Comparative pangenome analysis of Aspergillus flavus and Aspergillus oryzae reveals their phylogenetic, genomic, and metabolic homogeneity

Aspergillus flavus and Aspergillus oryzae are closely related fungal species with contrasting roles in food safety and fermentation. To comprehensively investigate their phylogenetic, genomic, and metabolic characteristics, we conducted an extensive comparative pangenome analysis using complete, dereplicated genome sets for both species. Phylogenetic analyses, employing both the entirety of the identified single-copy orthologous genes and six housekeeping genes commonly used for fungal classification, did not reveal clear differentiation between A. flavus and A. oryzae genomes. Upon analyzing the aflatoxin biosynthesis gene clusters within the genomes, we observed that non-aflatoxin-producing strains were dispersed throughout the phylogenetic tree, encompassing both A. flavus and A. oryzae strains. This suggests that aflatoxin production is not a distinguishing trait between the two species. Furthermore, A. oryzae and A. flavus strains displayed remarkably similar genomic attributes, including genome sizes, gene contents, and G + C contents, as well as metabolic features and pathways. The profiles of CAZyme genes and secondary metabolite biosynthesis gene clusters within the genomes of both species further highlight their similarity. Collectively, these findings challenge the conventional differentiation of A. flavus and A. oryzae as distinct species and highlight their phylogenetic, genomic, and metabolic homogeneity, potentially indicating that they may indeed belong to the same species.

Marinomonas rhodophyticola sp. nov. and Marinomonas phaeophyticola sp. nov., isolated from marine algae

Two Gram-stain-negative, facultatively aerobic, and motile rod bacteria, designated as strains KJ51-3T and 15G1-11T, were isolated from marine algae collected in the Republic of Korea. Both strains exhibited catalase- and oxidase-positive activities. Optimum growth conditions for strain KJ51-3T were observed at 30 °C and pH 6.0-8.0, with 1.0-7.0 % (w/v) NaCl, whereas strain 15G1-11T exhibited optimal growth at 30 °C, pH 7.0, and 1.0-5.0 % NaCl. Major fatty acids detected in both strains included C16 : 0, C10 : 0 3-OH and summed features 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and 8 (C18 : 1  ω7c and/or C18 : 1  ω6c). As for polar lipids, strain KJ51-3T contained phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol, and two unidentified phospholipids, whereas strain 15G1-11T had PE, PG, and an unidentified aminolipid. Ubiquinone-8 was the predominant respiratory quinone in both strains, with minor detection of ubiquinone-9 in strain KJ51-3T. The genomic DNA G+C contents were 44.0 mol% for strain KJ51-3T and 40.5 mol% for strain 15G1-11T. Phylogenetic analyses based on both 16S rRNA gene and genome sequences placed strains KJ51-3T and 15G1-11T into distinct lineages within the genus Marinomonas, most closely related to Marinomonas arctica 328T (98.6 %) and Marinomonas algicola SM1966T (98.3 %), respectively. Strains KJ51-3T and 15G1-11T exhibited a 94.6 % 16S rRNA gene sequence similarity and a 70.7 % average nucleotide identity (ANI), with ANI values of 91.9 and 79.3 % between them and M. arctica 328T and M. algicola SM1966T, respectively, indicating that they represent novel species. In summary, based on their phenotypic, chemotaxonomic, and phylogenetic properties, strains KJ51-3T and 15G1-11T are proposed to represent novel species within the genus Marinomonas, for which the names Marinomonas rhodophyticola sp. nov. (KJ51-3T=KACC 22756T=JCM 35591T) and Marinomonas phaeophyticola sp. nov. (15G1-11T=KACC 22593T=JCM 35412T) are respectively proposed.

Unraveling the carbohydrate metabolic characteristics of Leuconostoc mesenteroides J18 through metabolite and transcriptome analyses

The metabolic characteristics of Leuconostoc mesenteroides subsp. mesenteroides J18, which is mainly responsible for kimchi fermentation, on various carbon sources were investigated through carbon utilization, metabolite, and transcriptome analyses at different culture conditions (10 and 30 °C with/without 2.5% NaCl). The metabolic features of strain J18 were relatively similar across the four culture conditions. However, the metabolic characteristics of strain J18 showed significant variations depending on the carbon source. These distinct metabolic traits of strain J18 on various carbon sources were validated through transcriptomic analyses and the reconstruction of metabolic pathways. The transcriptional expression of the metabolic pathways in response to each carbon source consistently correlated with the production profiles of metabolites, including ethanol, acetoin, diacetyl, and riboflavin, in each carbon source. Our findings suggests that the abundance of Leu. mesenteroides during fermentation and the taste and flavor of fermented food products can be controlled by altering the carbon sources.

Roseibium algicola sp. nov. and Roseibium porphyridii sp. nov., isolated from marine red algae

Two Gram-stain-negative, strictly aerobic rods, designated as RMAR6-6T and KMA01T, exhibiting catalase- and oxidase-positive activities, were isolated from marine red algae in the Republic of Korea. Cells of strain RMAR6-6T exhibited flagellar motility, while those of strain KMA01T were non-motile. Strain RMAR6-6T exhibited optimal growth at 30-35°C and pH 7.0-8.0 with 4.0-6.0 % (w/v) NaCl, while strain KMA01T grew optimally at 30-35 °C, pH 7.0-8.0 and 2.0-5.0% NaCl. Both strains shared common major respiratory isoprenoid quinone (ubiquinone-10), cellular fatty acids (C18 : 0, C18: 1  ω7c 11-methyl, C20 : 1  ω7c and summed feature 8) and polar lipids (phosphatidylglycerol, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sulphoquinovosyldiacylglycerol). The genomic DNA G+C contents were 59.0 and 55.0 mol% for strains RMAR6-6T and KMA01T, respectively. With 98.5 % 16S rRNA gene similarity, 75.2 % average nucleotide identity (ANI) and 19.8 % digital DNA-DNA hybridization (dDDH) values, strains RMAR6-6T and KMA01T were identified as representing distinct species. Phylogenetic analyses based on both 16S rRNA gene and genome sequences revealed that strains RMAR6-6T and KMA01T formed distinct phylogenic lineages within the genus Roseibium, most closely related to Roseibium aggregatum IAM 12614T and Roseibium album CECT 5094T, respectively. The ANI and dDDH values between strain RMAR6-6T and R. aggregatum IAM 12614T were 87.5 and 33.3 %, respectively. Similarly, the values between KMA01T and R. album CECT 5094T were 74.2 % (ANI) and 19.3 % (dDDH). Based on phenotypic, chemotaxonomic and molecular characteristics, strains RMAR6-6T and KMA01T represent two novel species of the genus Roseibium, for which the names R. algicola sp. nov. (RMAR6-6T=KACC 22482T=JCM 34977T) and R. porphyridii sp. nov. (KMA01T=KACC 22479T=JCM 34597T) are proposed, respectively.

Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions

BACKGROUND

Enterococcus faecium and E. lactis are phylogenetically closely related lactic acid bacteria that are ubiquitous in nature and are known to be beneficial or pathogenic. Despite their considerable industrial and clinical importance, comprehensive studies on their evolutionary relationships and genomic, metabolic, and pathogenic traits are still lacking. Therefore, we conducted comparative pangenome analyses using all available dereplicated genomes of these species.

RESULTS

E. faecium was divided into two subclades: subclade I, comprising strains derived from humans, animals, and food, and the more recent phylogenetic subclade II, consisting exclusively of human-derived strains. In contrast, E. lactis strains, isolated from diverse sources including foods, humans, animals, and the environment, did not display distinct clustering based on their isolation sources. Despite having similar metabolic features, noticeable genomic differences were observed between E. faecium subclades I and II, as well as E. lactis. Notably, E. faecium subclade II strains exhibited significantly larger genome sizes and higher gene counts compared to both E. faecium subclade I and E. lactis strains. Furthermore, they carried a higher abundance of antibiotic resistance, virulence, bacteriocin, and mobile element genes. Phylogenetic analysis of antibiotic resistance and virulence genes suggests that E. faecium subclade II strains likely acquired these genes through horizontal gene transfer, facilitating their effective adaptation in response to antibiotic use in humans.

CONCLUSIONS

Our study offers valuable insights into the adaptive evolution of E. faecium strains, enabling their survival as pathogens in the human environment through horizontal gene acquisitions.

Neobacillus terrae sp. nov., isolated from mountain soil

A Gram-stain-positive, spore-forming and facultative aerobic bacterium, designated C11^T, was isolated from mountain soil collected in the Republic of Korea. The cells were motile rods with peritrichous flagella, and positive for catalase and oxidase activities. Strain C11^T grew at 15-45 °C (optimum, 30-37 °C) and pH 6.0-8.0 (optimum, pH 6.0) and in the presence of 0-1 % (w/v) NaCl (optimum, 0.5 %). Strain C11^T contained menaquinone-7 as the sole isoprenoid quinone and iso-C_15 : 0, iso-C_16 : 0 and anteiso-C_15 : 0 as the major fatty acids. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids. The G+C content of the genomic DNA was 38.8 mol%. Strain C11^T was most closely related to Neobacillus drentensis IDA1967^T and Mesobacillus foraminis CV53^T, with 98.0 and 97.7 %, 71.7 and 69.9 %, and 20.1 and 20.3 % 16S rRNA gene sequence similarity, average nucleotide identity, and digital DNA-DNA hybridization values, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences showed that strain C11^T was included in a phyletic lineage with members of the genus Neobacillus but was distinct from members of the genus Mesobacillus. Phenotypic, chemotaxonomic and molecular properties suggested that strain C11^T represents a novel species of the genus Neobacillus, for which the name Neobacillus terrae sp. nov. is proposed. The type strain is C11^T (=KACC 21661^T=JCM 33943^T).

Chitinophaga horti sp. nov., Isolated from Garden Soil

A strictly aerobic Gram-negative bacterium, designated R8^T, isolated from garden soil in South Korea was subjected to a taxonomic study. The cells were non-spore-forming, oxidase-positive and catalase-negative, and non-motile rods (without flagella). Growth was observed between 10 °C and 40 °C (optimum, 30 °C) and between pH 6.0 and 9.0 (optimum, pH 7.0) and in the presence of 0%-1.5% (w/v) NaCl (optimum, 0%). The G + C content of the genomic DNA was 49.9% and the major isoprenoid quinone was found to be menaquinone-7. The major fatty acids of strain R8^T were iso-C_15:0, C_16:1 ω5c, and summed feature 3 (comprising iso-C_15:0 2-OH and/or C_16:1 ω7c/ω6c). Phosphatidylethanolamine was identified as a major polar lipid. Comparative 16S rRNA gene sequence analysis showed that strain R8^T had the highest 16S rRNA gene sequence similarity of 98.3% with Chitinophaga sedimenti TFL-3 ^T. Phylogenetic analyses using 16S rRNA gene sequences and concatenated 92 marker protein sequences revealed that strain R8^T formed a robust phylogenetic lineage with C. sedimenti within the genus Chitinophaga. Average nucleotide identity and digital DNA-DNA hybridization values of strain R8^T to Chitinophaga species were less than 77.9% and 21.1%, respectively. The phenotypic, phylogenetic, and chemotaxonomic properties support that strain R8^T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga horti sp. nov. is proposed. The type strain is R8^T (= KACC 19895 ^T = JCM 33215 ^T).

Fabrication of fluorine-doped diamond-like carbon stamps for UV nanoimprint lithography

Two fluorine-doped diamond-like carbon (F-DLC) stamps with sub-100 nm line patterns were fabricated using a direct etching method. These were applied successfully to ultraviolet (UV) nanoimprint lithography without requiring an anti-adhesion layer coating. Tests were performed to determine the optimum fluorine concentration for the F-DLC stamps. The ideal stamp material consisted of 25 at.% F-DLC with a contact angle of 85°, UV transmittance of 16.4-26.8%, and hardness of 4.5 GPa. The O(2) plasma etch rate of the DLC was increased considerably by the fluorine doping, making it comparable to the etch rate of polymethyl methacrylate (PMMA). Thus, only PMMA was used as the etch mask in the fabrication of the stamps.

Comparison between anisometropic and strabismic amblyopia using functional magnetic resonance imaging

AIMS

To assess calcarine activation with functional magnetic resonance imaging (fMRI) in patients with anisometropic and strabismic amblyopia.

METHODS

14 amblyopes (eight anisometropic and six strabismic) were studied with fMRI using stimuli of checkerboards of various checker sizes and temporal frequencies. While T2* weighted MRI were obtained every 3 seconds for 6 minutes, patients viewed the stimuli monocularly with either the amblyopic or sound eye.

RESULTS

Amblyopic eyes showed reduced calcarine activation compared with contralateral sound eyes in fMRI in all subjects. The calcarine activation from amblyopic eyes in anisometropic amblyopes was more suppressed at higher spatial frequencies, while that from amblyopic eyes in strabismic amblyopes was more suppressed at lower spatial frequencies.

CONCLUSION

These results suggest that fMRI is a useful tool for the study of amblyopia in humans. The calcarine activation via amblyopic eyes because of anisometropia or strabismus has different temporospatial characteristics, which suggests differences in the neurophysiological mechanisms between two types of amblyopia.

Vertical strabismus in monofixation syndrome

PURPOSE

The manifest angle of the horizontal deviation in monofixation syndrome (MFS) has been reported to reach a maximum of 8 to 10 PD. Review of the literature, however, revealed no studies about the vertical deviation associated with MFS. The purpose of this study is to evaluate the range of the angle of the vertical deviation in MFS.

METHODS

Forty patients who had MFS with vertical strabismus in the distance primary position were included in this study. All fulfilled the criteria for monofixation, fusing Worth 4 dots at near but suppressing at distance and/or having stereoacuity between 3000 and 60 seconds of arc by using Titmus stereotest and a horizontal deviation within 8 PD of orthophoria by simultaneous prism and cover test. Patients were divided into 3 groups: patients with hypertropia without any dissociated vertical deviation (DVD) (group I), patients with only DVD (group II), and patients with both hypertropia and DVD (group III).

RESULTS

Eighteen patients (45.0%) had hypertropia only (group I), 15 (37.5%) had DVD only (group II), and 7 (17.5%) had both (group III). In groups I and III the angle of hypertropia by simultaneous prism and cover test was 2 to 6 PD (mean, 3.9 PD) and in group II and III the angle of DVD was 4 to 14 PD (mean, 7.5 PD) at distance.

CONCLUSIONS

These results suggest that in MFS the angle of hypertropia can range up to a maximum of 6 PD. However, monofixation was observed in patients with a larger absolute angle of DVD (up to 14 PD), possibly due to an intermittent nature of the DVD.

Medial rectus resection(s) with adjustable suture for intermittent exotropia of the convergence insufficiency type

BACKGROUND

The surgical results for intermittent exotropia of the convergence insufficiency type have been reported to be of varying success. The purpose of this study is to evaluate the surgical results of medial rectus muscle (MR) resection(s) with adjustable suture for this condition.

METHODS

Twenty-one consecutive patients with intermittent exotropia of the convergence insufficiency type were included in this retrospective study. All patients had a history of prolonged difficulties at near work unrelieved by nonsurgical treatment. Unilateral or bilateral MR resection(s) were done with the adjustable suture, which was tied at the first postoperative day. The target angle was an esotropia of 10 to 20 PD at distance and an esotropia of 5 to 10 PD at near. Postoperatively Fresnel prisms were used temporarily in patients manifesting a consecutive esotropia with diplopia at distance. Postoperative follow-up period was between 6 months and 24 months with a mean of 9.1 months.

RESULTS

MR resection(s) with the adjustable suture reduced the mean exodeviation at near from 25.7 to 3 PD. It also reduced the exodeviation at distance from 11.4 to -2 PD (esodeviation). The mean near-distance difference was collapsed from 14.3 PD preoperatively to 5 PD postoperatively.

CONCLUSIONS

MR resection(s) with adjustable suture combined with intentional postoperative aggressive overcorrection and the use of Fresnel prisms is useful in intermittent exotropia of the convergence insufficiency type. The intentional overcorrection during the immediate postoperative period at distance and near is required to prevent long-term undercorrection.

Effect of ADCON-L on adjustable strabismus surgery in rabbits

BACKGROUND/AIMS

In search of a way to prevent postoperative adhesion after strabismus surgery, an animal study was performed to assess the effect of a gel consisting of a polyglycan ester in a gelatin matrix (ADCON-L).

METHODS

Bilateral recessions of superior rectus muscle (SR) were performed on 16 rabbits. ADCON-L was applied beneath and over the SR in the right eyes of all rabbits, while the operative fields in the left eyes were irrigated with a balanced salt solution (BSS). The adjustment was performed on each SR at 4 and 7 days postoperatively on the same eye. The length and force of the adjustment and the degree of adhesion were recorded. At 3 weeks postoperatively, disinsertional force was measured in several of the eyes, and the other eyes were enucleated.

RESULTS

The length of the adjustment was longer and the force of the adjustment was less in the ADCON-L group than in the BSS treated group at 4 and 7 days postoperatively (p=0.00). A significant reduction (p=0.00) in the degree of adhesion was noted in eyes treated with ADCON-L. There was no significant difference in disinsertional force between the two groups. Histopathological evaluation of the muscle revealed decreased fibrosis of perimuscular connective tissue in eyes treated with ADCON-L at 3 weeks postoperatively.

CONCLUSION

This study suggests that ADCON-L helps to prevent postoperative adhesion in rabbits and enables adjustment twice within 7 days postoperatively without complications.

Reliability of an ear-bow arbitrary face-bow transfer instrument

STATEMENT OF PROBLEM

Accuracy of techniques for recording the orientation of the maxillary arch to the articulation of the temporomandibular joints has been reported. The variability contributed by the dentist and the equipment within a technique may also contribute to technical error.

PURPOSE

This study investigated the variability of a group of dentists who used an arbitrary ear-face-bow instrument to mount a maxillary cast.

MATERIAL AND METHODS

The same maxillary cast on a single experimental subject was mounted on an articulator with a common arbitrary ear-face-bow instrument. This cast was equipped with 4 reference points for the measurement of changes of spatial orientation of the cast, which were determined through coordinate measurements with a machinist's microscope. A repeated measures analysis of variance was used to determine statistically significant changes in spatial orientation with a Wilks' Lambda test to compare mean values.

RESULTS

A confidence interval of 95% demonstrated that any dentist might expect a range of +/-1.2 mm error in using this instrument/articulator combination. The 3 dentists did not demonstrate any significant differences in the spatial orientation of their mountings in the vertical or horizontal directions. However, there were significant differences in their mountings in linear distance changes of the patient's posterior right side.

CONCLUSION

A range of inherent error attributable to the operator using this instrument was recorded.

Electron microscopic study on overacting inferior oblique muscles

Overaction of the inferior oblique(IO) muscle is manifested by elevation of the adducted eye and from the clinical point of view there are two types of overaction. The primary type is of unknown cause, whereas the secondary type is usually related to the palsy of the ipsilateral superior oblique or contralateral superior rectus. An ultrastructural study on the overacting IO muscles was performed compared to normal IO muscles by electron microscopy. Of 16 biopsies of overacting IO muscles, four had primary overacting inferior obliques and twelve had secondary overacting inferior obliques due to paralysis of superior oblique muscle. Additional four IO muscle, obtained from patients with intraocular diseases served as control specimens. The most striking abnormalities were aggregations of mitochondria and degenerating mitochondrial profiles and increased vacuolization in primary and secondary overacting muscles. Many muscle fibers were in different stages of atrophy, and hypertrophy and regeneration of muscle fibers were sometimes visible. The results suggest that the primary overacting IO muscle might be the result of a paresis of the superior oblique muscle.

Medial transposition of the lateral rectus muscle in experimentally induced medial rectus paralysis

When the oculomotor nerve is completely paralyzed, the affected eye shows severe outward displacement and poor cosmetic appearance. Past results of many surgical procedures for oculomotor palsy have been generally unsatisfactory. We tried a new surgical approach experimentally, in which the disinserted lateral rectus muscle was used as an adductor by medial transposition of the muscle. Five adult cats underwent disinsertion of the medial rectus muscle of both eyes to induce iatrogenic medial rectus paralysis. The disinserted medial rectus was removed as far back as possible to prevent reattachment. Then, the right lateral rectus muscle was disinserted and passed beneath the superior rectus muscle and resutured to the sclera 4mm superoposterior to the medial rectus insertion site. After excision of the bilateral medial rectus, a large exotropia of an average 47.6 delta (42.0-55.5 delta) was induced. The medial transposition of the right lateral rectus produced an average 36.6 delta (24.8-45.8 delta) correction of the exotropia. A satisfactory cosmetic result was achieved by this procedure.

Clinical analysis of uveitis

Uveitis can be classified in a variety of ways and this fact makes it difficult to compare results. Therefore we classified uveitis by the location with the method of Henderly; anterior-, posterior-, intermediate- and panuveitis. We determined the frequency of occurrence, etiology and clinical characteristics of various forms of uveitis. We conducted a retrospective analysis of 683 patients with uveitis seen at Seoul National University Hospital from January 1978, to December 1987. The results were as follows. 1. 192 cases (28.1%) occurred as anterior uveitis, 218 cases (31.9%) as posterior uveitis, 166 cases (24.3%) as panuveitis and 107 cases (15.7%) as pars planitis. Posterior uveitis was the most common form of uveitis. 2. In cases of anterior uveitis, 142 cases (74.0%) were idiopathic, traumatic uveitis was seen in 18 cases. In posterior-uveitis, 111 cases (50.9%) were idiopathic, retinal vasculitis including Eales' disease in 60 cases (27.5%), toxoplasmosis in 23 cases (10.6%). In cases of panuveitis, idiopathic form occurred in 80 cases (48.2%), Behçet's disease in 41 cases (24.7%). The idiopathic form was the most common entity in all locations of uveitis.