SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Pilot study comparing yield from 16srRNA sequencing from frozen tissue vs. formalin-fixed paraffin-embedded (FFPE) tissue from the ileum and colon

Introduction: Next generation sequencing have made it possible to examine the microbiome of the GI tract without culture dependent methods. 16srRNA sequencing is currently the most frequently used sequencing method to examine the microbiome in the GI tract. As sequencing costs continues to decrease, thorough investigations of the microbiome in the GI tract is now easily accessible. However, several studies have shown large variation between the mucosal and fecal microbiome in humans. In inflammatory bowel disease (IBD), the mucosal microbiome is considered to be the most relevant for the pathogenesis. Mucosal tissue is only accessible during colonoscopy or surgery, and the availability of colon or ileum tissue is therefore the most important limiting factor in microbiome research in IBD. However the access to FFPE-tissue is immense compared to the availability of fresh tissue samples. Aims and methods: To compare the yield from 16srRNA sequencing on frozen tissue vs. FFPE from the same patient. Two patients scheduled for bowel resection because of cancer in the right hemicolon were included in this pilot study. Paired tissue biopsies were taken from the colon and ileum in both patients immediately after surgical bowel resection. One biopsy in the pair was frozen on liquid nitrogen and in -80 C and the other put on formalin for subsequent DNA isolation and sequencing analysis. DNA isolation were performed using Qiagen, QIAamp DNA mini kit for the frozen the tissue and Qiagen, QIAamp DNA FFPE tissue kit for FFPE tissue. 16srRNA sequencing, using Illumina Miseq platform were performed on both frozen tissue and FFPE tissue.

Biome: root:Host-associated:Human:Digestive system
Metagenome from an acidogenic thermophilic anaerobic reactor

Metagenome from an acidogenic thermophilic anaerobic reactor

Biome: root:Engineered:Bioreactor:Continuous culture
Pooled sputum DNA extracts from patients with severe asthma who received either placebo or azithromycin for 48 weeks

Pooled sputum DNA extracts from patients with severe asthma who received either placebo or azithromycin for 48 weeks (AMAZES trial)

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Yarwun Port Curtis Sediment Bacterial 16S rRNA (V6) 454 sequence

Samples were collected from the top 10cm of marine sediment from Port Curtis, Gladstone, Queensland, Australia. Sampling occurred over two tropical wet seasons (October to May) and two tropical dry seasons (June to September) between 2008 and 2010. Whole microbial DNA was extracted from subsamples and the V6 region of the bacterial 16S rRNA gene was sequenced by 454 pyrosequencing.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Comparison of DNA extraction methods for oral bacterial 16S rRNA-V4 sequencing using healthy Japanese adult samples

The project contains bacterial partial 16S rRNA V4 sequencing data of supragingival plaque samples pooled from multiple teeth of 12 healthy Japanese adults. The partial 16S rRNA V4 region (typically 259 base pairs) was PCR-amplified and sequenced using the Illumina MiSeq platform. Paired-end sequencing and dual index tag techniques were applied. All relevant research protocols and procedures were approved by Ethics Committee of Tohoku University School of Medicine, Sendai, Japan. All subjects provided written informed consent.

Biome: root:Host-associated:Human:Digestive system:Oral:Supragingival plaque
oxidative stress Methanoperedens nitroreducens

‘Candidatus Methanoperedens nitroreducens' is an archaeon that couples the anaerobic oxidation of methane to nitrate reduction. In this study we investigated the effect of oxygen exposure on an enrichment culture dominated by ‘Ca. M. nitroreducens' (83% enrichment). In batch activity assays supplemented with 5% oxygen in headspace we monitored the methanotrophic activity of both anaerobic and aerobic methanotrophs and investigated the gene expression of ‘Ca. M. nitroreducens'.

Biome: root:Engineered:Bioreactor:Continuous culture
Metagenomic sequencing of water samples

Amplicon sequencing of urban water samples by Illumina technology

Biome: root:Engineered:Wastewater
Mucosal microbiome and 5-ASA concentration in the left hemicolon and rectum in patients with quiescent ulcerative colitis

Introduction: 5- aminosalicylic acid (5-ASA) is the mainstay of treatment of patients with ulcerative colitis (UC). 5-ASA acts locally in the colonic mucosa and mucosal concentrations of 5-ASA are inversely correlated to disease activity. Previous studies have found large inter-individual variations in mucosal 5-ASA concentrations. Several explanatory models have been proposed, but is remains unintelligible why some patients have high 5-ASA concentrations, while others have low. Previous findings suggest that treatment with Asacol (pH-dependent release formulation) yields higher mucosal 5-ASA concentrations than Pentasa (time-dependent release formulation). The mucosal bacterial composition and fermentation products, such as short chain fatty acids, greatly impact pH-value in the colon and might therefore be correlated to 5-ASA concentration. Aim and method: In this cross-sectional non-randomized study, we have measured mucosal concentration of 5-ASA and its inactive metabolite acetyl-5-ASA (Ac-5-ASA) in the left hemicolon and rectum in patients with quiescent UC taking Mezavant, Asacol or Pentasa. Patients with quiescent UC using oral mesalazine monotherapy in the maximal dose recommended by the manufacturers (4.0-4.8g o.d.) were included. Eight hours after ingestion of mesalazine, patients underwent blood sample collection, followed by bowel preparation with enema and sigmoidoscopy. A total of six mucosal biopsies were collected 10, 25 and 40 cm from the anal verge. 5-ASA and Ac-5-ASA concentrations were measured in five biopsies and serum by high-performance liquid chromatography. The mucosal and fecal microbiome was explored using 16srRNA sequencing. Disease activity was assessed by Mayo score (MS), Geboes histological score (GS) and measurement of plasma ESR, CRP, blood leukocytes and fecal calprotectin concentrations.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Sigmoid colon
Oral bacterial 16S rRNA-V4 sequencing of three Japanese adults sampled in multiple time points during a day

The project contains bacterial partial 16S rRNA sequencing data of 81 supragingival plaque samples of incisor, premolar, and molar teeth. Samples were taken from three adult Japanese males for multiple time points during a day (forenoon, evening, and night for three days). Partial bacterial 16S rRNA V4 region (typically 258 or 259 base pairs) was amplified and sequenced based on the Illumina MiSeq paired-end read sequencing protocol. Ninety-six combinations of dual index tags (Illumina D-series) were utilized. The project also contains data of four sequencing replicates for a part (4/81) of DNA samples by an independent sequencer run. All relevant research protocols and procedures were approved by Ethics Committee of Tohoku University School of Medicine, Sendai, Japan. All subjects provided written informed consent.

Biome: root:Host-associated:Human:Digestive system:Oral:Supragingival plaque
Temporal dynamics of bacterial and fungal communities during the infection of Brassica rapa roots by the protist Plasmodiophora brassicae

This study was conducted to assess the temporal dynamics of rhizosphere and root microbiota during the development of Plasmodiophora brassicae in root hairs of Chinese cabbage (Brassica rapa subsp. pekinensis). After inoculation (or not) with P. brassicae, disease was assessed at five sampling date during the vegetative stage of plant growth. The first symptom of clubroot disease appeared 14 days after inoculation (DAI) and increased drastically between 14 and 35 DAI. The structure of microbial communities associated to rhizosphere soil and root samples was assessed at each sampling date through sequencing of bacterial (16S) and fungal (18S) molecular markers. Proteobacteria and Bacteroidetes bacterial phyla dominate the Chinese cabbage rhizosphere and root microbiota. Rhizosphere bacterial communities also contained Actinobacteria and Firmicutes to a higher extend than in the roots. Moreover, a dramatic shift of fungal communities of non-inoculated plants occurred between the two last sampling dates, especially in plant roots but also in their rhizosphere. Most of Ascomycota fungi dominant until then were replaced by a fungus assigned to the Chytriomycota phylum. Parasitic invasion by P. brassicae disrupted the rhizosphere and root-associated community assembly during the vegetative stage of plant growth. These effects occurred late during the secondary cortical infection stage of clubroot disease in plant roots. At this stage, Flavisolibacter and Streptomyces in the rhizosphere, and Bacillus in the roots, were drastically less abundant upon parasite invasion. Rhizosphere of plants colonized by P. brassicae was significantly more invaded by the Chytriomycota fungus, which could reflect a mutualistic relationship in this compartment between these two microorganisms.

Biome: root:Host-associated:Plants:Rhizosphere
A practical introduction to microbial molecular ecology through the use of iChips

In the context of anti-microbial resistance as one of the most serious issues faced globally by health providers, we explored a practical introduction to molecular microbial ecology. We designed field work and practical experiments for third year members of a four year undergraduate Masters Programme in which the students employed traditional and novel isolation techniques to identify antimicrobial activities from soil dwelling microorganisms. Students gained experience in isolating DNA from complex microbial communities, amplifying 16S rRNA genes and applied richness / diversity indices as well as principal coordinates analyses to the interpretation of the data they obtained from high throughput sequencing. Our results confirmed that isolation chips (iChips) facilitate the growth of a greater diversity and different species subset from the complex soil microorganism community than traditional plate spreading techniques. However, rarefaction of 16S rRNA amplicon sequencing data showed that the majority of observed species in soil remain unculturable by current methods. Based on the written reports produced by the students carrying out the work, we concluded that the described protocols are robust and informative, that these activities provide a good practical introduction to the theories and practice of molecular ecology and can be easily deployed to groups of six or more students in a cost-effective manner.

Biome: root:Environmental:Terrestrial:Soil:Loam
Coix seed helps mice to lose weight and it is associated with the regulation of the gut microbiota.

Coix seed is commonly used as food material and herbal medicine in Asian countries. Evidence showed it has hypolipidemic activity, and can decrease the level of serum lipid. But whether Coix seed takes effect by modulating the composition of the gut microbiota remains unknown. In our study, 44 mice were randomly allocated to three groups, receiving Chow, high fat, and high fat added Coix seeds diet for 5 weeks, respectively. Mice who received the high fat diet demonstrated significant increasing in body weight and fat mass compared with the Chow groups. Complementing Coix seed could help mice lose weight, and reduce the fat mass and total cholesterol. Through sequencing of the V4-V5 regions of 16S rRNA genes in fecal samples, we found the gut microbiota had a distinct change in HF diet group comparing to Chow group. Coix Seeds can regulate the abundance of serveral bacteria, which are probably contributed to losing weight and preventing diabetes.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
It was verified the impact of irrigation treatments (wet, optimal, dry and very dry) and three potato cultivars on soil microbial community.

The water management was classified into four soil water matric potential mean: -15 kPa (Wet), -25 kPa (Optimal), -30 kPa (Dry) and -45 kPa (Very Dry). The three potato cultivars used were Goldrush (most cultivated mid-season variety in Quebec), Envol (popular early variety), and Red Maria (mid-late to late variety).

Biome: root:Environmental:Terrestrial:Soil:Crop
Antibiotic-induced acceleration of Type 1 diabetes alters intestinal innate pathway maturation

The early-life intestinal microbiota plays a key role in shaping host immune system development. We found that a single early-life antibiotic course (1PAT) accelerated Type 1 diabetes (T1D) development in male NOD mice. The single course had strong and persistent effects on the intestinal microbiome, selecting for a highly metabolically active metagenome, with altered hepatic and serum metabolites. The exposure led to differential ileal and hepatic histone modification, and perturbed ileal gene expression, strongly affecting the normal maturational pattern. Earliest effects involved specific genes in innate immune pathways, with later effects on adaptive immunity. Microbiome analysis revealed four potential T1D-protective taxa and four T1D-accelerating taxa, and a network linking specific microbial taxa to differences in ileal gene expression was identified. This simplified animal model has improved understanding of the mechanisms by which early-life gut microbiome perturbations alter host intestinal responses, contributing to T1D.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine
Investigation of the microbial diversity and metabolic function of microorganisms in dust as compared to soil in dust source regions.

Deserts are known to be major sources of dust, which is transported as aerosols across regional and even transcontinental scales. Dust has been shown to have negative effects on human well-being, as it has been associated with inducing respiratory, allergic, and cardiovascular diseases. Dust particles are known to serve as carrier for microorganisms, such as fungal spores, viruses, bacteria, archaea, and protozoa. The aim of this study is to examine the microbial composition and metabolic potential of filter-, soil-dust-, and biocrusts samples collected on Barbados, on Cyprus, Sahara desert and during Air Quality and Climate Change in the Arabian Basin (AQABA) ship expedition leading through the Mediterranean Sea and around the Arabian Peninsula.

Biome: root:Environmental:Terrestrial:Soil
differential metatranscriptomics of bulk soil and compost

3 bulk soil samples and 3 compost samples have been sequenced to determine the functional differences of the microbial communities.

Biome: root:Environmental:Terrestrial:Soil:Loam
in situ v. ex situ biogas upgrading

This study compares the upgrading communities between in situ and ex situ operation during increasing flow rates of H2 and CO2, showing that the presence (in situ) or absence (ex situ) of feedstock strongly delineates these communities. This in turn governs community response to rates of H2 supply, with in situ communities showing a far greater susceptibility to inhibition, population flux, and displacement of methanogens (Methanothermobacter). In comparison, ex situ upgrading communities saw little change at much higher H2 flow rates, and instead encouraged larger populations of closely related methanogens (Methanobacterium). These large ex situ hydrogenotrophic populations were significantly associated with smaller, ‘satellite' populations of hydrogen-producing bacteria, indicating a thermophilic upgrading community centred on biogas metabolism.

Biome: root:Engineered:Bioreactor:Continuous culture
Microbiota of Citrus sinensis plants affected by Citrus Decline Disease

Citrus Decline Disease was recently-reported affecting several citrus species in Iran when grafted on a local rootstock variety, Bakraee. Preliminary studies found ‘Candidatus Phytoplasma aurantifoliae' and ‘Candidatus Liberibacter asiaticus' as putative etiological agents, but were not ultimately able to determine which one, or if an association of both, were causing the disease. The current study has the aim of characterizing the microbiota of citrus plants that are either asymptomatic, showing early symptoms, or showing late symptoms through amplification of the V1-V3 region of 16S rRNA gene using an Illumina sequencer in order to (i) clarify the etiology of the disease, and (ii) describe the microbiota associated to different symptom stages.

Biome: root:Host-associated:Plants
Antibiotic manufacturing effluent enriches resistance genes and alter the structure of microbial communities

In this work, we have examined sludge samples from a Croatian azithromycin production plant using shotgun metagenomics, to better understand the full diversity of known resistance genes, mobile genetic elements and the impact on taxonomic composition caused by extensive antibiotic selection pressures. We compare this data to sludge from a wastewater treatment plant receiving municipal sewage. We find that the sludge from pharmaceutical production harbors around three times as much resistance genes as the municipal sewage sludge, with particularly large enrichments of aminoglycoside, amphenicol and sulfonamide resistance genes. The findings highlight that antibiotic production does contribute to the development of antibiotic resistance also in European settings and indicate a large potential for co-selection of resistance genes to a variety of antibiotic classes.

Biome: root:Engineered:Wastewater:Activated Sludge
Investigating short- and long-term genome evolution of commensal bacteria using the Oligo-MM community

The functionality of the mammalian intestinal ecosystem is influenced by various host and external factors, affecting the composition, gene expression and evolution of the microbial community over time. In particular, bacterial genome evolution is mostly driven by small additive mutations and horizontal gene transfer (HGT), events which are normally selected for in the course of environmental changes.We have previously established a defined consortium of 12 cultivable murine isolates (Oligo-MM) in a gnotobiotic mouse model to study the role of the gut microbiota and its association with diseases. We now aim to use this model for investigating short- and long-term genome evolution of commensal bacteria, and for delineating microbiota-associated functions and metabolic potential in their natural host.

Biome: root:Host-associated:Mammals:Digestive system
Environmental DNA profiles capture the influence of treated wastewater effluent on water column bacterial composition in headwaters of the Rhine River

Rivers receive a wide range of micro-pollution from wastewater treatment plants (WWTPs). WWTP effluent adds nutrients and chemicals into streams and follows well-documented hydrological mixing patterns based on dilution. However, the hydrological mixing of planktonic microbial communities is less well-documented. We tested whether environmental DNA (eDNA) sampled from 24 headwater streams and WWTP effluent flowing into the economically important Rhine River followed predicted dilution patterns and characterized the bacterial communities using 16S rRNA amplicon sequencing. Total eDNA recovered from the effluent lacked a quantitative mixing relationship with receiving streams, suggesting that eDNA is influenced by more than hydrological dilution. The downstream 16S profiles highlighted a decrease in Cyanobacteria and Proteobacteria taxa and an increase in Firmicutes and TM7 taxa compared to the upstream. All resulting sequences were assigned in silico habitat descriptors, and these habitat descriptors matched expected values for the effluent (e.g., “wastewater”) and upstream (e.g., “freshwater lake”, “river”) for most streams, whereas the downstream habitat descriptors were a mixture between the two. Thus, we demonstrate that effluent alters water column bacterial communities in receiving streams. This qualitative alteration of bacterial communities warrants further investigation into how bacterial pollution from WWTPs affects ecosystem function and stress.

Biome: root:Engineered:Wastewater:Industrial wastewater
Porcupine Seabight 16S Ribosomal RNA

Porcupine Seabight 16S Ribosomal RNA

Biome: root:Environmental:Aquatic:Marine:Sediment
Prospecting of extreme microbial ecosystems associated to minerals (microbialites, microbial mats and endoevaporites) in Puna, Wetlands and Salars of Argentina, Chile and Bolivia

Puna wetlands and salars are unique extreme environments since they are located in high altitude saline deserts, largely influenced by volcanic activity. UV radiation, arsenic content, high salinity, and low dissolved oxygen content, together with extreme daily temperature fluctuations and oligotrophic conditions comprise an environment that recreates the early Earth and even extraterrestrial conditions.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Saline
This is a repeat of previous analysis but with human reads filtered out.

This is a repeat of previous analysis but with human reads filtered out.

Biome: root:Mixed
Metatranscriptome sequencing from  samples corresponding to size fractions for protists.

Metatranscriptome sequencing from  different depths to retain small and large cell size (Protists Organisms). The RNA was extracted and submitted to high throughput sequencing.

Biome: root:Environmental:Aquatic:Marine
In-planta sporulation mediates host-partner interactions in the alder-Frankia-ectomycorrhizae tripartite symbiosis

In-planta sporulation mediates host-partner interactions in the alder-Frankia-ectomycorrhizae tripartite symbiosisfastq files from metabarcoding on nifH gene.primer GCIWTHTAYGGIAARGGIGGIATHGGIAAATIGCRAAICCICCRCAIACIACRTCnifH barcode  TATGTCAG TATGTCAGSTR1barcode  TATGTCAG TAGTCGCASTR2barcode  TATGTCAG TACTATACSTR3barcode  TATGTCAG ACTAGATCSLB1barcode  TATGTCAG GATCGCGASLB2barcode  TATGTCAG CGCTCTCGSLB3barcode  TAGTCGCA ACACACACSOR1barcode  TAGTCGCA ACAGCACASOR2barcode  TAGTCGCA GTGTACATSOR3barcode  TAGTCGCA TATGTCAGSFF1barcode  TAGTCGCA TAGTCGCASFF2barcode  TAGTCGCA TACTATACSFF3barcode  TAGTCGCA ACTAGATCSTO1barcode  TAGTCGCA GATCGCGASTO2barcode  TAGTCGCA CGCTCTCGSTO3barcode  TACTATAC ACACACACSXF1barcode  TACTATAC ACAGCACASXF2barcode  TACTATAC GTGTACATSXF3barcode  TACTATAC TATGTCAGAgTR1barcode  TACTATAC TAGTCGCAAgTR2barcode  TACTATAC TACTATACAgTR3barcode  TACTATAC ACTAGATCAgLB1barcode  TACTATAC GATCGCGAAgLB2barcode  TACTATAC CGCTCTCGAgLB3barcode  ACTAGATC ACACACACAgXF1barcode  ACTAGATC ACAGCACAAgXF2barcode  ACTAGATC GTGTACATAgXF3barcode  ACTAGATC TATGTCAGAgFF1barcode  ACTAGATC TAGTCGCAAgFF2barcode  ACTAGATC TACTATACAgFF3barcode  ACTAGATC ACTAGATCAiTR1barcode  ACTAGATC GATCGCGAAiTR2barcode  ACTAGATC CGCTCTCGAiTR3barcode  GATCGCGA ACACACACAiLB1barcode  GATCGCGA ACAGCACAAiLB2barcode  GATCGCGA GTGTACATAiLB3barcode  GATCGCGA TATGTCAGAiXF1barcode  GATCGCGA TAGTCGCAAiXF2barcode  GATCGCGA TACTATACAiXF3barcode  GATCGCGA ACTAGATCAiFF1barcode  GATCGCGA GATCGCGAAiFF2barcode  GATCGCGA CGCTCTCGAiFF3barcode  CGCTCTCG ACACACACAvFF1barcode  CGCTCTCG ACAGCACAAvFF2barcode  CGCTCTCG GTGTACATAvFF3barcode  CGCTCTCG TATGTCAGAvXF1barcode  CGCTCTCG TAGTCGCAAvXF2barcode  CGCTCTCG TACTATACAvXF3

Biome: root:Host-associated:Plants