet to be characterized. In order to deepen the understanding of these peaks and to develop a more reasonable identification workflow, we applied proteogenomic approaches to assign the high-intensity peaks of MALDI–TOF spectra of two bacterial genera. First, the 3–22 kD proteomes of 5 Cutibacterium strains were profiled by UPLC–MS/MS, and the amino acid sequences were refined by referring to their genome in the public database. Then, the sequences were converted to m/z (x-axis) values based on their molecular masses. When the interspecies comparison of calculated m/z values was well-fitted to the observed peaks, the peak assignments for the five Cutibacterium species were confirmed. Second, the peak assignments for six Staphylococcus species were performed by using the above result for Cutibacterium and referring to ribosomal subunit proteins coded on the S10-spc-alpha operon (the S10-GERMS method), a previous proteomics report by Becher et al., and comprehensive genome analysis. We successfully assigned 13 out of 15 peaks for the Cutibacterium species and 11 out of 13 peaks for the Staphylococcus species. DNA-binding protein HU, the CsbD-like protein, and 50S ribosomal protein L7/L12 were observed in common. The commonality suggests they consist of high-intensity peaks in the MALDI spectra of other bacterial species. Our workflow may lead to the development of a more accurate species identification database of MALDI–TOF mass spectrometry based on genome data.

A Janus-Faced Bacterium: Host-Beneficial and -Detrimental Roles of Cutibacterium acnes

The bacterial species Cutibacterium acnes (formerly known as Propionibacterium acnes) is tightly associated with humans. It is the dominant bacterium in sebaceous regions of the human skin, where it preferentially colonizes the pilosebaceous unit. Multiple strains of C. acnes that belong to phylogenetically distinct types can co-exist. In this review we summarize and discuss the current knowledge of C. acnes regarding bacterial properties and traits that allow host colonization and play major roles in host-bacterium interactions and also regarding the host responses that C. acnes can trigger. These responses can have beneficial or detrimental consequences for the host. In the first part of the review, we highlight and critically review disease associations of C. acnes, in particular acne vulgaris, implant-associated infections and native infections. Here, we also analyse the current evidence for a direct or indirect role of a C. acnes-related dysbiosis in disease development or progression, i.e., reduced C. acnes strain diversity and/or the predominance of a certain phylotype. In the second part of the review, we highlight historical and recent findings demonstrating beneficial aspects of colonization by C. acnes such as colonization resistance, immune system interactions, and oxidant protection, and discuss the molecular mechanisms behind these effects. This new insight led to efforts in skin microbiota manipulation, such as the use of C. acnes strains as probiotic options to treat skin disorders.

Genomic description and characterization of Nigeribacterium massiliense gen. nov., sp. nov., isolated from the human gut

Strain Marseille-P1302 was isolated from the stool of a 2-year-old Nigerian boy suffering from Kwashiorkor, a form of severe acute malnutrition. The strain grows in aerobic atmosphere and bacterial cells are Gram-positive cocci ranging in diameter from 0.8 to 1 μm. Strain Marseille-P1302 exhibits a 16S rRNA sequence similarity of 94.97% with Brevilactibacter flavus strain VG341^T, but phylogenetically-closest species with standing in nomenclature is Brevilactibacter sinopodophylli strains KCTC 33808^Twith the sequence similarity of 93.41%. The draft genome of strain Marseille-P1302 is 2,934,258bp-long with a 70.38% G+C content, and contains 2,704 protein-coding genes and 55 RNAs that includes 9 rRNA genes. On the basis of these data, we propose the creation of the new genus Nigeribacterium gen. nov., with strain Marseille-P1302^T (= CSUR P1302 = DSM 29084) being the type strain of new species Nigeribacterium. massiliense gen. nov., sp. nov.

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.

Echocardiographic Findings in Children with Native Mitral Valve Masses Complicated by Systemic Embolization

• Case of mitral valve IMT with embolization. • Case of Streptococcus pneumoniae mitral valve endocarditis with embolization. • Use of 2D and 3D echocardiography for management of mitral valve masses.

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.

Complete Genome Sequences and Methylome Analyses of Cutibacterium acnes subsp. acnes Strains DSM 16379 and DSM 1897T

Cutibacterium acnes is a member of the normal human skin microbiome. However, it is also associated with skin disorders and persistent infections of orthopedic implants. Here, we announce complete genome sequences and methylomes of the C. acnes subsp. acnes strains DSM 1897^T and DSM 16379 together with their active restriction-modification systems.

Cutibacterium acnes is a member of the normal human skin microbiome. However, it is also associated with skin disorders and persistent infections of orthopedic implants. Here, we announce complete genome sequences and methylomes of the C. acnes subsp. acnes strains DSM 1897^T and DSM 16379 together with their active restriction-modification systems.

Red-Brown Pigmentation of Acidipropionibacterium jensenii Is Tied to Haemolytic Activity and cyl-Like Gene Cluster

The novel Acidipropionibacterium genus encompasses species of industrial importance but also those associated with food spoilage. In particular, Acidipropionibacterium acidipropionici, Acidipropionibacterium thoenii, and Acidipropionibacterium jensenii play an important role in food fermentation, as biopreservatives, or as potential probiotics. Notably, A. jensenii and A. thoenii can cause brown spot defects in Swiss-type cheeses, which have been tied to the rhamnolipid pigment granadaene. In the pathogenic bacterium Streptococcus agalactiae, production of granadaene depends on the presence of a cyl gene cluster, an important virulence factor linked with haemolytic activity. Here, we show that the production of granadaene in pigmented Acidipropionibacterium, including A. jensenii, A. thoenii, and Acidipropionibacterium virtanenii, is tied to haemolytic activity and the presence of a cyl-like gene cluster. Furthermore, we propose a PCR-based test, which allows pinpointing acidipropionibacteria with the cyl-like gene cluster. Finally, we present the first two whole genome sequence analyses of the A. jensenii strains as well as testing phenotypic characteristics important for industrial applications. In conclusion, the present study sheds light on potential risks associated with the presence of pigmented Acidipropionibacterium strains in food fermentation. In addition, the results presented here provide ground for development of a quick and simple diagnostic test instrumental in avoiding potential negative effects of Acidipropionibacterium strains with haemolytic activity on food quality.

Propionibacterium acnes and Acne Vulgaris: New Insights from the Integration of Population Genetic, Multi-Omic, Biochemical and Host-Microbe Studies

The anaerobic bacterium Propionibacterium acnes is believed to play an important role in the pathophysiology of the common skin disease acne vulgaris. Over the last 10 years our understanding of the taxonomic and intraspecies diversity of this bacterium has increased tremendously, and with it the realisation that particular strains are associated with skin health while others appear related to disease. This extensive review will cover our current knowledge regarding the association of P. acnes phylogroups, clonal complexes and sequence types with acne vulgaris based on multilocus sequence typing of isolates, and direct ribotyping of the P. acnes strain population in skin microbiome samples based on 16S rDNA metagenomic data. We will also consider how multi-omic and biochemical studies have facilitated our understanding of P. acnes pathogenicity and interactions with the host, thus providing insights into why certain lineages appear to have a heightened capacity to contribute to acne vulgaris development, while others are positively associated with skin health. We conclude with a discussion of new therapeutic strategies that are currently under investigation for acne vulgaris, including vaccination, and consider the potential of these treatments to also perturb beneficial lineages of P. acnes on the skin.