SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Using High Throughput Sequencing to Understand the Biodiversity of Oral Bacterial Communities

High throughput sequencing of 16S rRNA amplicons is a cost-effective method for evaluation of bacterial communities associated with oral diseases. However, before undertaking large-scale studies, it is necessary to understand the technique-associated limitations and intrinsic variability of the oral ecosystem, which may affect our ability to discover disease-associated biomarkers. In this work we evaluated bias in species representation using an in vitro-assembled mock community of oral bacteria. We then sequenced the salivary and buccal mucosa bacterial communities of five healthy subjects to investigate their diversity and differences within and between subjects. Mock community analysis revealed primer and DNA isolation biases and an overestimation of diversity that was reduced after eliminating singleton operational taxonomic units (OTUs). Sequencing of salivary and mucosal communities revealed 455 OTUs (0.3% dissimilarity) across all samples with only 78 of the OTUs present in all subjects. Salivary communities were more diverse, with 120-318 OTUs per subject, while in mucosa each subject had 63-136 OTUs. Total OTUs per subject estimated using CatchAll (an estimator that performed well in evenly distributed salivary and also in uneven mucosal communities), ranged from 145-369 for saliva and 111-377 for mucosa. Inter-subject variability in community structure was lower than site differences between salivary and mucosal communities within subjects. These differences were evident even at very low sequencing depths and were mainly explained by an over-representation of Streptococcus mitis and Gemella haemolysans in mucosa, while several taxa from the genera Neisseria, Porphyromonas, Prevotella, Fusobacterium, among others, showed higher affinity for saliva. In summary, we present an experimental and data analysis framework that will facilitate the design and interpretation of pyrosequencing-based studies of the oral flora. Despite challenges associated with this technique, we demonstrate its power for the evaluation of oral diversity and biogeography patterns.

Biome: root:Host-associated:Human:Digestive system:Oral
Oral cavity microbiome analysis vs. pneumonia risk

16S rRNA gene sequencing to compare the oral microbial profiles in community dwelling adults with those residing in healthcare environments that are known to have high epidemiologic risk for pneumonia (i.e., nursing home residents, and mechanically ventilated patients in intensive care units).  Our goal was to determine if there was an association between the oral microbial profile and subsequent development of pneumonia.   Using sterile cotton applicators, oral cavity samples were obtained and pooled for each subject from the anterior and posterior gingival crevice of each tooth, buccal mucosa, tongue, and the soft and hard palate. Using sterile cotton applicators, oral cavity samples were obtained with two swabs from the: 1) anterior and posterior gingival crevice of each tooth; and 2) buccal mucosa, tongue, and the soft and hard palate.

Biome: root:Host-associated:Human:Digestive system:Oral
Defining a core microbial community of healthy human oral cavity

The aim of this study was to define the healthy oral microbiome. We sampled and sequenced the V5-V6 hypervariable region of 16S rRNA from microbiomes obtained at several intraoral niches (dental surfaces, cheek, hard palate, tongue and saliva) in three healthy Caucasian male adults with no dental caries, no periodontal disease and no antibiotic use in the past three months. Samples were collected in the morning, 12 hours after tooth brushing and 2 hours after the last food and/or drink intake.

Biome: root:Host-associated:Human:Digestive system:Oral
Oral and nasal microbiome in Parkinson's disease

Parkinson's disease (PD) is associated with neurodegeneration in olfactory and gastrointestinal nervous tissues. Accordingly, PD patients frequently suffer from hyposmia, hyposalivation, and dysphagia. Since hyposmia and gastrointestinal dysfunction are frequently premotor symptoms, it has been speculated that an external, for example microbial, agent could trigger the pathologic process in the corresponding tissues with subsequent spreading to the central nervous system. We recently demonstrated that fecal microbiota of PD patients differ from those of control subjects. Based on these findings and the involvement of nasal and perioral tissues in PD, we compared the oral and nasal bacterial communities of 76 PD patients and 76 control subjects using a 16S rRNA gene sequencing approach. The sequencing was performed in a MiSeq machine.

Biome: root:Host-associated:Human
This study develops a framework for exploiting the oral microbiome for monitoring oral cancer development, progression and recurrence.

Individual bacteria and shifts in the composition of the microbiome have been associated with human diseases including cancer.  To investigate changes in the microbiome associated with oral cancers, we profiled cancers and anatomically matched contralateral normal tissue from the same patient by sequencing 16S rDNA hypervariable region amplicons.  In cancer samples from both a discovery and a subsequent confirmation cohort, abundance of Firmicutes (especially Streptococcus) and Actinobacteria (especially Rothia) was significantly decreased relative to contralateral normal samples from the same patient.  Significant decreases in abundance of these phyla were observed for pre-cancers, but not when comparing samples from contralateral sites (tongue and floor of mouth) from healthy individuals.  Weighted UniFrac principal coordinates analysis based on 12 taxa separated most cancers from other samples with greatest separation of node positive cases.  These studies begin to develop a framework for exploiting the oral microbiome for monitoring oral cancer development, progression and recurrence.

Biome: root:Host-associated:Human:Digestive system:Oral
The intestinal microbiota predisposes to the occurrence of traveller's diarrhoea and to the carriage of multidrug-resistant Enterobacteriaceae after travelling to tropical regions.

The risk of acquisition of multidrug-resistant Enterobacteriaceae (MRE) and of occurrence of diarrhea is particularly high when travelling to tropical regions, likely owing to suboptimal hygiene living conditions and uncontrolled antibiotic usage. To date, the link between MRE acquisition, traveller's diarrhoea and the microbiota composition in healthy people has not been addressed. Therefore, we analysed the composition of metabolically active microbiota by sequencing the total cDNA from faecal samples before and after the travelling.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Comparison of copper contaminated soils, with similar uncontaminated controls.

Two sites of long-term copper polluted soil were sampled, along with nearby uncontaminated controls. All treatments were carried out and sampled in triplicate. A third site was samples at a copper mine, though the control site was of a dissimilar soil type and only single samples of each were taken.Marker taxa and gene functional groups will be identified between polluted and control soils.

Biome: root:Environmental:Terrestrial:Soil:Contaminated
16S Amplicon sequencing of northwestern argentinian artisanal cheeses gDNA using V4 primers

The Northwest argentinian artisanal cheese is a handcrafted product made from raw cow milk. The ripening process occurs spontaneously and, probably, it is influenced by environmental conditions. Its sensory characteristics and safety are probably the result of the balance between microbial populations and their metabolic capacity. The 16S amplicon sequencing of three DNA samples (and their corresponding replicates) from different Northwest argentinian artisanal cheeses, was used to assess the taxonomic affiliation of the bacterial populations in that type of cheeses. The samples were processed using 16S amplicon sequencing on a  Mi-seq sequencer with 515/806 primers to V4 region, this was carried out at Molecular Research (MR DNA) service provider (www.mrdnalab.com, Shallowater, TX, USA) following the manufacturer's guidelines.

Biome: root:Engineered:Food production:Dairy products
Metagenomic data from an northwestern argentinian artisanal cheese

The Northwest argentinian artisanal cheese is a handcrafted product made from raw cow milk. The ripening process occurs spontaneously and, probably, it is influenced by environmental conditions. Its sensory characteristics and safety are probably the result of the balance between microbial populations and their metabolic capacity. A metagenome-based approach was used to assess the taxonomic affiliation and function potential for bacteriocin production of the bacterial populations in this type of cheese. The DNA sample was subjected to shot-gun sequencing based on ion semiconductor technology using an IonTorrent PGM system, this was carried out at Molecular Research (MR DNA) service provider (www.mrdnalab.com, Shallowater, TX, USA) following the manufacturer's guidelines.

Biome: root:Engineered:Food production:Dairy products
Microbial biogeography of French caves

Diversity comparison of four pristine caves with five anthropized caves in Dordogne region (France).

Biome: root:Environmental:Terrestrial:Deep subsurface
Endocarditis due to Neisseria meningitidis

We report a metagenomic analysis of a heart valve community acquired from a patient with blood culture negative infective endocarditis due to Neisseria meningitidis.

Biome: root:Host-associated:Human:Circulatory system
Community structure analysis in chronic periodontitis and novel oral sampling sites for detecting disease indicators

Periodontitis is an infectious and inflammatory disease of polymicrobial etiology that can lead to the destruction of bones and tissues that support the teeth. The management of chronic periodontitis (CP) relies heavily on elimination or at least control of known pathogenic consortia associated with the disease. Until now, microbial plaque obtained from the subgingival (SubG) sites has been the primary focus for bacterial community analysis using deep-sequencing. In addition to the use of SubG plaque, here we investigated whether plaque obtained from supragingival (SupG) and tongue dorsum sites can serve as alternatives for monitoring CP-associated bacterial biomarkers. Using SubG, SupG, and tongue plaque DNA from 11 healthy and 13 diseased subjects, we sequenced V3 regions (~200 bases) of the 16S rRNA gene using Illumina sequencing. For the first time, this study demonstrates that SupG and tongue dorsum plaque can serve as alternative sources for detecting and enumerating known and novel bacterial biomarkers of CP. This finding is clinically important because, in contrast with SubG sampling that requires trained professionals, obtaining plaque from SupG and tongue sites is convenient, minimally-invasive, and offers a novel means to track CP-biomarker organisms during treatment outcome monitoring.

Biome: root:Host-associated:Human:Digestive system:Oral
Moving pictures of the human microbiome

Understanding the normal temporal variation in the human microbiome is critical to developing treatments for putative microbiome-related afflictions such as obesity, Crohn's disease, inflammatory bowel disease, and malnutrition. Sequencing and computational technologies however have been a limiting factor in performing dense timeseries analysis of the human microbiome. Here we present the largest human microbiota timeseries analysis to date, covering two individuals at four body sites over 396 timepoints. Results: We find that despite stable differences between body sites and individuals, daily fluctuations in an individual's microbiota appear characteristic. Additionally, only a small fraction of the total within body site microbial communities appears to be present across all time points, suggesting that if a core temporal microbiome exists it is small. Many more taxa appear to be persistent but non-permanent community members. DNA sequencing and computational advances described here provide the ability to go beyond infrequent snapshots of our human-associated microbial ecology to high-resolution assessments of temporal variations over protracted periods, within and between body habitats and individuals. This capacity will allow us to define normal variation and pathologic states, and for assessing responses to therapeutic interventions.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Bacteria in domestic water-storage containers with or without mosquito larvae

In this study, bacteria in domestic water-storage containers in an Indian village were analysed. Bacteria were identified by 16S rRNA gene amplicon sequencing and identified bacteria were correlated to the presence of vector mosquitoes.

Biome: root:Environmental:Aquatic:Freshwater:Drinking water
Microbial modulations using fecal microbiota transplantation improves cerebral amyloidosis, taupathy and gliosis in ADLPAPT transgenic mice.

Cerebral amyloidosis and severe tauopathy in the brain are key pathological features of Alzheimer's disease (AD), resulting in reactive gliosis and behavioral abnormalities of learning and memory. Despite a strong influence of the intestinal microbiota on neurodevelopment and neurological disorders, a functional link between the gut microbiota and AD remains unknown. Using a newly developed ADLPAPT transgenic mouse model that overexpresses human mutant APP/PS1 and mutant tau, we examined the impact of the gut microbiota on AD pathogenesis. The composition of the gut microbiota in ADLPAPT mice differed from that of healthy wild type (WT) mice; these differences appeared in early life of ADLPAPT mice before AD pathogenesis. Also, ADLPAPT mice showed low-grade inflammation, high gut permeability and metabolic endotoxemia. RNA-Seq analysis of colonic tissue revealed that aging-related tissue degeneration and macrophage dysfunction occurred earlier in ADLPAPT mice, compared to WT mice. Interestingly, frequent transfer of fecal microbiota from the WT mice into ADLPAPT mice ameliorated Aβ plaque, neurofibrillary tangle formation and glial reactivity, thereby improving learning behavior in recipient mice. In addition, abnormalities in colonic gene expressions were recovered by fecal microbiota transfer. These findings suggest that gut microbial dysbiosis and gut microbiota-derived factors contribute to the development of AD.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
sputum from patients with bronchiectasis pooled together and sequenced for the purpose of investigating the effect of erythromycin on antibiotic resistance carriage

Determining the effects of antimicrobial therapies on airway microbiology at a population-level is essential. Such analysis allows, for example, surveillance of antibiotic-induced changes in pathogen prevalence, the emergence and spread of antibiotic resistance, and the transmission of multi-resistant organisms. However, current analytical strategies for understanding these processes are limited. Culture- and PCR-based assays for specific microbes require the a priori selection of targets, while antibiotic sensitivity testing typically provides no insight into either the molecular basis of resistance, or the carriage of resistance determinants by the wider commensal microbiota. Shotgun metagenomic sequencing provides an alternative approach that allows the microbial composition of clinical samples to be described in detail, including the prevalence of resistance genes and virulence traits. While highly informative, the application of metagenomics to large patient cohorts can be prohibitively expensive. Using sputum samples from a randomised placebo-controlled trial of erythromycin in adults with bronchiectasis, we describe a novel, cost-effective strategy for screening patient cohorts for changes in resistance gene prevalence. By combining metagenomic screening of pooled DNA extracts with validatory quantitative PCR-based analysis of candidate markers in individual samples, we identify population-level changes in the relative abundance of specific macrolide resistance genes. This approach has the potential to provide an important adjunct to current analytical strategies, particularly within the context of antimicrobial clinical trials.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Responses in Methane Production, Rumen metabolism and Microbial Community in Tropical Adapted Cattle Fed 3-Nitrooxypropanol

The aim of this study was to investigate the effects of 3-nitrooxypropanol (3-NOP) and chloroform on methane and hydrogen production, rumen metabolites and microbial community structure in cattle fed a tropical roughage diet. Eight rumen-fistulated steers were fed a roughage hay diet (Rhode grass; Chloris gayana). Four animals received the antimethanogenic compound chloroform (1.6 g choloroform-cyclodextrin /100 kg LW) while the other four received 3-NOP (2.5 g 3-NOP/ animal/ day) for 21 days. Methane reduction compared with control period was similar for both treatments (30 to 38 %) with no differences of H2 expelled between controls and treatments. Daily weight gain was significantly increased when animals were treated with 3-NOP compared with chloroform and control. Regarding the rumen fermentation parameters increases in ammonia, acetate and branched chain fatty acids were observed with both compounds compared with the controls. Also, methylamines, alcohols and dimethylsulfone concentrations were significantly increased with the treatments compared with control. The rumen microbiome analyses revealed a similar profile for both treatments, with a shift in operational taxonomic units (OTUs) assigned to the Prevotellaceae and Campylobacteraceae family. Moreover, major archaeal OTUs associated with Methanobrevibacter and Methanosphaera were significantly affected to varying extents based on the inhibitory treatments compared to the control. Also the abundance of the Methanobrevibacter spp was decreased by 3-NOP and chloroform, while the Methanomassiliicoccaceae family was inhibited only by 3-NOP. The results suggest that despite the specific mode of action of 3-NOP on methanogens, inhibition of methanogenesis by both compounds resulted in similar responses in metabolism and microbial community structure in the rumen. We hypothesized that these changes were driven by the redirection of metabolic hydrogen by both treatments. Therefore results from previous publications using chloroform as an inhibitor of methanogenesis may be useful in predicting rumen microbiome and fermentation responses to 3-NOP.

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Ring Test for fecal DNA extraction protocols in pigs

The PiGutNet COST action organised a ring test to evaluate different DNA extraction protocols for porcine gut microbiota. A set of pooled samples were distributed to several laboratories along Europe and each group performed a set of extraction protocols. Extracted DNA was subjected to 16S sequencing (V3-V4 region) in an Illumina MiSeq instrument.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Characterization of microbial communities during a Ground Tire Rubber (GTR) desulfurization process

The present study aims at evaluating the effectiveness of bioreactor-based ground tire rubber (GTR) biodesulfurization process using two bacterial strains in two different bioreactors: i) Gordonia desulfuricans DSM 44462T, and ii) Rhodococcus sp. AF21875. Automated ribosomal inter-genic spacer analysis (ARISA), and High Throughput Sequencing of 16S rRNA gene amplicons were used to analyze samples collected from the bioreactors over time to detect the persistence of the inoculated bacteria within the autochthonous communities, and to compare communities in the bioreactors. Furthermore, the abundance of total bacteria (16S rRNA gene) and biodesulfurization potential (dszA) were estimated using qPCR, in the bioreactors and on GTR before the treatment. ARISA showed that G. desulfuricans DSM 44462T was able to persist, while there are no clear evidences of Rhodococcus sp AF21875 persistence into the bioreactor due to the presence of matching ARISA fragments in the untreated GTR. In both bioreactors, a high abundance of genus Gordonia and Rhodococcus was observed, with an increase of dszA copy numbers over time. Vulcanizates containing biodesulfurized GTRs showed better mechanical and rheological properties than an untreated GTR vulcanizate and even comparable with a natural rubber reference.

Biome: root:Engineered:Bioreactor
Blue Mountains Swamp Archaea

Blue Mountains Swamp Archaea

Biome: root:Environmental:Aquatic:Freshwater:Wetlands:Swamp
Microbiome of deep dentinal caries lesions associated with symptomatic irreversible pulpitis

This study used a next-generation sequencing approach to identify the bacterial taxa occurring in the advanced front of caries biofilms associated with pulp exposure and irreversible pulpitis.

Biome: root:Host-associated:Human:Digestive system:Oral
Distinct and Complex Bacterial Profiles in Human Periodontitis and Health  Revealed by 16S Pyrosequencing

Periodontitis has a polymicrobial etiology within the framework of a complex microbial ecosystem. With advances in sequencing technologies comprehensive studies to elucidate bacterial community differences have recently become possible. We used 454 sequencing of 16S rDNA to compare subgingival bacterial communities from 29 periodontally healthy controls and 29 subjects with chronic periodontitis. Amplicons from both the V1-2 and V4 regions of the 16S gene were sequenced, yielding 1,393,579 sequences. They were identified by BLAST against a curated oral 16S database, and mapped to 16 phyla, 106 genera, and 596 species. 81% of sequences could be mapped to cultivated species. Differences between health- and periodontitis-associated bacterial communities were observed at all phylogenetic levels, and UniFrac and PCoA showed distinct community profiles in health and disease. Community diversity was higher in disease, and 123 species were identified that were significantly more abundant in disease, and 53 in health. Spirochaetes, Synergistetes, and Bacteroidetes were more abundant in disease, while the Proteobacteria were found at higher levels in healthy controls. Within the phylum Firmicutes, the class Bacilli was health-associated, while the Clostridia, Negativicutes, and Erysipelotrichia were associated with disease. These results implicate a number of taxa that will be targets for future research. Some, such as Filifactor alocis and many spirochetes were represented by a large fraction of sequences as compared to previously identified targets. Elucidation of these differences in community composition provides a basis for further understanding the pathogenesis of periodontitis.

Biome: root:Host-associated:Human:Digestive system:Oral
Coral and human-associated micro-eukaryotes.

Coral and human-associated micro-eukaryotes. PIs Javier del Campo and Patrick J. Keeling.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
DNA isolation and sampling kits comparison

Intestinal microbiome plays a key role in shaping human health. In large cohort microbiome studies a comfortable sampling kit is crucial for good compliance of volunteers. The kit should also provide material of good quality for sequencing. Also, different DNA isolation kits provide varying results due to different lysis procedures. We compared multiple sampling and DNA isolation kits to assess their applicability in cohort studies.

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