Salvaging high-quality genomes of microbial species from a meromictic lake using a hybrid sequencing approach.

Most of Earth's bacteria have yet to be cultivated. The metabolic and functional potentials of these uncultivated microorganisms thus remain mysterious, and the metagenome-assembled genome (MAG) approach is the most robust method for uncovering these potentials. However, MAGs discovered by conventional metagenomic assembly and binning are usually highly fragmented genomes with heterogeneous sequence contamination. In this study, we combined Illumina and Nanopore data to develop a new workflow to reconstruct 233 MAGs-six novel bacterial orders, 20 families, 66 genera, and 154 species-from Lake Shunet, a secluded meromictic lake in Siberia. With our workflow, the average N50 of reconstructed MAGs greatly increased 10-40-fold compared to when the conventional Illumina assembly and binning method were used. More importantly, six complete MAGs were recovered from our datasets. The recovery of 154 novel species MAGs from a rarely explored lake greatly expands the current bacterial genome encyclopedia.

Crusted scabies with scalp involvement in an institutionalized elderly.

Scabies is a common disease and typically described as a skin condition with sparing of face and scalp in adults. However, crusted scabies is not conventional scabies. It can also affect the scalp. Herein, we report an unusual case of crusted scabies with scalp infestation and suggest that for cases with suspicious lesions on scalp, immunocompromised patients or relapse cases, crusted scabies, special age groups, such as infant, young children, and the elderly, topical treatment of the scalp should be included.

Methanolobus halotolerans sp. nov., isolated from the saline Lake Tus in Siberia.

A halotolerant, psychrotolerant and methylotrophic methanogen, strain SY-01T, was isolated from the saline Lake Tus in Siberia. Cells of strain SY-01T were non-motile, cocci and 0.8-1.0 µm in diameter. The only methanogenic substrate utilized by strain SY-01T was methanol. The temperature range of growth for strain SY-01T was from 4 to 40 °C and the optimal temperature for growth was 30 °C. The pH range of growth was from pH 7.2 to 9.0, with optimal growth at pH 8.0. The NaCl range of growth was 0-1.55 M with optimal growth at 0.51 M NaCl. The G+C content of the genome of strain SY-01T was 43.6 mol % as determined by genome sequencing. Phylogenetic analysis revealed that strain SY-01T was most closely related to Methanolobus zinderi SD1T (97.3 % 16S rRNA gene sequence similarity), and had 95.5-97.2 % similarities to other Methanolobus species with valid names. Genome relatedness between strain SY-01T and DSM 21339T was computed using average nucleotide identity and digital DNA-DNAhybridization, which yielded values of 79.7 and 21.7 %, respectively. Based on morphological, phenotypic, phylogenetic and genomic relatedness data presented here, it is evident that strain SY-01T represents a novel species of the genus Methanolobus, and the name Methanolobus halotolerans sp. nov. is proposed. The type strain is SY-01T (=BCRC AR10051T=NBRC 113166 T=DSM 107642T).

The Mechanism of Onychomadesis (Nail Shedding) and Beau's Lines Following Hand-Foot-Mouth Disease.

BACKGROUND: Nail changes, including onychomadesis (nail shedding) and Beau's line, following hand-foot-mouth disease (HFMD) are a common emergence at the stage of late complications of HFMD. However, the exact mechanism is still unknown. Therefore, we conducted this study to elucidate the mechanism of nail changes following HFMD. METHODS: We collected 11 patients suffering from onychomadesis following HFMD. Nail samples from all of them were collected. Real time reverse transcription polymerase chain reaction (RT-PCR) and sequencing for human enteroviruses (HEV) were performed. Throat swabs for RT-PCR and sequencing for HEV were performed for three cases. RESULTS: RT-PCR demonstrated the presence of Coxackievirus A6 (CVA6) in nail samples from three patients and one with Echovirus. CONCLUSION: In conclusion, we believe that the major cause of onychomadesis following HFMD is that certain novel viruses, mostly CVA6, are virulent and may damage nail matrix. Direct injury caused by cutaneous lesions of HFMD around nail matrix is a minor cause. There are still other virulent HEV which may result in onychomadesis. In addition, the novel strain of CVA6 also causes atypical clinical presentations, such as adult involvement and delayed-onset palmar and plantar desquamation. Physicians should be familiar with atypical presentations caused by novel viruses to avoid misdiagnosis and even inform patients of the possibility of onychomadesis that may take place weeks later to reassure patients.

Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia.

Microorganisms are critical to maintaining stratified biogeochemical characteristics in meromictic lakes; however, their community composition and potential roles in nutrient cycling are not thoroughly described. Both metagenomics and metaviromics were used to determine the composition and capacity of archaea, bacteria, and viruses along the water column in the landlocked meromictic Lake Shunet in Siberia. Deep sequencing of 265 Gb and high-quality assembly revealed a near-complete genome corresponding to Nonlabens sp. sh3vir. in a viral sample and 38 bacterial bins (0.2-5.3 Mb each). The mixolimnion (3.0 m) had the most diverse archaeal, bacterial, and viral communities, followed by the monimolimnion (5.5 m) and chemocline (5.0 m). The bacterial and archaeal communities were dominated by Thiocapsa and Methanococcoides, respectively, whereas the viral community was dominated by Siphoviridae. The archaeal and bacterial assemblages and the associated energy metabolism were significantly related to the various depths, in accordance with the stratification of physicochemical parameters. Reconstructed elemental nutrient cycles of the three layers were interconnected, including co-occurrence of denitrification and nitrogen fixation in each layer and involved unique processes due to specific biogeochemical properties at the respective depths. According to the gene annotation, several pre-dominant yet unknown and uncultured bacteria also play potentially important roles in nutrient cycling. Reciprocal BLAST analysis revealed that the viruses were specific to the host archaea and bacteria in the mixolimnion. This study provides insights into the bacterial, archaeal, and viral assemblages and the corresponding capacity potentials in Lake Shunet, one of the three meromictic lakes in central Asia. Lake Shunet was determined to harbor specific and diverse viral, bacterial, and archaeal communities that intimately interacted, revealing patterns shaped by indigenous physicochemical parameters.

Effect of mouth-opening levels on sound field gain in the ear canal.

The human external auditory canal can become deformed when the mandible moves, and this changes the sound field in the external auditory canal. This study measured the sound field gain in the external auditory canal while varying mouth-opening in three levels. The mandible was fixed at the 1/3, the 2/3, and the maximal mouth-opening levels. Seven 65-dB tones of 200, 500, 1000, 2000, 4000, 6000, and 8000 Hz, which are the sound pressure level and frequency range when people are talking at a normal level, were adopted as the sound stimulus to measure sound field gains at 5, 10, 15, and 20 mm to the interior of the external auditory canal. The results show that, with the exception of the 1.25 dB decrease from 12.96 to 11.71 dB at a depth of 5 mm with a stimulus at 8000 Hz, the differences in the sound field gain at the other depths and stimulus frequencies were within 1 dB and were not statistically significant. These results suggest that mouth-opening level has no effect on the measurement of the sound field in the external auditory canal.

Methanolobus psychrotolerans sp. nov., a psychrotolerant methanoarchaeon isolated from a saline meromictic lake in Siberia.

A psychrotolerant, methylotrophic methanogen, strain YSF-03T, was isolated from the saline meromictic Lake Shira in Siberia. Cells of strain YSF-03T were non-motile, irregular cocci and 0.8-1.2 µm in diameter. The methanogenic substrates utilized by strain YSF-03T were methanol and trimethylamine. The temperature range of growth for strain YSF-03T was from 0 to 37 °C. The optimum growth conditions were 30-37 °C, pH 7.0-7.4 and 0.17 M NaCl. The G+C content of the genome of strain YSF-03T was 41.3 mol%. Phylogenetic analysis revealed that strain YSF-03T was most closely related to Methanolobus profundi MobMT (98.15 % similarity in 16S rRNA gene sequence). Genome relatedness between strain YSF-03T and MobMT was computed using the Genome-to-Genome Distance Calculator and average nucleotide identity, which gave values of 23.5 and 79.3 %, respectively. Based on the morphological, phenotypic, phylogenetic and genomic relatedness data presented here, it is evident that strain YSF-03T represents a novel species of the genus Methanolobus, for which the name Methanolobus psychrotolerans sp. nov. is proposed. The type strain is YSF-03T (=BCRC AR10049T=DSM 104044T=NBRC 112514T).

Alopecia syphilitica.

Alopecia syphilitica is a less common manifestation of secondary syphilis. It could present with other mucocutaneous symptoms of secondary syphilis or rarely present as the only symptom of secondary syphilis, the so-called "essential syphilitic alopecia." Herein, we present a case of essential syphilitic alopecia to remind physicians, especially for sexually active patients.

Bacterial Communities of Three Saline Meromictic Lakes in Central Asia.

Meromictic lakes located in landlocked steppes of central Asia (~2500 km inland) have unique geophysiochemical characteristics compared to other meromictic lakes. To characterize their bacteria and elucidate relationships between those bacteria and surrounding environments, water samples were collected from three saline meromictic lakes (Lakes Shira, Shunet and Oigon) in the border between Siberia and the West Mongolia, near the center of Asia. Based on in-depth tag pyrosequencing, bacterial communities were highly variable and dissimilar among lakes and between oxic and anoxic layers within individual lakes. Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria and Firmicutes were the most abundant phyla, whereas three genera of purple sulfur bacteria (a novel genus, Thiocapsa and Halochromatium) were predominant bacterial components in the anoxic layer of Lake Shira (~20.6% of relative abundance), Lake Shunet (~27.1%) and Lake Oigon (~9.25%), respectively. However, few known green sulfur bacteria were detected. Notably, 3.94% of all sequencing reads were classified into 19 candidate divisions, which was especially high (23.12%) in the anoxic layer of Lake Shunet. Furthermore, several hydro-parameters (temperature, pH, dissolved oxygen, H2S and salinity) were associated (P< 0.05) with variations in dominant bacterial groups. In conclusion, based on highly variable bacterial composition in water layers or lakes, we inferred that the meromictic ecosystem was characterized by high diversity and heterogenous niches.

Effects of porous-hydroxyapatite incorporated into glass-ionomer sealants.

The purpose of the present study was to evaluate the mechanical and chemical properties of a novel glass ionomer cement for use as a pit and fissure sealant containing a porous hydroxyapatite, namely, apatite ionomer cement (AIC). Control sealant samples were used Fuji III (GIC-S). The experiment sealant samples (AIC-S) consisted of porous spherical hydroxyapatite (HApS) particles added at 28 wt% to GIC-S powder. The GIC-S and AIC-S samples were evaluated through mechanical strength measurements, scanning electron microscopy observations, energy dispersive X-ray spectroscopy analysis, fluoride ion release tests, and antibacterial tests. The flexural strength of the AIC-S was significantly higher than that of GIC-S for each period, 1 h, 24 h and 1 year. The fluoride release dose for AIC-S was consistently higher than that for GIC-S. In addition, the antibacterial properties of AIC-S were superior to those of GIC-S. The novel AIC-S may be a more suitable sealant material for pits and fissures with intact and/or infected enamel.

Aliidiomarina shirensis sp. nov., a halophilic bacterium isolated from Shira Lake in Khakasia, southern Siberia, and a proposal to transfer Idiomarina maris to the genus Aliidiomarina.

Strain AIS(T), an aerobic halophilic, Gram-reaction-negative, heterotrophic bacterium isolated from the water of Shira Lake in Khakasia, southern Siberia, was characterized using a polyphasic approach. Our analysis of the 16S rRNA gene sequences showed that 'Aliidiomarina haloalkalitolerans', 'Aliidiomarina sanyensis', Idiomarina maris and AIS(T) formed a distinct lineage. The sequence similarities between AIS(T) and the type strains of species of the genera Idiomarina and Aliidiomarina were 91.6-95.1 % and 94.0-96.9 %, respectively. The major isoprenoid quinone of AIS(T) was ubiquinone 8 (Q-8). Predominant cellular fatty acids were iso-C17 : 0, iso-C15 : 0 and summed feature 9. The genomic DNA G+C content was 45.8 mol%. It is concluded that AIS(T) represents a novel species of the genus Aliidiomarina, and the name Aliidiomarina shirensis sp. nov. is herein proposed for it. The type strain is AIS(T) ( = JCM 17761(T) = BCRC 80327(T)). Based on its fatty acid profile and our phylogenetic analysis, we propose that Idiomarina maris be transferred to the genus Aliidiomarina.

Silver-containing hydrofiber dressing is an effective adjunct in the treatment of pemphigus vulgaris.

Pemphigus vulgaris is a life-threatening autoimmune bullous dermatosis and its management represents a major challenge to medical teams. The primary treatments for pemphigus vulgaris are oral steroids and immunosuppressants, but topical approaches also play a role in disease management. Here, we report a patient with pemphigus vulgaris involving 62% of the total body surface area, with initial poor clinical response to systemic steroids and topical silver sulfadiazine therapy. However, a marked improvement in wound healing and decreased patient discomfort were observed after application of silver-containing hydrofiber dressings (Aquacel-Ag). Therefore, silver-containing hydrofiber dressings may offer an effective adjunct in the treatment of patients with pemphigus vulgaris with extensive skin involvement. Our encouraging experience with these dressing patches may be extended to manage other large exudation wounds.

Prevalence of adult atopic dermatitis among nursing staff in a Taiwanese medical center: a pilot study on validation of diagnostic questionnaires.

BACKGROUND: Atopic dermatitis (AD) is a chronic, relapsing dermatosis. Previous studies have focused mostly on pediatric patients, and investigations emphasizing adult AD have been limited. OBJECTIVE: We set out to determine the 1-year prevalence and evaluate the validity of the International Study of Asthma and Allergies in Childhood (ISAAC) and United Kingdom Working Party (UKWP) AD questionnaires of adult AD in Taiwan. METHODS: We conducted a cross-sectional study among nursing staff at a university hospital. The 1-year prevalence of AD was assessed by ISAAC and UKWP questionnaires. Subsequently, the dermatologists' diagnosis based on Hanifin and Rajka criteria was used as a reference for validation. RESULTS: The overall response rate was 92.9%, equivalent to 1131 complete questionnaires. Ninety adult patients with AD (8%) were identified by dermatologists' diagnosis whereas ISAAC identified 107 (9.5%); sensitivity and specificity were 36.7% and 92.9%, respectively. UKWP identified 42 (3.7%) patients with AD; sensitivity and specificity were 42.2% and 99.6%, respectively. Using the receiver operating characteristic curve analysis, the UKWP criteria performed significantly better than its ISAAC counterpart. Further analysis indicated that modification of these criteria resulted in significant improvement in their diagnostic efficacy. More specifically, modified ISAAC showed 90.0% and 55.2% sensitivity and specificity, respectively, whereas modified UKWP demonstrated 82.2% and 94.2% sensitivity and specificity, respectively. LIMITATION: Most of the study subjects were female with a high educational background. CONCLUSION: Currently available questionnaire instruments do not perform well in the identification of adult patients with AD. Modification of the original questionnaires may allow for future large-scale epidemiologic studies.

Phakomatosis cesioflammea with late-onset glaucoma and acquired nevus spilus-like lesion - 15 years of follow-up.

Phakomatosis pigmentovascularis is a very rare disease characterized by coexistence of a capillary malformation with various melanocytic lesions, including dermal melanocytosis (Mongolian spots), nevus spilus, and nevus of Ota. As of now about 200 cases have been reported, most are of Japanese origin and about half of reported cases are associated with various systemic involvement. We present a 15-year-old Taiwanese male with phakomatosis cesioflammea who developed, during adolescence, a nevus spilus-like lesion and late-onset open angle glaucoma, suggesting that long-term ophthalmic follow-up is necessary in this type of patient.