The oral microbiome of early stage Parkinson’s disease and its relationship with functional measures of motor and non-motor function

Mihaila, Dragos; Donegan, Jordan; Barns, Sarah; LaRocca, Daria; Du, Qian; Zheng, Danny; Vidal, M.; Neville, Christopher; Uhlig, Richard; Middleton, Frank A.

doi:10.1371/journal.pone.0218252

Cited by 77 publications

(71 citation statements)

References 75 publications

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“…Furthermore, the treatment of oral pathologies connected to the dysbiosis of its microbiota has taken on a particular interest in the scientific community as numerous recent publications have found associations between this dysbiosis and various systemic diseases. In fact, some authors have related an increased concentration of bacteria of the Bacillus genus or the species Lactobacillus reuteri to the Autistic Spectrum Disorders and Parkinson's disease, respectively [22][23][24]. Similar evidence was found between Actinomyces and Atopobium genera and oesophageal squamous cell carcinoma, and between Prevotella spp.…”

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confidence: 72%

Personalized Dentistry: Approaching a New Way for Diagnosis and Treatment of Oral Diseases

Patini¹

2020

JPM

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For years, it has been thought that the field of dentistry was referring exclusively to some diseases that strictly affect the oral cavity. Dental caries, periodontal disease, and pathologies associated with their worsening were considered almost the only interest in scientific research in dentistry. Recent studies have begun to shed light on the effect of the oral microbiota on general health and on the crucial role of dentistry in its maintenance. In this way, we came to understand that the bacterial populations that make up the oral microbiota can vary profoundly between individuals and that contribute in a fundamental way to outlining the so-called “oral signature”. This characteristic is called into question to evaluate the susceptibility, or lack thereof, of the subject to the contraction of a wide range of pathologies, apparently not connected with oral health. From this evidence, it will also be possible to study therapeutic approaches aimed at the eradication of species considered at risk or colonization with species considered protective; thus, giving life to so-called “personalized dentistry”. Therefore, this Special Issue is aimed at spreading the scientific knowledge over the current limits in terms of new molecular and culturomic approaches towards the diagnosis of oral microbiota and the treatment techniques of eventually associated systemic diseases. In vivo studies and systematic literature reviews with quantitative analysis of results, when possible, will be given a high priority.

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confidence: 72%

Personalized Dentistry: Approaching a New Way for Diagnosis and Treatment of Oral Diseases

Patini¹

2020

JPM

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“…Gastrointestinal symptoms often precede the motor signs of PD. Recently, there are a number of studies conducted to study the connection between the gut microbiome and PD [3,[29][30][31][32][33]. We use a dataset released by Hill-Burns et al [30].…”

Section: A Human Gut Microbiome Dataset Related To Pdmentioning

confidence: 99%

Predictive analysis methods for human microbiome data with application to Parkinson’s disease

Dong

Chen

et al. 2020

PLoS ONE

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Microbiome data consists of operational taxonomic unit (OTU) counts characterized by zero-inflation, over-dispersion, and grouping structure among samples. Currently, statistical testing methods are commonly performed to identify OTUs that are associated with a phenotype. The limitations of statistical testing methods include that the validity of p-values/qvalues depend sensitively on the correctness of models and that the statistical significance does not necessarily imply predictivity. Predictive analysis using methods such as LASSO is an alternative approach for identifying associated OTUs and for measuring the predictability of the phenotype variable with OTUs and other covariate variables. We investigate three strategies of performing predictive analysis: (1) LASSO: fitting a LASSO multinomial logistic regression model to all OTU counts with specific transformation; (2) screening+GLM: screening OTUs with q-values returned by fitting a GLMM to each OTU, then fitting a GLM model using a subset of selected OTUs; (3) screening+LASSO: fitting a LASSO to a subset of OTUs selected with GLMM. We have conducted empirical studies using three simulation datasets generated using Dirichlet-multinomial models and a real gut microbiome data related to Parkinson's disease to investigate the performance of the three strategies for predictive analysis. Our simulation studies show that the predictive performance of LASSO with appropriate variable transformation works remarkably well on zero-inflated data. Our results of real data analysis show that Parkinson's disease can be predicted based on selected OTUs after the binary transformation, age, and sex with high accuracy (Error Rate = 0.199, AUC = 0.872, AUPRC = 0.912). These results provide strong evidences of the relationship between Parkinson's disease and the gut microbiome.

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“…9 Analysis of the microbiome state may also be informative for assessing risk of, diagnosing or managing disease. [10][11][12][13] The genus Lactobacillus encompasses an unusually diverse number of species that share the property of being found in nutrient-rich environments. 14 Lactobacilli have been exploited extensively for food preservation, 15 for biotechnological applications, 16 and as health-promoting "probiotics".…”

Section: Introductionmentioning

confidence: 99%

“… 9 Analysis of the microbiome state may also be informative for assessing risk of, diagnosing or managing disease. 10 – 13 …”

Section: Introductionmentioning

confidence: 99%

Metagenomic analysis reveals distinct patterns of gut lactobacillus prevalence, abundance, and geographical variation in health and disease

2020

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Lactobacilli are exploited extensively for food fermentation and biotechnology. Some food and gut isolates have been developed as probiotics, for which species that may be commensal to the human host are considered desirable. However, the robustness of defining original niches for lactobacilli-food, environment, the gut-is questionable, and culture-independent analyses of prevalence in different human populations is lacking. Here we analyzed the abundance of lactobacilli in 6,154 subjects from a database of highly curated fecal shotgun metagenomics data spanning 25 nationalities, with ages ranging from infancy to 102 years. Twenty-five species were detected, which we assigned into low, medium, and high prevalence groups. The microbiome of apparently healthy individuals could be categorized into 6 clusters or Lactobacillotypes (LbTypes), with three of the Lbtypes being dominated by L. delbrueckii, L. ruminis, L. casei, and the other three comprising a combination of different species. These Lactobacillus clusters exhibit distinct global abundance patterns. The cluster prevalences also display distinct age-specific trends influenced by geography, with overall lactobacillus prevalence increasing significantly with age in North America and Europe but declining with age in non-Westernized societies. Regression analysis stratified by regional location identified distinct associations of the Lactobacillotypes with age, BMI, and gender. Cirrhosis, fatty-liver, , IBD and T2D were characterized by net gain of lactobacilli, whereas hypertension patients harbored depleted lactobacillus levels. Collectively these data indicate that the species abundance of gut lactobacilli is moderated by geography, diet, and interaction with the whole microbiome, and has strong interactions with diseases associated with a western lifestyle.

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The oral microbiome of early stage Parkinson’s disease and its relationship with functional measures of motor and non-motor function

Cited by 77 publications

References 75 publications

Personalized Dentistry: Approaching a New Way for Diagnosis and Treatment of Oral Diseases

Personalized Dentistry: Approaching a New Way for Diagnosis and Treatment of Oral Diseases

Predictive analysis methods for human microbiome data with application to Parkinson’s disease

Metagenomic analysis reveals distinct patterns of gut lactobacillus prevalence, abundance, and geographical variation in health and disease

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