SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Microbiome variation in mesophotic corals

Here, we provide the first detailed assessment of the prokaryotic community associated withmultiple scleractinian corals over a depth gradient to the lower mesophotic realm (15-85 m).

Biome: root:Host-associated:Invertebrates:Cnidaria:Coral
marine metagenome Raw sequence reads

Adaptation to reef habitats through selection on the coral animal and its associated microbiome

Biome: root:Host-associated:Invertebrates:Cnidaria:Coral
Microbiota of Dipteran gut, plant litter and cow dung

Soil dwelling Dipteran larvae of Dilophus febrilis were fed with either one of the food sources cow dung (Bos primigenius taurus), dwarf shrub litter (Vaccinium gaultheroides) and grass litter (Dactylis glomerata). Afterwards the whole gut content of each specimen as well as its feeding source were extracted and analysed using massive parallel sequencing . The aim was to evaluate whether the microbial community in the Dipteran gut is species-specific or diet-related.

Biome: root:Host-associated:Insecta:Digestive system
Isolation and Identification of the Follicular Microbiome: Implications for Acne Research

In this study, we compare the both sequencing methods (16S vs. WGS) and collection methods (pore strip, glue strip, swab) to develop recommendations for collecting microbiome information for studies of acne vulgaris.

Biome: root:Host-associated:Human:Skin
Human Skin Microbiome Metagenome

Human Skin Microbiome

Biome: root:Host-associated:Human:Skin
Skin microbiome in human volunteers inoculated with H. ducreyi Raw sequence reads

The aim of this project was to investigate the interaction of the skin microbiome and Haemophilus ducreyi during experimental infection of human volunteers. We hypothesized that the skin microbiome influences susceptibility to H. ducreyi infection and that infection with H. ducreyi causes changes in the skin microbiome. To address these hypotheses, we collected skin swab samples prior to inoculation with H. ducreyi, at Days 1, 2 and 5 post-inoculation, at clinical endpoint, and at the test of cure visit. Samples from four dose-matched pairs of volunteers that either resolved the infection or formed pustules were subjected to barcoded amplification and pyrosequencing of the V1-V3 region of bacterial 16S rRNA genes. We compared alpha and beta diversity measurements of the microbiomes of resolvers and pustule formers, and determined signature bacteria that were associated with infection resolution or pustule formation.

Biome: root:Host-associated:Human:Skin
Oral tongue plaque Metagenome

To probe the microbial basis of halitosis in natural human populations, we em-ployed a longitudinal study design to compare the tongue microbiota associated with halitosis in 29 Chinese adults who underwent a consecutive three-day evaluation for the amount of volatile sulfur compounds (VSC) excreted orally. Three levels of the disease state (healthy, halitosis and severe halitosis) were defined based on the Halimeter value. Community structure of the tongue plaques was more sensitive to changes of disease state than to inter-personal variations or difference in sampling time. Within each subject, the structure of microbiota was relatively stable, while their variations were correlated with the change in Halimeter value. Severe halitosis micro-biota were the most conserved in community structure, whereas the healthy ones were relatively varied. Halitosis-associated bacteria were identified, among which the rela-tive abundance of Leptotrichia and Prevotella was positively correlated with halitosis severity whereas Haemophilus demonstrated a negative relationship with disease. Our study provided one of the first organismal profiles of disease-associated tongue mi-crobiota and revealed microbes that can potentially be used to evaluate halitosis state and progress.

Biome: root:Host-associated:Human:Digestive system:Oral:tongue dorsum
Human oral microbiome associated with OC regiment

Quantitative assessment of anti-gingivitis methods based on the microbiota holds great potential yet remains challenging. Although anti-gingivitis efficacy of different oral care products has been studied from clinical outcomes, we know little about their impacts on oral microbiota and its metabolic capabilities. Here, ninety one adults underwent controlled transitions from naturally occurring gingivitis, to healthy gingivae using different anti-gingivitis products. Oral care product regimen, which contains stannous chloride in toothpaste and cetylpyridinium chloride in mouthwash, showed significant better anti-plaque and anti-gingivitis efficacy than placebo toothpaste in twenty seven days parallel study. Microbial diversity for regimen group was significantly decreased from Baseline Day 0 to Day 27. Meanwhile, plaque microbiota structure exhibited a continuous transition along the first principal component, which correlated with changes of Mazza Gingival Index and Plaque Index. Thirteen oral bacteria tend to be affected by two antibacterial activess. Metabonomic analysis of saliva indicates reduced anaerobic fermentation and tissue degradation of oral microbiota. Interestingly, microbial parameters demonstrate the ability to predict treatment effects of different product and regression of gingivitis symptom. Thus, our study provided novel insight into impacts of oral care products on microbial clades and metabolic pathways of gingivitis.

Biome: root:Host-associated:Human:Digestive system:Oral:Supragingival plaque
Subgingival microbiome of from patients suffering from periodontitis and liver cirrhosis


Biome: root:Host-associated:Human:Digestive system:Oral:Supragingival plaque
microbial community diversities of subgingival plaque of 9 subjects

The microbial community diversities of subgingival plaque from 3 health subjects, 3 CP patients, 3 AgP patients.

Biome: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
Hemoparo

Chronic periodontitis subgingival samples in patients with HFE C282Y hemochromatosis.

Biome: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
Subgingival plaque and peri-implant biofilm

First permanent molars frequently present severe conditions in periodontitis cases. Implant restoration is an accepted means of replacing teeth lost due to periodontitis. The present investigation focused on the microbiome analysis of 10 healthy dental implants and 10 chronic periodontitis patients using 454-prosequencing of 16S rDNA. Subgingival plaque and peri-implant biofilm were sampled at the first permanent molar site before and after implant restoration.

Biome: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
human oral metagenome Metagenome

In five ten-year-old children, biofilm was collected from the upper first premolars and first molars using sterilized, UV-treated paper points inserted into the subgingival sulcus at eight sites.

Biome: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
healthy and stomatitis denture microbiome


Biome: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
Subgingival microbiome Metagenome

Subgingival microbiome in relation to clinical outcomes after the use of antibiotics in the treatment of periodontitis.

Biome: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
Dental Plaque 16s rRNA v6 amplicons

Characterization of the Dental Plaques of axial spondyloarthiritis patients

Biome: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
Human oral subgingival communities

16S sequencing of subgingival microbiota from subjects with chronic periodontitis and healthy subjects.

Biome: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
human oral metagenome Raw sequence reads

The present study aims to evaluate the composition of the subgingival plaque community associated with periodontal health and disease using high throughput sequencing approaches

Biome: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
Subgingival samples from Healthy / Periodontitis subjects Targeted Locus (Loci)

Subgingival samples from Healthy / Periodontitis subjects

Biome: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
Influence of DNA extraction on oral microbial profiles obtained via 16S rRNA gene sequencing- Supragingival plaque

Background and Objective: The advent of next-generation sequencing has significantly facilitated characterization of the oral microbiome. Despite great efforts in streamlining the processes of sequencing and data curation, upstream steps required for amplicon library generation could still influence 16S rRNA gene-based microbial profiles. Among upstream processes, DNA extraction is a critical step that could represent a great source of bias. Accounting for bias introduced by extraction procedures is important when comparing studies that use different methods. Identifying the method that best portrays communities is also desirable. Accordingly, the aim of this study was to evaluate bias introduced by different DNA extraction procedures on oral microbiome profiles.  Design: Four DNA extraction methods were tested on mock communities consisting of seven representative oral bacteria. Additionally, supragingival plaque samples were collected from 7 individuals and divided equally to test two commonly used DNA extraction procedures. Amplicon libraries of the 16S rRNA gene were generated and sequenced via 454-pyrosequencing.  Results: Evaluation of mock communities revealed that DNA yield and bacterial species representation varied with DNA extraction method. Despite producing the lowest yield of DNA, a method that included bead beating was the only protocol able to detect all seven species in the mock community. Comparison of the performance of two commonly used methods (crude lysis and a chemical/enzymatic lysis + column-based DNA isolation) on plaque samples showed no effect of extraction protocols on taxa prevalence but global community structure and relative abundance of individual taxa were affected. At the phylum level, the latter method improved the recovery of Actinobacteria, Bacteroidetes and Spirochaetes over crude lysis.  Conclusion: DNA extraction distorts microbial profiles in simulated and clinical oral samples, reinforcing the importance of careful selection of a DNA extraction protocol to improve species recovery and facilitate data comparison across oral microbiology studies.

Biome: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
Combined analysis of the salivary microbiome and host defence peptides predicts dental disease

Understanding the triad of host response, microbiome and disease status is potentially informative for disease prediction, prevention, early intervention and treatment. Using longitudinal assessment of saliva and disease status, we demonstrated that partial least squares modelling of microbial, immunological and clinical measures, grouped children according to future dental disease status. Saliva was collected and dental health assessed in 33 children aged 4 years, and again 1-year later. The composition of the salivary microbiome was assessed and host defense peptides in saliva were quantified. Principle component analysis of the salivary microbiome indicated that children clustered by age and not disease status. Similarly, changes in salivary host defense peptides occurred with age and not in response to, or preceding dental caries. Partial least squares modelling of microbial, immunological and clinical baseline measures clustered children according to future dental disease status. These data demonstrate that isolated evaluation of the salivary microbiome or host response failed to predict dental disease. In contrast, combined assessment of both host response together with the microbiome revealed clusters of health and disease. This type of approach is potentially relevant to myriad diseases that are modified by hostmicrobiome interactions.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Exercise frequency is associated with the oral microbiota of student athletes and non-athletes

We investigated the oral microbiota from human saliva samples of undergraduate student athletes and non-athletes, by sequencing 16S rDNA using high-throughput next-generation Illumina sequencing.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Oral microbiome of young adults

Oral microbiota associated with recurrent aphthous stomatitis in young adults

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Human saliva Targeted Locus (Loci)

This study aimed at investigating the salivary microbiota of fourteen non progressor (NP) and fourteen progressor (P) patients with immunoglobulin A nephropathy (IgAN).

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Human saliva microbiota Targeted Locus (Loci)

African celiac children''s saliva as affected by gluten-free diet

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Omnivorous, vegetarian and vegan saliva Targeted Locus (Loci)

Omnivorous, vegetarian and vegan saliva microbiota

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Transplantation-associated long-term immunosuppression promotes oral colonization by potentially opportunistic pathogens without impacting other members of the salivary bacteriome

Solid-organ transplant recipients rely on pharmacological immunosuppression to prevent allograft rejection. The effect of such chronic immunosuppression on the microflora at mucosal surfaces is not known. We evaluated the salivary bacterial microbiome of 20 transplant recipients and 19 non-immunosuppressed controls via 454-pyrosequencing of 16S rRNA gene amplicons. Alpha-diversity and global community structure did not differ between transplant and control subjects. However, principal coordinate analysis showed differences in community membership. Taxa more prevalent in transplant subjects included operational taxonomic units (OTUs) of potentially opportunistic Gammaproteobacteria such as Klebsiella pneumoniae, Pseudomonas fluorescens, Acinetobacter sp., Vibrio spp., Enterobacteriaceae sp. and the genera Acinetobacter and Klebsiella. Transplant subjects had increased proportions of Pseudomonas aeruginosa, Acinetobacter sp., Enterobacteriaceae sp. and Enterococcus faecalis, among other OTUs, while increased genera included Klebsiella, Acinetobacter, Staphylococcus and Enterococcus. Furthermore, in transplant subjects, the dose of the immunosuppressant prednisone positively correlated with bacterial richness, while prednisone and mycophenolate mofetil doses positively correlated with the prevalence and proportions of transplant-associated taxa. Correlation network analysis of OTU relative abundance revealed a cluster containing potentially opportunistic pathogens as transplant-associated. This cluster positively correlated with serum levels of C-reactive protein, suggesting a link between the resident flora at mucosal compartments and systemic inflammation. Network connectivity analysis revealed opportunistic pathogens as highly connected to each other and to common oral commensals, pointing to bacterial interactions that may influence colonization. This work demonstrates that immunosuppression aimed at limiting T-cell-mediated responses creates a more permissive oral environment for potentially opportunistic pathogens without affecting other members of the salivary bacteriome.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Saliva in oral cavity Targeted Locus (Loci)

to study the microbe in oral cavity of patients with dental decay

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Human oral saliva Metagenome

Microbial community survey of human saliva samples with and without oral lichen plauns

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
microbial diversity on human oral cavity

To study the microbial diversity in saliva of oral cavity of human

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Identification of salivary microbiota associated with oral malodor using 16S pyrosequencing

Both hydrogen sulfide (H2S) and methyl mercaptan (CH3SH) are frequently detected in large amounts in malodorous mouth air. We investigated the bacterial composition of saliva of 30 subjects with severe oral malodor exhibiting extreme CH3SH/H2S ratios (high H2S but low CH3SH concentrations, n = 14; high CH3SH but low H2S concentrations, n = 16) and 13 subjects without malodor, using barcoded pyrosequencing analysis of the 16S rRNA gene. Phylogenetic community analysis with the UniFrac distance metric revealed a distinct bacterial community structure in each malodor group. The H2S group showed higher proportions of the genera Neisseria, Fusobacterium, Porphyromonas and SR1 than the other two groups, whereas the CH3SH group had higher proportions of the genera Prevotella, Veillonella, Atopobium, Megasphaera, and Selenomonas. Our results suggested that distinct bacterial populations in the oral microbiota are involved in production of high levels of H2S and CH3SH in the oral cavity.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Human Saliva Microbiome

16S rRNA sequencing of the saliva microbiome of healthy human adult individuals

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Teeth bacterium Metagenome

To examine using 16S rDNA sequencing normal and pathogenic periodontal microflora.

Biome: root:Host-associated:Human:Digestive system:Oral:Periodontal pockets
UW - Children''s Health Cohort, Adult Participant''s Buccal Oral Microbiomes, 16S rDNA V5V6 PCR Sequences

Thinning ((T) Summer June 2005) and Nonspray ((N) Winter January 2006) Farmworker Buccal Oral 16S rDNA V5V6 PCR Microbiome raw sequence reads from the University of Washington''s Children''s Health Farmworker Cohort. Study goals were to characterize the oral microbiome of Washington State''s Yakima Valley Hispanic Farmworkers to assess human oral bacterial census diversity within a cohort with agricultural environmental bacterial exposures including farming, plant, animal and rural bacterial sources.

Biome: root:Host-associated:Human:Digestive system:Oral:buccal mucosa
human oral  metagenome Raw sequence reads

human oral surface mucosa metagenome Raw sequence reads

Biome: root:Host-associated:Human:Digestive system:Oral:buccal mucosa
molecular charactarization of endodontic infection in humans

Illumina Miseq platform sequencing can be used to explore person to person and temporal variation in oral microbiome composition of endodontic infection.

Biome: root:Host-associated:Human:Digestive system:Oral
human oral metagenome Raw sequence reads

create a new oral biofilm model where native oral biofilm is grown in vivo and then transferred to a biofilm reactor system.

Biome: root:Host-associated:Human:Digestive system:Oral
plaque, saliva, tongue coating metagenome

To exploring the oral microflora of preschool children

Biome: root:Host-associated:Human:Digestive system:Oral
Human-associated samples Metagenome

Using saliva (PK) and plaque (TK) samples of normal subjects as controls, we undertook a large-scale molecular analyses of 16S rDNA sequences to better characterize four crucial features of disease-associated oral microbiota in primary dentition: 1) the structure and composition of microbial communities from both saliva (PQ) and plaque (TQ) in patients with caries; 2) the structure and composition of microbial communities from both saliva (PS) and plaque (PQ) in patients with pigment; 3) the structure and composition of microbial communities from both saliva (PSQ) and plaque (TSQ) in patients with the mixture of caries and pigment; and 4) bacterial co-infection patterns linked with those three disease types.

Biome: root:Host-associated:Human:Digestive system:Oral
Human Oral Swabs Raw sequence reads

Human Oral Microbiome Samples

Biome: root:Host-associated:Human:Digestive system:Oral
Development and pyrosequencing analysis of an in-vitro oral biofilm model

The aim of this study was to develop an in vitro oral biofilm model using the Calgary Biofilm Device. The composition of the biofilms was determined by pyrosequencing of 16S rRNA genes.

Biome: root:Host-associated:Human:Digestive system:Oral
Microcosm Targeted Locus (Loci)

Microbial diversity based on 16S rDNA

Biome: root:Host-associated:Human:Digestive system:Oral
Saliva of human Targeted Locus (Loci)

Oral microbiology study

Biome: root:Host-associated:Human:Digestive system:Oral
Human current and never smokers

The goals of the study were to examine the role played by smoking in creating at-risk-for-harm oral microbial communities

Biome: root:Host-associated:Human:Digestive system:Oral
Human oral metagenome

Microbial diversity in dental caries and plaque

Biome: root:Host-associated:Human:Digestive system:Oral
Oral microbiome of leukemia patients

Oral microbial diversity of acute lymphoblastic leukemia patients was investigated and compared with that of healthy control subjects.  Supragingival plaque samples from acute lymphoblastic leukemia patients and healthy control subjects.

Biome: root:Host-associated:Human:Digestive system:Oral
Species within oral squamous cell carcinoma and control tissues -  Metagenome

Species within oral squamous cell carcinoma and control tissues - Metagenome

Biome: root:Host-associated:Human:Digestive system:Oral
Oral Bacterial Metagenome - Young Healthy Arabs

Bacterial community of oral cavity in young healthy Arabs

Biome: root:Host-associated:Human:Digestive system:Oral
Microbiome of Oral Leukoplakia

16s profiling of Oral Leukoplakia using V1V2 amplification and sequencing on MiSeq

Biome: root:Host-associated:Human:Digestive system:Oral
human oral metagenome

We use metagenomic analyses to investigate the complex relationship between the oral microbiome and caries in preschool children. A total of 41 preschoolers, aged 3-5 years were recruited. Saliva samples were collected, followed by DNA extraction, Illumina high-throughput sequencing and metagenomics analyses of the oral microbial communities.

Biome: root:Host-associated:Human:Digestive system:Oral
oral metagenome Metagenome

Our purposes were to utilize culture-independent molecular techniques to extend our knowledge on the breadth of bacterial diversity in the healthy human oral cavity in Egyptian individuals.

Biome: root:Host-associated:Human:Digestive system:Oral
Oral cancer bacteriome - preliminary study Metagenome

Bacterial species present within oral cancer tissue

Biome: root:Host-associated:Human:Digestive system:Oral
The human oral microbiota and interleukin 8 levels

The present study describes a 16S rRNA gene-targeted sequencing analysis in a cohort of healthy human partecipants. Nutritional habits and dental hygiene are compared with the oral microbial communities and with interleukin 8 levels in the oral cavity.

Biome: root:Host-associated:Human:Digestive system:Oral
Oral microbiome Raw sequence reads

Comparison of bacterial community diversity in human plaque and saliva samples using four different DNA extraction methods.

Biome: root:Host-associated:Human:Digestive system:Oral
human oral metagenome Metagenome

The study aims to characterize oral microbiome in HIV infection and periodontal disease. Sequencing data includes 16s v3-4 amplicon for dental plaque, cheek, and saliva samples.

Biome: root:Host-associated:Human:Digestive system:Oral
Alcohol and tobacco consumption affects bacterial richness in oral cavity biofilms

V1 16S rDNA sequences derived from human oral swab samples.

Biome: root:Host-associated:Human:Digestive system:Oral
Human oral microbiome

Human oral microbiome of non diabetic and diabetic subjects

Biome: root:Host-associated:Human:Digestive system:Oral
Oral Microbiome Metagenome

Oral Microbiome Characterization

Biome: root:Host-associated:Human:Digestive system:Oral