scholarly journals The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 878 ◽  
Author(s):  
Maria A. Sierra ◽  
Qianhao Li ◽  
Smruti Pushalkar ◽  
Bidisha Paul ◽  
Tito A. Sandoval ◽  
...  
Keyword(s):  
16S Rrna ◽  
Oral Microbiome ◽  
Data Curation ◽  
Ribosomal Database Project ◽  
Β Diversity ◽  
Bioinformatics Tools ◽  
Large Databases ◽  
Α Diversity ◽  
Reference Databases ◽  
Taxonomical Classification

There is currently no criterion to select appropriate bioinformatics tools and reference databases for analysis of 16S rRNA amplicon data in the human oral microbiome. Our study aims to determine the influence of multiple tools and reference databases on α-diversity measurements and β-diversity comparisons analyzing the human oral microbiome. We compared the results of taxonomical classification by Greengenes, the Human Oral Microbiome Database (HOMD), National Center for Biotechnology Information (NCBI) 16S, SILVA, and the Ribosomal Database Project (RDP) using Quantitative Insights Into Microbial Ecology (QIIME) and the Divisive Amplicon Denoising Algorithm (DADA2). There were 15 phyla present in all of the analyses, four phyla exclusive to certain databases, and different numbers of genera were identified in each database. Common genera found in the oral microbiome, such as Veillonella, Rothia, and Prevotella, are annotated by all databases; however, less common genera, such as Bulleidia and Paludibacter, are only annotated by large databases, such as Greengenes. Our results indicate that using different reference databases in 16S rRNA amplicon data analysis could lead to different taxonomic compositions, especially at genus level. There are a variety of databases available, but there are no defined criteria for data curation and validation of annotations, which can affect the accuracy and reproducibility of results, making it difficult to compare data across studies.

scholarly journals Clinical Detection of Chronic Rhinosinusitis through Next-Generation Sequencing of the Oral Microbiota

2020 ◽  
Vol 8 (6) ◽  
pp. 959 ◽  
Author(s):  
Ben-Chih Yuan ◽  
Yao-Tsung Yeh ◽  
Ching-Chiang Lin ◽  
Cheng-Hsieh Huang ◽  
Hsueh-Chiao Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
Chronic Rhinosinusitis ◽  
Oral Microbiome ◽  
Oral Microbiota ◽  
Upper Respiratory Tract ◽  
Aerobic Culture ◽  
Β Diversity ◽  
Α Diversity ◽  
Significant Difference ◽  
Anaerobic Infections

Chronic rhinosinusitis (CRS) is the chronic inflammation of the sinus cavities of the upper respiratory tract, which can be caused by a disrupted microbiome. However, the role of the oral microbiome in CRS is not well understood. Polymicrobial and anaerobic infections of CRS frequently increased the difficulty of cultured and antibiotic therapy. This study aimed to elucidate the patterns and clinical feasibility of the oral microbiome in CRS diagnosis. Matched saliva and nasal swabs were collected from 18 CRS patients and 37 saliva specimens from normal volunteers were collected for 16S rRNA sequencing. The α-diversity of the saliva displayed no significant difference between control and CRS patients, whereas the β-diversity was significantly different (p = 0.004). Taxonomic indices demonstrated that Veillonella dispar, Rothia mucilaginosa, and Porphyromonas endodontalis were enriched, while Campylobacter and Cardiobacterium were reduced in the saliva of CRS patients. These microbial markers could significantly distinguish CRS patients from control (AUC = 0.939). It is noted that the 16S rRNA results of the nasal swab were consistent with the nasopharynx aerobic culture, and additionally detected multiple pathogens in CRS patients. In summary, these results indicated these oral microbiomes may provide a novel signal for CRS detection and that NGS may be an alternative approach for CRS diagnosis.

The microbial characteristics of patients with esophageal squamous cell carcinoma before and after immunotherapy.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e16016-e16016
Author(s):  
Jing Zuo ◽  
Wenjing Lv ◽  
Yudong Wang ◽  
Zhisong Fan ◽  
Li Feng ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
16S Rrna ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Fecal Samples ◽  
Β Diversity ◽  
Α Diversity ◽  
Before And After ◽  
New Ideas

e16016 Background: Esophageal squamous cell carcinoma (ESCC) is a common malignancy without effective therapy. Immune checkpoint–oriented immunotherapies have shown considerable promise and the advent of esophageal microbiome provides researchers with new ideas. Methods: DNA was extracted from blood, oral mucosal, saliva, urine, fecal samples from 20 ESCC patients before and after immunotherapy. Total microbial genomic DNA samples were extracted using an OMEGA Soil DNA Kit (D5625-01). The V3–V4 regions of bacterial 16S rRNA genes were amplified by PCR using the forward primer and the reverse primer and were sequenced with Illumina MiSeq platform. In order to comprehensively evaluate the α diversity of microbial communities, we used Chao1 and Observed Species indices to characterize the richness, Shannon and Simpson indices to characterize the diversity. PCoA were used to analyze differences in β diversity. Functions of 16S rRNA sequences were predicted using the PICRUSt2 and KEGG databases. Results: A comparison of blood, oral mucosal, saliva, urine, fecal samples of ESCC patients before and after immunotherapy showed that α diversity was not statistically significant. In terms of β diversity, no statistically significant differences were detected within blood, oral mucosal, saliva, urine, fecal samples of ESCC patients before and after immunotherapy. In ESCC patients treated before immunotherapy, the α diversity and β diversity of blood, oral mucosal, saliva, urine, fecal samples were different, and in ESCC patients treated after immunotherapy had the same rule. At the phylum level, the top 5 microbes in ESCC patients before and after immunotherapy were Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria. At the genus level, the top 5 microbes in ESCC patients before immunotherapy were Aquabacterium, Streptococcus, Prevotella, Veillonella, Bacteroides, and in ESCC patients after immunotherapy were Aquabacterium, Streptococcus, Prevotella, Faecalibacterium, Veillonella. In terms of the microbial functions in ESCC patients before and after immunotherapy, the metabolic pathways accounted for the most. Conclusions: This study is conducive to exploring new mechanisms for tumor cells to evade host immune surveillance, providing new ideas and new strategies for the microecology-based immunotherapy of ESCC.

scholarly journals Microbiome Profiles of Ligature-Induced Periodontitis in Nonhuman Primates across the Life Span

2019 ◽  
Vol 87 (6) ◽  
Author(s):  
Sreenatha Kirakodu ◽  
Jin Chen ◽  
Janis Gonzalez Martinez ◽  
Octavio A. Gonzalez ◽  
Jeffrey Ebersole
Keyword(s):  
Nonhuman Primates ◽  
Age Groups ◽  
Amplicon Sequencing ◽  
Young Adolescent ◽  
Oral Microbiome ◽  
Host Responses ◽  
Content Type ◽  
Β Diversity ◽  
16S Amplicon Sequencing ◽  
Α Diversity

ABSTRACT This investigation compared the microbiomes colonizing teeth during the initiation, progression, and resolution of periodontitis in nonhuman primates (Macaca mulatta) at different ages. Subgingival plaque samples were collected at baseline; 0.5, 1, and 3 months following ligature-induced periodontitis; and following naturally occurring disease resolution at 5 months. Samples were analyzed using 16S amplicon sequencing to identify bacterial profiles across age groups: young (<3 years of age), adolescent (3 to 7 years), adult (12 to 15 years), and aged (17 to 23 years). α-Diversity of the microbiomes was greater in the adult/aged samples than in the young/adolescent samples. β-Diversity of the samples demonstrated clear age group differences, albeit individual variation in microbiomes between animals within the age categories was noted. Phylum distributions differed between the young/adolescent animals and the adult/aged animals at each of the time points, showing an enrichment of the phyla Spirochetes, Fusobacteria, and Bacteroidetes associated with periodontitis. Major differences in the top 50 operational taxonomic units (OTUs) were noted in the young and adolescent microbiomes during initiation and progression postligation compared to the adult and aged animals. The proportions of a large number of species in the top 50 OTUs were lower at baseline and in resolved disease microbiomes in the young samples, while profiles in adolescent animals were more consistent with the disease microbiomes. Microbiome profiles for resolution for adults and aged animals appeared more resilient and generally maintained a pattern similar to that of disease. Use of the model can expand our understanding of the crucial interactions of the oral microbiome and host responses in periodontitis.

scholarly journals Influence of 16S rRNA Reference Databases in Amplicon-Based Environmental Microbiome Research

2021 ◽  
Author(s):  
Meganathan P. Ramakodi
Keyword(s):  
16S Rrna ◽  
Reference Database ◽  
P Value ◽  
Ribosomal Database Project ◽  
Core Microbiome ◽  
Microbiome Composition ◽  
Common Reference ◽  
Microbiome Research ◽  
Reference Databases ◽  
The Impact

Abstract Purpose: The reference databases play a pivotal role in amplicon microbiome research but the sequence content and taxonomic information available in common reference databases differ. Studies on mock community and human health microbiome have revealed the problems associated with the choice of reference database on the outcome. Nonetheless, the influence of reference databases in environmental microbiome studies is not explicitly illustrated. Methods: This study analyzed the amplicon (V1V3, V3V4, V4V5 and V6V8) data of 128 soil samples and evaluated the impact of 16S rRNA databases, Genome Taxonomy Database (GTDB), Ribosomal Database Project (RDP), SILVA and Consensus Taxonomy (ConTax), on microbiome inference. Results: The analyses showed that the distribution of observed amplicon sequence variants was significantly different (P-value < 2.647e-12) across four datasets, generated based on different databases for each amplicon region. In addition, the beta diversity was also found to be altered by different databases. Further investigation revealed that the microbiome composition inferred by different databases vary significantly (P-value=0.001), irrespective of amplicon regions. Importantly, the study found that the core-microbiome structure in environmental studies could be altered by the reference databases. Conclusion: In summary, this present study illustrates that the choice of reference database could influence the outcome of environmental microbiome research.

scholarly journals Sex Variations in the Oral Microbiomes of Youths with Severe Periodontitis

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Ya-Qiong Zhao ◽  
Ying-Hui Zhou ◽  
Jie Zhao ◽  
Yao Feng ◽  
Zheng-Rong Gao ◽  
...  
Keyword(s):  
Immune System ◽  
16S Rrna ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Β Diversity ◽  
Severe Periodontitis ◽  
Rrna Gene Sequencing ◽  
Dominant Bacteria

Objective. Periodontitis is an inflammatory disease of microbial etiology caused primarily by dysbiosis of the oral microbiota. Our aim was to compare variations in the composition of the oral microbiomes of youths with severe periodontitis according to gender. Methods. Subgingival plaque samples collected from 17 patients with severe periodontitis (11 males and 6 females) were split for 16S rRNA gene sequencing. The composition, α-diversity, and β-diversity of the patients’ oral microbiomes were compared between the males and the females. Linear discriminant analysis effect size (LEfSe) was used to analyze the specific taxa enriched in the two groups. Functional profiles (KEGG pathways) were obtained using PICRUSt based on 16S rRNA gene sequencing data. Results. The Chao1 index and phylogenetic diversity whole tree were significantly higher in males than in females. The Simpson and Shannon indices were not significantly different between the two groups. β-Diversity suggested that the samples were reasonably divided into groups. The Kruskal-Wallis test based on the relative abundance of species, combined with the LEfSe analysis showed that the dominant bacteria in males were Pseudomonas and Papillibacter, whereas the dominant bacteria in women were Fusobacteriales and Tannerella. KEGG analysis predicted that the variation in the oral microbiome may be related to the immune system in women, whereas immune system diseases were the dominant pathway in men. Conclusion. We found sex-specific differences in the oral microbiome in a sample of youths with severe periodontitis. The differences may be related to changes in immune homeostasis and lead to a better understanding of periodontitis.

scholarly journals Salivary microbiome profiling reveals a dysbiotic schizophrenia-associated microbiota

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Ying Qing ◽  
Lihua Xu ◽  
Gaoping Cui ◽  
Liya Sun ◽  
Xiaowen Hu ◽  
...  
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Oral Microbiome ◽  
Disease Stage ◽  
First Episode ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Β Diversity ◽  
Metabolic Functions ◽  
Α Diversity ◽  
Rrna Gene Sequencing

AbstractSchizophrenia is a debilitating mental disorder and often has a prodromal period, referred to as clinical high risk (CHR) for psychosis, prior to the first episode. The etiology and pathogenesis of schizophrenia remain unclear. Despite the human gut microbiome being associated with schizophrenia, the role of the oral microbiome, which is a vital player in the mouth–body connection, is not well understood. To address this, we performed 16S rRNA gene sequencing to investigate the salivary microbiome in 85 patients with drug-naïve first-episode schizophrenia (FES), 43 individuals at CHR, and 80 healthy controls (HCs). The salivary microbiome of FES patients was characterized by higher α-diversity and lower β-diversity heterogeneity than those of CHR subjects and HCs. Proteobacteria, the predominant phylum, was depleted, while Firmicutes and the Firmicutes/Proteobacteria ratio was enriched, in a stepwise manner from HC to CHR to FES. H2S-producing bacteria exhibited disease-stage-specific enrichment and could be potential diagnostic biomarkers for FES and CHR. Certain salivary microbiota exhibited disease-specific correlation patterns with symptomatic severities, peripheral pro-inflammatory cytokines, thioredoxin, and S100B in FES. Furthermore, the metabolic functions from inferred metagenomes of the salivary microbiome were disrupted in FES, especially amino acid metabolism, carbohydrate metabolism, and xenobiotic degradation. This study has established a link between salivary microbiome alterations and disease initiation and provided the hypothesis of how the oral microbiota could influence schizophrenia.

scholarly journals Differential Signature of the Microbiome and Neutrophils in the Oral Cavity of HIV-Infected Individuals

2021 ◽  
Vol 12 ◽  
Author(s):  
Eliana Perez Rosero ◽  
Samantha Heron ◽  
Juan Jovel ◽  
Conar R. O’Neil ◽  
Shannon Lee Turvey ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Immune Cell ◽  
16S Rrna Gene Sequencing ◽  
Surface Expression ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Healthy Individuals ◽  
Β Diversity ◽  
Α Diversity ◽  
Wide Range

HIV infection is associated with a wide range of changes in microbial communities and immune cell components of the oral cavity. The purpose of this study was to evaluate the oral microbiome in relationship to oral neutrophils in HIV-infected compared to healthy individuals. We evaluated oral washes and saliva samples from HIV-infected individuals (n=52) and healthy controls (n=43). Using 16S-rRNA gene sequencing, we found differential β-diversity using Principal Coordinate Analysis (PCoA) with Bray-Curtis distances. The α-diversity analysis by Faith’s, Shannon, and observed OTUs indexes indicated that the saliva samples from HIV-infected individuals harbored significantly richer bacterial communities compared to the saliva samples from healthy individuals. Notably, we observed that five species of Spirochaeta including Spirochaetaceae, Spirochaeta, Treponema, Treponema amylovorum, and Treponema azotonutricum were significantly abundant. In contrast, Helicobacter species were significantly reduced in the saliva of HIV-infected individuals. Moreover, we found a significant reduction in the frequency of oral neutrophils in the oral cavity of HIV-infected individuals, which was positively related to their CD4+ T cell count. In particular, we noted a significant decline in CD44 expressing neutrophils and the intensity of CD44 expression on oral neutrophils of HIV-infected individuals. This observation was supported by the elevation of soluble CD44 in the saliva of HIV-infected individuals. Overall, the core oral microbiome was distinguishable between HIV-infected individuals on antiretroviral therapy compared to the HIV-negative group. The observed reduction in oral neutrophils might likely be related to the low surface expression of CD44, resulting in a higher bacterial diversity and richness in HIV-infected individuals.

Patterns in diversity and composition of the microbenthos of subarctic intertidal beaches with different morphodynamics

2020 ◽  
Vol 648 ◽  
pp. 19-38
Author(s):  
AI Azovsky ◽  
YA Mazei ◽  
MA Saburova ◽  
PV Sapozhnikov
Keyword(s):  
Species Abundance ◽  
Abundance Ratio ◽  
Wave Action ◽  
Coarse Grained ◽  
Sediment Properties ◽  
Β Diversity ◽  
Α Diversity ◽  
Wide Range ◽  
Similar Mode ◽  
Abundance And Diversity

Diversity and composition of benthic diatom algae and ciliates were studied at several beaches along the White and Barents seas: from highly exposed, reflective beaches with coarse-grained sands to sheltered, dissipative silty-sandy flats. For diatoms, the epipelic to epipsammic species abundance ratio was significantly correlated with the beach index and mean particle size, while neither α-diversity measures nor mean cell length were related to beach properties. In contrast, most of the characteristics of ciliate assemblages (diversity, total abundance and biomass, mean individual weight and percentage of karyorelictids) demonstrated a strong correlation to beach properties, remaining low at exposed beaches but increasing sharply in more sheltered conditions. β-diversity did not correlate with beach properties for either diatoms or ciliates. We suggest that wave action and sediment properties are the main drivers controlling the diversity and composition of the intertidal microbenthos. Diatoms and ciliates, however, demonstrated divergent response to these factors. Epipelic and epipsammic diatoms exhibited 2 different strategies to adapt to their environments and therefore were complementarily distributed along the environmental gradient and compensated for each other in diversity. Most ciliates demonstrated a similar mode of habitat selection but differed in their degree of tolerance. Euryporal (including mesoporal) species were relatively tolerant to wave action and therefore occurred under a wide range of beach conditions, though their abundance and diversity were highest in fine, relatively stable sediments on sheltered beaches, whereas the specific interstitial (i.e. genuine microporal) species were mostly restricted to only these habitats.

scholarly journals Microbiome of Odontogenic Abscesses

2021 ◽  
Vol 9 (6) ◽  
pp. 1307
Author(s):  
Sebastian Böttger ◽  
Silke Zechel-Gran ◽  
Daniel Schmermund ◽  
Philipp Streckbein ◽  
Jan-Falco Wilbrand ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Oral Microbiome ◽  
Minor Role ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Bacterial Strains ◽  
16S Rrna Gene Analysis ◽  
Odontogenic Infections ◽  
Odontogenic Abscess

Severe odontogenic abscesses are regularly caused by bacteria of the physiological oral microbiome. However, the culture of these bacteria is often prone to errors and sometimes does not result in any bacterial growth. Furthermore, various authors found completely different bacterial spectra in odontogenic abscesses. Experimental 16S rRNA gene next-generation sequencing analysis was used to identify the microbiome of the saliva and the pus in patients with a severe odontogenic infection. The microbiome of the saliva and the pus was determined for 50 patients with a severe odontogenic abscess. Perimandibular and submandibular abscesses were the most commonly observed diseases at 15 (30%) patients each. Polymicrobial infections were observed in 48 (96%) cases, while the picture of a mono-infection only occurred twice (4%). On average, 31.44 (±12.09) bacterial genera were detected in the pus and 41.32 (±9.00) in the saliva. In most cases, a predominantly anaerobic bacterial spectrum was found in the pus, while saliva showed a similar oral microbiome to healthy individuals. In the majority of cases, odontogenic infections are polymicrobial. Our results indicate that these are mainly caused by anaerobic bacterial strains and that aerobic and facultative anaerobe bacteria seem to play a more minor role than previously described by other authors. The 16S rRNA gene analysis detects significantly more bacteria than conventional methods and molecular methods should therefore become a part of routine diagnostics in medical microbiology.

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.

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