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103 results for “oral microbiome”
Supplementary information from: An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research
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Data from: Oral exposure to benzalkonium chlorides in male and female mice reveals sex-dependent alteration of the gut microbiome and bile acid profile
<p>Benzalkonium chlorides (BACs) are commonly used disinfectants in a variety of consumer and food-processing settings, and the COVID-19 pandemic has led to increased usage of BACs. The prevalence of BACs raises the concern that BAC exposure could disrupt the gastrointestinal microbiota, thus interfering with the beneficial functions of the microbes. We hypothesize that BAC exposure can alter the gut microbiome diversity and composition, which will disrupt bile acid homeostasis along the gut-liver axis. In this study, male and female mice were exposed orally to d<sub>7</sub>-C12- and d<sub>7</sub>-C16-BACs at 120 µg/g/day for one week. UPLC-MS/MS analysis of liver, blood, and fecal samples of BAC-treated mice demonstrated the absorption and metabolism of BACs. Both parent BACs and their metabolites were detected in all exposed samples. Additionally, 16S rRNA sequencing was carried out on the bacterial DNA isolated from the cecum intestinal content. For female mice, and to a lesser extent in males, we found that treatment with either d<sub>7</sub>-C12- or d<sub>7</sub>-C16-BAC led to decreased alpha diversity and differential composition of gut bacteria with notably decreased actinobacteria phylum. Lastly, through a targeted bile acid quantitation analysis, we observed decreases in secondary bile acids in BAC-treated mice, which was more pronounced in the female mice. This finding is supported by decreases in bacteria known to metabolize primary bile acids into secondary bile acids, such as the families of Ruminococcaceae and Lachnospiraceae. Together, these data signify the potential impact of BACs on human health through disturbance of the gut microbiome and gut-liver interactions.</p>
HiPR-FISH Oral Microbiome Experiments 4
<p>This dataset contains z-stacks of a HiPR-FISH experiment on an oral microbiome.</p>
HiPR-FISH Oral Microbiome Experiments 2
<p>This dataset contains a z-stack of a HiPR-FISH experiment on a oral microbiome.</p>
HiPR-FISH Oral Microbiome Experiments 1
<p>This dataset contains images of a HiPR-FISH experiments on an oral plaque microbiome.</p>
HiPR-FISH Oral Microbiome Experiments 3
<p>This dataset contains a z-stack of a HiPR-FISH experiment on an oral microbiome.</p>
Stability of oral and faecal microbiome at room temperature: impact on diversity
<p>When collecting oral and faecal samples for large epidemiological microbiome studies, optimal storage conditions such as immediate freezing, are not always feasible. It is fundamental to study the impact of temporary room temperature (RT) storage and shipping on the microbiome diversity obtained in different types of samples. We performed a pilot study aimed to validate the sampling protocol based on the viability of the 16S rRNA gene sequencing in microbiome samples.</p> <p>Faecal and oral samples from five participants were collected and preserved in different conditions: i) 70% ethanol; ii) in a FIT tube for stool samples; and iii) in a chlorhexidine solution for oral wash samples. Four aliquots were prepared per sample, which were stored at RT, and frozen at days 0, 5, 10 and 15, respectively.</p>
Agta hunter-gatherer oral microbiomes are shaped by contact network structure
<p>Here we investigate the effects of extensive sociality and mobility on the oral microbiome of 138 Agta hunter-gatherers from the Philippines. Our comparisons of microbiome composition showed that the Agta are more similar to Central African Bayaka hunter-gatherers than to neighbouring farmers. We also defined the Agta social microbiome as a set of 137 oral bacteria (only 7% of 1980 amplicon sequence variants) significantly influenced by social contact (quantified through wireless sensors of short-range interactions). We show that large interaction networks including strong links between close kin, spouses, and even unrelated friends, can significantly predict bacterial transmission networks across Agta camps. Finally, we show that more central individuals to social networks are also bacterial supersharers. We conclude that hunter-gatherer social microbiomes are predominantly pathogenic and were shaped by evolutionary tradeoffs between extensive sociality and disease spread.<strong> </strong></p>
Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Mapping MGEs in oral plaque biofilms at high specificity
<p>We stained for the GFP gene in samples that contained mixtures of plaque and GFP-transformed E. coli. We mapped mefE, an AMR gene located on a plasmid and encoding an antibiotic efflux pump, in the plaque metagenomic data of volunteer A but not volunteer B. To test the efficacy of gel embedding and clearing, we used orthogonal FISH probes, designed to not target any sequence in the plaque. We identified a T7-like prophage via metagenomic analysis and developed probes targeting its capsB gene, which encodes the minor capsid protein. We identified a highly prevalent prophage of the class Caudoviricetes with a large terminase gene, termL, and were able to design a large set of FISH probes to stain in three different colors simultaneously. We identified three non-plasmid AMR genes within metagenome assembled genomes: patA, patB, and adeF.</p>
Oral Probiotic Administration to Modulate the Airway Microbiome in Obese Asthmatic Subjects
ClinicalTrials.gov study NCT03157518. IPD Sharing: NO. Countries: 1. Publications: 6.
Data from: Oral exposure to benzalkonium chlorides in male and female mice reveals sex-dependent alteration of the gut microbiome and bile acid profile
Open the record for dataset details and reuse information.
HiPR-FISH Oral Microbiome Experiments 5
<p>This dataset contains HiPR-FISH images from a longitudinal experiment on a human oral microbiome.</p>
Data from: Oral microbiomes from hunter-gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet
Maladaptation to modern diets has been implicated in several chronic disorders. Given the higher prevalence of disease such as dental caries and chronic gum diseases in industrialized societies, we sought to investigate the impact of different subsistence strategies on oral health and physiology, as documented by the oral microbiome. To control for confounding variables such as environment and host genetics, we sampled saliva from three pairs of populations of hunter-gatherers and traditional farmers living in close proximity in the Philippines. Deep shotgun sequencing of salivary DNA generated high-coverage microbiomes along with human genomes. Comparing these microbiomes with publicly available data from individuals living on a Western diet revealed that abundance ratios of core species were significantly correlated with subsistence strategy, with hunter-gatherers and Westerners occupying either end of a gradient of Neisseria against Haemophilus, and traditional farmers falling in between. Species found preferentially in hunter-gatherers included microbes often considered as oral pathogens, despite their hosts' apparent good oral health. Discriminant analysis of gene functions revealed vitamin B5 autotrophy and urease-mediated pH regulation as candidate adaptations of the microbiome to the hunter-gatherer and Western diets, respectively. These results suggest that major transitions in diet selected for different communities of commensals and likely played a role in the emergence of modern oral pathogens.
Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders, MetaPhlAn 3 profiles
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The Effects of Oral Probiotics and Herbal Supplementation on the Gut Microbiome and Sebum Excretion Rate in Non-Cystic Acne
ClinicalTrials.gov study NCT05919810. IPD Sharing: NO. Countries: 1. Publications: 1.
Dietary Nitrate and the Oral Microbiome in Children With Primary Hypertension
ClinicalTrials.gov study NCT07236125. IPD Sharing: NO. Countries: 1. Publications: 3.
The Effect of Probiotic Lactobacillus Reuteri Prodentis Consumption on Gingival Crevicular Fluid Inflammatory Response and Metagenomic Profiles of Oral Microbiome in Orthodontic Patients.
ClinicalTrials.gov study NCT04847960. IPD Sharing: Not stated. Countries: 1. Publications: 24.
Effect of Gut Microbiome Intervention on Aging Via Oral FMT
ClinicalTrials.gov study NCT05598112. IPD Sharing: YES. Countries: 1. Publications: 5.
Role of the Oral Microbiome in Blood Pressure Regulation in Pregnancy
ClinicalTrials.gov study NCT03930693. IPD Sharing: NO. Countries: 1. Publications: 1.
Oral Microbiome in Carotid Atherosclerosis
ClinicalTrials.gov study NCT07296965. IPD Sharing: UNDECIDED. Countries: 1. Publications: 3.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.