scholarly journals Comparison of oral microbiome profiles in 18-month-old infants and their parents

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ryutaro Jo ◽  
Kazuma Yama ◽  
Yuto Aita ◽  
Kota Tsutsumi ◽  
Chikako Ishihara ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Dental Caries ◽  
Oral Bacteria ◽  
Oral Microbiome ◽  
Commensal Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Deciduous Dentition ◽  
The Difference ◽  
Generation Sequencing

AbstractThe onset and progress of dental caries and periodontal disease is associated with the oral microbiome. Therefore, it is important to understand the factors that influence oral microbiome formation. One of the factors that influence oral microbiome formation is the transmission of oral bacteria from parents. However, it remains unclear when the transmission begins, and the difference in contributions of father and mother. Here, we focused on the oral microbiome of 18-month-old infants, at which age deciduous dentition is formed and the oral microbiome is likely to become stable, with that of their parents. We collected saliva from forty 18-month-old infants and their parents and compared the diversity and composition of the microbiome using next-generation sequencing of 16S rRNA genes. The results showed that microbial diversity in infants was significantly lower than that in parents and composition of microbiome were significantly different between infants and parents. Meanwhile, the microbiome of the infants was more similar to that of their mothers than unrelated adults. The bacteria highly shared between infants and parents included not only commensal bacteria but also disease related bacteria. These results suggested that the oral microbiome of the parents influences that of their children aged < 18 months.

scholarly journals Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease

mBio ◽  
2019 ◽  
Vol 10 (2) ◽  
Author(s):  
Gajender Aleti ◽  
Jonathon L. Baker ◽  
Xiaoyu Tang ◽  
Ruth Alvarez ◽  
Márcia Dinis ◽  
...  
Keyword(s):  
Dental Caries ◽  
Small Molecules ◽  
Gene Clusters ◽  
Signaling Molecules ◽  
Oral Bacteria ◽  
Oral Microbiome ◽  
Communication Media ◽  
Biosynthetic Gene ◽  
Colonization Resistance ◽  
Biosynthetic Gene Clusters

ABSTRACT Small molecules are the primary communication media of the microbial world. Recent bioinformatic studies, exploring the biosynthetic gene clusters (BGCs) which produce many small molecules, have highlighted the incredible biochemical potential of the signaling molecules encoded by the human microbiome. Thus far, most research efforts have focused on understanding the social language of the gut microbiome, leaving crucial signaling molecules produced by oral bacteria and their connection to health versus disease in need of investigation. In this study, a total of 4,915 BGCs were identified across 461 genomes representing a broad taxonomic diversity of oral bacteria. Sequence similarity networking provided a putative product class for more than 100 unclassified novel BGCs. The newly identified BGCs were cross-referenced against 254 metagenomes and metatranscriptomes derived from individuals either with good oral health or with dental caries or periodontitis. This analysis revealed 2,473 BGCs, which were differentially represented across the oral microbiomes associated with health versus disease. Coabundance network analysis identified numerous inverse correlations between BGCs and specific oral taxa. These correlations were present in healthy individuals but greatly reduced in individuals with dental caries, which may suggest a defect in colonization resistance. Finally, corroborating mass spectrometry identified several compounds with homology to products of the predicted BGC classes. Together, these findings greatly expand the number of known biosynthetic pathways present in the oral microbiome and provide an atlas for experimental characterization of these abundant, yet poorly understood, molecules and socio-chemical relationships, which impact the development of caries and periodontitis, two of the world’s most common chronic diseases. IMPORTANCE The healthy oral microbiome is symbiotic with the human host, importantly providing colonization resistance against potential pathogens. Dental caries and periodontitis are two of the world’s most common and costly chronic infectious diseases and are caused by a localized dysbiosis of the oral microbiome. Bacterially produced small molecules, often encoded by BGCs, are the primary communication media of bacterial communities and play a crucial, yet largely unknown, role in the transition from health to dysbiosis. This study provides a comprehensive mapping of the BGC repertoire of the human oral microbiome and identifies major differences in health compared to disease. Furthermore, BGC representation and expression is linked to the abundance of particular oral bacterial taxa in health versus dental caries and periodontitis. Overall, this study provides a significant insight into the chemical communication network of the healthy oral microbiome and how it devolves in the case of two prominent diseases.

scholarly journals Next Generation Sequencing Discoveries of the Nitrate-Responsive Oral Microbiome and Its Effect on Vascular Responses

2019 ◽  
Vol 8 (8) ◽  
pp. 1110 ◽  
Author(s):  
Melissa M. Grant ◽  
Daniel Jönsson
Keyword(s):  
Nitric Oxide ◽  
Next Generation Sequencing ◽  
Human Condition ◽  
Oral Microbiome ◽  
Oral Microbiota ◽  
Next Generation ◽  
Contributing Factors ◽  
Future Directions ◽  
Generation Sequencing

Cardiovascular disease is a worldwide human condition which has multiple underlying contributing factors: one of these is long-term increased blood pressure—hypertension. Nitric oxide (NO) is a small nitrogenous radical species that has a number of physiological functions including vasodilation. It can be produced enzymatically through host nitric oxide synthases and by an alternative nitrate–nitrite–NO pathway from ingested inorganic nitrate. It was discovered that this route relies on the ability of the oral microbiota to reduce nitrate to nitrite and NO. Next generation sequencing has been used over the past two decades to gain deeper insight into the microbes involved, their location and the effect of their removal from the oral cavity. This review article presents this research and comments briefly on future directions.

scholarly journals Illumina-based sequencing analysis of pathogenic microorganisms in dental caries patients of different Chinese ethnic groups

2019 ◽  
Vol 47 (10) ◽  
pp. 5037-5047
Author(s):  
Chen Yun ◽  
Li Zhiyan ◽  
Zhao Chong ◽  
Liu Jing ◽  
Zhang Xin ◽  
...  
Keyword(s):  
Dental Caries ◽  
Ethnic Groups ◽  
High Throughput Sequencing ◽  
Community Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Control Group ◽  
Sequencing Analysis ◽  
Pathogenic Microorganisms ◽  
Effective Prevention

Objective To analyze the pathogenic community diversity of dental caries patients from Tu, Hui, Tibetan, and Han Chinese ethnic groups. Methods Forty saliva samples were collected from the following patients with dental caries: Tu from Huzhu County (n = 10), Hui from Ping’an County (n = 10), Han from Xining city (n = 10), and Tibetan from Yushu (n = 10). High-throughput sequencing of bacterial 16S rRNA genes (V3-V4) was performed using the Illumina MiSeq sequencing platform. Results Based on 97% similarity clustering, operational taxonomic units of Tu, Hui, Tibetan, and Han ethnic groups were 181, 210, 38, and 67, respectively. In Tu patients, 11 phyla, 19 classes, and 89 genera were identified, compared with 13 phyla, 21 classes, and 113 genera in Hui patients, two phyla, four classes, and 21 genera in Tibetan patients, five phyla, nine classes, and 34 genera in Han patients, and four phyla, five classes, and 12 genera from the control group. The main pathogens of dental caries included Veillonella, Aggregatibacter, Leptotrichia, Bacteroides, Granulicatella, Streptococcus, and Prevotella. Conclusion The pathogenic microorganisms of dental caries differ greatly among Tu, Hui, Tibetan, and Han ethnic groups. These findings provide a theoretical basis for the effective prevention and treatment of dental caries in different Chinese populations.

scholarly journals Antimicrobial and Substantivity Properties of Silver Nanoparticles against Oral Microbiomes Clinically Isolated from Young and Young-Adult Patients

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
León Francisco Espinosa-Cristóbal ◽  
Carolina Holguín-Meráz ◽  
Erasto Armando Zaragoza-Contreras ◽  
Rita Elizabeth Martínez-Martínez ◽  
Alejandro Donohue-Cornejo ◽  
...  
Keyword(s):  
Silver Nanoparticles ◽  
Young Adult ◽  
Dental Caries ◽  
Periodontal Disease ◽  
Dental Plaque ◽  
Bacterial Species ◽  
Inhibitory Effect ◽  
Oral Bacteria ◽  
Oral Microbiome ◽  
Oral Biofilms

The dental plaque is an oral microbiome hardly associated to be the etiological agent of dental caries and periodontal disease which are still considered serious health public problems. Silver nanoparticles (AgNPs) have demonstrated to have good antimicrobial properties affecting a wide variety of microorganisms, including oral bacteria; however, there is no scientific information that has evaluated the antimicrobial effect of AgNPs against clinical oral biofilms associated with dental caries and periodontal disease. The aim of this study was to determine the antimicrobial and substantivity effects of AgNPs in oral biofilms isolated clinically from patients with dental caries and periodontal disease. Sixty-seven young and young-adult subjects with dental caries and periodontal disease were clinically sampled through the collection of subgingival dental plaque. The inhibitory effect of AgNPs was performed with standard microbiological assays by triplicate using two sizes of particle. Polymerase chain reaction (PCR) assay was used to identify the presence of specific bacterial species. All AgNPs showed an inhibitory effect for all oral biofilms for any age and, generally, any gender (p>0.05); however, the effectiveness of the antimicrobial and substantivity effects was related to particle size, time, and gender (p<0.05). The identified microorganisms were S. mutans, S. sobrinus, S. sanguinis, S. gordonii, S. oralis, P. gingivalis, T. forsythia, and P. intermedia. The AgNPs could be considered as a potential antimicrobial agent for the control and prevention of dental caries and periodontal disease.

Next-generation sequencing ordering trends in the cancer trajectory.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 10104-10104
Author(s):  
Joseph Ma ◽  
Chelsea Hagmann ◽  
Alexandra Dullea ◽  
Winnie S Wang ◽  
Warren Yau ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Cancer Patients ◽  
Advanced Cancer ◽  
Metastatic Disease ◽  
Primary Objective ◽  
Next Generation ◽  
Advanced Cancer Patients ◽  
The Difference ◽  
Generation Sequencing ◽  
Tumor Profiling

10104 Background: Next-generation sequencing (NGS) molecular tumor profiling is increasingly being ordered for advanced cancer patients to evaluate non-traditional therapeutic options. The timing of when NGS is ordered relative to date of diagnosis, palliative care (PC) consultation, and death remains unknown. The primary objective of this study was to examine NGS ordering patterns among cancer patients. Methods: This was a single center, retrospective data analysis in cancer patients at our institution between January 2011 and February 2016. Cancer patients ≥16 yrs of age were identified from a tumor registry and matched to an existing NGS tumor profiling database. Additional data were collected from an electronic medical record and compiled into a single database. Differences in the date of when NGS was ordered compared to date of diagnosis, PC consultation, and/or date of death were determined. A Mann-Whitney rank sum test examined differences in patients where NGS was ordered relative to the date of PC consultation. Logistic regression examined variables possibly associated with PC consultation. Results: Analysis included 1596 (807 women) cancer patients. Mean±SD age was 55.5±15.2 years, 30.8% (n = 492) of patients had metastatic disease, with breast and lung the most common cancers. The difference between date of cancer diagnosis and date of NGS order was 1053.6±1568.5 days (n = 1546). The difference between date of NGS order and date of death was 221.2.4±186.6 days. Two-hundred and fifty-one patients (15.7%) received a PC consultation, of which 82 patients had a NGS order before the PC consultation and 169 patients had a NGS order after the PC consultation. The mean difference in number of days between a NGS order before versus after a PC consultation was 147.3±216.8 vs. 179.8±169.7 days (p < 0.005). Four-hundred and sixty-six (29%) patients have died with 121 receiving a PC consultation. Metastatic disease, but not age and sex, was associated with PC completion (OR 1.7; 95%CI 1.27-2.21). Conclusions: NGS was frequently ordered near the time of death. PC consultations were completed in a minority of patients. NGS ordering in advanced cancer patients may serve as a trigger for PC consultation.

scholarly journals Although host-related factors are important for the formation of gut microbiota, environmental factors cannot be ignored

2020 ◽  
Author(s):  
YeonGyun Jung ◽  
Dorsaf Kerfahi ◽  
Huy Quang Pham ◽  
HyunWoo Son ◽  
Jerald Conrad Ibal ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Genetic Background ◽  
Intestinal Microflora ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Related Factors ◽  
Present Evidence ◽  
The Difference

The gut microbiome is essential to human health. However, little is known about the influence of the environment versus host-related factors (e.g. genetic background, sex, age, and body mass) in the formation of human intestinal microflora. Here, we present evidence in support of the importance of host-related factors in the establishment and maintenance of individual gut assemblages. We collected fecal samples (n = 249) from 44 Korean naval trainees and 39 healthy people living in Korea over eight weeks and sequenced the bacterial 16S rRNA genes. The following hypotheses were tested: 1) microbiome function is linked to its diversity, community structure, and genetic host-related factors, and 2) preexisting host-related factors have a more significant effect on gut microbiome formation and composition than environmental factors. For each individual, the difference between the initial gut microbiota and that after eight weeks was negligible even though the 44 naval trainees lived in the same area and received the same diet, the same amount of exercise, and the same amount of physical stress during the study. This suggests that host-related factors, rather than environmental factors, is a key determinant of individual gut microflora. Moreover, eight weeks of physical training and experiencing the same environmental conditions resulted in an increase in the species Bifidobacterium, Faecalibacterium, and Roseburia in most trainees, suggesting a healthier intestinal environment.

scholarly journals Case Report: Metagenomics Next-Generation Sequencing Can Help Define the Best Therapeutic Strategy for Brain Abscesses Caused by Oral Pathogens

2021 ◽  
Vol 8 ◽  
Author(s):  
Zhonghui Ma ◽  
Su Yan ◽  
Haoxin Dong ◽  
Huifen Wang ◽  
Yonggang Luo ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Brain Abscess ◽  
Genomic Analysis ◽  
Critical Factor ◽  
Oral Microbiome ◽  
Next Generation ◽  
Gram Staining ◽  
Brain Abscesses ◽  
Generation Sequencing

Brain abscesses are associated with an increased long-term risk of new seizures and increased mortality within several years after infection. Common microorganisms that cause brain abscesses include bacteria, fungi, and mycoplasma. We report a 75-year-old man with a brain abscess caused by Prevotella denticola, an oral pathogen. Based on the clinical condition, we suspected that the patient had a blood-borne brain abscess, and he received antibiotics and systemic supportive treatment. The patient developed shock for the second time after negative Gram-staining results. Metagenomics next-generation sequencing showed one strain from the oral microbiome, confirming our hypothesis, and targeted antibiotic treatment was administered quickly. Thus, we report a case in which genomic analysis was the critical factor in determining the best antimicrobial therapy for administration.

scholarly journals Identification of the bacterial biosynthetic gene clusters of the oral microbiome illuminates the unexplored social language of bacteria during health and disease

2018 ◽  
Author(s):  
Gajender Aleti ◽  
Jonathon L. Baker ◽  
Xiaoyu Tang ◽  
Ruth Alvarez ◽  
Márcia Dinis ◽  
...  
Keyword(s):  
Dental Caries ◽  
Small Molecules ◽  
Gene Clusters ◽  
Signaling Molecules ◽  
Oral Bacteria ◽  
Oral Microbiome ◽  
Communication Media ◽  
Biosynthetic Gene ◽  
Colonization Resistance ◽  
Biosynthetic Gene Clusters

ABSTRACTSmall molecules are the primary communication media of the microbial world. Recent bioinformatics studies, exploring the biosynthetic gene clusters (BGCs) which produce many small molecules, have highlighted the incredible biochemical potential of the signaling molecules encoded by the human microbiome. Thus far, most research efforts have focused on understanding the social language of the gut microbiome, leaving crucial signaling molecules produced by oral bacteria, and their connection to health versus disease, in need of investigation. In this study, a total of 4,915 BGCs were identified across 461 genomes representing a broad taxonomic diversity of oral bacteria. Sequence similarity networking provided a putative product class for over 100 unclassified novel BGCs. The newly identified BGCs were cross-referenced against 254 metagenomes and metatranscriptomes derived from individuals with either good oral health, dental caries, or periodontitis. This analysis revealed 2,473 BGCs, which were differentially represented across the oral microbiomes associated with health versus disease. Co-abundance network analysis identified numerous inverse correlations between BGCs and specific oral taxa. These correlations were present in health, but greatly reduced in dental caries, which may suggest a defect in colonization resistance. Finally, corroborating mass spectrometry identified several compounds with homology to products of the predicted BGC classes. Together, these findings greatly expand the number of known biosynthetic pathways present in the oral microbiome and provide an atlas for experimental characterization of these abundant, yet poorly understood, molecules and socio-chemical relationships, which impact the development of caries and periodontitis, two of the world’s most common chronic diseases.IMPORTANCEThe healthy oral microbiome is symbiotic with the human host, importantly providing colonization resistance against potential pathogens. Dental caries and periodontitis are two of the world’s most common and costly chronic infectious diseases, and are caused by a localized dysbiosis of the oral microbiome. Bacterially produced small molecules, often encoded by BGCs, are the primary communication media of bacterial communities, and play a crucial, yet largely unknown, role in the transition from health to dysbiosis. This study provides a comprehensive mapping of the BGC repertoire of the human oral microbiome and identifies major differences in health compared to disease. Furthermore, BGC representation and expression is linked to the abundance of particular oral bacterial taxa in health versus dental caries and periodontitis. Overall, this study provides a significant insight into the chemical communication network of the healthy oral microbiome, and how it devolves in the case of two prominent diseases.

scholarly journals Oral Microbiome of Children Living in an Isolated Area in Myanmar

2020 ◽  
Vol 17 (11) ◽  
pp. 4033 ◽  
Author(s):  
Yoshiaki Nomura ◽  
Ryoko Otsuka ◽  
Ryo Hasegawa ◽  
Nobuhiro Hanada
Keyword(s):  
Dental Caries ◽  
Oral Microbiome ◽  
Community Level ◽  
Operational Taxonomic Units ◽  
The Core ◽  
Hypervariable Regions ◽  
Extraction And Purification ◽  
Supragingival Plaque ◽  
Systemic Health ◽  
Generation Sequencing

Several studies have shown that the oral microbiome is related to systemic health, and a co-relation with several specific diseases has been suggested. The oral microbiome depends on environmental- and community-level factors. In this observational study, the oral microbiomes of children of isolated mountain people were analyzed with respect to the core oral microbiome and etiology of dental caries. We collected samples of supragingival plaque from children (age 9–13) living in the Chin state of Myanmar. After DNA extraction and purification, next-generation sequencing of the V3–V4 hypervariable regions of the 16S rRNA was conducted. From thirteen subjects, 263,458 valid reads and 640 operational taxonomic units were generated at a 97% identity cut-off value. At the phylum level, Proteobacteria was the most abundant, followed by Firmicutes and Bacteroides. Forty-four bacteria were detected in total from all the subjects. For children without dental caries, Proteobacteria was abundant. In contrast, in children with dental caries, Firmicutes and Bacteroides were abundant. The oral microbiome of children living in an isolated area may be affected by environmental- and community-level factors. Additionally, the composition of the oral microbiome may affect the risk of dental caries.

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