OTUs clustering should be avoided for defining oral microbiome

This in silico investigation aimed to: 1) evaluate a set of primer pairs with high coverage, including those most commonly used in the literature, to find the different oral species with 16S rRNA gene amplicon similarity/identity (ASI) values ≥97%; and 2) identify oral species that may be erroneously clustered in the same operational taxonomic unit (OTU) and ascertain whether they belong to distinct genera or other higher taxonomic ranks. Thirty-nine primer pairs were employed to obtain amplicon sequence variants (ASVs) from the complete genomes of 186 bacterial and 135 archaeal species. For each primer, ASVs without mismatches were aligned using BLASTN and their similarity values were obtained. Finally, we selected ASVs from different species with an ASI value ≥97% that were covered 100% by the query sequences. For each primer, the percentage of species-level coverage with no ASI≥97% (SC-NASI≥97%) was calculated. Based on the SC-NASI≥97% values, the best primer pairs were OP_F053-KP_R020 for bacteria (65.05%), KP_F018-KP_R002 for archaea (51.11%), and OP_F114-KP_R031 for bacteria and archaea together (52.02%). Eighty percent of the oral-bacteria and oral-archaea species shared an ASI≥97% with at least one other taxa, including Campylobacter, Rothia, Streptococcus, and Tannerella, which played conflicting roles in the oral microbiota. Moreover, around a quarter and a third of these two-by-two similarity relationships were between species from different bacteria and archaea genera, respectively. Furthermore, even taxa from distinct families, orders, and classes could be grouped in the same cluster. Consequently, irrespective of the primer pair used, OTUs constructed with a 97% similarity provide an inaccurate description of oral-bacterial and oral-archaeal species, greatly affecting microbial diversity parameters. As a result, clustering by OTUs impacts the credibility of the associations between some oral species and certain health and disease conditions. This limits significantly the comparability of the microbial diversity findings reported in oral microbiome literature.

Download Full-text

Oral Microbiota Identifies Patients in Early Onset Rheumatoid Arthritis

Microorganisms ◽

10.3390/microorganisms9081657 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1657

Author(s):

Anders Esberg ◽

Linda Johansson ◽

Ingegerd Johansson ◽

Solbritt Rantapää Dahlqvist

Keyword(s):

Rheumatoid Arthritis ◽

Early Onset ◽

Amplicon Sequencing ◽

Oral Bacteria ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Microbiota ◽

Disease Manifestation ◽

Periodontal Status ◽

Quality Register

Rheumatoid arthritis (RA) is the most common autoimmune inflammatory disease, and single periodontitis-associated bacteria have been suggested in disease manifestation. Here, the oral microbiota was characterized in relation to the early onset of RA (eRA) taking periodontal status into consideration. 16S rRNA gene amplicon sequencing of saliva bacterial DNA from 61 eRA patients without disease-modifying anti-rheumatic drugs and 59 matched controls was performed. Taxonomic classification at 98.5% was conducted against the Human Oral Microbiome Database, microbiota functions were predicted using PICRUSt, and periodontal status linked from the Swedish quality register for clinically assessed caries and periodontitis. The participants were classified into three distinct microbiota-based cluster groups with cluster allocation differences by eRA status. Independently of periodontal status, eRA patients had enriched levels of Prevotella pleuritidis, Treponema denticola, Porphyromonas endodontalis and Filifactor alocis species and in the Porphyromonas and Fusobacterium genera and functions linked to ornithine metabolism, glucosylceramidase, beta-lactamase resistance, biphenyl degradation, fatty acid metabolism and 17-beta-estradiol-17-dehydrogenase metabolism. The results support a deviating oral microbiota composition already in eRA patients compared with healthy controls and highlight a panel of oral bacteria that may be useful in eRA risk assessment in both periodontally healthy and diseased persons.

Download Full-text

Variations of Oral Microbiome in Chronic Insomnia Patients with Different Tongue Features

The American Journal of Chinese Medicine ◽

10.1142/s0192415x20500445 ◽

2020 ◽

Vol 48 (04) ◽

pp. 923-944 ◽

Cited By ~ 2

Author(s):

Meng Liu ◽

Xiting Wang ◽

Fengzhi Wu ◽

Ning Dai ◽

Mindan Chen ◽

...

Keyword(s):

Relative Abundance ◽

16S Rrna Gene Sequencing ◽

Oral Bacteria ◽

Oral Microbiome ◽

Chronic Insomnia ◽

Rrna Gene ◽

Oral Microbiota ◽

Healthy Individuals ◽

Tongue Diagnosis ◽

Therapeutic Decision Making

Chronic insomnia is a disease which brings intense mental pain and disturbing complications to patients worldwide. The oral microbiome exhibits a mechanistic influence on human health. Therefore, it is crucial to understand the oral microbial diversity in insomnia. Tongue diagnosis has been considered a critical basic procedure in insomnia therapeutic decision-making in Traditional Chinese Medicine (TCM). Hence, it is significant to elucidate the various oral microbiome differences in chronic insomnia patients with different tongue features. In this paper, we used 16S rRNA gene sequencing and bioinformatics analysis to investigate dynamic changes in oral bacterial profile and correlations between chronic insomnia patients and healthy individuals, as well as in patients with different tongue coatings. Moreover, the relationship between the severity of insomnia and oral microbiota was explored. Our findings showed that chronic insomnia patients harbored a significantly higher diversity of oral bacteria when compared to healthy controls. More importantly, the results revealed that the diversity and relative abundance of the bacterial community was significantly altered among different tongue coatings in patients but not in healthy individuals. Oral bacteria with a relative abundance [Formula: see text]1% and [Formula: see text] among different tongue groups were considered remarkable bacteria, which included three phyla Proteobacteria, Bacteroidetes, Gracilibacteria, and four genera, Streptococcus, Prevotella_7, Rothia, and Neisseria. Our findings indicate that changes in oral microbiome correlate with tongue coatings in patients with chronic insomnia. Thus, the remarkable microbiome may provide inspiration for further studies on the correlation between tongue diagnosis and oral microbiome in chronic insomnia patients.

Download Full-text

The Human Oral Microbiome

Journal of Bacteriology ◽

10.1128/jb.00542-10 ◽

2010 ◽

Vol 192 (19) ◽

pp. 5002-5017 ◽

Cited By ~ 1462

Author(s):

Floyd E. Dewhirst ◽

Tuste Chen ◽

Jacques Izard ◽

Bruce J. Paster ◽

Anne C. R. Tanner ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Species Level ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Microbiota ◽

16S Rrna Gene Sequences ◽

Culture Independent ◽

Health And Disease

ABSTRACT The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome is comprised of over 600 prevalent taxa at the species level, with distinct subsets predominating at different habitats. The oral microbiome has been extensively characterized by cultivation and culture-independent molecular methods such as 16S rRNA cloning. Unfortunately, the vast majority of unnamed oral taxa are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic anchors. The first aim of this research was to collect 16S rRNA gene sequences into a curated phylogeny-based database, the Human Oral Microbiome Database (HOMD), and make it web accessible (www.homd.org ). The HOMD includes 619 taxa in 13 phyla, as follows: Actinobacteria, Bacteroidetes, Chlamydiae, Chloroflexi, Euryarchaeota, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes, SR1, Synergistetes, Tenericutes, and TM7. The second aim was to analyze 36,043 16S rRNA gene clones isolated from studies of the oral microbiota to determine the relative abundance of taxa and identify novel candidate taxa. The analysis identified 1,179 taxa, of which 24% were named, 8% were cultivated but unnamed, and 68% were uncultivated phylotypes. Upon validation, 434 novel, nonsingleton taxa will be added to the HOMD. The number of taxa needed to account for 90%, 95%, or 99% of the clones examined is 259, 413, and 875, respectively. The HOMD is the first curated description of a human-associated microbiome and provides tools for use in understanding the role of the microbiome in health and disease.

Download Full-text

Niche-Specialist And Age-Related Microbial Ecosystem: Correlation Analysis With Immune Cells In Oral Homeostasis

10.21203/rs.3.rs-829179/v1 ◽

2021 ◽

Author(s):

Dongjia Lin ◽

Lisa Yang ◽

Qiannan Hu ◽

Dikan Wang ◽

Wenxiao Dai ◽

...

Keyword(s):

Correlation Analysis ◽

Immune Cells ◽

Immune Cell ◽

Oral Bacteria ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Microbiota ◽

Life Stages ◽

Microbial Ecosystem ◽

Age Related

Abstract Background: The oral microbial ecosystem, with distinct characteristics in structure and evolution, plays an important role in the mucosal homeostasis. The characterization of baseline microbial and functional diversity in the oral microbiome has been discussed, yet the taxon-taxon relationships, and the role of the microbes themselves to the host mucosa are still lack of discussing. In addition, the current literature seems insufficient to draw a definitive conclusion about a possible impact of ageing on the oral microbiota. Therefore, the study focuses on the spatial and temporal characteristics of the oral microbial ecosystem, and its correlation with immune cell in oral homeostasis. Results: The V3V4 region of 16S rRNA gene of 30 samples from different sites (gingiva, palate, buccal, tongue) and life stages (adult, old) was analyzed. Flow cytometry was used to investigate the residing immune cells. The niche-specialist and age-related communities, characterized by alterations in microbiota structure, taxon-taxon relationship, microbial functions, and immune cell inhabiting, have been addressed. Interestingly, network analysis shows more antagonistic interactions in gingiva, palatal site, and old mice saliva, where harbor a richer diversity. While in buccal mucosa and tongue, it appears more synergic interactions to maintain the ecosystem balance. Functional analysis reveals that the significant factor that determines the niche for a microbe is its local habitat in the content of one specific age, which includes its immediate neighbors. Correlation analysis suggests strong associations between distinct oral bacteria and Th cells exist in different life stages. Conclusions: Our findings propose that the oral microbial ecosystem, with niche-specialist and age-related characteristics, has unique evolution and co-evolution with the host to maintain oral homeostasis, which provides critical insights on mucosal microbiology.

Download Full-text

Frequency of Selenomonas Noxia in Oral Microbiota of Obese and Normal Weight People in Duhok-Iraq

Science Journal of University of Zakho ◽

10.25271/sjuoz.2019.7.4.674 ◽

2019 ◽

Vol 7 (4) ◽

pp. 120-124

Author(s):

Roshna M. Qadir ◽

Mahde S. Abdulrahman

Keyword(s):

Oral Bacteria ◽

Normal Weight ◽

Oral Microbiome ◽

Oral Microbiota ◽

Obese People ◽

Overweight People ◽

Significant Difference ◽

Overweight Group ◽

Oral Carriage ◽

Selenomonas Noxia

Obesity represents one of the major problematic health issues worldwide. Recent evidences suggest that obesity is related with the alteration of the oral microbiome. The aim of this study was to measure the salivary bacterial Selenomonas noxia in Duhok population. A total of 155 saliva samples were collected from individuals (aged between 19-35 years) of both genders (86 females and 69 males). The individuals were divided into three groups (obese, overweight, and normal weight) based on their body mass index. Bacterial genomic DNA was extracted from saliva samples. Molecular detections of Selenomonas noxia were performed by the polymerase chain reaction. Among the 155 participants, 34.1% were obese, 26.4% overweight and 39.3% normal weight individuals. The prevalence rate of oral S. noxia among all people was 82.6%. The highest rate of S. noxia was in obese people (86.8%), followed by overweight (85.4%) and normal weight people (77%). The prevalence of S. noxia in overweight people was statistically significant in compare with the normal weight people (p<0.0001). Moreover, the oral carriage of S. noxia was highest among the overweight females (94.5%) followed by obese females (88.9%). However, no significant difference was found compared to males. The result revealed that it is possible to assume that the expansion of S. noxia in saliva is due to obesity. Moreover, the composition of salivary microbiome may lead to the risk that the overweight group is at risk of future obesity. However, further investigations are required with larger sample and participants with different socioeconomic status in order to address the exact link between obesity and oral bacteria. This could lead to a new and promising therapeutic way for improving human's health.

Download Full-text

Impact of Oropharyngeal Administration of Colostrum in Preterm Newborns’ Oral Microbiome

Nutrients ◽

10.3390/nu13124224 ◽

2021 ◽

Vol 13 (12) ◽

pp. 4224

Author(s):

Ramon V. Cortez ◽

Andrea Fernandes ◽

Luiz Gustavo Sparvoli ◽

Marina Padilha ◽

Rubens Feferbaum ◽

...

Keyword(s):

Preterm Infants ◽

16S Rrna Gene Sequencing ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Microbiota ◽

Alpha And Beta Diversity ◽

Longitudinal Observational Study ◽

Key Factor ◽

Rrna Gene Sequencing ◽

Preterm Newborns

The initial colonization of the human microbiota is of paramount importance. In this context, the oropharyngeal administration of colostrum is a safe, viable, and well-tolerated practice even by the smallest preterm infants. Therefore, this study evaluated the effects of oropharyngeal administration of colostrum on the establishment of preterm infants’ oral microbiota. A longitudinal observational study was carried out with 20 premature neonates, divided into two groups: one receiving the protocol (Oropharyngeal Administration of Colostrum; OAC) and the other one receiving Standard Caare (SC). Saliva samples were collected from the newborns weekly during the study period (from the day of birth until the 21st day of life) for analysis of oral microbiota through 16S rRNA gene sequencing. We observed that the colonization of the oral microbiota of preterm newborns preseanted a higher relative abundance of Staphylococcus on the 7th day of life, mainly in the OAC group. Additionally, an increased abundance of Bifidobacterium and Bacteroides was observed in the OAC group at the first week of life. Regarding alpha and beta diversity, time was a key factor in the oral modulation of both groups, showing how dynamic this environment is in early life.

Download Full-text

Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study

Gut ◽

10.1136/gutjnl-2016-312580 ◽

2016 ◽

Vol 67 (1) ◽

pp. 120-127 ◽

Cited By ~ 177

Author(s):

Xiaozhou Fan ◽

Alexander V Alekseyenko ◽

Jing Wu ◽

Brandilyn A Peters ◽

Eric J Jacobs ◽

...

Keyword(s):

Pancreatic Cancer ◽

Case Control Study ◽

Case Control ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Microbiota ◽

Increased Risk ◽

Oral Pathogens ◽

Nested Case Control ◽

Control Study

ObjectiveA history of periodontal disease and the presence of circulating antibodies to selected oral pathogens have been associated with increased risk of pancreatic cancer; however, direct relationships of oral microbes with pancreatic cancer have not been evaluated in prospective studies. We examine the relationship of oral microbiota with subsequent risk of pancreatic cancer in a large nested case–control study.DesignWe selected 361 incident adenocarcinoma of pancreas and 371 matched controls from two prospective cohort studies, the American Cancer Society Cancer Prevention Study II and the National Cancer Institute Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. From pre-diagnostic oral wash samples, we characterised the composition of the oral microbiota using bacterial 16S ribosomal RNA (16S rRNA) gene sequencing. The associations between oral microbiota and risk of pancreatic cancer, controlling for the random effect of cohorts and other covariates, were examined using traditional and L1-penalised least absolute shrinkage and selection operator logistic regression.ResultsCarriage of oral pathogens, Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans, were associated with higher risk of pancreatic cancer (adjusted OR for presence vs absence=1.60 and 95% CI 1.15 to 2.22; OR=2.20 and 95% CI 1.16 to 4.18, respectively). Phylum Fusobacteria and its genus Leptotrichia were associated with decreased pancreatic cancer risk (OR per per cent increase of relative abundance=0.94 and 95% CI 0.89 to 0.99; OR=0.87 and 95% CI 0.79 to 0.95, respectively). Risks related to these phylotypes remained after exclusion of cases that developed within 2 years of sample collection, reducing the likelihood of reverse causation in this prospective study.ConclusionsThis study provides supportive evidence that oral microbiota may play a role in the aetiology of pancreatic cancer.

Download Full-text

Analysis of the Effects of Dietary Pattern on the Oral Microbiome of Elite Endurance Athletes

Nutrients ◽

10.3390/nu11030614 ◽

2019 ◽

Vol 11 (3) ◽

pp. 614 ◽

Cited By ~ 17

Author(s):

Nida Murtaza ◽

Louise Burke ◽

Nicole Vlahovich ◽

Bronwen Charlesson ◽

Hayley O’Neill ◽

...

Keyword(s):

Discriminant Analysis ◽

Relative Abundance ◽

Distance Measure ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Microbiota ◽

Unifrac Distance ◽

Linear Discriminant ◽

Principal Coordinates ◽

Low Carbohydrate

Although the oral microbiota is known to play a crucial role in human health, there are few studies of diet x oral microbiota interactions, and none in elite athletes who may manipulate their intakes of macronutrients to achieve different metabolic adaptations in pursuit of optimal endurance performance. The aim of this study was to investigate the shifts in the oral microbiome of elite male endurance race walkers from Europe, Asia, the Americas and Australia, in response to one of three dietary patterns often used by athletes during a period of intensified training: a High Carbohydrate (HCHO; n = 9; with 60% energy intake from carbohydrates; ~8.5 g kg−1 day−1 carbohydrate, ~2.1 g kg−1 day−1 protein, 1.2 g kg−1 day−1 fat) diet, a Periodised Carbohydrate (PCHO; n = 10; same macronutrient composition as HCHO, but the intake of carbohydrates is different across the day and throughout the week to support training sessions with high or low carbohydrate availability) diet or a ketogenic Low Carbohydrate High Fat (LCHF; n = 10; 0.5 g kg−1 day−1 carbohydrate; 78% energy as fat; 2.1 g kg−1 day−1 protein) diet. Saliva samples were collected both before (Baseline; BL) and after the three-week period (Post treatment; PT) and the oral microbiota profiles for each athlete were produced by 16S rRNA gene amplicon sequencing. Principal coordinates analysis of the oral microbiota profiles based on the weighted UniFrac distance measure did not reveal any specific clustering with respect to diet or athlete ethnic origin, either at baseline (BL) or following the diet-training period. However, discriminant analyses of the oral microbiota profiles by Linear Discriminant Analysis (LDA) Effect Size (LEfSe) and sparse Partial Least Squares Discriminant Analysis (sPLS-DA) did reveal changes in the relative abundance of specific bacterial taxa, and, particularly, when comparing the microbiota profiles following consumption of the carbohydrate-based diets with the LCHF diet. These analyses showed that following consumption of the LCHF diet the relative abundances of Haemophilus, Neisseria and Prevotella spp. were decreased, and the relative abundance of Streptococcus spp. was increased. Such findings suggest that diet, and, in particular, the LCHF diet can induce changes in the oral microbiota of elite endurance walkers.

Download Full-text

Comparison of Oral Microbiota Collected Using Multiple Methods and Recommendations for New Epidemiologic Studies

mSystems ◽

10.1128/msystems.00156-20 ◽

2020 ◽

Vol 5 (4) ◽

Cited By ~ 2

Author(s):

Yukiko Yano ◽

Xing Hua ◽

Yunhu Wan ◽

Shalabh Suman ◽

Bin Zhu ◽

...

Keyword(s):

Beta Diversity ◽

Epidemiologic Studies ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Microbiota ◽

Collection Method ◽

Two Samples ◽

Relative Abundances ◽

Collection Methods ◽

Diversity Metrics

ABSTRACT Epidemiologic studies use various biosample collection methods to study associations between human oral microbiota and health outcomes. However, the agreement between the different methods is unclear. We compared a commercially available OMNIgene ORAL kit to three alternative collection methods: Saccomanno’s fixative, Scope mouthwash, and nonethanol mouthwash. Oral samples were collected from 40 individuals over 4 visits. Two samples were collected from each subject per visit: one with OMNIgene and one with an alternative method. DNA was extracted using the DSP DNA Virus Pathogen kit, and the V4 region of the 16S rRNA gene was PCR amplified and sequenced using MiSeq. Oral collection methods were compared based on alpha and beta diversity metrics and phylum- and genus-level relative abundances. All alpha diversity metrics were significantly lower for Saccomanno’s fixative than for OMNIgene (P < 0.001), whereas the two mouthwashes were more similar to OMNIgene. Principal-coordinate analysis (PCoA) using the Bray-Curtis and weighted UniFrac beta diversity matrices showed large differences in the microbial compositions of samples collected with Saccomanno’s compared to those with OMNIgene and the mouthwashes. Clustering by collection method was not observed in unweighted UniFrac PCoA plots, suggesting differences in relative abundances but not specific taxa detected by the collection methods. Relative abundances of most taxa were significantly different between OMNIgene and the other methods at each taxonomic level, with Saccomanno’s showing the least agreement with OMNIgene. There were clear differences in oral microbial communities between the four oral collection methods, particularly for Saccomanno’s fixative. IMPORTANCE We compared four different oral collection methods for studying the human oral microbiome: an OMNIgene ORAL kit, Scope mouthwash, nonethanol mouthwash, and Saccomanno’s fixative. Our study shows that the type of the collection method can have a large impact on the results of an oral microbiome analysis. We recommend that one consistent oral collection method should be used for all oral microbiome comparisons. While Scope and nonethanol mouthwashes are less expensive and provide results similar to those with OMNIgene, Saccomanno’s fixative may be unfavorable due to the microbial differences detected in this study. Our results will help guide the design of future oral microbiome studies.

Download Full-text

Single-Cell Genomics and the Oral Microbiome

Journal of Dental Research ◽

10.1177/0022034520907380 ◽

2020 ◽

Vol 99 (6) ◽

pp. 613-620 ◽

Cited By ~ 2

Author(s):

M. Balachandran ◽

K.L. Cross ◽

M. Podar

Keyword(s):

Microbial Community ◽

Single Cell ◽

Single Cells ◽

Oral Bacteria ◽

Oral Microbiome ◽

Oral Microbiota ◽

Oral Diseases ◽

Interspecies Interactions ◽

Single Cell Genomics

The human oral cavity is one of the first environments where microbes have been discovered and studied since the dawn of microbiology. Nevertheless, approximately 200 types of bacteria from the oral microbiota have remained uncultured in the laboratory. Some are associated with a healthy oral microbial community, while others are linked to oral diseases, from dental caries to gum disease. Single-cell genomics has enabled inferences on the physiology, virulence, and evolution of such uncultured microorganisms and has further enabled isolation and cultivation of several novel oral bacteria, including the discovery of novel interspecies interactions. This review summarizes some of the more recent advances in this field, which is rapidly moving toward physiologic characterization of single cells and ultimately cultivation of the yet uncultured. A combination of traditional microbiological approaches with genomic-based physiologic predictions and isolation strategies may lead to the oral microbiome being the first complex microbial community to have all its members cultivable in the laboratory. Studying the biology of the individual microbes when in association with other members of the community, in controlled laboratory conditions and in vivo, should lead to a better understanding of oral dysbiosis and its prevention and reversion.

Download Full-text