Oral Microbiome Metabolism Takahashi, N.
Journal of Dental Research,
12/2015, Letnik:
94, Številka:
12
Book Review, Journal Article
Recenzirano
Recent advances in molecular biology have facilitated analyses of the oral microbiome (“Who are they?”); however, its functions (e.g., metabolic activities) are poorly understood (“What are they ...doing?”). This review aims to summarize our current understanding of the metabolism of the oral microbiome. Saccharolytic bacteria—including Streptococcus, Actinomyces, and Lactobacillus species—degrade carbohydrates into organic acids via the Embden-Meyerhof-Parnas pathway and several of its branch pathways, resulting in dental caries, while alkalization and acid neutralization via the arginine deiminase system, urease, and so on, counteract acidification. Proteolytic/amino acid–degrading bacteria, including Prevotella and Porphyromonas species, break down proteins and peptides into amino acids and degrade them further via specific pathways to produce short-chain fatty acids, ammonia, sulfur compounds, and indole/skatole, which act as virulent and modifying factors in periodontitis and oral malodor. Furthermore, it is suggested that ethanol-derived acetaldehyde can cause oral cancer, while nitrate-derived nitrite can aid caries prevention and systemic health. Microbial metabolic activity is influenced by the oral environment; however, it can also modify the oral environment, enhance the pathogenicity of bacteria, and induce microbial selection to create more pathogenic microbiome. Taking a metabolomic approach to analyzing the oral microbiome is crucial to improving our understanding of the functions of the oral microbiome.
Dental biofilms produce acids from carbohydrates that result in caries. According to the extended caries ecological hypothesis, the caries process consists of 3 reversible stages. The microflora on ...clinically sound enamel surfaces contains mainly non-mutans streptococci and Actinomyces, in which acidification is mild and infrequent. This is compatible with equilibrium of the demineralization/remineralization balance or shifts the mineral balance toward net mineral gain (dynamic stability stage). When sugar is supplied frequently, acidification becomes moderate and frequent. This may enhance the acidogenicity and acidurance of the non-mutans bacteria adaptively. In addition, more aciduric strains, such as ‘low-pH’ non-mutans streptococci, may increase selectively. These microbial acid-induced adaptation and selection processes may, over time, shift the demineralization/remineralization balance toward net mineral loss, leading to initiation/progression of dental caries (acidogenic stage). Under severe and prolonged acidic conditions, more aciduric bacteria become dominant through acid-induced selection by temporary acid-impairment and acid-inhibition of growth (aciduric stage). At this stage, mutans streptococci and lactobacilli as well as aciduric strains of non-mutans streptococci, Actinomyces, bifidobacteria, and yeasts may become dominant. Many acidogenic and aciduric bacteria are involved in caries. Environmental acidification is the main determinant of the phenotypic and genotypic changes that occur in the microflora during caries.
8q24.21 is a frequently amplified genomic region in colorectal cancer (CRC). This region is often referred to as a ‘gene desert’ due to lack of any important protein-coding genes, highlighting the ...potential role of noncoding RNAs, including long noncoding RNAs (lncRNAs) located around the proto-oncogeneMYC. In this study, we have firstly evaluated the clinical significance of altered expression of lncRNAs mapped to this genomic locus in CRC.
A total of 300 tissues, including 280 CRC and 20 adjacent normal mucosa specimens were evaluated for the expression of 12 lncRNAs using qRT-PCR assays. We analyzed the associations between lncRNA expression and various clinicopathological features, as well as with recurrence free survival (RFS) and overall survival (OS) in two independent cohorts.
The expression of CCAT1, CCAT1-L, CCAT2, PVT1, and CASC19 were elevated in cancer tissues (P=0.039, <0.001, 0.018, <0.001, 0.002, respectively). Among these, high expression of CCAT1 and CCAT2 was significantly associated with poor RFS (P=0.049 and 0.022, respectively) and OS (P=0.028 and 0.015, respectively). These results were validated in an independent patient cohort, in which combined expression of CCAT1 and CCAT2 expression was significantly associated with a poor RFS (HR:2.60, 95% confidence interval CI: 1.04–6.06,P=0.042) and a poor OS (HR:8.38, 95%CI: 2.68–37.0,P<0.001). We established a RFS prediction model which revealed that combined expression of CCAT1, CCAT2, and carcinoembryonic antigen was a significant determinant for efficiently predicting RFS in stage II (P=0.034) and stage III (P=0.001) CRC patients.
Several lncRNAs located in 8q24.21 locus are highly over-expressed in CRC. High expression of CCAT1 and CCAT2 significantly associates with poor RFS and OS. The expression of these two lncRNAs independently, or in combination, serves as important prognostic biomarkers in CRC.
Synthetic DNA is durable and can encode digital data with high density, making it an attractive medium for data storage. However, recovering stored data on a large-scale currently requires all the ...DNA in a pool to be sequenced, even if only a subset of the information needs to be extracted. Here, we encode and store 35 distinct files (over 200 MB of data), in more than 13 million DNA oligonucleotides, and show that we can recover each file individually and with no errors, using a random access approach. We design and validate a large library of primers that enable individual recovery of all files stored within the DNA. We also develop an algorithm that greatly reduces the sequencing read coverage required for error-free decoding by maximizing information from all sequence reads. These advances demonstrate a viable, large-scale system for DNA data storage and retrieval.
In this essay we propose an extension of the caries ecological hypothesis to explain the relation between dynamic changes in the phenotypic/genotypic properties of plaque bacteria and the ...demineralization/remineralization balance of the caries process. Dental plaque represents a microbial ecosystem in which non-mutans bacteria (mainly non-mutans streptococci and Actinomyces) are the key microorganisms responsible for maintaining dynamic stability on the tooth surface (dynamic stability stage). Microbial acid adaptation and subsequent acid selection of ‘low-pH’ non-mutans bacteria play a critical role for destabilizing the homeostasis of the plaque by facilitating a shift of the demineralization/remineralization balance from ‘net mineral gain’ to ‘net mineral loss’ (acidogenic stage). Once the acidic environment has been established, mutans streptococci and other aciduric bacteria may increase and promote lesion development by sustaining an environment characterized by ‘net mineral loss’ (aciduric stage). Hence, high proportions of mutans streptococci and/or other aciduric bacteria may be considered biomarkers of sites of particularly rapid caries progression. This cascade of events may change the surface texture of caries lesions from smooth to rough (enamel) or hard to soft (dentin). These clinical surface features can be reversed at any stage of lesion development provided that the acidogenic/aciduric properties of the biofilm are resolved. From an ecological point of view it is therefore not only important to describe which bacteria are involved in caries, but also to know what the bacteria are doing.
Oral Microbiome Metabolism Takahashi, N
Journal of dental research,
12/2015, Letnik:
94, Številka:
12
Journal Article
Recenzirano
Recent advances in molecular biology have facilitated analyses of the oral microbiome (“Who are they?”); however, its functions (e.g., metabolic activities) are poorly understood (“What are they ...doing?”). This review aims to summarize our current understanding of the metabolism of the oral microbiome. Saccharolytic bacteria—including Streptococcus, Actinomyces, and Lactobacillus species—degrade carbohydrates into organic acids via the Embden-Meyerhof-Parnas pathway and several of its branch pathways, resulting in dental caries, while alkalization and acid neutralization via the arginine deiminase system, urease, and so on, counteract acidification. Proteolytic/amino acid–degrading bacteria, including Prevotella and Porphyromonas species, break down proteins and peptides into amino acids and degrade them further via specific pathways to produce short-chain fatty acids, ammonia, sulfur compounds, and indole/skatole, which act as virulent and modifying factors in periodontitis and oral malodor. Furthermore, it is suggested that ethanol-derived acetaldehyde can cause oral cancer, while nitrate-derived nitrite can aid caries prevention and systemic health. Microbial metabolic activity is influenced by the oral environment; however, it can also modify the oral environment, enhance the pathogenicity of bacteria, and induce microbial selection to create more pathogenic microbiome. Taking a metabolomic approach to analyzing the oral microbiome is crucial to improving our understanding of the functions of the oral microbiome.
A quick and easy method to detect Fusobacterium species has been developed to utilize magnetic nanoparticles' magnetic response and is applied by switching magnetic fields. The bacterium can be ...detected without the washing process. The magnetic nanoparticles and Fusobacterium species are bound by an antigen-antibody reaction and aggregated into a spherical shape using a needle-shaped magnetic yoke. The aggregation of magnetic nanoparticles improves the signal-to-noise ratio to detect the bacterium. We report that a clear tendency for the concentration of Fusobacterium nucleatum can be derived by analyzing the amount of reverse magnetization and the correlation coefficient of a waveform, as well as checking the principal component analysis. This analysis is useful for an accurate evaluation of the antigen. Specific detection of Fusobacterium nucleatum was demonstrated through the cross-reaction using Candida albicans . The optical density (OD) sensitivity value was around 10 −4 -10 −3 .
Power generation performance and long‐term durability of ammonia‐fueled solid oxide fuel cell (SOFC) systems are investigated with SOFC stacks consisting of 30 planar anode‐supported cells. SOFC ...systems with three different operation modes are employed: direct ammonia, external decomposition and autothermal decomposition. A novel BaO/Ni/Sm2O3/MgO catalyst is newly developed for the external ammonia cracker, whereas a Co‐Ce‐Zr composite oxide catalyst is used for the autothermal ammonia cracker. Initial performance measurement and 1,000 h long‐term durability test of the stacks are conducted. The stack fueled with direct ammonia achieves 1 kW power output with 52% direct current (DC) electrical efficiency; a slight decrease in its performance compared with the stack with the mixture fuel of hydrogen and nitrogen is attributed to the decrease in the stack temperature caused by the endothermic ammonia decomposition reaction. The external ammonia cracker helps to maintain the stack temperature, improving the initial performance of the stack. The stack performance with the autothermal ammonia cracker is also comparable to those with the other operation modes. It is also demonstrated that the stacks fueled with ammonia have excellent stability during the long‐term tests and 57% energy conversion efficiency at ca. 700 W electrical output is achieved with the external ammonia cracker.
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