Oral Phenotype and Salivary Microbiome of Individuals With Papillon–Lefèvre Syndrome

Papillon–Lefèvre syndrome (PLS) is an autosomal recessive rare disease, main characteristics of which include palmoplantar hyperkeratosis and premature edentulism due to advanced periodontitis (formerly aggressive periodontitis). This study aimed to characterize the oral phenotype, including salivary parameters, and the salivary microbiome of three PLS sisters, comparatively. Two sisters were toothless (PLSTL1 and PLSTL2), and one sister had most of the teeth in the oral cavity (PLST). Total DNA was extracted from the unstimulated saliva, and the amplicon sequencing of the 16S rRNA gene fragment was performed in an Ion PGM platform. The amplicon sequence variants (ASVs) were obtained using the DADA2 pipeline, and the taxonomy was assigned using the SILVA v.138. The main phenotypic characteristics of PLS were bone loss and premature loss of primary and permanent dentition. The PLST sister presented advanced periodontitis with gingival bleeding and suppuration, corresponding to the advanced periodontitis as a manifestation of systemic disease, stage IV, grade C. All three PLS sisters presented hyposalivation as a possible secondary outcome of the syndrome. Interestingly, PLST salivary microbiota was dominated by the uncultured bacteria Bacterioidales (F0058), Fusobacterium, Treponema, and Sulfophobococcus (Archaea domain). Streptococcus, Haemophilus, and Caldivirga (Archaea) dominated the microbiome of the PLSTL1 sister, while the PLSTL2 had higher abundances of Lactobacillus and Porphyromonas. This study was the first to show a high abundance of organisms belonging to the Archaea domain comprising a core microbiome in human saliva. In conclusion, a PLST individual does have a microbiota different from that of the periodontitis’ aggressiveness previously recognized. Due to an ineffective cathepsin C, the impairment of neutrophils probably provided a favorable environment for the PLS microbiome. The interactions of Bacteroidales F0058, Caldivirga, and Sulfophobococcus with the microbial consortium of PLS deserves future investigation. Traditional periodontal therapy is not efficient in PLS patients. Unraveling the PLS microbiome is essential in searching for appropriate treatment and avoiding early tooth loss.

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Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

Microbiome ◽

10.1186/s40168-020-00961-3 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Ya Wang ◽

Yan Yan ◽

Kelsey N. Thompson ◽

Sena Bae ◽

Emma K. Accorsi ◽

...

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Comprehensive Evaluation ◽

Amplicon Sequencing ◽

Human Saliva ◽

Rrna Gene ◽

Propidium Monoazide ◽

Functional Profiling ◽

Subway System ◽

Compositional Diversity

Abstract Background High-throughput sequencing provides a powerful window into the structural and functional profiling of microbial communities, but it is unable to characterize only the viable portion of microbial communities at scale. There is as yet not one best solution to this problem. Previous studies have established viability assessments using propidium monoazide (PMA) treatment coupled with downstream molecular profiling (e.g., qPCR or sequencing). While these studies have met with moderate success, most of them focused on the resulting “viable” communities without systematic evaluations of the technique. Here, we present our work to rigorously benchmark “PMA-seq” (PMA treatment followed by 16S rRNA gene amplicon sequencing) for viability assessment in synthetic and realistic microbial communities. Results PMA-seq was able to successfully reconstruct simple synthetic communities comprising viable/heat-killed Escherichia coli and Streptococcus sanguinis. However, in realistically complex communities (computer screens, computer mice, soil, and human saliva) with E. coli spike-in controls, PMA-seq did not accurately quantify viability (even relative to variability in amplicon sequencing), with its performance largely affected by community properties such as initial biomass, sample types, and compositional diversity. We then applied this technique to environmental swabs from the Boston subway system. Several taxa differed significantly after PMA treatment, while not all microorganisms responded consistently. To elucidate the “PMA-responsive” microbes, we compared our results with previous PMA-based studies and found that PMA responsiveness varied widely when microbes were sourced from different ecosystems but were reproducible within similar environments across studies. Conclusions This study provides a comprehensive evaluation of PMA-seq exploring its quantitative potential in synthetic and complex microbial communities, where the technique was effective for semi-quantitative purposes in simple synthetic communities but provided only qualitative assessments in realistically complex community samples.

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Similarity of salivary microbiome in parents and adult children

10.7287/peerj.preprints.27565 ◽

2019 ◽

Author(s):

Kati Sundström ◽

Pashupati P Mishra ◽

Mikko J Pyysalo ◽

Terho Lehtimäki ◽

Pekka J Karhunen ◽

...

Keyword(s):

Adult Children ◽

Bacterial Communities ◽

Bacterial Species ◽

Amplicon Sequencing ◽

Human Saliva ◽

Oral Microbiome ◽

Rrna Gene ◽

Genus Level ◽

Abundant Genus ◽

Dna Profiles

Background: Human saliva contains approximately 700 bacterial species but the relatedness of salivary bacteria from parents to adult children is not investigated in humans. The objectives were to investigate the entirety of salivary bacterial DNA profiles and whether and how families share these profiles and also compare these communities between adult parent-off-spring pairs using 16S rRNA gene amplicon sequencing. Results: The most abundant phyla in two separate families were Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria and Actinobacteria. Family ties explained 13 % of the variance between individuals’ bacterial communities (R2=0.13; P=0.001). Mothers shared more OTUs with their adult children compared to fathers, but this linkage seemed to be weaker in the family with older adult children. We identified 29 differentially abundant genus level OTUs (FDR < 0.05) between the families, which accounted for 31 % of the total identified genus level OTUs Conclusions: Our results indicate that adult family members share bacterial communities and adult children were more similar to mothers than fathers. Our results suggest implicitly that a similarity in oral microbiome between parent-child pairs is present, but may change over time.

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Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

10.21203/rs.3.rs-59563/v2 ◽

2020 ◽

Author(s):

Ya Wang ◽

Yan Yan ◽

Kelsey N. Thompson ◽

Sena Bae ◽

Emma K. Accorsi ◽

...

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Comprehensive Evaluation ◽

Amplicon Sequencing ◽

Human Saliva ◽

Rrna Gene ◽

Propidium Monoazide ◽

Functional Profiling ◽

Subway System ◽

Compositional Diversity

Abstract Background High-throughput sequencing provides a powerful window into the structural and functional profiling of microbial communities, but it is unable to characterize only the viable portion of microbial communities at scale. There is as yet not one best solution to this problem. Previous studies have established viability assessments using propidium monoazide (PMA) treatment coupled with downstream molecular profiling (e.g. qPCR or sequencing). While these studies have met with moderate success, most of them focused on the resulting “viable” communities without systematic evaluations of the technique. Here, we present our work to rigorously benchmark “PMA-seq” (PMA treatment followed by 16S rRNA gene amplicon sequencing) for viability assessment in synthetic and realistic microbial communities. Results PMA-seq was able to successfully reconstruct simple synthetic communities comprising viable/heat-killed Escherichia coli and Streptococcus sanguinis. However, in realistically complex communities (computer screens, computer mice, soil and human saliva) with E. coli spike-in controls, PMA-seq did not accurately quantify viability (even relative to variability in amplicon sequencing), with its performance largely affected by community properties such as initial biomass, sample types and compositional diversity. We then applied this technique to environmental swabs from the Boston subway system. Several taxa differed significantly after PMA treatment, while not all microorganisms responded consistently. To elucidate the “PMA-responsive” microbes, we compared our results with previous PMA-based studies and found that PMA-responsiveness varied widely when microbes were sourced from different ecosystems but were reproducible within similar environments across studies. Conclusions This study provides a comprehensive evaluation of PMA-seq exploring its quantitative potential in synthetic and complex microbial communities, where the technique was effective for semi-quantitative purposes in simple synthetic communities, but provided only qualitative assessments in realistically complex community samples.

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Similarity of salivary microbiome in parents and adult children

PeerJ ◽

10.7717/peerj.8799 ◽

2020 ◽

Vol 8 ◽

pp. e8799 ◽

Cited By ~ 2

Author(s):

Kati Sundström ◽

Pashupati P. Mishra ◽

Mikko J. Pyysalo ◽

Terho Lehtimäki ◽

Pekka J. Karhunen ◽

...

Keyword(s):

Adult Children ◽

Bacterial Communities ◽

Nuclear Family ◽

Bacterial Species ◽

Large Family ◽

Amplicon Sequencing ◽

Human Saliva ◽

Oral Microbiome ◽

Rrna Gene ◽

Genus Level

Background Human saliva contains approximately 700 bacterial species. It has been reported that the salivary microbiome of a large family of closely related individuals consisting of multiple households is similar but the relatedness of salivary bacteria between generations of parents and their children has not yet been investigated. The objectives were to investigate the entirety of salivary bacterial DNA profiles and whether and how families share these profiles and also compare these communities between grandparents and their first daughter generations (F1) using 16S rRNA gene amplicon sequencing. Results The most abundant phyla in two separate families were Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria and Actinobacteria. Family ties explained 13% of the variance between individuals’ bacterial communities (R2 = 0.13; P = 0.001). Mothers shared more OTUs with adult children compared to fathers, but this linkage seemed to be weaker in the nuclear family with older adult children. We identified 29 differentially abundant genus level OTUs (FDR < 0.05) between families, which accounted for 31% of the total identified genus level OTUs. Conclusions Our results indicate that adult family members share bacterial communities and adult children were more similar to mothers than fathers. The observed similarity in oral microbiome between parent–child pairs seemed to weaken over time. We suggest that our analysis approach is suitable for relatedness study of multigenerational salivary bacteria microbiome.

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Similarity of salivary microbiome in parents and adult children

10.7287/peerj.preprints.27565v1 ◽

2019 ◽

Author(s):

Kati Sundström ◽

Pashupati P Mishra ◽

Mikko J Pyysalo ◽

Terho Lehtimäki ◽

Pekka J Karhunen ◽

...

Keyword(s):

Adult Children ◽

Bacterial Communities ◽

Bacterial Species ◽

Amplicon Sequencing ◽

Human Saliva ◽

Oral Microbiome ◽

Rrna Gene ◽

Genus Level ◽

Abundant Genus ◽

Dna Profiles

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Seagrass leaf reddening alters the microbiome of Zostera muelleri

Marine Ecology Progress Series ◽

10.3354/meps13409 ◽

2020 ◽

Vol 646 ◽

pp. 29-44

Author(s):

V Hurtado-McCormick ◽

T Kahlke ◽

D Krix ◽

A Larkum ◽

PJ Ralph ◽

...

Keyword(s):

Significant Proportion ◽

Amplicon Sequencing ◽

High Irradiance ◽

Rrna Gene ◽

Core Microbiome ◽

Microbiome Composition ◽

Operational Taxonomic Units ◽

Normal Green ◽

White Tissue ◽

Leaf Reddening

Seagrasses host an extremely diverse microbiome that plays fundamental roles in seagrass health and productivity but may be sensitive to shifts in host physiology. Here, we observed a leaf reddening phenomenon in Zostera muelleri and characterized bacterial assemblages associated with green and reddened leaves to determine whether this change in leaf pigmentation stimulates shifts in the seagrass microbiome. Using 16S rRNA gene amplicon sequencing, we observed that the microbiome associated with 4 different leaf pigmentation categories (i.e. green, white, purple and black) differed significantly, with substantial changes in microbiome composition when the tissue is whitened (non-pigmented). Actinobacteria, Rhodobacteraceae, Erythrobacter, Sulfitobacter and Granulosicoccus were enriched in black and/or purple tissues and discriminated these microbiomes from those associated with green leaves. Contrastingly, all ‘discriminatory’ zero-radius operational taxonomic units (zOTUs) were depleted within the communities associated with white samples. While 40% of the abundant zOTUs identified were exclusively associated with a single pigmentation category, only 3% were shared across all categories, indicating partitioning of the phyllosphere microbiome. However, a significant proportion of the ‘normal’ (green) leaf core microbiome was also retained in the core communities associated with black (70%) and purple (70%) tissues. Contrastingly, no core zOTUs were maintained in the white tissues. These results indicate that environmentally driven physiological shifts in seagrasses, such as leaf reddening expressed in response to high irradiance, can impact the seagrass leaf microbiome, resulting in significant shifts in the microbiome of reddened leaves with the most extreme expression (in white tissue of reddened leaves).

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Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

10.21203/rs.3.rs-59563/v1 ◽

2020 ◽

Author(s):

Ya Wang ◽

Yan Yan ◽

Kelsey N. Thompson ◽

Sena Bae ◽

Emma K. Accorsi ◽

...

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Comprehensive Evaluation ◽

Amplicon Sequencing ◽

Human Saliva ◽

Rrna Gene ◽

Propidium Monoazide ◽

Functional Profiling ◽

Subway System ◽

Compositional Diversity

Abstract Background: High-throughput sequencing provides a powerful window into the structural and functional profiling of microbial communities, but it is unable to characterize only the viable portion of microbial communities at scale. There is as yet not one best solution to this problem. Previous studies have established viability assessments using propidium monoazide (PMA) treatment coupled with downstream molecular profiling (e.g. qPCR or sequencing). While these studies have met with moderate success, most of them focused on the resulting “viable” communities without systematic evaluations of the technique. Here, we present our work to rigorously benchmark “PMA-seq” (PMA treatment followed by 16S rRNA gene amplicon sequencing) for viability assessment in synthetic and realistic microbial communities. Results: PMA-seq was able to successfully reconstruct simple synthetic communities comprising viable/heat-killed Escherichia coli and Streptococcus sanguinis . However, in realistically complex communities (computer screens, computer mice, soil and human saliva) with E. coli spike-in controls, PMA-seq did not accurately quantify viability, with its performance largely affected by community properties such as initial biomass, sample types and compositional diversity. We then applied this technique to environmental swabs from the Boston subway system. Several taxa differed significantly after PMA treatment, while not all microorganisms responded consistently. To elucidate the “PMA-responsive” microbes, we compared our results with previous PMA-based studies and found that PMA-responsiveness varied widely when microbes were sourced from different ecosystems but were reproducible within similar environments across studies. Conclusions: This study provides a comprehensive evaluation of PMA-seq exploring its quantitative accuracy in synthetic and complex microbial communities, where the technique was effective for semi-quantitative purposes in simple synthetic communities, but provided only qualitative assessments in realistically complex community samples.

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Periodontal Manifestations in a Patient with Haim-Munk Syndrome

European Journal of Dentistry ◽

10.1055/s-0039-1697849 ◽

2010 ◽

Vol 04 (03) ◽

pp. 338-340

Author(s):

Kamile Erciyas ◽

Serhat Inaloz ◽

A. Fuat Erciyas

Keyword(s):

Autosomal Recessive ◽

Alveolar Bone ◽

Bone Destruction ◽

Autosomal Recessive Disorder ◽

Aggressive Periodontitis ◽

Pes Planus ◽

Rare Autosomal Recessive Disorder ◽

Rare Anomaly ◽

Palmoplantar Hyperkeratosis

Haim-Munk syndrome is an extremely rare autosomal recessive disorder characterized clinically by palmoplantar hyperkeratosis, aggressive periodontitis with severe alveolar bone destruction, onychogryphosis, pes planus, arachnodactyly, and acro-osteolysis. Consanguinity seems a notable prerequisite. The aim of this study was therefore to report one case of this syndrome and to focus on the periodontal manifestations, in order to attract the attention of dental clinicians to this rare anomaly. (Eur J Dent 2010;4:338-340)

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Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

Genome Biology ◽

10.1186/s13059-019-1831-z ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 14

Author(s):

Robert C. Kaplan ◽

Zheng Wang ◽

Mykhaylo Usyk ◽

Daniela Sotres-Alvarez ◽

Martha L. Daviglus ◽

...

Keyword(s):

Community Health ◽

Gut Microbiome ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Shannon Index ◽

Health Study ◽

Rrna Gene ◽

Cross Sectional ◽

Hispanic Community ◽

The Usa

Abstract Background Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment. Results Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA. Conclusions Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.

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Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals

Microbiome ◽

10.1186/s40168-021-01012-1 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Janis R. Bedarf ◽

Naiara Beraza ◽

Hassan Khazneh ◽

Ezgi Özkurt ◽

David Baker ◽

...

Keyword(s):

Parkinson’S Disease ◽

16S Rrna ◽

16S Rrna Gene ◽

False Positive ◽

Gene Sequencing ◽

Bacterial Biomass ◽

16S Rrna Gene Sequencing ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Rrna Gene Sequencing

Abstract Background Recent studies suggested the existence of (poly-)microbial infections in human brains. These have been described either as putative pathogens linked to the neuro-inflammatory changes seen in Parkinson’s disease (PD) and Alzheimer’s disease (AD) or as a “brain microbiome” in the context of healthy patients’ brain samples. Methods Using 16S rRNA gene sequencing, we tested the hypothesis that there is a bacterial brain microbiome. We evaluated brain samples from healthy human subjects and individuals suffering from PD (olfactory bulb and pre-frontal cortex), as well as murine brains. In line with state-of-the-art recommendations, we included several negative and positive controls in our analysis and estimated total bacterial biomass by 16S rRNA gene qPCR. Results Amplicon sequencing did detect bacterial signals in both human and murine samples, but estimated bacterial biomass was extremely low in all samples. Stringent reanalyses implied bacterial signals being explained by a combination of exogenous DNA contamination (54.8%) and false positive amplification of host DNA (34.2%, off-target amplicons). Several seemingly brain-enriched microbes in our dataset turned out to be false-positive signals upon closer examination. We identified off-target amplification as a major confounding factor in low-bacterial/high-host-DNA scenarios. These amplified human or mouse DNA sequences were clustered and falsely assigned to bacterial taxa in the majority of tested amplicon sequencing pipelines. Off-target amplicons seemed to be related to the tissue’s sterility and could also be found in independent brain 16S rRNA gene sequences. Conclusions Taxonomic signals obtained from (extremely) low biomass samples by 16S rRNA gene sequencing must be scrutinized closely to exclude the possibility of off-target amplifications, amplicons that can only appear enriched in biological samples, but are sometimes assigned to bacterial taxa. Sequences must be explicitly matched against any possible background genomes present in large quantities (i.e., the host genome). Using close scrutiny in our approach, we find no evidence supporting the hypothetical presence of either a brain microbiome or a bacterial infection in PD brains.

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