CSMD: a computational subtraction-based microbiome discovery pipeline for species-level characterization of clinical metagenomic samples.

MOTIVATION: Microbiome analyses of clinical samples with low microbial biomass are challenging because of the very small quantities of microbial DNA relative to the human host, ubiquitous contaminating DNA in sequencing experiments and the large and rapidly growing microbial reference databases. RESULTS: We present computational subtraction-based microbiome discovery (CSMD), a bioinformatics pipeline specifically developed to generate accurate species-level microbiome profiles for clinical samples with low microbial loads. CSMD applies strategies for the maximal elimination of host sequences with minimal loss of microbial signal and effectively detects microorganisms present in the sample with minimal false positives using a stepwise convergent solution. CSMD was benchmarked in a comparative evaluation with other classic tools on previously published well-characterized datasets. It showed higher sensitivity and specificity in host sequence removal and higher specificity in microbial identification, which led to more accurate abundance estimation. All these features are integrated into a free and easy-to-use tool. Additionally, CSMD applied to cell-free plasma DNA showed that microbial diversity within these samples is substantially broader than previously believed. AVAILABILITY AND IMPLEMENTATION: CSMD is freely available at https://github.com/liuyu8721/csmd. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Association between obesity and dental caries in Chinese children.

The study sought to analyze the association between dental caries and obesity in Chinese children, and to investigate the protective and risk factors of dental caries. A total of 280 children aged 7-12 years voluntarily answered the caries examination and questionnaire. Caries was measured using the International Caries Detection and Assessment System. According to the Chinese body mass index, the participants were grouped overweight or normal-weight. The logistic regression model showed no correlation between dental caries and obesity. Drinking yogurt and chewing gum are protective factors, whereas oral breathing and genetic predisposition to caries are risk factors.

Correction to "An Electrochemical Sensor for Quantitation of the Oral Health Care Agent Chlorogenic Acid Based on Bimetallic Nanowires with Functionalized Reduced Graphene Oxide Nanohybrids".

[This corrects the article DOI: 10.1021/acsomega.1c06612.].

A new strategy for browning regulation: Flos Sophorae Immaturus extract and thermal treatment modulates nitric oxide and reactive oxygen species network in fresh-cut potatoes.

Browning discoloration is a critical issue that negatively affects the quality of fresh-cut products and their industrial growth. Although many individual anti-browning technologies have been adopted, very few reports on the combination use of natural product extracts and physical methods exist. This study investigated the use of Flos Sophorae Immaturus extract in conjunction with thermal treatment and discovered that the combination effectively retarded browning in fresh-cut potatoes. Accordingly, the activities of polyphenol oxidase, peroxidase, and phenylalanine ammonia-lyase, as well as phenol accumulation, were effectively regulated. Meanwhile, this combination treatment also allowed for the modulation of nitric oxide synthase, superoxide dismutase, and catalase activities, while also regulating the concentrations of nitric oxide, superoxide anion, and hydrogen peroxide. Furthermore, the duplex treatment also regulated the antioxidant capacity and malondialdehyde concentrations. In addition, 39 phytoactive compounds, including protocatechuic acid, quercetin, (-)-alpha-pinene, and matrine, were identified in the extract, which may function as the anti-browning composition. These findings suggest that the combination technology modulated the dynamic equilibrium of production and clearance of nitric oxide and reactive oxygen species, thereby reducing browning deterioration. This is, to our knowledge, the first report of the combined application of Flos Sophorae Immaturus and thermal treatment, which may offer a novel option for fresh-cut preservation. PRACTICAL APPLICATION: The feasibility of integrating a novel highly efficient, safe, environmentally friendly, and easy-to-operate anti-browning alternative, with the ability to integrate into the existing processing line was investigated. The color of sliced potato chips was significantly improved (73.4%) by dipping them in a 0.01% Flos Sophorae Immaturus solution for 5 min and then in 55°C water for 2 min. In this regard, superior browning alleviation may depend on the regulation of the browning reaction and the NO-ROS network. This method has a promising future for making fresh-cut products more appealing to consumers and may provide guidance for fresh-cut producers and related industries.

An Electrochemical Sensor for Quantitation of the Oral Health Care Agent Chlorogenic Acid Based on Bimetallic Nanowires with Functionalized Reduced Graphene Oxide Nanohybrids.

Chlorogenic acid (CGA), a phenolic acid from coffee, has been regarded as a powerful ingredient against oxidative stress and inflammation. Meanwhile, its healing feature to interfere with periodontal disease (PD) makes it a promising drug candidate. However, the existing methods for chlorogenic acid detection limit its practical application in purification and further pharmacological study in stomatology due to their lack of accuracy and productivity. Therefore, it is crucial to find a forceful approach to precisely evaluate CGA for an in-depth anti-PD study. In this work, we reported a facile and controllable synthesis of Pt@Pd nanowires (NWs) in a non-compacted core-shell structure with high electrocatalytic activity. In addition, polyethylenimine (PEI)-capped reduced graphene oxide (rGO) nanoflakes provided large binding sites for a network structure composed of interweaved Pt@Pd nanowires and protected hemin from self-destruction, which empowered Pt@Pd NWs-Hemin-PEI-rGO nanohybrids to own a large electroactive surface area and great electrochemical property for CGA detection. The enzyme-free electrochemical sensor based on Pt@Pd NWs-Hemin-PEI-rGO displayed a favorable capacity for trace CGA detection with a detection limit of 7.8 nM and a wide linear range of 0.5 µM to 4 mM. The exceptional sensitivity and selectivity of the sensor made it accomplish the measurements of chlorogenic acid in soft drinks and coffee with high consistency of HPLC results. The satisfactory performance of the obtained sensor enables it to be used for quality control and study of drug metabolism in PD treatments.

Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease.

Background: Dry eye disease (DED) is a multifactorial inflammatory disease of the ocular surface. It is hypothesized that dysbiosis of the conjunctival microbiota contributes to the development of DED. However, species-level compositions of the conjunctival microbiota in DED and the potential dysbiosis involving microorganisms other than bacteria remain largely uncharacterized. Methods: We collected conjunctival impression samples from a cohort of 95 individuals, including 47 patients with DED and 48 healthy subjects. We examined the conjunctival microbiota of these samples using shotgun metagenomic sequencing and analyzed microbial dysbiosis in DED at the species level. Results: The conjunctival microbiota in DED exhibited a decreased α-diversity and an increased inter-individual variation. The α-diversity of female patients with DED was higher than that of male patients. Despite a decreased prevalence in DED, 23 microbial species were identified to show abnormally high abundance in DED samples positive for the species. Among these species, a fungal species Malassezia globosa was enriched female patients. In addition, distinct patterns of associations with disease status were observed for different species of the same genus. For DED subtypes, Staphylococcus aureus and S. capitis were associated with meibomian gland dysfunction (MGD), whereas S. hominis was enriched in patients solely with aqueous tear deficiency (ATD). The microbiota of patients with a mixed type of diagnosis was more similar to MGD patients than ATD patients. Conclusion: We demonstrated that the conjunctival microbiota dysbiosis in DED is characterized by significant heterogeneity. Microbial signatures may offer novel insights into the complicated etiology of DED and potentially promote the development of personalized treatment for DED in the future.

Implementation of fragile X syndrome carrier screening during prenatal diagnosis: A pilot study at a single center.

BACKGROUND: Fragile X syndrome (FXS) is the most common inherited form of intellectual disability. Prenatal screening of FXS allows for early identification and intervention. The present study explored the feasibility of FXS carrier screening during prenatal diagnosis for those who were not offered screening early in pregnancy or prior to conception. METHODS: Pregnant women to be offered amniotic fluid testing were recruited for the free voluntary carrier screening at a single center between August, 2017 and September, 2019. The number of CGG repeats in the 5' un-translated region of the fragile X mental retardation gene 1 (FMR1) was determined. RESULTS: 4286 of 7000 (61.2%) pregnant women volunteered for the screening. Forty (0.93%), five (0.11%), and three (0.07%) carriers for intermediate mutation (45-54 repeats), premutation (55-200 repeats) and full mutation (>200 repeats) of the FMR1 gene were identified respectively. None of the detected premutation alleles were inherited by the fetuses. Of the three full mutation carrier mothers, all had a family history and one transmitted a full mutation allele to her male fetus. CONCLUSION: Implementation of FXS carrier screening during prenatal diagnosis may be considered for the need to increase screening for FXS.

Identification of an intraocular microbiota.

The current dogma in ophthalmology and vision research presumes the intraocular environment to be sterile. However, recent evidence of intestinal bacterial translocation into the bloodstream and many other internal organs including the eyes, found in healthy and diseased animal models, suggests that the intraocular cavity may also be inhabited by a microbial community. Here, we tested intraocular samples from over 1000 human eyes. Using quantitative PCR, negative staining transmission electron microscopy, direct culture, and high-throughput sequencing technologies, we demonstrated the presence of intraocular bacteria. The possibility that the microbiome from these low-biomass communities could be a contamination from other tissues and reagents was carefully evaluated and excluded. We also provide preliminary evidence that a disease-specific microbial signature characterized the intraocular environment of patients with age-related macular degeneration and glaucoma, suggesting that either spontaneous or pathogenic bacterial translocation may be associated with these common sight-threatening conditions. Furthermore, we revealed the presence of an intraocular microbiome in normal eyes from non-human mammals and demonstrated that this varied across species (rat, rabbit, pig, and macaque) and was established after birth. These findings represent the first-ever evidence of intraocular microbiota in humans.

Gastrointestinal symptoms and fecal nucleic acid testing of children with 2019 coronavirus disease: a systematic review and meta-analysis.

In order to understand the clinical manifestations and incidence of gastrointestinal symptoms of coronavirus disease (COVID-19) in children and discuss the importance of fecal nucleic acid testing.We retrospectively analyzed studies on gastrointestinal symptoms and fecal nucleic acid detection in pediatric COVID-19 patients from January 1, 2020 to August 10, 2020, including prospective clinical studies and case reports. The results of fecal nucleic acid detection were analyzed systematically. Stata12.0 software was used for meta-analysis.The results showed that the most common gastrointestinal symptoms in children with COVID-19 were vomiting and diarrhea, with a total incidence of 17.7% (95% Cl 13.9-21.5%). However, the prevalence of gastrointestinal symptoms in other countries (21.1%, 95% CI 16.5-25.7%) was higher compared to China (12.9%, 95% CI 8-17.7%). In Wuhan, the pooled prevalence was much higher (41.3%, 95% CI 3.2-79.4%) compared to areas outside Wuhan in China (7.1%, 95% CI 4.0-10.3%). The positive rate of fecal nucleic acid testing in COVID-19 children was relatively high at 85.8% (91/106). Additionally, 71.2% (52/73) were still positive for fecal nucleic acid after respiratory tract specimens turned negative. One and two weeks after the respiratory tract specimens turned nucleic acid-negative, 45.2% (33/73) and 34.2% (25/73) patients, respectively, remained fecal nucleic acid-positive. The longest interval between the respiratory tract specimens turning negative and fecal specimens turning negative exceeded 70 days. Conclusions and relevance: gastrointestinal symptoms in pediatric COVID-19 are relatively common. Attention should be paid to the detection of fecal nucleic acids in children. Fecal nucleic acid-negative status should be considered as one of the desegregation standards.

Metagenomic analysis reveals gestational diabetes mellitus-related microbial regulators of glucose tolerance.

AIMS: Recent studies have suggested a possible association between microbiota and gestational diabetes (GDM). However, the results are inconsistent. Our objective was to investigate further the relationship between GDM and microbiota and verify the potential microbial marker. METHODS: Two complementary approaches were used for the demonstration. First, we compared the gut microbial composition of 23 GDM patients and 26 non-GDM ethnically Chinese Han pregnant women, by using whole-metagenome shotgun sequencing of their stool samples collected at the third trimester. Second, we used Q-PCR (quantitative polymerase chain reaction) to evaluate the gut microbial composition in the stool samples from another cohort of 150 Chinese pregnant women (113 Control and 37 GDM), to further confirm the potential microbial marker. RESULTS: The gut microbiota of GDM women show lower albeit not statistically significant (p = 0.18) alpha diversity at the species level than non-GDM women. However, the species-level beta-diversity or between-sample diversity measured by Bray-Curtis distance shows significant differences (p < 2.2e-16) between the two groups. The species Bacteroides dorei positively correlated with both OGTT (oral glucose tolerance test) 0-Hour (p = 0.0099) and OGTT 1-Hour (p = 0.0070). There is a similar trend between Bacteroides sp. 3_1_33FAA and both OGTT 0-Hour (p = 0.014) and OGTT 1-Hour (p = 0.0101) response variables. The species Alistipes putredinis negatively correlated with OGTT 1-Hour (p = 0.0172) and OGTT 2-Hour (p = 0.0147). Q-PCR validation further confirmed the association between the glucose tolerance loci of Bacteroides dorei and OGTT response. CONCLUSIONS: Gut microbiome is related to the diabetic status of Chinese women during pregnancy. Specific species such as Bacteroides dorei associate with glucose response and could be potential monitoring and therapeutic microbial markers for GDM.

Geographic Difference Shaped Human Ocular Surface Metagenome of Young Han Chinese From Beijing, Wenzhou, and Guangzhou Cities.

Purpose: Microbial ecosystems interact with the human body and affect human health. The microbial community on the ocular surface remains an underexplored territory despite its importance as the first line of defense barrier that protects the eye and ultimately sight. We investigated how age and sex affected human ocular surface microbiome, and in the present study wanted to understand how geographic difference shaped the microbiome in the ocular surface. Methods: We collected conjunctival specimens of 172 eyes from 86 healthy volunteers living in three Chinese cities, namely, Guangzhou, Wenzhou, and Beijing. Using the direct metagenomic shotgun sequencing approach, we characterized how geographic difference affected the human ocular microbiome. Results: We surveyed the taxonomic composition and metabolic function of the microbiota on human ocular surface. We showed that the ocular surface microbiota was composed of bacteria, viruses, and fungi. A geographical difference in both composition and function of the conjunctival microbiome suggests that the environment people lived in shapes their conjunctival microbiome, especially the dominate species. Conclusions: Our study provides a reference catalog of the healthy conjunctival metagenome and raises a concern for environmental influences on the ocular surface microbiome.

Inhibition of Experimental Age-Related Macular Degeneration by ZQMT in Mice.

BACKGROUND: Age-related macular degeneration (AMD) is a progressive and irreversible eye disease. The anti-vascular endothelial growth factor (VEGF) therapy has revolutionized the treatment of neovascular AMD. However, the expense for such treatment is quite high. METHODS: We used a traditional Chinese medicine ZQMT as an alternative therapeutic regimen for AMD. We employed two in vivo animal models mimicking dry and wet AMD respectively to assess the therapeutic efficacy of ZQMT on treating AMD-related retinopathy. AMD-related retinopathy in Crb1rd8 mice was evaluated from week 1 to 8 by fundus photography. Laser-induced choroidal neovascularization (CNV) was evaluated by fluorescein angiography and histopathology. RESULTS: ZQMT increased CX3CR1 expression in murine CD4+ T cells either cultured in vitro or directly isolated from animals treated with ZQMT. We also performed both in vitro and in vivo studies to confirm that ZQMT has no apparent toxic effects. ZQMT alleviated AMD-related retinopathy in both Crb1rd8 and CNV models. Depletion of CCL2 and CX3CR1 in Crb1rd8 mice abolished the efficacy of ZQMT, suggesting that CCL2 and/or CX3CR1 may underlie the mechanisms of ZQMT in treating AMD-related retinopathy in mice. CONCLUSION: In summary, our study supports the protective roles of a traditional Chinese medicine ZQMT in AMD.

[Determination of trace elements in hair of mice infected with Trichinella spiralis].

Mice were divided into 3 groups: heavy infection group with 80 mice each was fed with 400 muscle larvae of Trichinella spiralis, light infection group with 60 mice each was fed by 200 larvae, and uninfected control (60 mice) . The content of Cu, Zn and Fe in the dorsal hair samples was measured in the week of 1, 3, 5, 7, 9, 11, 13 and 15 after infection. Results indicated that the content of Zn, Cu and Fe in the two experimental groups reduced considerably in comparison to the control (P < 0.05), especially for that of Zn and Cu. Lower content was found in the heavily infected mice than in those with light infection (P < 0.05).

Comparison of the effect of four decalcifying agents combined with 60°C 3% sodium hypochlorite on smear layer removal.

INTRODUCTION: The objective of this study was to compare the efficacy on smear layer removal of 4 decalcifying agents: 17% ethylenediaminetetraacetic acid (EDTA), 20% citric acid, BioPure MTAD, and SmearClear. METHODS: Forty-five single-rooted human teeth were used and prepared up to ProTaper F3. After each instrumentation, 1 mL of 3% NaOCl at 60°C was irrigated for 1 minute. All the samples were randomly divided into 5 groups according to the final irrigants: 17% EDTA, 20% citric acid, BioPure MTAD, SmearClear, and 3% NaOCl (control). The smear layer removal of all groups at the apical, middle, and coronal thirds was observed under the thermal field emission scanning electron microscope. RESULTS: The EDTA group was significantly more effective than the SmearClear and MTAD groups (P < .05). The efficacy of all three thirds in the EDTA, MTAD, and SmearClear groups can be arranged as coronal, middle, and apical thirds (P < .05) from excellent to poor. However, in the citric acid group, the coronal two thirds were significantly better than the apical third (P < .05), and there was no statistical significance between the coronal and middle thirds (P > .05). CONCLUSIONS: The 4 decalcifying agents could effectively, but not completely, remove the smear layer, especially in the apical third. The efficacy of 17% EDTA was better than that of MTAD and SmearClear.