Actinomyces dentalis sp. nov., from a human dental abscess

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.

The Oral Microbiome as Mediator between Oral Hygiene and Its Impact on Nasopharyngeal Carcinoma

Oral hygiene and the alteration of the oral microbiome have been linked to nasopharyngeal carcinoma (NPC). This study aimed to investigate whether the oral microbiome plays a mediating role in the relationship between oral hygiene and NPC, and identify differential microbial taxonomies that potentially mediated this association. We conducted a case–control study that involved 218 NPC patients and 192 healthy controls. The 16S rRNA gene sequencing of the V4 region was performed to evaluate the composition of the oral microbiome. Mediation analysis was applied to explore the relationship among oral hygiene, the oral microbiome and NPC. We found that dental fillings and poor oral hygiene score were associated with increased risks of NPC (OR = 2.51 (1.52–4.25) and OR = 1.54 (1.02–2.33)). Mediation analysis indicated that dental fillings increased the risk of NPC by altering the abundance of Erysipelotrichales, Erysipelotrichaceae, Solobacterium and Leptotrichia wadei. In addition, Leptotrichia wadei also mediated the association between oral hygiene score and the risk of NPC. Our study confirmed that poor oral hygiene increased the risk of NPC, which was partly mediated by the oral microbiome. These findings might help us to understand the potential mechanism of oral hygiene influencing the risk of NPC via the microbiome.

Actinomyces wuliandei sp. nov., Corynebacterium liangguodongii sp. nov., Corynebacterium yudongzhengii sp. nov. and Oceanobacillus zhaokaii sp. nov., isolated from faeces of Tibetan antelope in the Qinghai-Tibet plateau of China

Eight Gram-stain-positive, rod-shaped bacterial strains were isolated from faeces of Tibetan antelopes on the Tibet-Qinghai Plateau of China. Genomic sequence analysis showed that the strains belong to the genera Actinomyces (strains 299^T and 340), Corynebacterium (strains 2184^T, 2185, 2183^T and 2189) and Oceanobacillus (strains 160^T and 143), respectively, with a percentage of similarity for the 16S rRNA gene under the species threshold of 98.7 % except for strains 160^T and 143 with Oceanobacillus arenosus CAU 1183^T (98.8 %). The genome sizes (and genomic G+C contents) were 3.1 Mb (49.4 %), 2.5 Mb (64.9 %), 2.4 Mb (66.1 %) and 4.1 Mb (37.1 %) for the type strains 299^T, 2183^T, 2184^T and 160^T, respectively. Two sets of the overall genome relatedness index values between our isolates and their corresponding closely related species were under species thresholds (95 % for average nucleotide identity, and 70 % for digital DNA-DNA hybridization). These results, together with deeper genotypic, genomic, phenotypic and biochemical analyses, indicate that these eight isolates should be classified as representing four novel species. Strain 299^T (=CGMCC 1.16320^T=JCM 33611^T) is proposed as representing Actinomyces wuliandei sp. nov.; strain 2184^T (=CGMCC 1.16417^T=DSM 106203^T) is proposed as representing Corynebacterium liangguodongii sp. nov.; strain 2183^T (=CGMCC 1.16416^T=DSM 106264^T) is proposed as representing Corynebacterium yudongzhengii sp. nov.; and strain 160^T (=CGMCC 1.16367^T=DSM 106186^T) is proposed as representing Oceanobacillus zhaokaii sp. nov.

Actinomyces lilanjuaniae sp. nov., isolated from the faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau

Two novel, Gram-stain-positive, non-motile, facultatively anaerobic, rod-shaped bacteria (strains 2129^T and 2119) were isolated from the faeces of Tibetan antelopes (Pantholops hodgsonii) on the Qinghai-Tibet Plateau, PR China. The 16S rRNA gene sequences of the strains showed highest similarity values to Actinomyces timonensis DSM 23838^T (92.9 and 92.8 %, respectively), and phylogenetic analysis based on 16S rRNA gene and genomic sequences indicated that strains 2129^T and 2119 represent a new lineage. Strains 2129^T and 2119 could ferment d-adonitol and d-xylose, but were unable to utilize d-mannose and d-melibiose nor produce esterase (C4) and proline arylamidase. The G+C contents of the two strains were both 69.0 mol%. Their genomes exhibited less than 40.4 % relatedness in DNA-DNA hybridization tests (below 70 % as the recommended threshold for new species) with all available genomes of the genus Actinomyces in the NCBI database. The major fatty acids of the two strains were C_18 : 1ω9c and C_16 : 0, and the major polar lipids were diphosphatidylglycerol, glycolipid, phosphatidylinositol, phosphatidyl inositol mannoside and phosphoglycolipid. Based on the results of genotypic, phenotypic and biochemical analyses, it is proposed that the two unidentified bacteria be classified as representing a novel species, Actinomyces lilanjuaniae sp. nov. The type strain is 2129^T (=CGMCC 4.7483^T=DSM 106426^T).

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.

Members of the Oral Microbiota Are Associated with IL-8 Release by Gingival Epithelial Cells in Healthy Individuals

The triggers for the onset of oral diseases are still poorly understood. The aim of this study was to characterize the oral bacterial community in healthy humans and its association with nutrition, oral hygiene habits, and the release of the inflammatory marker IL-8 from gingival epithelial cells (GECs) with and without stimulation by bacterial endotoxins to identify possible indicator operational taxonomic units (OTUs) associated with inflammatory marker status. GECs from 21 healthy participants (13 females, 8 males) were incubated with or without addition of bacterial lipopolysaccharides (LPSs), and the oral microbiota was profiled using 16S rRNA gene-targeted sequencing. The basal IL-8 release after 6 h was between 9.9 and 98.2 pg/ml, and bacterial communities were characteristic for healthy oral microbiota. The composition of the oral microbiota was associated with basal IL-8 levels, the intake of meat, tea, white wine, sweets and the use of chewing gum, as well as flossing habits, allergies, gender and body mass index. Additionally, eight OTUs were associated with high basal levels of IL-8 and GEC response to LPS, with high basal levels of IL-8, and 1 with low basal levels of IL8. The identification of indicator bacteria in healthy subjects with high levels of IL-8 release is of importance as they may be promising early warning indicators for the possible onset of oral diseases.

Prevalence of Actinomyces spp. in patients with chronic periodontitis

This study investigated the prevalence of Actinomyces spp. in shallow, deep and very deep pockets of patients with chronic periodontitis compared to healthy controls and correlated the results with clinical status. Twenty patients with chronic periodontitis and 15 healthy subjects were enrolled in this study. Clinical indices were recorded in a six-point measurement per tooth. From each patient samples of supra and subgingival plaque were taken separately from teeth with shallow, deep and very deep pockets. Samples of supragingival plaque and sulcular microflora were collected from the healthy subjects. All the samples were cultivated on different media at 37̊C in an anaerobic atmosphere for 7 days. All the suspect colonies were identified using a rapid ID 32 A system (bioMèrieux) and MALDI-TOF-MS analysis using an Autoflex II Instrument (Bruker Daltonics) together with in house developed identification software and a reference spectra database. A total of 977 strains were identified as Actinomyces. Actinomyces naeslundii/oris/johnsonii (430 isolates) was the most prevalent species and was found in all patients and in almost all of the healthy subjects. Significant differences (p=0.003) between the groups were found for Actinomyces odontolyticus/meyeri and Actinomyces israelii which were associated with periodontitis patients. Actinomyces dentalis was found in higher percentage (p=0.015) in the periodontitis group. Actinomyces gerencseriae and Actinomyces massiliensis were significantly more often found supragingivally than subgingivally (p=0.004, p=0.022, respectively) in the periodontitis group. Whether some Actinomyces species, definitely important plaque formers, are actively involved in the pathogenicity of chronic periodontitis needs further investigation.

Actinomyces and related organisms in human infections

Actinomyces israelii has long been recognized as a causative agent of actinomycosis. During the past 3 decades, a large number of novel Actinomyces species have been described. Their detection and identification in clinical microbiology laboratories and recognition as pathogens in clinical settings can be challenging. With the introduction of advanced molecular methods, knowledge about their clinical relevance is gradually increasing, and the spectrum of diseases associated with Actinomyces and Actinomyces-like organisms is widening accordingly; for example, Actinomyces meyeri, Actinomyces neuii, and Actinomyces turicensis as well as Actinotignum (formerly Actinobaculum) schaalii are emerging as important causes of specific infections at various body sites. In the present review, we have gathered this information to provide a comprehensive and microbiologically consistent overview of the significance of Actinomyces and some closely related taxa in human infections.

Rapid identification of oral Actinomyces species cultivated from subgingival biofilm by MALDI-TOF-MS

BACKGROUND

Actinomyces are a common part of the residential flora of the human intestinal tract, genitourinary system and skin. Isolation and identification of Actinomyces by conventional methods is often difficult and time consuming. In recent years, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has become a rapid and simple method to identify bacteria.

OBJECTIVE

The present study evaluated a new in-house algorithm using MALDI-TOF-MS for rapid identification of different species of oral Actinomyces cultivated from subgingival biofilm.

DESIGN

Eleven reference strains and 674 clinical strains were used in this study. All the strains were preliminarily identified using biochemical methods and then subjected to MALDI-TOF-MS analysis using both similarity-based analysis and classification methods (support vector machine [SVM]). The genotype of the reference strains and of 232 clinical strains was identified by sequence analysis of the 16S ribosomal RNA (rRNA).

RESULTS

The sequence analysis of the 16S rRNA gene of all references strains confirmed their previous identification. The MALDI-TOF-MS spectra obtained from the reference strains and the other clinical strains undoubtedly identified as Actinomyces by 16S rRNA sequencing were used to create the mass spectra reference database. Already a visual inspection of the mass spectra of different species reveals both similarities and differences. However, the differences between them are not large enough to allow a reliable differentiation by similarity analysis. Therefore, classification methods were applied as an alternative approach for differentiation and identification of Actinomyces at the species level. A cross-validation of the reference database representing 14 Actinomyces species yielded correct results for all species which were represented by more than two strains in the database.

CONCLUSIONS

Our results suggest that a combination of MALDI-TOF-MS with powerful classification algorithms, such as SVMs, provide a useful tool for the differentiation and identification of oral Actinomyces.

Actinomyces naturae sp. nov., the first Actinomyces sp. isolated from a non-human or animal source

Three facultatively anaerobic, Gram-positive staining, rod-shaped, non-spore forming, flagellated bacterial strains, BL-75, BL-79(T) and BL-104, were isolated from chlorinated solvent-contaminated groundwater. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed them to represent a distinct lineage within the genus Actinomyces with sequence identities in the range of <88-95.4% with previously described Actinomyces species. The strains were oxidase and catalase negative. Nitrate was not reduced. Esculin was hydrolyzed. Growth occurred in the temperature range of 20-43°C (optimum 30-37°C) and pH range 4.5-9.0 (optimum pH 6.5). Substrates supporting growth included various mono-, di-, and tri-saccharides. The end products of glucose fermentation were acetate, lactate, succinate and formate. Fermentative growth was observed in the presence of near saturation concentrations of perchloroethene (PCE) and toluene and in the presence of 1,2-dichloroethane and 1,1,2-trichloroethane at concentrations up to at least 24.4 mM and 11.2 mM, respectively. The dominant cellular fatty acids when grown in peptone/yeast extract/glucose (PYG) medium were C(18:1) ω9c, C(16:0), and C(14:0). The peptidoglycan was found to contain the amino acids alanine, glutamic acid, lysine, and ornithine at approximate molar ratios of 1.7 Ala: 2.3 Glu: 1.3 Lys: 1.0 Orn. The cell wall sugars were found to include rhamnose and mannose. The polar lipids were found to include diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phospholipid (PL), phosphoglycolipids (PGL), and glycolipids (GL). The main respiratory quinone of strain BL-79(T) was MK-9(H(4)), with minor components MK-10(H(4)) and MK-8(H(4)). The DNA mol% G+C content of the type strain is 69.8%. On the basis of phylogenetic and phenotypic characteristics, these strains could be differentiated from previously described species of the genus Actinomyces. Strains BL-75, BL-79(T) and BL-104 are designated as a novel species, for which the name Actinomyces naturae sp. nov. is proposed. This is the first Actinomyces species isolated from an environmental rather than human or animal sources. The type strain of Actinomyces naturae is BL-79(T) (= CCUG 56698(T) = NRRL B-24670(T)).

pH of pus collected from periapical abscesses

AIM

To determine the pH of pus collected from periapical abscesses.

METHODOLOGY

Forty patients (Male = 17/Female = 23) between the ages 17 and 37 years, each with a periapical abscess and with no relevant medical history, were recruited. All the participants had moderate-to-severe pain on percussion accompanied by localized or generalized swelling. At least 1 mL of pus was aspirated from each participant using a No 20 gauge needle. A pH meter was used to define the pH of the pus immediately following aspiration.

RESULT

The mean pH of pus from the periapical abscesses of patients was 6.68 +/- 0.324 with a range between 6.0 and 7.3. There was no statistically significant difference in pH by gender or age.

CONCLUSION

The mean pH of pus from periapical abscesses was generally acidic, but some samples (two female and three male) were neutral and some samples (four female and one male) were alkaline.

Actinomyces hominis sp. nov., isolated from a wound swab

A coryneform bacterium (strain 1094(T)) was isolated from a wound swab taken from an 89-year-old female patient. Chemotaxonomic investigations suggested that this bacterium was related to the genera Actinomyces, Arcanobacterium and Actinobaculum. Phylogenetic analysis of 16S rRNA gene sequences showed that strain 1094(T) was most closely related to Actinomyces europaeus CCUG 32789 A(T) (94.3 % similarity). Phenotypically, the isolate could be separated from its closest phylogenetic neighbours on the basis of being positive for catalase, CAMP reaction, acid phosphatase, N-acetyl-beta-glucosaminidase and raffinose fermentation. Based on the data presented, it is proposed that strain 1094(T) should be classified in a novel species, Actinomyces hominis sp. nov. The type strain is 1094(T) (=CCUG 57540(T) =DSM 22168(T)).

Actinomyces timonensis sp. nov., isolated from a human clinical osteo-articular sample

Gram-positive, non-spore-forming rods were isolated from a human osteo-articular sample (strain 7400942(T)). Based on cellular morphology and the results of biochemical analysis, this strain was tentatively identified as a novel species of the genus Actinomyces. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the bacterium was closely related to the type strain of Actinomyces denticolens (96.9 % 16S rRNA gene sequence similarity). A comparison of biochemical traits showed that strain 7400942(T) was distinct from A. denticolens in a number of characteristics, i.e. in contrast with A. denticolens, strain 7400942(T) was negative for nitrate reduction and for beta-galactosidase, alpha-glucosidase and alanine arylamidase activities, it was positive for acid production from N-acetylglucosamine, melezitose and glycogen, and it was negative for acid production from turanose. Matrix-assisted laser-desorption/ionization time-of-flight MS protein analysis confirmed that strain 7400942(T) represents a novel species, as scores obtained for its spectra were significant (>2.2) only with strain 7400942(T). On the basis of phenotypic data and phylogenetic inference, it is proposed that this strain should be designated Actinomyces timonensis sp. nov.; the type strain is strain 7400942(T) (=CSUR P35(T)=CCUG 55928(T)).

Actinomyces massiliensis sp. nov., isolated from a patient blood culture

Gram-positive, non-spore-forming rods (strain 4401292(T)) were isolated from a human blood sample. Based on cellular morphology and the results of biochemical tests, this strain was tentatively identified as belonging to an undescribed species of the genus Actinomyces. Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that the bacterium was related closely to Actinomyces gerencseriae (95.1 % 16S rRNA gene sequence similarity), Actinomyces israelii (95.2 %), Actinomyces oricola (95.2 %), Actinomyces ruminicola (93.3 %) and Actinomyces dentalis (91.4 %). The predominant fatty acids were C18 : 1omega9c and C16 : 0. On the basis of phenotypic data and phylogenetic inference, the novel species Actinomyces massiliensis sp. nov. is proposed; the type strain is 4401292(T) (=CSUR P18(T)=CCUG 53522(T)).

Actinomyces--gathering evidence of human colonization and infection

The roles of the 'classical'Actinomyces spp. as colonizers of oral cavities of man and animals, in development of intra-oral infections and as agents of actinomycosis have been well documented. This mini-review focuses on perceptions of human colonization and infection that have emerged in the past decade, largely as a result of advances in classification, identification and direct detection from clinical material. Arguably, of the greatest importance is the recognition of actinomycosis as a major factor and indicator of poor prognosis in both infected osteoradionecrosis and bisphosphonate-associated osteonecrosis of the jaws. Among recently described species, Actinomyces graevenitzii has been isolated almost exclusively from oral and respiratory sites and may be a causative agent of actinomycosis. Conversely, several other Actinomyces spp. are isolated commonly from superficial soft tissue infections. Members of the genus Actinobaculum, which is closely related to Actinomyces, are strongly associated with urosepsis. Isolation and identification of Actinomyces and related genera by conventional methods remain difficult. Diagnosis is commonly belated and based solely upon histological findings. Development of direct detection methods may aid patient management and further elucidate clinical associations.

Actinomyces ruminicola sp. nov., isolated from cattle rumen

Two obligate anaerobic bacterial strains, B71Tand D471, were isolated from cattle rumen. The novel strains were Gram-positive and rod-shaped. The strains hydrolysed xylan and starch, fermented some mono-, di- and oligosaccharides and produced formic, acetic and lactic acids as end products from glucose. Growth of the isolates was observed at 20–55 °C and pH 6.5–9.0. The DNA G+C contents of strains B71Tand D471 were 68.06 and 68.26 mol%, respectively. Although the two novel strains met the genus description forActinomyces, some phenotypic characteristics, such as optimum growth temperature, requirement for O2and the end products of fermentation, distinguished them from previously described members of the genus. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that the novel strains belonged to the genusActinomyces(88.3–93.6 % sequence similarity) and formed a distinct line within the clade containingActinomyces bovis. On the basis of these results, a novel species,Actinomyces ruminicolasp. nov., is proposed. The type strain is B71T(=JCM 13352T=CGMCC 1.5030T).