SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Colonic transit time relates to bacterial metabolism and mucosal turnover in the gut

Little is known about how colonic transit time relates to human colonic metabolism, and its importance for host health, although stool consistency, a proxy for colonic transit time, has recently been negatively associated with gut microbial richness. Here we show that colonic transit time in humans, assessed using radiopaque markers, is associated with overall gut microbial composition, diversity and metabolism. We find that a long colonic transit time associates with high microbial richness and is accompanied by a shift in colonic metabolism from carbohydrate fermentation to protein catabolism as reflected by microbial metabolites in urine, which results in a number of deleterious protein-derived metabolites. Additionally, longer colonic transit time correlates with metabolites reflecting reduced renewal of the colonic mucosa. Together, this suggests that high gut microbial richness does not per se imply a healthy gut microbial ecosystem, and contributes to the understanding of the aetiology of diseases where increased transit time is a risk factor.

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

The objective of this study was to investigate the general characteristics and environmental factors, such as dietary pattern and physical activities, of elderly women from Seoul and Jeju Island, and to characterize the composition of their fecal microbiota

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Analisi metagenomica ( ITS2) su suolo rizosferico di nocciolo

Piante di nocciolo di 4 anni di due varieta' diverse (Tonda di Giffoni e Mortarella) concimate con fertilizzante di sintesi (NPK), compost di sansa, zolfo e bentonite, zolfo e bentonite + compost di sansa

Biome: root:Environmental:Terrestrial:Soil:Crop
Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention

16s rRNA sequences from fecal samples from obese participants enrolled in the DIETFITS randomized clinical trial. Participants were randomized to either a low-carbohydrate or low-fat dietary intervention for 1 year. Fecal samples were collected prior to diet initiation and after 10 weeks of dietary intervention.

Biome: root:Host-associated:Human:Digestive system
Observational Study on the Diagnostic Evaluation of the Intestinal Microbiota of Patients With COVID-19. (EDIFICE)

In the context of the COVID-19 pandemic, the role of the gut microbiome is yet unknown. The aim of this trial is to evaluate the clinical contribution of the gut microbiome composition and diversity on the disease severity and to estimate the viral load in stool samples.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Dietary intervention of people with Parkinson's disease

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

"BioSolWest is a research project focused on assessing the soil biological health in the western region of Paraná, Brazil. Over a span of two years, we conducted a comprehensive study in 14 rural properties with clayey and sandy soils. Parameters such as carbon biomass, basal respiration, qCO2, microbial biomass nitrogen, and fungal and bacterial quantities were evaluated using epifluorescence microscopy. The project also involved metagenomic analysis (shotgun) to examine the microbial composition in the best and worst performing samples each year. Through this project, we aim to gain insights into the soil's biological characteristics and promote sustainable agricultural practices in the region."

Biome: root:Environmental:Terrestrial:Soil
PfSGS

Plant Growth-Promoting Rhizobacteria (PGPR) play a pivotal role in agriculture, enhancing plant growth, controlling pathogens, and offering environmentally-friendly alternatives to agrochemicals. Among them, Pseudomonas species are well-known inhabitants of the rhizosphere due to their competitive potential and adaptability to various environments. In this study, the aim was to investigate the effect of different doses of Pseudomonas fluorescens on soybean cultivation and its impact on the soil microbial composition and the soil-plant system.

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of PRJNA797778 data set (Vaginal Microbiome Research Consortium).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA797778, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Reproductive system:Vagina.

Biome: root:Host-associated:Human:Reproductive system:Vagina
CForBio.metagenome

This study collected 36 soil samples from 12 Chinese forests to investigate how soil microbes response to environmental changes.

Biome: root:Environmental:Terrestrial:Soil:Loam:Forest soil
Effects of Dietary Fiber Intervention on Gut Microbiota in Healthy People

Aim of this project was to investgigate the effect of fiber-rich diets in the human gut microbiome. The participants were asked to visit the study center sober and received the intervention meal or placebo meal. Additionally, a capsule with food coloring was administered. The intake of the dye stains the stool green which helps to associate collected stool samples and food intake. 16S rRNA gene was sequenced at ZIEL Core Facility Microbiome, Technical University Munich, Germany.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Human intervention study: anthocyanins supplementation and the impacts on gut microbiota

Dietary polyphenols are natural compounds occurring in plants, including foods such as fruits, vegetables, cereals, tea, coffee and wine. Epidemiological studies and associated meta-analyses strongly suggest that long term consumption of diets rich in plant polyphenols offer protection against development several chronic diseases. In this study, the long term consumption of anthocyanin-rich fruit juice impacts the gut microbiota enriching specific bacteria and increase the expression of important antioxidative markers.

Biome: root:Host-associated:Human:Digestive system
The effect of nutritional intervention with lactoferrin, galactooligosacharides and vitamin D on the gut microbiota composition of healthy elderly women

in the present study, we examined the effect of bovine lactoferrin, galactoligosacharides and vitamind D on the gut microbiota composition of 25 elderly women. Participants were distributed into two groups receiving either the dietary intervention (n=12) or the placebo treatment (n=13) for a total period of 9 weeks. During the first 3 weeks of the study, the intervention group consumed 1 g/day bLF, followed by 3 weeks of 1 g/day bLF and 2.64g/day active galactooligosaccharides (GOS), and 3 weeks of 1 g/day bLF, 2.64g/day GOS and 20 μg/day of vitamin D. The placebo group received maltodextrin, in matching dosages with the supplements administrated to the intervention group. Fecal bacterial composition was profiled using partial 16S rRNA gene amplicon sequencing and short-chain fatty acids analysis (SCFA) concentrations were determined with high liquid performance chromatography. Finally, the fecal levels of calprotectin, zonulin, and alpha-1-antitrypsin were measured, as markers of gastrointestinal barrier and inflammation.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Influence of gut microbiota on short-term low carbohydrate diet intervention for weight loss therapy

To date, much progress has been made in dietary therapy for obese patients. A low-carbohydrate diet (LCD) has reached a revival in its clinical use during the past decade with undefined mechanisms and debatable efficacy. Gut microbiota has been suggested to promote energy harvesting. Here, we propose that gut microbiota contributes to the inconsistent outcome under LCD. To test this hypothesis, patients with obesity or overweight were randomly assigned either to a normal diet (ND) or LCD group with ad libitum energy intake for 12 weeks. Using matched sampling, the microbiome profile at baseline and end-stage was examined. The relative abundance of butyrate-producing bacteria, Porphyromonadaceae Parabacteroides and Ruminococcaceae Oscillospira, was markedly increased after LCD intervention for 12 weeks. Moreover, within LCD group, participants with a higher relative abundance of Bacteroidaceae Bacteroides at baseline exhibited a better response to LCD intervention and achieved greater weight loss outcomes. Nevertheless, the adoption of an artificial neural network (ANN)-based prediction model greatly surpasses general linear model in predicting weight loss outcomes after LCD intervention. Therefore, gut microbiota served as a positive outcome predictor has the potential to predict weight loss outcomes after short-term LCD intervention. Gut microbiota may help to guide the clinical application of short-term LCD intervention to develop effective weight loss strategies.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Systems Biology of Lipid Accumulating Organisms

Characterization of microbial communities at the genomic, transcriptomic, proteomic and metabolomic levels, with a special interest on lipid accumulating bacterial populations, which are naturally enriched in biological wastewater treatment systems and may be harnessed for the conversion of mixed lipid substrates (wastewater) into biodiesel. The project aims to elucidate the genetic blueprints and the functional relevance of specific populations within the community. It focuses on within-population genetic and functional heterogeneity, trying to understand how fine-scale variations contribute to differing lipid accumulating phenotypes. Insights from this project will contribute to the understanding the functioning of microbial ecosystems, and improve optimization and modeling strategies for current and future biological wastewater treatment processes.  This BioProject contains datasets derived from the same biological wastewater treatment plant. The date includes metagenomes, metatranscriptomes and organisms isolated in pure cultures.

Biome: root:Engineered:Wastewater
EMG produced TPA metagenomics assembly of PRJNA217052 data set (Fiji COMP).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA217052, and was assembled with metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Mixed.

Biome: root:Mixed
EMG produced TPA metagenomics assembly of PRJEB28367 data set (Metagenomic Analysis of the Marine Sponge, Cinachyrella keukenthali: Insights into an Emerging Model Sponge).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB28367, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Porifera.

Biome: root:Host-associated:Porifera
Metatranscriptome24H1-3

Metatranscriptome, 24h of culture15NaNO3

Biome: root:Environmental:Terrestrial:Soil:Agricultural
EMG produced TPA metagenomics assembly of the Metagenomes and metatranscriptomes from the diffuse hydrothermal vents of Axial Seamount from 2013 (2013 'Omics from the diffuse hydrothermal vents of Axial Seamount) data set

The 2013 'Omics from the diffuse hydrothermal vents of Axial Seamount Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB7866. This project includes samples from the following biomes : Hydrothermal vents.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents:Microbial mats
EMG produced TPA metagenomics assembly of PRJNA777294 data set (Tracking Genomic Characteristics across Oceanic Provinces: Contrasting Early and Mature Plastic Biofilm Communities).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA777294, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.

Biome: root:Environmental:Aquatic:Marine
Human bronchoalveolar lavage, oral wash, nasal swab and saline/reagent control microbiota 16S rRNA gene amplicon sequencing

No studies to date have examined the relationship within an individual between bacterial communities along sites of the upper aerodigestive tract. Our objective was to perform an intra-subject and inter-site analysis to determine the contribution of two upper mucosal sites (mouth and nose) as source communities for the bacterial microbiome of the lower sites (lungs and stomach). Oral wash, bronchoalveolar lavage (BAL), nasal swab, and gastric aspirate samples were collected from 28 healthy subjects.

Biome: root:Host-associated:Human
Microbial community study upland peatland site, Northumberland

Comparative study of microbial communities between restored and degraded peatland sites from Whitelee Moor, Northumberland National Park

Biome: root:Environmental:Terrestrial:Soil
Humpback Whale Blow Metagenome Raw sequence reads

This Bioproject comprised the amplification of bacterial 16S rRNA gene derived from humpback whale blow in Hervey Bay, Queensland, Australia, with an aim to assess theinterannual difference and core microbiota.

Biome: root:Host-associated:Mammals:Respiratory system
Using drones to sample whale blow microbiota

We developed a low-cost multirotor UAV incorporating a sterile petri dish with a remotely operated ‘flip lid’ to sample whale blow with minimal disturbance to the whales. This design addressed several sampling challenges: accessibility; safety; cost, and critically, minimized the collection of atmospheric and seawater microbiota and other potential sources of sample contamination. We collected 59 samples of blow from northward migrating humpback whales off Sydney, Australia and used high throughput sequencing of bacterial ribosomal gene markers to identify putative respiratory tract microbiota. Model-based comparisons with seawater and drone-captured air demonstrated that our system minimized external sources of contamination and successfully captured sufficient material to identify whale blow-specific microbial taxa.

Biome: root:Host-associated:Mammals:Respiratory system
Whale blow 16S rRNA gene Raw sequence reads

This Bioproject comprised the amplification of the 16S rRNA gene in the blow of humpback, gray, blue and long-finned pilot whales off the coast of Eastern Australia, Mexico and in the Alboran Sea (Mediterranean). We aimed to compare the blow microbiota of two whale species with different levels of sociality, by analysing the alpha and beta diversity of the microbial communities and the core bacteria.

Biome: root:Host-associated:Mammals:Respiratory system
Marine metagenomes Metagenome

Marine amplicons from Australian marine (benthic and pelagic environments

Biome: root:Environmental:Aquatic:Marine
HoloFood Chicken Caecum Metagenome – extreme sizes batch

Metagenomic raw reads from selected HoloFood chicken caecum samples. Samples within this batch come from animals with weights at the extremes of the distribution curve. Samples selected for this batch were randomised among trials (feed), age, and breed to overcome batch effect.

Biome: root:Host-associated:Birds:Digestive system
hypersaline lake metagenome Genome sequencing and assembly

Cultivation of a vampire: 'Candidatus Absconditicoccus praedator'. We report the first stable cultivation of an association between the ultrasmall Candidate Phyla Radiation bacterium M39-6, which we named 'Ca. Absconditicoccus praedator', and its host Halorhodospira halophila M39-5, an obligately photosynthetic and anaerobic purple sulphur bacterium; we also carry out an in-depth characterization of their biology. Both were isolated from the hypersaline alkaline Lake Hotontyn Nur (Mongolia).

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
Potential of fecal microbiota for early stage detection of colorectal cancer

Several bacterial species have been implicated in the development of colorectal carcinoma (CRC), but CRC-associated changes of fecal microbiota and their potential for cancer screening remain to be explored. Here we used metagenomic sequencing of fecal samples to identify taxonomic markers that distinguished CRC patients from tumor-free controls in a study population of 156 participants. Accuracy of metagenomic CRC detection was similar to the standard fecal occult blood test (FOBT) and when both approaches were combined, sensitivity improved >45% relative to the FOBT while maintaining its specificity. Accuracy of metagenomic CRC detection did not differ significantly between early and late-stage cancer and could be validated in independent patient and control populations (N=335) from different countries. CRC-associated changes in the fecal microbiome at least partially reflected microbial community composition at the tumor itself, indicating that observed gene pool differences may reveal tumor-related host-microbe interactions. Indeed, we deduced a metabolic shift from fiber degradation in controls to utilization of host carbohydrates and amino acids in CRC patients accompanied by an increase of lipopolysaccharide metabolism.

Biome: root:Host-associated:Human:Digestive system
Genomics and transcriptomics of enrichment cultures of marine methanotroph

The Iheya North Knoll in the mid-Okinawa Trough is a methane-rich deep-sea hydrothermal field. To cultivate methane-oxidizing bacteria from the Iheya North field, a continuous flow-through reactor cultivation was conducted using gill tissue of Bathymodiolus japonicus as an inoculum. The enriched culture consisting mainly of methane-oxidizing bacteria was subjected to genetic analyses to investigate their metabolic characteristics.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents
EMOSE (2017) Inter-Comparison of Marine Plankton Metagenome Analysis Methods

This study includes experiments from the following five sequencing strategies: 1) Shotgun DNA sequencing; 2) Amplicon sequencing after 18S amplification by PCR using 1391F/EukB primer set. Library were constructed according to Illumina Library protocol without any sizing; 3) Amplicon sequencing after 16S amplification by PCR using 515F/926R primer set. Library were constructed according to Illumina Library protocol without any sizing; 4) Amplicon sequencing after 16S amplification by PCR using 515F/926R primer set. Library were constructed according to Illumina Library protocol with a sizing step selecting the 450-650 bp fragments; and 5) Amplicon sequencing after 16S amplification by PCR using 515F/926R primer set. Library were constructed according to Illumina Library protocol with a sizing step selecting the 650-850 bp fragments.

Biome: root:Environmental:Aquatic:Marine
Human Gut Microbiome in a Multiplex Family Study of Type 1 Diabetes Mellitus

Recent evidence from high-resolution molecular studies suggests links between microbial dysbiosis in the gastrointestinal tract and a number of complex chronic diseases including diabetes mellitus. The present study forms a pilot study for the larger Luxembourg-based Diabetes Multiplex Family Study (MUST). Within the pilot study, we investigate the interplay of the gastrointestinal microbiota, lifestyle and genetic background in an observational study of families with two or more individuals affected by type 1 diabetes mellitus. Faecal samples which have undergone comprehensive biomolecular extractions are currently analysed using a multi-omics approach. Anthropometric data, including demographics, medical history, health status, medication, and dietary habits of all study participants were collected and are integrated with molecular data.

Biome: root:Host-associated:Human:Digestive system
HoloFood Chicken Caecum+Ileum Metagenome – non-targeted metabolomics batch

Metagenomic raw reads from a subset of the HoloFood chicken caecum and ileum samples. This batch is the metagenomic counterpart of animals sampled for non-targeted metabolomics; all samples come from male animals under control treatment and aged 35 days.

Biome: root:Host-associated:Birds:Digestive system
SARS-CoV-2 genome sequencing and assembly from COVID-19 autopsy tissue specimens

Viral sequence analysis of tissue specimens from fatal COVID-19 cases collected for multiple studies.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
EMG produced TPA metagenomics assembly of PRJEB4352 data set (Shotgun Sequencing of Tara Oceans DNA samples corresponding to size fractions for protist).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB4352, and was assembled with megahit v1.2.9. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.

Biome: root:Environmental:Aquatic:Marine
EMG produced TPA metagenomics assembly of PRJEB6608 data set (Metatranscriptome sequencing of Tara Oceans DNA samples corresponding to size fractions for  prokaryotes.).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB6608, and was assembled with metaSPAdes v3.14.1 and megahit v1.2.9. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic.

Biome: root:Environmental:Aquatic:Marine
EMG produced TPA metagenomics assembly of PRJNA385854 data set (Marine metagenomes from the bioGEOTRACES project).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA385854, and was assembled with SPAdes v3.12.0 and megahit v1.2.9. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.

Biome: root:Environmental:Aquatic:Marine
lungbiome: Microbiome and cytokine signatures of bacterial pneumonia and tracheobronchitis

Lung transplant recipients routinely acquire infectious diseases such as bacterial pneumonia and tracheobronchitis. These two diseases are difficult to distinguish from each other, or from non-infectious airway colonization because there is considerable overlap in their signs and symptoms and respiratory culture findings. In this project, we explored the microbiome and cytokine signatures of lung transplant recipients with bacterial pneumonia, tracheobronchitis and non-infectious airway colonization.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Respiratory and intestinal dysbiosis induced by acuter LPS challenge

Systemic inflammatory response syndrome (SIRS) is a severe condition which may lead to multiple organ failure, shock and death. SIRS is often accompanied by intestinal dysbiosis. However, the mechanism, role and details of microbiome alterations during the early phase of acute SIRS are not completely understood. This project characterizes the dynamic alterations of both the respiratory and intestinal microbiome during the early phase of acute SIRS.

Biome: N/A
Respiratory mycobiome of critically ill COVID patients

To understand the role of the respiratory mycobiome in critically ill COVID-19 patients and the additional impact of a CAPA diagnosis. A multi-national study of 39 COVID-19 patients in intensive care units with and without CAPA. Respiratory mycobiome was profiled using ITS1 sequencing

Biome: N/A
CF airway microbiota within baseline clinical state

The study is focused on the variation in measures of CF airway microbiota within baseline clinical state, and factors that relate to this variation. The primary objective of this study was to quantify variation in measures of CF airway microbiota within periods of baseline clinical state. Additional objectives included identifying clinical variables associated with variation in measures of airway microbiota, determining within-subject changes in airway microbiota over time, and determining the impact of sampling interval on measures of microbiota.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung