Metabolomics reveals high fructose-1,6-bisphosphate from fluoride-resistant Streptococcus mutans.

BACKGROUND: Fluoride-resistant Streptococcus mutans (S. mutans) strains have developed due to the wide use of fluoride in dental caries prevention. However, the metabolomics of fluoride-resistant S. mutans remains unclear. OBJECTIVE: This study aimed to identify metabolites that discriminate fluoride-resistant from wild-type S. mutans. MATERIALS AND METHODS: Cell supernatants from fluoride-resistant and wild-type S. mutans were collected and analyzed by liquid chromatography-mass spectrometry. Principal components analysis and partial least-squares discriminant analysis were performed for the statistical analysis by variable influence on projection (VIP > 2.0) and p value (Mann-Whitney test, p < 0.05). Metabolites were assessed qualitatively using the Human Metabolome Database version 2.0 ( http://www.hmdb.ca ), or Kyoto Encyclopedia of Genes and Genomes ( http://www.kegg.jp ), and Metaboanalyst 6.0 ( https://www.metaboanalyst.ca ). RESULTS: Fourteen metabolites differed significantly between fluoride-resistant and wild-type strains in the early log phase. Among these metabolites, 5 were identified. There were 32 differential metabolites between the two strains in the stationary phase, 13 of which were identified. The pyrimidine metabolism for S. mutans FR was matched with the metabolic pathway. CONCLUSIONS: The fructose-1,6-bisphosphate concentration increased in fluoride-resistant strains under acidic conditions, suggesting enhanced acidogenicity and acid tolerance. This metabolite may be a promising target for elucidating the cariogenic and fluoride resistant mechanisms of S. mutans.

Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments.

BACKGROUND: Mangrove wetlands are coastal ecosystems with important ecological features and provide habitats for diverse microorganisms with key roles in nutrient and biogeochemical cycling. However, the overall metabolic potentials and ecological roles of microbial community in mangrove sediment are remained unanswered. In current study, the microbial and metabolic profiles of prokaryotic and fungal communities in mangrove sediments were investigated using metagenomic analysis based on PacBio single-molecule real time (SMRT) and Illumina sequencing techniques. RESULTS: Comparing to Illumina short reads, the incorporation of PacBio long reads significantly contributed to more contiguous assemblies, yielded more than doubled high-quality metagenome-assembled genomes (MAGs), and improved the novelty of the MAGs. Further metabolic reconstruction for recovered MAGs showed that prokaryotes potentially played an essential role in carbon cycling in mangrove sediment, displaying versatile metabolic potential for degrading organic carbons, fermentation, autotrophy, and carbon fixation. Mangrove fungi also functioned as a player in carbon cycling, potentially involved in the degradation of various carbohydrate and peptide substrates. Notably, a new candidate bacterial phylum named as Candidatus Cosmopoliota with a ubiquitous distribution is proposed. Genomic analysis revealed that this new phylum is capable of utilizing various types of organic substrates, anaerobic fermentation, and carbon fixation with the Wood-Ljungdahl (WL) pathway and the reverse tricarboxylic acid (rTCA) cycle. CONCLUSIONS: The study not only highlights the advantages of HiSeq-PacBio Hybrid assembly for a more complete profiling of environmental microbiomes but also expands our understanding of the microbial diversity and potential roles of distinct microbial groups in biogeochemical cycling in mangrove sediment. Video Abstract.

Deep sequencing reveals comprehensive insight into the prevalence, mobility, and hosts of antibiotic resistance genes in mangrove ecosystems.

Mangrove receives aquaculture wastewater and urban sewage, and thus is a potential reservoir for antibiotic resistance genes (ARGs). However, there is a dearth of a comprehensive profile of ARGs in mangrove ecosystems. We used metagenomic techniques to uncover the occurrence, host range, and potential mobility of ARGs in six mangrove ecosystems in southeastern China. Based on deep sequencing data, a total of 348 ARG subtypes were identified. The abundant ARGs were associated with acriflavine, bacitracin, beta-lactam, fluoroquinolone, macrolide-lincosamide-streptogramin, and polymyxin. Resistance genes tetR, aac(6')-Iae, aac(3)-IXa, vanRA, vanRG, and aac(3)-Ig were proposed as ARG indicators in mangrove ecosystems that can be used to evaluate the abundance of 100 other co-occurring ARGs quantitatively. Remarkably, 250 of 348 identified ARG subtypes were annotated as mobile genetic elements-associated ARGs, indicating a high potential risk of propagation of ARGs in mangrove ecosystems. By surveying the distribution of ARGs in 6281 draft genomes, more than 42 bacterial phyla were identified as the putative hosts of the ARGs. Among them, 21.97% were potentially multidrug-resistant hosts, including human and animal opportunistic pathogens. This research adds to our understanding of the distribution and spread of antibiotic resistomes in mangrove ecosystems, helping improve ARG risk assessment and management worldwide.

Biogeography, Assembly Patterns, Driving Factors, and Interactions of Archaeal Community in Mangrove Sediments.

Archaea are a major part of Earth's life. They are believed to play important roles in nutrient biogeochemical cycling in the mangrove. However, only a few studies on the archaeal community in mangroves have been reported. In particular, the assembly processes and interaction patterns that impact the archaeal communities in mangroves have not been investigated to date. Here, the biogeography, assembly patterns, and driving factors of archaeal communities in seven representative mangroves across southeastern China were systematically analyzed. The analysis revealed that the archaeal community is more diverse in surface sediments than in subsurface sediments, and more diverse in mangroves at low latitudes than at high latitudes, with Woesearchaeota and Bathyarchaeota as the most diverse and most abundant phyla, respectively. Beta nearest-taxon index analysis suggested a determinant role of homogeneous selection on the overall archaeon community in all mangroves and in each individual mangrove. In addition, the conditionally rare taxon community was strongly shaped by homogeneous selection, while stochastic processes shaped the dominant taxon and always-rare taxon communities. Further, a moderate effect of environmental selection on the archaeal community was noted, with the smallest effect on the always-rare taxon community. Mangrove location, mean annual temperature, and salinity were the major factors that greatly affected the community composition. Finally, network analysis revealed comprehensive cooccurrence relationships in the archaeal community, with a crucial role of Bathyarchaeota. This study expands the understanding of the biogeography, assembly patterns, driving factors, and cooccurrence relationships of the mangrove archaeal community and inspires functional exploration of archaeal resources in mangrove sediments. IMPORTANCE As a key microbial community component with important ecological roles, archaea merit the attention of biologists and ecologists. The mechanisms controlling microbial community diversity, composition, and biogeography are central to microbial ecology but poorly understood. Mangroves are located at the land-ocean interface and are an ideal environment for examining the above questions. We here provided the first-ever overview of archaeal community structure and biogeography in mangroves located along an over-9,000-km coastline of southeastern China. We observed that archaeal diversity in low-latitude mangroves was higher than that in high-latitude mangroves. Furthermore, our data indicated that homogeneous selection strongly controlled the assembly of the overall and conditionally rare taxon communities in mangrove sediments, while the dominant taxon and always-rare taxon communities were mainly controlled by dispersal limitation.

High-Level Diversity of Basal Fungal Lineages and the Control of Fungal Community Assembly by Stochastic Processes in Mangrove Sediments.

Fungi are key components of microbial communities in mangrove wetlands, with important roles in the transformation of nutrients and energy. However, existing studies typically focus on cultivable fungi and seldom on the structure and driving factors of entire fungal communities. The compositions, community assembly, and interaction patterns of mangrove fungal communities on a large scale remain elusive. Here, biogeography, assembly, and co-occurrence patterns of fungal communities in mangroves across eastern to southern China were systematically analyzed by targeting the entire internal transcribed spacer (ITS) region with high-throughput Pacific Biosciences single-molecule real-time sequencing. The analysis revealed a high level of fungal diversity, including a number of basal fungal lineages not previously reported in mangroves, such as Rozellomycota and Chytridiomycota. Beta nearest-taxon index analyses suggested a determinant role of dispersal limitation on fungal community in overall and most individual mangroves, with support from the strong distance-decay patterns of community similarity. Further, nonmetric multidimensional scaling analyses revealed similar biogeographies of dominant and rare fungal communities. A minor role of environmental selection on the fungal community was noted, with geographical location and sediment depth as crucial factors driving the distribution of both, the dominant and rare taxa. Finally, network analysis revealed high modularized co-occurrence patterns of fungal community in mangrove sediments, and the keystone taxa might play important roles in microbial interactions and ecological functions. The investigation expands our understanding of biogeography, assembly patterns, driving factors, and co-occurrence relationships of mangrove fungi and will spur the further functional exploration and protection of fungal resources in mangroves. IMPORTANCE As key components of microbial community in mangroves, fungi have important ecological functions. However, the fungal community in mangroves on a large scale is generally elusive, and mangroves are declining rapidly due to climate change and anthropogenic activities. This work provides an overview of fungal community structure and biogeography in mangrove wetlands along a >9,000-km coastline across eastern to southern China. Our study observed a high number of basal fungal lineages, such as Rozellomycota and Chytridiomycota, in mangrove sediments. In addition, our results highlight a crucial role of dispersal limitation and a minor role of environmental selections on fungal communities in mangrove sediments. These novel findings add important knowledge about the structure, assembly processes, and driving factors of fungal communities in mangrove sediments.

Comparison of the formation ability of two types of machine-made nickel-titanium instruments in simulated curved root canals / 口腔疾病防治

Objective@#To compare ProTaper Universal (PU) and M3-L instruments in preparing curved root canals and to provide a reference for clinical applications.@*Methods@#Twenty resin-simulated curved single root canals were randomly divided into two groups. Root canal preparation was performed with a PU nickel-titanium file or an M3-L nickel-titanium file. Root canal preparation time, root canal length before and after preparation and root canal deviation were recorded.@*Results@#In the M3-L group, the displacement measured at the 4th to 7th sites was less than that in the PU group (P < 0.05), but there was no significant difference between the other two groups (P > 0.05); The length of the root canal before and after root canal preparation in the M3-L group was （14.90 ± 1.92）mm and （14.57 ± 1.13）mm, respectively, and the difference between the two groups was not statistically significant (t=3.18, P=0.058). The root canal length before and after root canal preparation in the PU group was（14.53 ± 1.53）mm and （14.28 ± 1.39）mm, respectively. The difference between the two groups was not statistically significant（t=2.12,P=0.124）; The average preparation time of the M3-L group [（110.15 ± 10.43）s] was less than that in the PU group [（330.48 ± 12.62）s] (P < 0.05).@*Conclusion @#The M3-L nickel-titanium file has better central positioning ability and is less time-consuming than the PU nickel-titanium file in root canal bending preparation.

Adhesive interfacial characteristics and the related bonding performance of four self-etching adhesives with different functional monomers applied to dentin.

OBJECTIVES: To examine the interfacial chemical and morphological characteristics of four self-etching adhesives bonded to dentin with different functional monomers. Further, to evaluate the effects of this interaction between functional monomers and dentin on short-term in vitro bonding performance of the four adhesives. METHODS: Clearfil SE Bond (CSE) and Scotchbond Universal (SU) containing 10-methacryloxydecyl dihydrogen phosphate (10-MDP), Optibond XTR (OX) containing glycero-phosphate dimethacrylate (GPDM), and Adper Easy One (AEO) containing 6-methacryloyloxyhexyl dihydrogen phosphate (6-MHP) were applied to the dentin surface according to the instructions supplied with each. Interaction between the functional monomers and dentin was characterized using thin-film X-ray diffraction (TF-XRD) and scanning electron microscopy (SEM). The hydrophilicity of each acidic monomer was also assessed by chemical structure drawing software. Micro-tensile bond strength (µTBS) and nanoleakage were used to evaluate the bonding effectiveness of the adhesives, either immediately or after thermo-cycling (5°C-55°C) for 5000 cycles. RESULTS: TF-XRD showed that both CSE and SU exhibited 10-MDP-Ca nano-layering at the adhesive interface, but with different intensity when reacted with dentin. OX, that contains GPDM, demineralized the dentin surface more severely, forming long resin tags into the dentinal tubules, and gained the highest µTBS at the immediate time-point. Thermo-cycling adversely affected the µTBS and nanoleakage of AEO and OX, but had no significant influence on CSE and SU which contain 10-MDP. CONCLUSIONS: Self-etching adhesives containing different structures/concentrations of functional monomers produced adhesive interfaces with obviously different chemical and morphological characteristics, which may have a direct impact on bonding effectiveness. CLINICAL SIGNIFICANCE: Our findings support the concept that the stable chemical bonding produced by 10-MDP to the Ca of hydroxyapatite is advantageous for durability of adhesive-dentin bonds. In contrast a higher immediate bond strength was achieved with the functional monomer GPDM that etched and wetted the dentin surface better.

Comparative analysis of two 16S rRNA gene-based PCR primer sets provides insight into the diversity distribution patterns of anammox bacteria in different environments.

Due to the high divergence among 16S rRNA genes of anammox bacteria, different diversity pattern of the community could be resulted from using different primer set. In this study, the efficiencies and specificities of two commonly used sets, Amx368F/Amx820R and Brod541F/Amx820R, were evaluated by exploring the diversity characteristics of anammox bacteria in sediments from marine, estuary, and freshwater wetland. Statistical analysis indicated that the base mispairing rate between bases on 16S rRNA gene sequences retrieved by Amx368F/Amx820R and their corresponding ones on primer Brod541F was quite high, suggesting the different efficiency and specificity of Amx368F/Amx820R and Brod541F/Amx820R. Further experimental results demonstrated that multiple genera of anammox bacteria, including Ca. Scalindua, Ca. Brocadia, and Ca. Kuenenia, were able to be detected by Amx368F/Amx820R, but only Ca. Scalindua could be retrieved by Brod541F/Amx820R. Moreover, the phylogenetic clusters of Ca. Scalindua by Amx368F/Amx820R were different completely from those by Brod541F/Amx820R, presenting a significant complementary effect. By joint application of these two primer sets, the diversity distribution patterns of anammox bacteria in different environments were analyzed. Almost all retrieved sequences from marine sediments belonged to Ca. Scalindua. Sequences from freshwater wetland were affiliated to Ca. Brocadia and two new clusters, while high diversity of anammox bacteria was found in estuary, including Ca. Scalindua, Ca. Brocadia, and Ca. Kuenenia, corresponding to the river-sea intersection environmental feature. In total, these two prime sets have different characteristic for anammox bacteria detecting from environmental samples, and their combined application could achieve better diversity display of anammox community.