SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Metagenomics of the Microbiome in Oral Health and Disease

The development of dental caries in children provides a disease model that is well suited to a metagenomic investigation since the timeframe of caries development can be monitored within a defined study period during which longitudinal studies can be conducted. Dental caries has a well-established link to discrete, but only partially characterized changes in the dental plaque microbiome. Our study endeavors to define the relative abundance of many species comprising the dental plaque microbiome in twin pairs discordant for dental caries in association and longitudinal studies. The study power afforded by the use of discordant twin pairs for dental caries is substantially greater than similar studies using unrelated individuals. Next, we will compare the caries-free and caries-active microbiomes by deep metagenomic sequencing to identify differentially abundant genes and metabolic pathways. Lastly, we will determine the functional relevance of differentially abundant species, strains and genes by conducting targeted meta-transcriptomic studies. The statistical significance of all of the datasets will be determined which will allow for the widespread identification of species, strains, genes and transcripts associated with dental caries and dental health. These approaches are likely to enhance our understanding of dental caries onset and development and may enable in the future the development of novel treatment strategies.

Biome: root:Host-associated:Human:Digestive system:Oral
Microbiota between subgingival plaque and gingival tissue in periodontitis

Comparison of microbiota between subgingival plaque and tissue in periodontitis patients

Biome: root:Host-associated:Human:Digestive system:Oral
Human oral microbiota in periodontitis and health

We investigated the oral microbiota in saliva, supragingival and subgingival plaque of Chinese adults with and without periodontits to obtain a comprehensive view of the oral bacterial communities and identify periodontitis associated bacteria

Biome: root:Host-associated:Human:Digestive system:Oral
Oral active microbiota of dental caries

Identifying the microbial species in caries lesions is instrumental to determine the etiology of dental caries. However, a significant proportion of bacteria in carious lesions have not been cultured, and the use of molecular methods has been limited to DNA-based approaches, which detect both active and inactive or dead microorganisms. To identify the RNA-based, metabolically active bacterial composition of caries lesions at different stages of disease progression in order to provide a list of potential etiological agents of tooth decay. Non-cavitated enamel caries lesions (n=15) and dentin caries lesions samples (n=12) were collected from 13 individuals. RNA was extracted and cDNA constructed, which was used to amplify the 16S rRNA gene. The resulting 780 bp PCR products were pyrosequenced using Titanium-plus chemistry and the sequences obtained were used to determine the bacterial composition.

Biome: root:Host-associated:Human:Digestive system:Oral
Predictive modeling of early childhood caries via spatial-temporal variations of oral microbiota (Validataion study)

The strong correlation between bacterial communities and main factors (e.g., time and disease state) both between subjects and within subjects within a given niche thus suggested that oral microbiota could potentially model ECC onset. To test this hypothesis, the 34-children study cohort sampled two times during one year (T1, T3) were used as a train set for model construction, and an additional 24 child subjects were recruited and then each sampled at two time points (T3 and T4) for model validation: 14 patients including 7 experiencing caries-onset (HC group) and 7 experiencing caries- exacerbation (CC group) and ten healthy-steady controls (HH group).

Biome: root:Host-associated:Human:Digestive system:Oral
Predictive modeling of early childhood caries via spatial-temporal variations of oral microbiota

Principles for exploiting the spatial and temporal variations of microbiota for modeling chronic infections are not well established. Early Childhood Caries (ECC) is the most common disease in children and is irreversible once started; thus, its preventive intervention is crucial but usually difficult. Here we simultaneously tracked the development of microbiota at two distinct oral niches (plaque and saliva) for 34 four-year-old preschoolers over one year. During the tracked period, 10 children stayed free of caries (HHH group), 14 entered from health into cariogenesis (HCC group and HHC group), while the remaining 10 experienced caries exacerbation (CCC group).

Biome: root:Host-associated:Human:Digestive system:Oral
Liyan_caries_2011

37 samples of human oral metagenome related to Caries

Biome: root:Host-associated:Human:Digestive system:Oral
Casey periodontitis 2016

This studyexamined the saliva and subgingival microbiota of subjects with chronic periodontitis before andafter scaling and root planing and subjects without disease

Biome: root:Host-associated:Human:Digestive system:Oral
Carious dentine Genome sequencing

16S rRNA gene sequences from carious dentine

Biome: root:Host-associated:Human:Digestive system:Oral
Bacterial community development in experimental gingivitis

Current knowledge of the microbial composition of dental plaque in early gingivitis is based largely on microscopy and cultural methods, which do not provide a comprehensive description of oral microbial communities. This study used 454-pyrosequencing of the V1-V3 region of 16S rRNA genes (approximately 500 bp) to characterize the composition of plaque during the transition from periodontal health to gingivitis. A total of 20 healthy volunteers abstained from oral hygiene for two weeks, allowing plaque to accumulate and gingivitis to develop. Plaque samples were analyzed at baseline, and after one and two weeks. In addition, plaque samples from 20 chronic periodontitis patients were analyzed for cross-sectional comparison to the experimental gingivitis cohort.

Biome: root:Host-associated:Human:Digestive system:Oral
P&G gingivitis Targeted Locus

Gingivitis is the most common gum infection, yet its etiology remains elusive. We designed a retrogression-progression model (RPM) to simulate the development and reoccurrence of gingivitis. Fifty adults underwent a controlled transition from naturally occurring gingivitis (NG) to healthy gingivae (Baseline), then back to experimental gingivitis (EG). Within-subject temporal dynamics in taxonomic structure (for the 150 plaque microbiota samples) and functional profiles (for 18 of them) were observed via 16S rRNA gene and shotgun metagenomic sequencing respectively.  16S barcoded pyrosequencing for 273 oral plaque samples.

Biome: root:Host-associated:Human:Digestive system:Oral
Dental Calculus Metagenome (archaeological)

The purpose of this study was to investigate oral microbiome, dietary, and host DNA in archaeological human dental calculus (mineralized dental plaque), dentine, and bone using shotgun metagenomics and targeted 16S rRNA deep sequencing approaches. The samples in this study were obtained from four skeletons (G12, B17, B61, and B78) from the medieval site of Dalheim, Germany (ca. AD 950-1200). The skeletons exhibited osteological evidence of periodontal disease. A total of nine indexed Illumina shotgun metagenomic libraries were prepared from B61 and G12 dental calculus using different extraction and decontamination protocols. The nine indexed libraries were pooled and sequenced on a single Illumina HiSeq 2000 lane. A total of 32 indexed 454 targeted 16S rRNA libraries (V3, V5, and V6 regions) were prepared from paired dental calculus and dentine samples from G12, B17, B61, and B78, as well as from carious dentine and abscessed bone from B17. The 32 indexed libraries were pooled and sequenced on a 454 GS Junior. The genetic data associated with this project (including contig assemblies) are also available at MG-RAST in Project 365: http://metagenomics.anl.gov/linkin.cgi?project=365. Shotgun proteomic data associated with this project have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org/) via the PRIDE partner repository with the dataset identifier PXD000412 and DOI 10.6019/PXD000412.

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

Oral Microbiota

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

Microbiome associated with periodontal health and disease

Biome: root:Host-associated:Human:Digestive system:Oral
NGS approaches to metagenomics of gut microbiome

We compare the performance of 16S rRNA amplicon sequencing and shotgun metagenomics to perform taxonomic analysis of gut microbiome

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
feces metagenome

The 89 fresh feces samples (including 47 modified Kato-Katz thick smear-positive volunteers and 42 healthy controls from five rural communities) were collected in duplicate, with one for microscopic examination, and another one immediately stored at -80? until DNA extraction. All of the subjects were found no other parasite eggs (such as horkworms, roundworm, whipworm, pinworm, Taenia) by microscope.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Human gut metagenome and metatranscriptome raw sequence reads.

We conducted metagenomic and metatranscriptomic sequencing of the human gut microbiome among 308 participants enrolled in a subcohort of men nested within the Health Professionals Follow-up Study. Using a previously validated self-sampling stool collection method (PMID24843156), participants provided up to four stool samples  one set of samples collected approximately 48 hours apart followed by a second set approximately 6 months later. DNA extracted from 929 stool samples and RNA extracted from 378 stool samples was reverse-transcribed to cDNA and sequenced using the Illumina HiSeq platform. Raw data were filtered to remove low quality and human reads. Metagenomic and metatranscriptomic read data were then profiled for functional and taxonomic composition using the HUMAnN2 and MetaPhlAn2 platforms respectively.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Microbiome and Worm Infection

A study of the bacterial community of worm infected human stool via MetaGenomic Shotgun (MGS) data and 16s assembly data analysis

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
human stool bacteria 16s rDNA v4 region sequencing

bacterial alterions in C.difficile infection and alerations after fecal microbiota transplantation

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Impact of experimental Necator americanus infection on human gut microbiota


Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Association between oral and gut microbiota in Periodontal Disease

Is it possible that the relationship between periodontitis and these diseases are indirectly linked to disturbances on the intestinal microbiome?

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
The prebiotic fructooligosaccharide modulates metabolic dynamics and IgA production in the human gut ecosystem

Fructooligosaccharide (FOS), a prebiotic well known for its health-promoting properties, can improve the human gut ecosystem most likely through changes in its microbial composition. However, the detailed mechanism(s) of action of FOS in the modulation of the gut ecosystem remains obscure. Traditional methods of profiling microbes and metabolites could barely show any significant features due to the existence of large interindividual differences, but our novel microbe-metabolite correlation approach, combined with fecal IgA measurements, has revealed that the induction of mucosal IgA by FOS supplementation correlated with the presence of specific bacteria. Furthermore, the metabolic dynamics of butyrate, L-phenylalanine, L-lysine and tyramine were positively correlated with the dynamics of these bacteria and IgA production, whereas p-cresol was negatively correlated. Taken together, our focused intraindividual analysis with omics approaches is a powerful strategy for uncovering the gut molecular network and could provide a new vista for understanding the human gut ecosystem.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Fecal microbiota of toddlers Metagenome

Fecal samples attained from 18-27 month old toddlers were pyrosequenced to ascertain the effect of maternal obesity, temperament, and other variables upon the fecal microbiota.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Targeted Gene amplicons raw sequence reads

Sequencing of targeted genes like frc, but and buk genes from the microbial origin. Amplicons generated from gDNA from stool samples.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Homo sapiens fecal microbiome transplant

The objective of the study was to investigate the efficacy of fresh, frozen or lyophilized fecal microbiota transplantation (FMT) via colonoscopy in patients with recurrent C. difficile associated diarrhea (RCDAD). After a course of oral vancomycin we performed FMT in 36 patients with =3 bouts of RCDAD. FMT products from thoroughly screened healthy donors after filtering stools twice were given as single (non-pooled) product either as fresh, frozen (-80C) or lyophilized. Patients submitted fresh stools pre- and on 7, 14 and 30 days post-FMT. Bacterial DNA was extracted and the V4 region of the 16S rRNA gene was amplified by PCR and amplicons were sequenced on the MiSeq (Illumina) platform. The unique aspects of this study are the comparative efficacy in different patients with recurrent CDI of FMT using the same donor providing either fresh or frozen product, or the successful use of lyophilized FMT products.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Metagenome from fecal samples collect from healty human subject during probiotic intervention trial


Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
16s-based microbiome metagenome

Microbiome Analysis of IBS Patients

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Human gut microbiota from the ALADDIN study

Characterization of mothers and infants microbiota

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Human Feces Samples Metagenome

This study investigates the transfer of viral populations during human fecal microbiota transplants.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
A Longitudinal Study of Pediatric Subjects with Newly Diagnosed Inflammatory Bowel Disease


Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Raw sequence reads of human sleep apnea patients gut microbiome

Gut microbiome of patients with sleep apnea

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Alterations of the human gut microbiome in multiple sclerosis

The gut microbiome plays an important role in normal immune function and has been implicated in several autoimmune disorders. Here we use high-throughput 16S rRNA sequencing to investigate the gut microbiome in subjects with multiple sclerosis (MS, n=61) and healthy controls (n=43). Alterations in the gut microbiome in MS include increases in the genera Methanobrevibacter and Akkermansia and decreases in Butyricimonas, and correlate with variations in the expression of genes involved in dendritic cell maturation, interferon signaling and NF-kB signaling pathways in circulating T cells and monocytes. Patients on disease-modifying treatment show increased abundances of the genera Prevotella and Sutterella, and decreased Sarcina, compared to untreated patients. MS patients of a second cohort show elevated breath methane compared to controls, consistent with our observation of increased gut Methanobrevibacter in MS in the first cohort. Further study is required to assess whether the observed alterations in the gut microbiome play a role in, or are a consequence of, MS pathogenesis.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Comparison of the fecal microbiota during variable collection and storage methods

Sample collection from in-patients can be challenging and potentially impacted by collection method variability. We used 16S rRNA-based sequencing to compare the microbiota profiles of variably stored and collected samples. Stool from three different patients were evaluated at different freezing and handling conditions. Additionally, rectal swabs were compared to a stool sample, collected from eight different patients over the course of 24 hours. Storage conditions did not significantly impact the microbial community, and only minor differences were observed between rectal swabs and stool. We conclude that fecal microbial communities did not change substantially after various transport and storage conditions. Rectal swabs are a suitable alternative for assessing the microbiota when fresh stool is not easily obtained.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
16S rRNA profiling of "Allergy" and "Healthy" human faecal samples


Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Shallow coastal lagoon Metagenome

In the present study, Sediment bacterial communities in monospecific stands of four habitats (mudflats and mono-specific plots of the seagrass Zostera noltei and the saltmarsh plants Juncus maritimus and Spartina maritima) were investigated.

Biome: root:Host-associated:Human:Digestive system:Large intestine
Human gut environment Targeted loci environmental

Here we associate microbial community membership with distinct phenotypes of colorectal lesion. By performing 16S rRNA gene sequencing on mucosal biopies obtained from colorectal cancer-free patients, patients with adenomatous polyps, and patients with adenocarcinomas, we characterized the taxonomic configurations of microbial community to examine how disease progression is associated with changes in microbial community types.

Biome: root:Host-associated:Human:Digestive system:Large intestine
Human gut metagenome and metatranscriptome in the inflammatory bowel disease (iHMP/HMP2)

We examined the dynamics of microbiome functionality in Inflammatory bowel disease (IBD) by profiling metagenomic and metatranscriptomic sequencing of the human gut microbiome among 100 individuals sampled over a one year period. Here, we present the first results based on the functional analysis of 78 paired metagenomes/metatranscriptomes and 222 additional metagenomes.

Biome: root:Host-associated:Human:Digestive system:Intestine
Children Gut Microbiota 16S

Study aimed to assess the effects of helminths and protozoa parasites in the bacterial gut microbiota of children.

Biome: root:Host-associated:Human:Digestive system
Changes in duodenal tissue-associated microbiota following hookworm infection and consecutive gluten challenges in humans with coeliac disease

A reduced diversity of the commensal microbiota is associated with the development of several inflammatory diseases. Recent reports in humans and animal models have demonstrated the beneficial therapeutic effects of infections by parasitic worms (helminths) in some inflammatory disorders, such as inflammatory bowel disease (IBD) and coeliac disease (CeD). Interestingly, these studies have described how helminths may alter the intestinal microbiota, potentially representing a mechanism by which they regulate inflammation. However, for practical reasons, these reports have primarily analysed the fecal microbiota. In the present investigation, we have assessed, for the first time, the changes in the microbiota at the site of infection by a parasitic helminth (hookworm) and gluten-dependent inflammation in humans with CeD using biopsy tissue from the duodenum. Our results demonstrate that hookworm infection and gluten exposure were associated with increases in the richness and diversity of the tissue-resident microbiota within the intestine. This may represent one mechanism by which these parasites may restore intestinal immune homeostasis and exert a therapeutic benefit in CeD, and potentially other inflammatory disorders.

Biome: root:Host-associated:Human:Digestive system
16S rDNA sequences of human oral and gut microbiome Raw sequence reads

The goals of this study is to expose the relevance between environmental microbiome and microbiome from human oral and gut

Biome: root:Host-associated:Human:Digestive system
Intestinal microbiota of the patients with Hirschsprungs disease Raw sequence reads

Hirschsprung-associated enterocolitis (HAEC) is a life-threatening complication of Hirschsprungs disease (HD). Despite the pathological mechanisms are still unclear, studies have shown that HAEC has close relationship with intestinal microbiota disturbance. This study aimed to investigate the characterization of the intestinal microbiome of HD with or without enterocolitis. During routine or emergency surgery we collected 35 intestinal content samples from five patients with HAEC and eight HD patients, including three HD patients with a history of enterocolitis (HAEC remission, HAEC-R). Using Illumina-MiSeq high-throughput sequencing, we sequenced the V4 region of bacterial 16S rRNA, and operational taxonomic units (OTUs) were defined by 97% sequence similarity. Principal coordinate analysis (PCoA) of weighted UniFrac distances was performed to compare the diversity of each intestinal microbiome sample. The microbiota differed significantly between the HD patients (characterized by Bacteroidetes) and HAEC patients (characterized by Proteobacteria), and the microbiota of HAEC-R patients was more similar to that of HAEC patients. We also observed that specimens from different intestinal sites in each HD patient differed significantly, whilst specimens from different intestinal sites in each HAEC and HAEC-R patients were more similar. In conclusion, the microbiome pattern of HAEC-R patients was more similar to that of HAEC patients than HD patients. HD patients have a relatively distinct, more stable community than HAEC and HAEC-R patients, suggesting that enterocolitis may either be caused by or result in a disruption of the patients uniquely adapted intestinal flora. The intestinal microbiota associated with enterocolitis may persist following resolution of symptoms, and could be implicated in the symptom recurrence.

Biome: root:Host-associated:Human:Digestive system
Human oral or faecal metagenome Raw sequence reads

Faecal or oral microbiomes of persons administered different antibiotics.

Biome: root:Host-associated:Human:Digestive system
Human nasal and oral cavities microbiota 16S rRNA gene amplicon sequencing

The purpose of this study was to document and compare the bacterial communities found in the nasal and oral cavities of healthy humans.

Biome: root:Host-associated:Human