SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Development of an in-vitro, three stage model of the equine hindgut, inoculated with faeces.

An in-vitro model of the equine hindgut was developed to aid with the understanding of the bacteria that reside within the large intestine horses. This model utilises the bacteria in faeces to initiate bacterial populations, so that there is no need for invasive sample collection. These are the sequencing files from the sequencing of the 16S rRNA gene of samples from the gut model and gastrointestinal content that accompany the journal paper for the validation of our equine hindgut model.

Biome: root:Host-associated:Mammals:Digestive system
This study includes multiple samples simulating a human oral community with 13 bacterial species

This is a simulation study. Reads have been simulated using BBmap.

Biome: root:Engineered:Modeled:Simulated communities (microbial mixture)
Bacteria in Anopheles darlingi breeding sites in Manaus, the Amazon, Brazil

In this study bacterial community composition in Anopheles darlingi breeding waters was investigated. Four sites in Manaus Brazil were sampled by taking surface water. The water samples were DNA extracted and 16S rRNA genes were amplified and sequenced by MiSeq. The reads were then analysed and compared between the sites.

Biome: root:Environmental:Aquatic:Freshwater:Lotic
JoanneHStudy

JoanneHStudy

Biome: root:Mixed
Defining the microbial response to colitis through integrated host and microbiome profiling: Replication data set

This is a replication study of E-MTAB-3562  ( http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3562/ ) and  complementary transcription profiling data from the mouse hosts have also been deposited at ArrayExpress under accession number E-MTAB-3590 ( http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3590/ )

Biome: root:Host-associated:Mammals:Digestive system
Soil microbial response to organic disturbances

We employed a deep 16S amplicon sequencing approach to evaluate the recovery of the native soil microbiome after multiple disturbances caused by the application of organic vinasse residue, inorganic nitrogen (N) or a combination of both during the sugarcane crop-growing season.

Biome: root:Environmental:Terrestrial:Soil:Loam:Contaminated
Breast Cancer Metagenomics

Breast Cancer Metagenomics

Biome: root:Host-associated:Human:Skin
Metagenomic investigation of six depths from the anchialine Bundera sinkhole

Bundera sinkhole is an anchialine ecosystem located in north-western Australia. It has a highly stratified physico-chemical profile which is reflected in the microbial community structure of each strata. This study is the first to perform shotgun metagenomics on communities inhabiting a selection of depths: 2, 8, 17, 18, 22 and 28 m.

Biome: root:Environmental:Aquatic:Marine:Coastal
Microbial community in Trachea-oropharynx of Diabetic patient was compared with healthy controls and bacterial pneumonia

The aim of this study is to produce a healthy control metataxonomic data of bacterial community in tracheal-oropharynx using endotracheal tube which can be used for sputa studies which would involve various pathological conditions including bacterial infectious pneumonia. Furthermore, we also investigated samples from diabetic patients as infection-free risk group which is frequently requested patients in clinical environment.

Biome: root:Host-associated:Human:Respiratory system
Plant nutrient resource use strategies shape active rhizosphere microbiota through root exudation

Plant nutrient resource strategies have the potential to strongly influence plant-microorganism interactions, due to the competition between plants and microorganisms for soil nutrient acquisition and/or conservation. In the present study, we investigate whether plant nutrient use strategies could influence rhizosphere microbial activities via root exudation, and contribute to the microbiota diversification of active bacterial communities colonizing the root-adhering soil and inhabiting the root tissues.

Biome: root:Host-associated:Plants:Rhizosphere
Effect of short- and medium- chain fatty acids on gut microbiome of gilthhead sea bream (Sparus aurata)

This study aimed to evaluate the potential beneficial effects of SCFAs, used as a feed additive, on intestinal microbiota composition. For this purpose, a specific combination of short and medium chain fatty acids was tested in juvenile gilthead sea bream (Sparus aurata) fed a plant-based diet. The Illumina MiSeq platform for high-throughput amplicon sequencing of 16S rRNA gene, and QIIME pipeline were used to analyse and characterize the whole microbiome associated to both, feeds and S.aurata intestine. In summary our findings clearly indicated that SCFAs positively modulated the fish intestinal microbiota by increasing the number of beneficial lactic acid bacteria, namely Lactobacillus, and reducing Gammaproteobacteria that include several potential pathogenic bacteria.

Biome: root:Host-associated:Fish:Digestive system:Intestine
Antarctic Snow Algae 2014/15 16S and 18S Illumina Seq of snow algae communities around Ryder Bay, Antarctica

Antarctic Snow Algae 2014/15 16S and 18S Illumina Seq of snow algae communities around Ryder Bay, Antarctica. DNA extracted from green phase dominant and red phase dominant blooms on the snow surface. Field samples collected by Matt Davey (Univeristy of Cambridge, Department of Plant Sciences).

Biome: root:Environmental:Aquatic:Freshwater:Ice
There are 3 zooplankton samples from 3 different ponds, we collected sample and use the fresh samples to do DNA extraction directly, then mix them with adjustment guided by the number of species within each of them. At last, use Hiseq-2599 PE-150 to do NGS work

These 3 samples come from 3 different freshwater ponds. Our lab used the fresh sample to easy the DNA extraction pipeline.  Our primary goal of this experiment is testing the mitochondrial metagenomic strategy in zooplankton, for phylogenetic diversity and molecular ecology research

Biome: root:Environmental:Aquatic:Freshwater:Pond
Root Herbivory Shapes The Dynamic Of Oilseed Root And Rhizosphere Microbial Communities Through Chemical Changes

Interactions between plants and herbivorous insects are known to influence the evolution of plant defenses. Recent studies are unravelling the impact of microorganisms from the rhizosphere on such interactions and are gradually changing our perception, but the reverse effect has seldom been investigated. Herbivore attacks on plants could represent important perturbations for belowground communities. Our study aimed at determining how plant herbivory influences resistance and resilience of root and rhizosphere microbial community assemblages and whether potential changes in root metabolites and elemental compounds during herbivory can explain microbial community dynamics. We further questioned the influence of initial soil microbial diversity on these interactions. We conducted our study on a crop plant, oilseed rape (Brassica napus) and one of its major belowground pest, the cabbage root fly (Delia radicum). Soils of different initial microbial diversity were obtained through a removal-recolonization method. Root and rhizosphere sampling targeted different stages of the herbivore development: i) the hatching stage which corresponds to the initiation of herbivory, ii) the third larval instar which corresponds to the peak of herbivory and iii) adult emergence which corresponds to the end of herbivory. Bacterial communities were more affected by herbivory than fungi communities, which appeared very variable. Herbivory was associated to an increase of γ-Proteobacteria and of 5 bacterial dominant genera belonging to this phylum and Firmicutes. Root communities were more resilient than rhizosphere communities. This resilience was partly visible at the root metabolite and nutrient level, which reached back a more stable state at the end of herbivory. But herbivory also induced an increase of sulfur-containing compounds, as well as a couple amino acids and sugars. Three bacterial genera were positively correlated to most metabolites and negatively to nutrients. Further researches would help to identify the biological function of the microbial genera impacted by plant infestation and their potential implication in the plant defense.

Biome: root:Host-associated:Plants:Rhizosphere
Endocarditis due to Cardiobacterium hominis

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

Biome: root:Host-associated:Human
Effect of chewing gum on the oral microbiome

Characterisation of the human plaque microbiota before and after the administration of maltitol chewing gums or base chewing gums for two weeks. Study subjects are healthy individuals or patients with caries. Microbiome analysis is performed by 16S profiling of variable regions V1-V2 using Roche 454 GS-FLX sequencing.

Biome: root:Host-associated:Human:Digestive system:Oral
Oral and Vaginal Microbiota of Mother''s and Their Infant and Toddler Daughters

Using high-throughput sequencing of the 16s rRNA gene, we studied the oral and vaginal microbiome of girls less than 15 months of age and compared those sites to those of their mothers.

Biome: root:Host-associated:Human
Hydraulic retention time affects bacterial community structure in an As-rich acid mine drainage (AMD) biotreatment process

Arsenic removal consecutive to microbiological iron oxidation and precipitation is an effective process for treating As-rich acid mine drainage (AMD). Here, we  studied the effect of hydraulic retention time (HRT) - a key operating parameter that drives water treatment process performances - on water physico-chemistry, precipitate mineralogy, and bacterial community that develops in a bench-scale bioreactor treating AMD from the Reigous Creek (Carnoulès mine, France). System efficiency regarding Fe(II) and As(III) oxidation and As removal was monitored during 19 days. At the end, the mineralogy (As and Fe bearing phases) and bacterial communities in the biogenic precipitate were analyzed by X-ray absorption spectroscopy and high-throughput 16S rRNA gene sequencing, respectively. The percentage of Fe(II) oxidation (10–47 %) and As removal (19–37 %) increased with increasing HRT. Arsenic was trapped in the biogenic precipitates as As(III)-bearing schwertmannite and amorphous ferric arsenate, with a decrease of As/Fe ratio with increasing HRT. The bacterial community in the biogenic precipitates differed widely from that of the original feed water. Fe-oxidizing bacteria were dominant whatever the HRT but the proportion of Gallionella and Ferrovum genera shifted notably, from respectively 65 and 12 % at low HRT, to 23 and 51 % at high HRT. This shift was associated with physicochemical changes in pH, dissolved oxygen and Fe(III) concentrations in the treated water. A genetic potential for As(III) oxidation was evidenced through the detection of aioA genes at all HRT and As-oxidizing Thiomonas genera was always present as a minority member of the community but HRT did not appear to control As(III) oxidation in the present experiment. To our knowledge, this is the first evidence of the role of HRT as a driver of bacterial community structure in bioreactors exploiting the microbial Fe(II) oxidation process for AMD treatment.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Acid Mine Drainage
Immediate transcriptional response of microbial communities present in soil to the presence of toluene and Pseudomonas veronii inoculation

This study project for a complete characterization and interpretation of the functional response of local microbial communities present in different type soils upon contamination of toluene.

Biome: root:Environmental:Terrestrial:Soil:Oil-contaminated
Compilation of different anaerobic digester microbial communities analysed through 16S rRNA gene amplicon sequencing during continuous and long term operation for conversion of non pre-treated microalgae into biogas

Microbial communities have an indigenous and strong potential to acclimatize to different substrates. Anaerobic bioreactors can be used for not only treating several waste streams, but also converting them into valuable products including energy. The resulting product of anaerobic reduction of the organic matter is biogas, whose high content in methane provides it a high energetic potential. Among the different sources of organic matter that can be converted into energy are the microalgae. These microorganisms are a promising renewable source as a biofuel as their culture has a low environmental footprint. The main bottleneck for their use in full scale biogas-producing systems is their disruption, as their cell wall bodies are often hard to hydrolyze. This study focuses on the analysis of different anaerobic bioreactors treating microalgae biomass. Microbial analysis of the communities involved in this process provides valuable information about relevant microorganisms that enhance the microalgae disruption. Several phylotypes have been revealed in this study after taxonomic assignment of the open reference clusters found after 16S rRNA gene amplicon sequencing analysis.

Biome: root:Engineered:Biogas plant:Wet fermentation
Gut microbiome changes in IL10 -/- mice fed westernized diet

IL10-/- Balb/c mice (enterocolitis model) fed with a high fat, high sucrose or control diet for 16 weeks. Feces samples taken at start, then every 4 weeks. Monitored for colitis.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Development of an oral mucosa model to study host-microbiome interactions during wound healing

Crosstalk between the human host and its microbiota is reported to influence various diseases such as mucositis. Fundamental research in this area is however complicated by the timeframe restrictions during which microbe-host interactions can be studied in vitro. The model proposed in this paper consists of an oral epithelium and biofilm to study microbe-host crosstalk in vitro in non-infectious conditions up to 72 h. Microbiota derived from oral swabs were cultured on an agar/mucin layer and challenged with monolayers of keratinocytes grown on plastic or collagen type I layers embedded with fibroblasts. The overall microbial biofilm composition in terms of species diversity remained representative for the oral microbiome, whilst the epithelial cell morphology and viability were unaffected. Applying the model to investigate wound healing revealed a reduced healing of 30% in presence of microbiota, which was not caused by a reduction of the proliferation index (52.1–61.5) or a significantly increased number of apoptotic (1-1.13) or necrotic (32-30.5%) cells. Since the model allows the separate study of the microbial and cellular exometabolome, the biofilm and epithelial characteristics after co-culturing, it is applicable for investigations within fundamental research and for the discovery and development of agents that promote wound healing.

Biome: root:Host-associated:Human:Digestive system:Oral
16S amplicon sequence analysis of microbial communities in the oral cavity, stomach and gut

The V1 and V2 region of the 16S ribosomal RNA gene. 45 individuals (18 PPI-users and 22 PPI-nonusers) in total.

Biome: root:Host-associated:Human:Digestive system
MICROBIOLOGICAL AND BIOINFORMATICS ANALYSIS OF PRIMARY SJOGREN'S SYNDROME PATIENTS WITH NORMAL SALIVATION

Background: Reduced salivation is considered a major clinical feature of most but not all cases of primary Sjögren's syndrome (pSS). Reduced saliva flow may lead to changes in the salivary microbiota. These changes have mainly been studied with culture that typically recovers only 65% of the bacteria present.

Objective: This study was to use high throughput sequencing, covering both cultivated and not-yet-cultivated bacteria, to assess the bacterial microbiota of whole saliva in pSS patients with normal salivation.

Methods: Bacteria of whole unstimulated saliva from nine pSS patients with normal salivation flow and from nine healthy controls were examined by high throughput sequencing of the hypervariable region V1V2 of 16S rRNA using the 454 GS Junior system. Raw sequence reads were subjected to a species-level, reference-based taxonomy assignment pipeline specially designed for studying the human oral microbial community. Each of the sequence reads was BLASTN-searched against a database consisting of reference sequences representing 1,156 oral and 12,013 non-oral species. Unassigned reads were then screened for high-quality non-chimeras and subjected to de novo species-level operational taxonomy unit (OTU) calling for potential novel species. Downstream analyses, including alpha and beta diversities, were analyzed using the Quantitative Insights into Microbial Ecology (QIIME) pipeline. To reveal significant differences between the microbiota of control saliva and Sjögren's saliva, a statistical method introduced in Metastats www.metastats.cbcb.umd.edu was used.

Results: Saliva of pSS patients with normal salivation had a significantly higher frequency of Firmicutes compared with controls (p=0.004). Two other major phyla, Synergistetes and Spirochaetes, were significantly depleted in pSS (p=0.001 for both). In addition, we saw a nearly 17% decrease in the number of genera in pSS (25 vs. 30). While Prevotella was almost equally abundant in both groups (25% in pSS and 22% in controls), about a twofold increase in pSS of Streptococcus (28% vs. 17%) and Veillonella (26% vs. 12%) was detected. Prevotella melaninogenica was the major species in controls (13%) while Veillonella atypica and the Veillonella parvula groups dominated in patient samples (14 and 14%). The scarcity in bacterial species in pSS compared with controls was also demonstrated by alpha and beta diversity analyses, as well as read abundance depicted in a phylogenetic tree.

Conclusions: While Firmicutes was significantly higher in pSS patients than in controls, Synergistetes and Spirochaetes were significantly lower. The number of bacterial genera and species was also lower. These data showed that microbial dysbiosis is another key characteristic of pSS whole saliva which can occur independent of hyposalivation.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Temporal stability of the salivary microbiome and its association with salivary markers of oxidative stress

Salivary markers of oxidative stress are associated with periodontal status and are altered in patients with periodontitis or caries. It has been hypothesized that the composition of oral microbiome and the presence of specific bacterial species might be associated with some salivary markers of oxidative stress. The day to day variability of salivary markers of oxidative stress has been described. More detailed studies are needed for the assessment of salivary microbiome stability. The objective of the present study is to study temporal stability of saliva microbiome and to analyze its association to variations of salivary markers of oxidative stress.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Effect of oral immunization with the Ty21a typhoid vaccine on local and systemic immune responses and the gut microbiota in adults

The resident microbial consortia of the human gastrointestinal tract play an integral role in modulating the immune response both locally and systemically. However, detailed information regarding the correlates of protective immunity after vaccine administration in relation to the gastrointestinal microbiota is absent. In this study, the licensed oral attenuated typhoid vaccine Ty21a was administered in a clinical study to investigate whether oral immunization resulted in alterations of the microbiota and identify immune responses that may alter microbiota composition. The gastrointestinal microbiota was characterized from stool samples by pyrosequencing of the bacterial 16S ribosomal gene.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Human oral microbiome (root canal, apical abscess, and oral cavity) Targeted Locus

Background: Endodontic infections are a leading cause of oro-facial pain and tooth loss in western countries, and may lead to severe life-threatening infections.  These infections are polymicrobial with high bacterial diversity.  Understanding the spatial transition of microbiota from normal oral cavities through the infected root canal to the acute periapical abscess can improve our knowledge of the pathogenesis of endodontic infections and lead to more effective treatment. We obtained samples from the oral cavity, infected root canal and periapical abscess of 8 patients (5 with localized and 3 with systemic infections). Microbial populations in these samples were analyzed using next-generation sequencing of 16S rRNA amplicons. Bioinformatics tools and statistical tests with rigorous criteria were used to elucidate the spatial transition of the microbiota from normal to diseased sites. Results: On average, 10,000 partial 16S rRNA gene sequences were obtained from each sample.  All sequences fell into 11 different bacterial phyla.  The microbial diversity in root canal and abscess samples was significantly lower than in the oral samples.  Streptococcus was the most abundant genus in oral cavities while Prevotella and Fusobacterium were most abundant in diseased samples.  Root canal and periapical abscess microbiota were more similar to each other than to the oral cavity microbiota. Using rigorous criteria and novel bioinformatics tools, we found that Granulicatella adiacens, Eubacterium yurii, Prevotella melaninogenica, Prevotella salivae, Streptococcus mitis, and Atopobium rimae were over-represented in diseased samples.  Conclusions: We used a novel approach and high-throughput methodologies to describe microbial transition from normal to diseased oral sites in the same individuals    Eight patients with root canal infections (5 with systemic infections and 3 with localized infection) undergone treatment. Samples were obtained from three sampling sites in each patient. Oral (OS): samples collected from the subjects by rubbing 3 fine paper points against patient''s cheek mucosa, lateral boarder of the tongue and supragingival plaque at the contra lateral side away from the affected tooth. Root Canal (RC): samples collected from the root canal space of the diseased tooth using 3 fine paper points. Abscess Aspiration (AS): the area of the swelling was aspirated with a syringe that has a 16 gauge needle, and expressed into a sterile vial.

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