Comparative Analysis of Primers Used for 16S rRNA Gene Sequencing in Oral Microbiome Studies

Microbiological profile of molars with advanced furcation defects before and after surgical and non-surgical periodontal treatment: A pilot randomized controlled trial

OBJECTIVES

To describe the microbiological composition of subgingival dental plaque of class III periodontal furcation-involved defects (FI) after surgical or non-surgical periodontal therapy.

METHODS

Twenty participants contributed with a class III FI and a periodontally healthy site (HS) each. FI molars were randomised either to repeated non-surgical periodontal treatment (NSPT) (10) or surgical treatment (10). Periodontal clinical parameters and subgingival plaque were collected at baseline and 6 months after the treatment from both furcation and healthy sites. Microbial analysis was conducted by sequencing the V3-V4 region of the 16S rRNA gene.

RESULTS

In total, 80 subgingival plaque samples were analysed. Differences in richness, diversity, oxygen metabolism, microbial composition, were observed when comparing class III furcation defects with HS (p < 0.05) both at baseline and 6 months later. At 6-months, significant reduction in PPD (p < 0.01) and increase of REC (p < 0.01) was detected in surgically treated sites (PPD: 3.55 ± 1.4, REC: 3.95 ± 1.7) compared to NSPT sites (PPD: 5.4 ± 1.3, REC: 2.92 ± 0.98). Higher levels of aerobic genera and an increase of Streptococcus mutans, Streptococcus oralis, and Streptococcus gordonii were detected in surgically treated sites compared to NSPT.

CONCLUSIONS

The microbial composition of class III furcation defects after surgical periodontal therapy showed higher level of aerobic and acidogenic microbial flora compared with furcation defects treated with a non-surgical approach.

CLINICAL SIGNIFICANCE

While surgical treatment of class III furcation defects improves pocket depths, it also leads to an increase in acidogenic microflora potentially predisposing to caries.

Oral microbiome changes in subjects with obesity following bariatric surgery compared to lean counterparts

Introduction

This study aimed to compare oral microbiome profiles between obese and lean individuals without clinical periodontitis, and to assess changes in the oral microbiome of obese subjects following bariatric surgery.

Methods

Individuals with a body mass index (BMI) > 30 were enrolled in the obese group, whereas those with a BMI < 23 served as controls. The obese surgery group, which consented to bariatric surgery, was followed up at 1, 3, and 6 months with clinical examinations. Oral examinations were conducted and periodontal disease was classified based on probing results. Saliva, buccal and subgingival microbiome samples were analyzed for community diversity, relative bacterial abundance, and differential abundance between control (n = 24) and obese group (n = 31). To evaluate effect size and statistical power, we used micropower, a simulation-based method for Permutational Multivariate Analysis of Variance-based β-diversity comparisons.

Results

The obese group exhibited distinct alpha diversity (buccal: Chao1 p = 0.0002, Shannon p = 0.0003, supragingival: Shannon p < 0.0001) compared with the control group. Bray-Curtis distance analysis indicated significant disparities in microbiome composition distribution in saliva (p = 0.003), buccal (p = 0.002), and subgingival plaque samples (p = 0.001). Although the obese and normal weight groups exhibited no significant periodontal differences, the obese group showed distinct species associated with periodontal disease, especially in subgingival plaque including Filifactor alocis, Peptostreptococcaceae spp., Prevotella spp., and Treponema maltophilum. Cluster analysis of the obese surgery group indicated the emergence of microbiomes associated with a healthy state that increased over time including Streptococcus salivarious and various Veillonella spp., whereas clusters containing periodontal pathogens including Porphyromonas spp., tended to diminish.

Discussion

The oral microbiome at 6 months post-bariatric surgery indicates a potential shift toward a healthy periodontal state, suggesting that weight loss interventions may positively impact oral microbial communities even in the absence of clinical periodontitis.

Culturable Human Microorganisms and the Impact of Transportation Conditions on Cultivability

The composition of the human microbiome is a critical health indicator, and culture-independent methodologies have substantially advanced our understanding of human-associated microorganisms. However, precise identification and characterization of microbial strains require culture-based techniques. Recently, the resurgence of culturomics, combined with high-throughput sequencing technology, has reduced the high labor demand of pure culture methods, facilitating a more efficient and comprehensive acquisition of culturable microbial strains. This study employed an integrated approach combining culturomic and high-throughput sequencing to identify culturable microorganisms on the human scalp and in human saliva and feces. Several Staphylococcus strains were identified from the scalp, whereas anaerobic microorganisms were dominant in the saliva and fecal samples. Additionally, the study highlighted the beneficial effects of transportation conditions (liquid nitrogen treatment, dry ice transport, and dimethyl sulfoxide [DMSO] buffer) in preserving culturable microorganisms. A robust methodology was developed for the large-scale acquisition of culturable microorganisms with optimized transport conditions that enhance the potential for isolating a greater diversity of culturable strains.

Distinctive salivary oral microbiome in patients with burning mouth syndrome depending on pain intensity compared to healthy subjects

Background/purpose

Burning moouth syndrome (BMS) is a chronic pain condition similar to neuropathic pain. It is characterized by a persistent burning sensation in the oral cavity. Despite the lack of clarity regarding the etiology of BMS, recent studies have reported an association between the gut microbiome and neuropathic pain. However, few studies have investigated the association between the oral microbiome and orofacial pain, such as BMS. This study aimed to compare the oral microbial profiles of healthy controls (HC) and patients with BMS.

Materials and methods

The BMS group was further divided into BMS_low and BMS_high groups according to pain intensity. A total of 60 patients with BMS (BMS_low, n = 16; BMS_high, n = 44) and 30 HC provided saliva samples, which were sequenced and analyzed for the V1-V2 region of the 16S rRNA gene.

Results

The alpha diversity was similar among the three groups. However, a significant difference in the distribution of microbiome composition was observed between BMS_high and HC, as revealed by the Bray-Curtis distance analysis (P < 0.01). At the genus level, Prevotella and Alloprevotella were the most abundant genera in the BMS group. Compared to HC, BMS_high exhibited a relatively higher abundance of bacterial species. Some bacteria, including Prevotella spp., exhibit an increasing pattern with subjective pain intensity.

Conclusion

These results suggest the potential involvement of oral microbiota in BMS pathogenesis. Additionally, variations in the microbiome may occur not only in the presence or absence of pain, but also with pain severity.

Microbiomic insights into the oral microbiome's role in type 2 diabetes mellitus: standardizing approaches for future advancements

The burgeoning field of microbiomics has unveiled significant insights into the role of the oral microbiome in the pathophysiology of Type 2 Diabetes Mellitus (T2DM), with this review focusing on recent advancements in diabetic oral microbiology, its clinical applications, and identifying factors that may affect study interpretations. A comprehensive review across various databases, including PubMed and Google Scholar, was conducted to collate original research data published in the past five years, specifically targeting studies exploring the impact of the oral microbiome on T2DM and emphasizing research that employs microbiomic approaches in clinical patient populations. The findings delineate the intricate interplay between T2DM and oral microbiome dysbiosis, highlighting significant microbial shifts following periodontal and antidiabetic treatments, and pointing to the complexity of the relationship between oral health and systemic disease. The observed oral microbial shifts in T2DM underscore the critical need for standardized research methodologies in microbiomic studies, suggesting that by adopting a unified approach, future research can more effectively elucidate the oral microbiome's role in T2DM. This could pave the way for innovative diagnostic and therapeutic strategies in managing T2DM and its oral health complications, thus making a pertinent overview of the work within the field.

Oral specimens as a tool for accurate metagenomic analysis: A pilot study

OBJECTIVES

Acute oral mucosal damage, as well as other inflammatory processes seem to be related to dysbiosis of the oral microbiome. The need to study changes in the oral microbiome led us to hypothesize what type of sample would provide the most representative picture of the entire human oral microbiome.

MATERIALS AND METHODS

An observational, and cross-sectional study was carried out. Six healthy adult participants provided 3 different sample types each, that included saliva, oral rinse and mucosal biopsy tissue. We performed 16S rRNA sequencing of the V3-V4 region of the 18 samples using Illumina MiSeq technology.

RESULTS

Participants were 27 ± 6,3 years old. Bacterial alpha diversity was higher in oral rinse samples compared to whole unstimulated saliva and oral mucosa tissue (p = 0,005). However, saliva specimens showed a 56 % relative abundance of identified species followed by a 30 % in oral rinse and only 1 % in tissue samples.

CONCLUSIONS

This study found differences on oral microbiome composition for each type of sample. Oral rinse should be chosen when higher alpha diversity is needed, whereas whole unstimulated saliva should be more appropriate for larger amount of bacterial DNA.

CLINICAL RELEVANCE

The results obtained demonstrate the importance of a correct choice of the optimal type of oral sample for microbiome studies due to the differences found in its composition.

Clinical Evaluation of Microbial Communities and Associated Biofilms with Breast Augmentation Failure

The incidence of breast implant illness (BII) and BII-related explant procedures has not decreased with current surgical and treatment techniques. It is speculated the main underlying cause of BII complications is the result of chronic, sub-clinical infections residing on and around the implant. The infection, and subsequent biofilm, produce antagonistic compounds that drive chronic inflammation and immune responses. In this study, the microbial communities in over 600 consecutive samples of infected explant capsules and tissues were identified via next-generation sequencing to identify any commonality between samples. The majority of the bacteria identified were Gram-positive, with Cutibacterium acnes and Staphylococcus epidermidis being the dominant organisms. No correlation between sample richness and implant filling was found. However, there was a significant correlation between sample richness and patient age. Due to the complex nature, breast augmentation failures may be better addressed from a holistic approach than one of limited scope.

Impact of cell lysis treatment before saliva metagenomic DNA extraction on the oral microbiome and the associated resistome

OBJECTIVES

The human oral microbiome, a complex ecosystem linked to oral and systemic health, harbors a diverse array of microbial populations, including antimicrobial resistance genes (ARGs). As a critical component of the One Health approach to tackle antibiotic resistance, comprehending the oral resistome's composition and diversity is imperative. The objective of this study was to investigate the impact of chemical cell lysis treatment using MetaPolyzyme on the detectability of the oral microbiome, resistome, and DNA quality and quantity.

MATERIALS AND METHODS

Saliva samples were collected from five healthy individuals, and each of the samples was subjected to DNA extraction with and without the treatment with MetaPolyzyme. Through metagenomic sequencing, we analyzed, assessed, and compared the microbial composition, resistome, and DNA characteristics between both groups of extracted DNA.

RESULTS

Our study revealed that MetaPolyzyme treatment led to significant shifts in the detectability of microbial composition, favoring Gram-positive bacteria, notably Streptococcus, over Gram-negative counterparts. Moreover, the MetaPolyzyme treatment also resulted in a distinct change in ARG distribution. This shift was characterized by an elevated proportion of ARGs linked to fluoroquinolones and efflux pumps, coupled with a reduction in the prevalence of tetracycline and β-lactam resistance genes when compared with the nontreated group. Alpha diversity analysis demonstrated altered species and ARG distribution without affecting overall diversity, while beta diversity analysis confirmed significant differences in the taxonomical composition and oral resistome between treated and nontreated groups.

CONCLUSIONS

These findings underscore the critical role of cell lysis treatment in optimizing oral metagenomic studies and enhance our understanding of the oral resistome's dynamics in the context of antimicrobial resistance.

Exploring the diversity and functional profile of microbial communities of Brazilian soils with high salinity and oil contamination

Environmental pollution associated with the petroleum industry is a major problem worldwide. Microbial degradation is extremely important whether in the extractive process or in bioremediation of contaminants. Assessing the local microbiota and its potential for degradation is crucial for implementing effective bioremediation strategies. Herein, contaminated soil samples of onshore oil fields from a semiarid region in the Northeast of Brazil were investigated using metagenomics and metataxonomics. These soils exhibited hydrocarbon contamination and high salinity indices, while a control sample was collected from an uncontaminated area. The shotgun analysis revealed the predominance of Actinomycetota and Pseudomonadota, while 16S rRNA gene amplicon analysis of the samples showed Actinomycetota, Bacillota, and Pseudomonadota as the most abundant. The Archaea domain phylotypes were assigned to Thermoproteota and Methanobacteriota. Functional analysis and metabolic profile of the soil microbiomes exhibited a broader metabolic repertoire in the uncontaminated soil, while degradation pathways and surfactant biosynthesis presented higher values in the contaminated soils, where degradation pathways of xenobiotic and aromatic compounds were also present. Biosurfactant synthetic pathways were abundant, with predominance of lipopeptides. The present work uncovers several microbial drivers of oil degradation and mechanisms of adaptation to high salinity, which are pivotal traits for sustainable soil recovery strategies.

Comparison of the full-length sequence and sub-regions of 16S rRNA gene for skin microbiome profiling

The skin microbiome plays a pivotal role in human health by providing protective and functional benefits. Furthermore, its inherent stability and individual specificity present novel forensic applications. These aspects have sparked considerable research enthusiasm among scholars across various fields. However, the selection of specific 16S rRNA hypervariable regions for skin microbiome studies is not standardized and should be validated through extensive research tailored to different research objectives and targeted bacterial taxa. Notably, third-generation sequencing (TGS) technology leverages the full discriminatory power of the 16S gene and enables more detailed and accurate microbial community analyses. Here, we conducted full-length 16S sequencing of 141 skin microbiota samples from multiple human anatomical sites using the PacBio platform. Based on this data, we generated derived 16S sub-region data through an in silico experiment. Comparisons between the 16S full-length and the derived variable region data revealed that the former can provide superior taxonomic resolution. However, even with full 16S gene sequencing, limitations arise in achieving 100% taxonomic resolution at the species level for skin samples. Additionally, the capability to resolve high-abundance bacteria (TOP30) at the genus level remains generally consistent across different 16S variable regions. Furthermore, the V1-V3 region offers a resolution comparable with that of full-length 16S sequences, in comparison to other hypervariable regions studied. In summary, while acknowledging the benefits of full-length 16S gene analysis, we propose the targeting of specific sub-regions as a practical choice for skin microbial research, especially when balancing the accuracy of taxonomic classification with limited sequencing resources, such as the availability of only short-read sequencing or insufficient DNA.IMPORTANCESkin acts as the primary barrier to human health. Considering the different microenvironments, microbial research should be conducted separately for different skin regions. Third-generation sequencing (TGS) technology can make full use of the discriminatory power of the full-length 16S gene. However, 16S sub-regions are widely used, particularly when faced with limited sequencing resources including the availability of only short-read sequencing and insufficient DNA. Comparing the 16S full-length and the derived variable region data from five different human skin sites, we confirmed the superiority of the V1-V3 region in skin microbiota analysis. We propose the targeting of specific sub-regions as a practical choice for microbial research.

Soil pH, developmental stages and geographical origin differently influence the root metabolomic diversity and root-related microbial diversity of Echium vulgare from native habitats

Improved understanding of the complex interaction between plant metabolism, environmental conditions and the plant-associated microbiome requires an interdisciplinary approach: Our hypothesis in our multiomics study posited that several environmental and biotic factors have modulating effects on the microbiome and metabolome of the roots of wild Echium vulgare plants. Furthermore, we postulated reciprocal interactions between the root metabolome and microbiome. We investigated the metabolic content, the genetic variability, and the prokaryotic microbiome in the root systems of wild E. vulgare plants at rosette and flowering stages across six distinct locations. We incorporated the assessment of soil microbiomes and the measurement of selected soil chemical composition factors. Two distinct genetic clusters were determined based on microsatellite analysis without a consistent alignment with the geographical proximity between the locations. The microbial diversity of both the roots of E. vulgare and the surrounding bulk soil exhibited significant divergence across locations, varying soil pH characteristics, and within the identified plant genetic clusters. Notably, acidophilic bacteria were characteristic inhabitants of both soil and roots under acidic soil conditions, emphasizing the close interconnectedness between these compartments. The metabolome of E. vulgare significantly differed between root samples from different developmental stages, geographical locations, and soil pH levels. The developmental stage was the dominant driver of metabolome changes, with significantly higher concentrations of sugars, pyrrolizidine alkaloids, and some of their precursors in rosette stage plant roots. Our study featured the complex dynamics between soil pH, plant development, geographical locations, plant genetics, plant metabolome and microbiome, shedding light on existing knowledge gaps.

Microbial diagnostics in periodontal diseases

Microbial analytical methods have been instrumental in elucidating the complex microbial etiology of periodontal diseases, by shaping our understanding of subgingival community dynamics. Certain pathobionts can orchestrate the establishment of dysbiotic communities that can subvert the host immune system, triggering inflammation and tissue destruction. Yet, diagnosis and management of periodontal conditions still rely on clinical and radiographic examinations, overlooking the well-established microbial etiology. This review summarizes the chronological emergence of periodontal etiological models and the co-evolution with technological advances in microbial detection. We additionally review the microbial analytical approaches currently accessible to clinicians, highlighting their value in broadening the periodontal assessment. The epidemiological importance of obtaining culture-based antimicrobial susceptibility profiles of periodontal taxa for antibiotic resistance surveillance is also underscored, together with clinically relevant analytical approaches to guide antibiotherapy choices, when necessary. Furthermore, the importance of 16S-based community and shotgun metagenomic profiling is discussed in outlining dysbiotic microbial signatures. Because dysbiosis precedes periodontal damage, biomarker identification offers early diagnostic possibilities to forestall disease relapses during maintenance. Altogether, this review highlights the underutilized potential of clinical microbiology in periodontology, spotlighting the clinical areas most conductive to its diagnostic implementation for enhancing prevention, treatment predictability, and addressing global antibiotic resistance.

Comparison of the performance of MiSeq and NovaSeq in oral microbiome study

Objective

Next generation sequencing is commonly used to characterize the microbiome structure. MiSeq is most commonly used to analyze the microbiome due to its relatively long read length. Illumina also introduced the 250 × 2 chip for NovaSeq. The purpose of this study was to compare the performance of MiSeq and NovaSeq in the context of oral microbiome study.

Methods

Total read count, read quality score, relative bacterial abundance, community diversity, and correlation between two platforms were analyzed. Phylogenetic trees were analyzed for Streptococcus and periodontopathogens.

Results

NovaSeq produced significantly more read counts and assigned more operational taxonomic units (OTUs) compared to MiSeq. Community diversity was similar between MiSeq and NovaSeq. NovaSeq were able to detect more unique OTUs compared to MiSeq. When phylogenetic trees were constructed for Streptococcus and periodontopathogens, both platforms detected OTUs for most of the clades.

Conclusion

Taken together, while both MiSeq and NovaSeq platforms effectively characterize the oral microbiome, NovaSeq outperformed MiSeq in terms of read counts and detection of unique OTUs, highlighting its potential as a valuable tool for large scale oral microbiome studies.

Microbial Profiles in Oral Lichen Planus: Comparisons with Healthy Controls and Erosive vs. Non-Erosive Subtypes

Recent studies have begun exploring the potential involvement of microbiota in the pathogenesis of oral lichen planus (OLP), yet comprehensive investigations remain limited. Hence, this study aimed to compare the microbial profiles in saliva samples obtained from patients with OLP against those from healthy controls (HC), along with a comparison between erosive (E) and non-erosive (NE) OLP patients. Saliva samples were collected from 60 OLP patients (E: n = 25, NE: n = 35) and 30 HC individuals. Analysis revealed no significant differences in alpha diversity, as assessed by the Chao1 and Shannon index, across the three groups. However, Bray-Curtis distance analysis indicated a significant disparity in microbiome composition distribution between HC and E-OLP, as well as HC and NE-OLP groups. The six most abundant phyla observed across the groups were Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Fusobacteria, and Saccharibacteria (TM7). Notably, OLP groups exhibited a higher prevalence of Bacteroidetes. Prevotella emerged as the predominant genus in the OLP groups, while Capnocytophaga showed a relatively higher prevalence in E-OLP compared to NE-OLP. This study's findings indicate a notable difference in microbiota composition between HC and patients with OLP. Additionally, differences in the microbiome were identified between the E-OLP and NE-OLP groups. The increase in the proportion of certain bacterial species in the oral microbiome suggests that they may exacerbate the inflammatory response and act as antigens for OLP.

From wolves to humans: oral microbiome resistance to transfer across mammalian hosts

The mammalian mouth is colonized by complex microbial communities, adapted to specific niches, and in homeostasis with the host. Individual microbes interact metabolically and rely primarily on nutrients provided by the host, with which they have potentially co-evolved along the mammalian lineages. The oral environment is similar across mammals, but the diversity, specificity, and evolution of community structure in related or interacting mammals are little understood. Here, we compared the oral microbiomes of dogs with those of wild wolves and humans. In dogs, we found an increased microbial diversity relative to wolves, possibly related to the transition to omnivorous nutrition following domestication. This includes a larger diversity of Patescibacteria than previously reported in any other oral microbiota. The oral microbes are most distinct at bacterial species or strain levels, with few if any shared between humans and canids, while the close evolutionary relationship between wolves and dogs is reflected by numerous shared taxa. More taxa are shared at higher taxonomic levels including with humans, supporting their more ancestral common mammalian colonization followed by diversification. Phylogenies of selected oral bacterial lineages do not support stable human-dog microbial transfers but suggest diversification along mammalian lineages (apes and canids). Therefore, despite millennia of cohabitation and close interaction, the host and its native community controls and limits the assimilation of new microbes, even if closely related. Higher resolution metagenomic and microbial physiological studies, covering a larger mammalian diversity, should help understand how oral communities assemble, adapt, and interact with their hosts.IMPORTANCENumerous types of microbes colonize the mouth after birth and play important roles in maintaining oral health. When the microbiota-host homeostasis is perturbed, proliferation of some bacteria leads to diseases such as caries and periodontitis. Unlike the gut microbiome, the diversity of oral microbes across the mammalian evolutionary space is not understood. Our study compared the oral microbiomes of wild wolves, dogs, and apes (humans, chimpanzees, and bonobos), with the aim of identifying if microbes have been potentially exchanged between humans and dogs as a result of domestication and cohabitation. We found little if any evidence for such exchanges. The significance of our research is in finding that the oral microbiota and/or the host limit the acquisition of exogenous microbes, which is important in the context of natural exclusion of potential novel pathogens. We provide a framework for expanded higher-resolution studies across domestic and wild animals to understand resistance/resilience.