scholarly journals Metagenomic Analysis of Dental Plaque on Pit and Fissure Sites With and Without Caries Among Adolescents

2021 ◽  
Vol 11 ◽  
Author(s):  
Liangyue Pang ◽  
Yinuo Wang ◽  
Yun Ye ◽  
Yan Zhou ◽  
Qinghui Zhi ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Acid Metabolism ◽  
Taxonomic Composition ◽  
Metagenomic Sequencing ◽  
Anatomical Structures ◽  
Tooth Surfaces ◽  
The Relationship ◽  
Carbohydrate Digestion ◽  
Level 2 ◽  
Microbiota Diversity

Caries is one of the most prevalent infectious diseases worldwide and is driven by the dysbiosis of dental biofilms adhering to tooth surfaces. The pits and fissured surfaces are the most susceptible sites of caries. However, information on the taxonomic composition and functional characteristics of the plaque microbiota in the pit and fissure sites is very limited. This study aimed to use metagenomic sequencing analyses to investigate the relationship between the plaque microbiome in the pit and fissure site and caries in adolescents. A total of 20 adolescents with active pit and fissure surface caries were involved as well as 20 age-matched, caries-free teenagers for control tests. Plaque samples were collected from the pit and fissure site and were subjected to metagenomic analyses, in which the microbial communities were investigated. Our results showed that the microbiota diversity was similar between those two groups. At the species level, the relative abundances of A. gerencseriae, P. acidifaciens, P. multisaccharivorax, S. oralis, S. mutans, and P. denticolens were higher in the caries-active group. N. elongata, C. hominis, and A. johnsonii were relatively more abundant in the caries-free groups. Functional analysis suggested that the metabolic pathway was the most abundant pathway, and the functional traits of the level 2 pathways included amino acid metabolism, metabolism of cofactors, and vitamins and carbohydrate metabolism. Our results also revealed that the caries group displayed several alterations in metabolic pathways, including enriched functions in carbohydrate digestion and absorption. This study suggested that in addition to the specific anatomical structures of the pit and fissured surfaces, the fundamental differences in the plaque microbiome may also be related to the susceptibility of pit and fissure caries.

scholarly journals Interplay between the human gut microbiome and host metabolism

2019 ◽  
Author(s):  
Alessia Visconti ◽  
Caroline I. Le Roy ◽  
Fabio Rosa ◽  
Niccolo Rossi ◽  
Tiphaine C. Martin ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Metabolic Pathways ◽  
Taxonomic Composition ◽  
Metagenomic Sequencing ◽  
Human Gut ◽  
Metabolic Potential ◽  
Microbial Ecosystem ◽  
Microbiome Composition ◽  
Shotgun Metagenomic Sequencing ◽  
Key Species

AbstractThe human gut is inhabited by a complex and metabolically active microbial ecosystem regulating host health. While many studies have focused on the effect of individual microbial taxa, the metabolic potential of the entire gut microbial ecosystem has been largely under-explored. We characterised the gut microbiome of 1,004 twins via whole shotgun metagenomic sequencing (average 39M reads per sample). We observed greater similarity, across unrelated individuals, for functional metabolic pathways (82%) than for taxonomic composition (43%). We conducted a microbiota-wide association study linking both taxonomic information and microbial metabolic pathways with 673 blood and 713 faecal metabolites (Metabolon, Inc.). Metabolic pathways associated with 34% of blood and 95% of faecal metabolites, with over 18,000 significant associations, while species-level results identified less than 3,000 associations, suggesting that coordinated action of multiple taxa is required to affect the metabolome. Finally, we estimated that the microbiome mediated a crosstalk between 71% of faecal and 15% of blood metabolites, highlighting six key species (unclassified Subdoligranulum spp., Faecalibacterium prausnitzii, Roseburia inulinivorans, Methanobrevibacter smithii, Eubacterium rectale, and Akkermansia muciniphila). Because of the large inter-person variability in microbiome composition, our results underline the importance of studying gut microbial metabolic pathways rather than focusing purely on taxonomy to find therapeutic and diagnostic targets.

scholarly journals Identification of the relationship between the gut microbiome and feed efficiency in a commercial pig cohort

2021 ◽  
Author(s):  
Hui Jiang ◽  
Shaoming Fang ◽  
Hui Yang ◽  
Congying Chen
Keyword(s):  
Amino Acid ◽  
16S Rrna ◽  
Gut Microbiome ◽  
Feed Efficiency ◽  
Amino Acid Metabolism ◽  
Acid Metabolism ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
The Relationship

Abstract Feed efficiency is an economically important trait in pig production. Gut microbiota plays an important role in energy harvest, nutrient metabolism and fermentation of dietary indigestible components. Whether and which gut microbes affect feed efficiency in pigs are largely unknown. Here, a total of 208 healthy Duroc pigs were used as experimental materials. Feces and serum samples were collected at the age of 140d. We first performed 16S rRNA gene and metagenomic sequencing analysis to investigate the relationship between the gut microbiome and porcine residual feed intake (RFI). 16S rRNA gene sequencing analysis detected 21 OTUs showing the tendency to correlation with the RFI (P < 0.01). Metagenomic sequencing further identified that the members of Clostridiales, e.g. Ruminococcus flavefaoiens, Lachnospiraceae bacterium 28-4 and Lachnospiraceae phytofermentans, were enriched in pigs with low RFI (high feed efficiency), while 11 bacterial species including five Prevotella spp., especially, the Prevotella copri, had higher abundance in pigs with high RFI. Functional capacity analysis suggested that the gut microbiome of low RFI pigs had high abundance of the pathways related to amino acid metabolism and biosynthesis, but low abundance of the pathways associated with monosaccharide metabolism and lipopolysaccharide biosynthesis. Serum metabolome and fecal short chain fatty acids (SCFAs) were determined by UPLC-QTOF/MS and gas chromatograph, respectively. Propionic acid in feces and the serum metabolites related to amino acid metabolism were negatively correlated with the RFI. The results from this study may provide potential gut microbial biomarkers that could be used for improving feed efficiency in pig production industry.

scholarly journals The efficiency and mechanism of vermicompost in enhancing the composting of swine manure as an additive

2021 ◽  
Author(s):  
Xiaoxia Hao ◽  
Xinyuan Ma ◽  
Lin Bai
Keyword(s):  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Pathogenic Bacteria ◽  
Acid Metabolism ◽  
Swine Manure ◽  
Functional Genes ◽  
Beneficial Bacteria ◽  
Metabolic Capacity ◽  
Level 3 ◽  
Level 2

Abstract Vermicompost was used as an additive in swine manure composting, and the expression of bacterial functional genes on biotransformation of nutrient was investigated. Results showed that vermicompost extended the thermophilic period to 12 days, decreased the NH4+ -N/NO3− -N ratio to 0.85 and increased GI value to 166%. With vermicompost addition, higher relative abundances of Firmicutes were observed in substrate at the beginning. The dominant phyla of Proteobacteria was decreased in thermophilic stage, as well as its pathogenic related genera Acinetobacter and Stenotrophomonas, while the potentially beneficial genera Actinomadura and Chryseolinea were increased. And the activities of primary functional genes associated with metabolisms of carbohydrate, amino acid and xenobiotics at the level 2 and fatty acid metabolism at the level 3 were enhanced during the thermophilic phase. Besides, most dominant genera showed strengthened correlations with NO3−-N and GI with vermicompost amendment, and they were the strongest environmental factors for bacterial communities. Network analysis showed dominant genera Pseudomonas, Acinetobacter, Stenotrophomonas Oceanobacter associated metabolic pathways increased from two to three with vermicompost added in substrate. These results indicated that vermicompost promoted the composting efficiency by increasing the potentially beneficial bacteria, decreasing pathogenic bacteria and enhancing the metabolic capacity of bacterial communities.

scholarly journals Gut Microbiota, Combined with Metabolomics, Reveals the Mechanism of Curcumol on Liver Fibrosis in Mice

2022 ◽  
Author(s):  
Yang Zheng ◽  
Jiahui Wang ◽  
Jiaru Wang ◽  
Ruizhu Jiang ◽  
Tianjian Liang ◽  
...  
Keyword(s):  
Liver Fibrosis ◽  
Gut Microbiota ◽  
Metabolic Pathways ◽  
Acid Metabolism ◽  
Intestinal Flora ◽  
Pathological Process ◽  
Arachidonic Acid Metabolism ◽  
Liver Inflammation ◽  
16S Rrna Analysis ◽  
The Relationship

Abstract Background:Liver fibrosis is a reversible pathological process, and its prevention and treatment are of great significance to patients with chronic liver disease. This study combined 16S rRNA analysis of gut microbiota and plasma metabolomics to explore the mechanism of curcumol’s effect on liver fibrosis in mice. The results will help to clarify the relationship between the gut microbiota and metabolites in the process of liver fibrosis.Results:Molecular biological testing found that curcumol could significantly improve the pathological changes of liver tissue and inhibit the occurrence of liver inflammation. Intestinal flora testing found that curcumol could significantly change the abundances of Veillonellaceae, Prerotella_oulorum, and Alistipes_finegoldii. Metabolomics analysis found that curcumol’s anti-hepatic fibrosis effect may be related to its regulation of arachidonic acid metabolism. Correlation analysis suggested that curcumol regulated the abundances of Bacteroidota and Bacteroides and participated in the metabolism of Prostaglandin B2.Conclusions:When liver fibrosis occurs, the intestinal flora and metabolic network will be altered. The effect of curcumol on liver fibrosis may be related to its regulation of intestinal flora and the resulting interference with metabolic pathways, thereby regulating liver inflammation.

Isoleucine Plays an Important Role for Maintaining Immune Function

2019 ◽  
Vol 20 (7) ◽  
pp. 644-651 ◽  
Author(s):  
Changsong Gu ◽  
Xiangbing Mao ◽  
Daiwen Chen ◽  
Bing Yu ◽  
Qing Yang
Keyword(s):  
Amino Acids ◽  
Acid Metabolism ◽  
Branched Chain Amino Acids ◽  
Whole Body ◽  
Immune Functions ◽  
Host Defense Peptides ◽  
Innate And Adaptive Immunity ◽  
Physiological Functions ◽  
Branched Chain ◽  
The Relationship

Branched chain amino acids are the essential nutrients for humans and many animals. As functional amino acids, they play important roles in physiological functions, including immune functions. Isoleucine, as one of the branched chain amino acids, is also critical in physiological functions of the whole body, such as growth, immunity, protein metabolism, fatty acid metabolism and glucose transportation. Isoleucine can improve the immune system, including immune organs, cells and reactive substances. Recent studies have also shown that isoleucine may induce the expression of host defense peptides (i.e., β-defensins) that can regulate host innate and adaptive immunity. In addition, isoleucine administration can restore the effect of some pathogens on the health of humans and animals via increasing the expression of β-defensins. Therefore, the present review will emphatically discuss the effect of isoleucine on immunity while summarizing the relationship between branched chain amino acids and immune functions.

scholarly journals Curves on K3 surfaces in divisibility 2

2021 ◽  
Vol 9 ◽  
Author(s):  
Younghan Bae ◽  
Tim-Henrik Buelles
Keyword(s):  
Modular Forms ◽  
K3 Surfaces ◽  
Initial Condition ◽  
Smooth Curves ◽  
Holomorphic Anomaly ◽  
Holomorphic Anomaly Equation ◽  
Anomaly Equation ◽  
Degeneration Formula ◽  
The Relationship ◽  
Level 2

Abstract We prove a conjecture of Maulik, Pandharipande and Thomas expressing the Gromov–Witten invariants of K3 surfaces for divisibility 2 curve classes in all genera in terms of weakly holomorphic quasi-modular forms of level 2. Then we establish the holomorphic anomaly equation in divisibility 2 in all genera. Our approach involves a refined boundary induction, relying on the top tautological group of the moduli space of smooth curves, together with a degeneration formula for the reduced virtual fundamental class with imprimitive curve classes. We use double ramification relations with target variety as a new tool to prove the initial condition. The relationship between the holomorphic anomaly equation for higher divisibility and the conjectural multiple cover formula of Oberdieck and Pandharipande is discussed in detail and illustrated with several examples.

scholarly journals Mitochondrial Sirtuins in Reproduction

Antioxidants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1047
Author(s):  
Giovanna Di Emidio ◽  
Stefano Falone ◽  
Paolo Giovanni Artini ◽  
Fernanda Amicarelli ◽  
Anna Maria D’Alessandro ◽  
...  
Keyword(s):  
Stress Responses ◽  
Metabolic Pathways ◽  
Redox Balance ◽  
Antioxidant Defenses ◽  
Metabolic Abnormalities ◽  
Female Reproduction ◽  
Mitochondrial Dysfunctions ◽  
Early Embryos ◽  
The Relationship

Mitochondria act as hubs of numerous metabolic pathways. Mitochondrial dysfunctions contribute to altering the redox balance and predispose to aging and metabolic alterations. The sirtuin family is composed of seven members and three of them, SIRT3-5, are housed in mitochondria. They catalyze NAD+-dependent deacylation and the ADP-ribosylation of mitochondrial proteins, thereby modulating gene expression and activities of enzymes involved in oxidative metabolism and stress responses. In this context, mitochondrial sirtuins (mtSIRTs) act in synergistic or antagonistic manners to protect from aging and aging-related metabolic abnormalities. In this review, we focus on the role of mtSIRTs in the biological competence of reproductive cells, organs, and embryos. Most studies are focused on SIRT3 in female reproduction, providing evidence that SIRT3 improves the competence of oocytes in humans and animal models. Moreover, SIRT3 protects oocytes, early embryos, and ovaries against stress conditions. The relationship between derangement of SIRT3 signaling and the imbalance of ROS and antioxidant defenses in testes has also been demonstrated. Very little is known about SIRT4 and SIRT5 functions in the reproductive system. The final goal of this work is to understand whether sirtuin-based signaling may be taken into account as potential targets for therapeutic applications in female and male infertility.

scholarly journals Comprehensive transcriptome and metabolome profiling reveal metabolic mechanisms of Nitraria sibirica Pall. to salt stress

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Huanyong Li ◽  
Xiaoqian Tang ◽  
Xiuyan Yang ◽  
Huaxin Zhang
Keyword(s):  
Salt Stress ◽  
Amino Acid ◽  
Salt Tolerance ◽  
Metabolic Pathways ◽  
Amino Acid Metabolism ◽  
Acid Metabolism ◽  
Sulfur Metabolism ◽  
Enrichment Analysis ◽  
Extracellular Region ◽  
Nitraria Sibirica

AbstractNitraria sibirica Pall., a typical halophyte that can survive under extreme drought conditions and in saline-alkali environments, exhibits strong salt tolerance and environmental adaptability. Understanding the mechanism of molecular and physiological metabolic response to salt stress of plant will better promote the cultivation and use of halophytes. To explore the mechanism of molecular and physiological metabolic of N. sibirica response to salt stress, two-month-old seedlings were treated with 0, 100, and 400 mM NaCl. The results showed that the differentially expressed genes between 100 and 400 mmol L−1 NaCl and unsalted treatment showed significant enrichment in GO terms such as binding, cell wall, extemal encapsulating structure, extracellular region and nucleotide binding. KEGG enrichment analysis found that NaCl treatment had a significant effect on the metabolic pathways in N. sibirica leaves, which mainly including plant-pathogen interaction, amino acid metabolism of the beta alanine, arginine, proline and glycine metabolism, carbon metabolism of glycolysis, gluconeogenesis, galactose, starch and sucrose metabolism, plant hormone signal transduction and spliceosome. Metabolomics analysis found that the differential metabolites between the unsalted treatment and the NaCl treatment are mainly amino acids (proline, aspartic acid, methionine, etc.), organic acids (oxaloacetic acid, fumaric acid, nicotinic acid, etc.) and polyhydric alcohols (inositol, ribitol, etc.), etc. KEGG annotation and enrichment analysis showed that 100 mmol L−1 NaCl treatment had a greater effect on the sulfur metabolism, cysteine and methionine metabolism in N. sibirica leaves, while various amino acid metabolism, TCA cycle, photosynthetic carbon fixation and sulfur metabolism and other metabolic pathways have been significantly affected by 400 mmol L−1 NaCl treatment. Correlation analysis of differential genes in transcriptome and differential metabolites in metabolome have found that the genes of AMY2, BAM1, GPAT3, ASP1, CML38 and RPL4 and the metabolites of L-cysteine, proline, 4-aminobutyric acid and oxaloacetate played an important role in N. sibirica salt tolerance control. This is a further improvement of the salt tolerance mechanism of N. sibirica, and it will provide a theoretical basis and technical support for treatment of saline-alkali soil and the cultivation of halophytes.

scholarly journals Transitions in oral and gut microbiome of HPV+ oropharyngeal squamous cell carcinoma following definitive chemoradiotherapy (ROMA LA-OPSCC study)

2021 ◽  
Author(s):  
Marc Oliva ◽  
Pierre H. H. Schneeberger ◽  
Victor Rey ◽  
Matthew Cho ◽  
Rachel Taylor ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Taxonomic Composition ◽  
Oropharyngeal Squamous Cell Carcinoma ◽  
Oral Microbiome ◽  
Metagenomic Sequencing ◽  
Α Diversity ◽  
16S Rna ◽  
The Impact

Abstract Background Oral and gut microbiomes have emerged as potential biomarkers in cancer. We characterised the oral and gut microbiomes in a prospective observational cohort of HPV+ oropharyngeal squamous cell carcinoma (OPSCC) patients and evaluated the impact of chemoradiotherapy (CRT). Methods Saliva, oropharyngeal swabs over the tumour site and stool were collected at baseline and post-CRT. 16S RNA and shotgun metagenomic sequencing were used to generate taxonomic profiles, including relative abundance (RA), bacterial density, α-diversity and β-diversity. Results A total of 132 samples from 22 patients were analysed. Baseline saliva and swabs had similar taxonomic composition (R2 = 0.006; p = 0.827). Oropharyngeal swabs and stool taxonomic composition varied significantly by stage, with increased oral RA of Fusobacterium nucleatum observed in stage III disease (p < 0.05). CRT significantly reduced the species richness and increased the RA of gut-associated taxa in oropharyngeal swabs (p < 0.05), while it had no effect in stool samples. These findings remained significant when adjusted by stage, smoking status and antibiotic use. Conclusions Baseline oral and gut microbiomes differ by stage in this HPV+ cohort. CRT caused a shift towards a gut-like microbiome composition in oropharyngeal swabs. Stage-specific features and the transitions in oral microbiome might have prognostic and therapeutic implications.

Sign in / Sign up

Export Citation Format

Share Document