SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Dietary intervention with a probiotic Bifidobacterium modulates dominant bacterial taxa in an enterotype-dependent fashion and normalizes butyrate levels in the gut of healthy adults

The modulation of the intestinal microbial ecosystem is considered to be the first target to establish probiotic efficacy in a healthy population.  A randomized, double-blind, crossover, placebo-controlled intervention study was conducted to determine the impact of the probiotic strain Bifidobacterium bifidum BB on the intestinal microbial ecology of adult healthy volunteers of both sexes. High-throughput 16S ribosomal RNA gene sequencing was used to characterize the fecal microbiota before and after four weeks of daily probiotic cells consumption.  This work shows that the intake of one billion live B. bifidum BB cells affects the relative abundance of dominant taxa in the fecal microbiota and modulates the fecal levels of butyrate. Specifically the relative abundance of family Prevotellaceae (P=0.041) and genus Prevotella (P=0.034) was significantly decreased, whereas the relative abundance of families Ruminococcaceae (P=0.039) and Rikenellaceae (P=0.010) was significantly increased. Although the overall composition of the microbiota was not affected, the dependency of the probiotic intervention on the enterotype has been highlighted observing the major effects of BB on microbiota composition in the Prevotella-dominated enterotype rather than the Bacteroides-dominated one. In addition, we observed a normalizing effect on fecal butyrate levels during the probiotic intervention. In conclusion, our study demonstrates that a single daily administration of B. bifidum BB can modify the human intestinal microbial ecology in healthy (not diseased) adults in a significant fashion. These findings can convey the need to reassess the notion of probiotics’ inability to influence the complex and stable intestinal microbial ecosystem of a healthy individual.

Biome: root:Host-associated:Human:Digestive system
Gut microbiota after dietary intervention

We analyzed the impact of a gut microbiota-targeted dietary intervention on the chronic inflammation underlying metabolic syndrome.  Human feces from central obese volunteers after whole grains, traditional Chinese medicinal foods, and prebiotics (WTP diet) dietary intervention.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Immune dysregulation associated with respiratory illness in elite athletes

ABSTRACTRationale: Elite athletes are susceptible to respiratory tract infection (RTI) leading to significant training and in-competition time loss.Objective: This prospective study aimed to understand RTI susceptibility in elite athletes through systematic clinical and immune phenotyping in a cohort of 121 elite Olympic athletes.Methods/measurements: We performed comprehensive clinical and respiratory function phenotyping to identify athletes highly susceptible and non-susceptible to RTI. Baseline T and B cell peripheral lymphotype phenotyping was performed by flow cytometry with findings validated by mass cytometry in repeat samples. Viral immune response was analysed through peripheral blood mononuclear cell (PBMC) stimulation assays. Further immune phenotyping was performed through 16s rRNA microbial sequencing of oropharyngeal swabs and global untargeted plasma metabolomic profiling. Findings were compared to non-athlete healthy controls.Main Results: Clinical phenotyping revealed 23 athletes as highly susceptible to RTI with 23 athletes non-susceptible. Immune phenotyping revealed that highly susceptible athletes had a significantly reduced peripheral memory T regulatory cell compartment compared to non-susceptible athletes and healthy controls. The PBMC immune response to viral ligands in highly susceptible athletes also revealed a pro-inflammatory skewed T helper 2 response. Analysis of the oropharyngeal microbiome revealed reduced bacterial biomass in elite athletes compared to healthy controls. Metabolomic profiling revealed significant differences in sphingolipid pathway metabolites between RTI highly susceptible, non-susceptible athletes and healthy controls.Conclusion: in this study we highlight a RTI-susceptible elite athlete endotype and show the presence of a persistent reduction in circulating memory T regulatory cells with further evidence of bacterial dysbiosis and metabolic dysregulation of the sphingolipid pathway.

Biome: root:Host-associated:Human:Respiratory system:Nasopharyngeal:Pharynx
Lung and gut microbiota profiling in intensive care unit patients: a prospective pilot study

Gut and lung microbiome play an important role in the host defense and can be predictive of clinical outcome in critically ill patients. However, the interplay between the gut and lung microbiota over time during severe illness is not fully understood and remains to be defined. This study aims to assess the longitudinal changes of the lung and gut microbiota in critically ill patients with and without infection.
Methods: We performed a prospective, observational cohort study in the intensive care unit (ICU) at Lausanne university hospital. A total of 73 endotracheal aspirates and 93 rectal-swabs were obtained from 38 critically ill adults who required mechanical ventilation. Lung and gut microbiota were characterized using bacterial 16S ribosomal RNA sequencing. The primary outcomes were the bacterial burden, community diversity and community composition of lung and gut microbiota. Secondary outcomes were ICU length of stay and ventilator-free days determined at 28 days after admission.
Results: We found a loss of alpha diversity during ICU stay which was more pronounced in infected patients than uninfected patients. The gut microbiome, more than the lung microbiome, became more dissimilar at discharge between uninfected and infected patients. The lung microbiome of patients who developed pneumonia was progressively enriched with Enterobacteriaceae and other Proteobacteria. Alpha diversity index in the lungs and Mogibacterium gut relative abundance predicted the length of mechanical ventilation.
Conclusion: Key features of the lung microbiome predicted outcome in critically ill patients. Lung and gut microbiome dysbiosis showed similar trends in critically ill patients, the interplay of gut-lung axis remains yet to be further evaluated.

Biome: root:Mixed
Bacterial microbiomes of lungs of male C57BL/6J mice optionally treated with high-fat diet to induce obesity

Briefly, male, 2-3-month old, C57BL/6J mice were treated with high-fat diet for 16 weeks to induce obesity. Age/sex-matched control mice were fed normal diet. DNA was isolated from lungs after sacrificing mice using Qiagen® DNeasy PowerSoil Kit. 16S PCR and library preparation were as per Illumina® Metagenomics Guide, using the guide's suggested V3-V4 primers; Kapa Biosystems® KAPA HiFi ReadyMix for PCR, with 35 cycles and 25 ng DNA input (when available; otherwise entire DNA sample). Indexing was with Nextera® XT v2 combinatorial dual index kit, 8 cycles of PCR. Negative controls used were for DNA extraction (three) and 16S PCR (no template; two). One positive control was ZymoBIOMICSTM Microbial Community DNA Standard, Zymo® cat. #6305). All libraries were sequenced together, at ~8 pM each, with 10% PhiX library spike-in, on Illumina® MiSeq with v3 reagents, to obtain 300 b paired-end reads.

Biome: root:Host-associated:Mammals:Respiratory system:Pulmonary system
EMG produced TPA metagenomics assembly of PRJNA340216 data set (Gut microbiota and metagenomic diversity of omnivore, vegetarian and vegan healthy subjects).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA340216, and was assembled with megahit v1.2.9. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system
Epipelagic bacterial communities of Canadian lakes

The NSERC Canadian LakePulse Network is a scientific initiative assessing environmental issues affecting Canadian lakes. Through multidisciplinary projects, LakePulse researchers use tools in lake science, spatial modelling, analytical chemistry, public health, and remote sensing to assess the status of over 600 lakes across various ecozones in Canada. The impacts of land-use, climate change and contaminants on lake health will be assessed to develop policies for better lake management.

Biome: root:Environmental:Aquatic:Freshwater:Lake
Dietary interventions rapidly affect gut microbiota diversity and function and the host lipid mediator response in a healthy population

This study investigates mechanisms regulating the interactions between the diet, host lipid mediators and the gut microbiome.

Biome: root:Host-associated:Human:Digestive system
Higher bacterial DNAemia can affect the impact of a polyphenol-rich dietary pattern on biomarkers of intestinal permeability and cardiovascular disease risk in older subjects

Scope. Aging is characterized by increased systemic low-grade inflammation, altered gut microbiota composition and enhanced intestinal permeability (IP). The intake of polyphenol-rich (PR) foods is proposed as a promising strategy to positively affect the gut microbiota-immune system-intestinal barrier (IB) axis. In this context, the MaPLE project was designed to test the hypothesis that a PR dietary pattern may preserve and/or improve IB function in older people. Here, we tested the hypothesis that the dietary intervention might have affected the presence of bacterial factors in the bloodstream of the older volunteers participating in the MaPLE trial. Methods and results. We quantified the presence of bacterial DNA in blood by qPCR targeting the 16S rRNA gene (16S; bacterial DNAemia). Blood DNA was  taxonomically profiled via 16S sequencing. We found that higher blood 16S levels are associated to higher BMI and markers of IP, inflammation and dyslipidemia. Subjects with higher bacterial DNAemia could benefit more from the PR-dietary intervention as demonstrated by the reduction of the markers related to IP, inflammation and dyslipidemia. Finally, we found that the bacterial DNA detected in blood mostly belong to γ-Proteobacteria, whose abundance significantly decreased after the PR-diet in subjects with higher bacterial DNAemia at baseline.Conclusion. This study shows that the efficacy of the PR diet could depend on bacterial DNAemia. Bacterial DNAemia may be a relevant marker to evaluate in order to test the efficacy of dietary interventions based on PR-foods in the older populations.

Biome: root:Host-associated:Human:Circulatory system:Blood
Gut microbiome of infants at 3, 6, and 12 months of age, with different dietary interventions. Raw sequence reads

We sought to determine how the infant gut microbiota evolve during infancy, in particular in relation to hygiene-related environmental factors, allergic and atopic disorders, and a randomized dietary intervention. Therefore, 288 healthy, exclusively breastfed infants were enrolled in a dietary intervention study from three months of age. 70 were followed up at six and twelve months to study the evolution of their gut microbiota, using 16S ribosomal RNA gene targeted amplicon sequencing.

Biome: root:Host-associated:Human:Digestive system
Gut microbiome composition after spices intervention

Short-term changes in dietary intake can induce changes in the gut microbiome. While various polyphenols and polyphenol-rich foods have been shown to modulate gut microflora to different extents, the acute influence of polyphenol-rich mixed spices, typically consumed, as curry meals worldwide has not been explored in a controlled setting. We, therefore, investigated the effects of a single serving of mixed spices Indian curry consumption, in two separate doses, on the gut microbiome in young, healthy, Singaporean Chinese males.This study has shown a single serving of mixed spices containing Indian curry can significantly modify certain commensal microbes, particularly in those people who do not regularly consume these spices.

Biome: root:Host-associated:Human:Digestive system
EMG produced TPA metagenomics assembly of PRJEB36528 data set (Real-time tracking of Tomato brown rugose fruit virus (ToBRFV) outbreaks in the Netherlands using Nextstrain.).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB36528, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants.

Biome: root:Host-associated:Plants
EMG produced TPA metagenomics assembly of PRJNA726355 data set (Responsiveness of rhizosphere bacteria assembled from manipulated soil microbiome suppressed Ralstonia solanacearum invasion).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA726355, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of PRJNA789467 data set (Disentangling the genetic basis of rhizosphere microbiome assembly in tomato (metagenomics part)).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA789467, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of PRJNA743714 data set (Survey of viruses of wild Solanum species in South Africa).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA743714, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Phylloplane.

Biome: root:Host-associated:Plants:Phylloplane
EMG produced TPA metagenomics assembly of PRJNA781422 data set (NGS study of Czech honey bee virome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA781422, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.

Biome: root:Host-associated:Insecta
EMG produced TPA metatranscriptomics assembly of PRJNA411946 data set (Illumina metagenomics RNA sequencing of the virome of wild bees in Belgium).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA411946, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.

Biome: root:Host-associated:Insecta
EMG produced TPA metagenomics assembly of PRJNA685398 data set (Honey bee gut microbiome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA685398, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.

Biome: root:Host-associated:Insecta:Digestive system
EMG produced TPA metagenomics assembly of PRJEB30847 data set (Shotgun metagenome sequence library from bulk soil and rhizosphere samples of wild and domesticated barley genotypes).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB30847, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of PRJNA494922 data set (Characterisation of the UK honey bee metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA494922, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.

Biome: root:Host-associated:Insecta
EMG produced TPA metatranscriptomics assembly of PRJNA395704 data set (Metatranscriptome_Rhizosphere_Barley Transcriptome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA395704, and was assembled with megahit v1.2.9, metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of PRJNA745270 data set (metagenomics sequence of manure and unmanured rhizosphere soil of tomato plant).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA745270, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of PRJNA763981 data set (SOYBEAN RHIZOSPHERE METAGENOMICS).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA763981, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of PRJNA653702 data set (Soil microbial communities from Nachusa Grasslands, Illinois, United States - SOY_050217 metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA653702, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizoplane:Soil.

Biome: root:Host-associated:Plants:Rhizoplane:Soil
Impact of a moderate caloric restriction on the gut microbiota composition and diversity of Italian obese patients

Although it is known that the gut microbiota (GM) can be modulated by diet, the impact of specific dietary interventions on its composition and diversity in obese patients remain to be ascertained. The present work aimed to evaluate the impact of a moderately hypocaloric Mediterranean diet on the GM of obese and overweight patients (OB). The GM of 23 OB patients (F/M= 20/3) was compared before and after 3 months of the nutritional intervention (NI). Fecal samples were analyzed by Illumina MiSeq sequencing of the 16S rRNA gene. After 3 months of NI, patients presented a statistically significant reduction of the body weight and fat mass, along with changes in the relative abundance of many microbial patterns. We observed an increased abundance in several Bacteroidetes taxa (i.e. Sphingobacteriaceae, Sphingobacterium, Bacteroides spp, Prevotella stercorea) and depletion of many Firmicutes taxa (i.e. Lachnospiraceae members, Ruminococcaceae and Ruminococcus, Veillonellaceae, Catenibacterium, Megamonas). In addition, the phylum Proteobacteria showed an increased abundance, while the genus Sutterella, within the same phylum, decreased after the intervention. Metabolic pathways related to membrane transport and cell motility showed a decreased expression after the NI.

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

The healthy Finnish controls were previously recruited as part of a dietary intervention investigating the effects of partly replacing animal proteins with plant proteins on health; the inclusion and exclusion criteria have been described elsewhere (PMID: 34837522). The fecal samples derived from 50 Finnish controls that were age-, sex- and BMI-matched with the Pakistani controls were included in the present study.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Modulation of dyslipidemic children fecal microbial ecosystem by dietary intervention with hazelnuts as source of unsaturated fatty acids.

The possibility to modulate the intestinal microbial ecosystem (IME) gains increasing interest due to its potential consequences on human health. The relative abundance of specific intestinal bacterial taxa may be potentially modulated through dietary interventions. The aim of this project is to describe the fluctuation of bacterial taxa and short chain fatty acids induced in fecal samples from 15 dyslipidemic children by hazelnuts consumption as the main source of unsaturated fatty acids.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Gut microbiota with the intervention of dietary oils

Dietary fats have important influences on the human body and the intestinal bacterial. This research investigated the effects of twelve common dietary fats intervention in mice, and the gut microbiota were analyzed. The dietary oils include olive oil, soybean oil, peanut oil, rapeseed oil, sunflower oil, palm oil, sesame oil, walnut oil, linseed oil, corn oil, camellia oil, and lard

Biome: root:Host-associated:Mammals:Digestive system
Baterial 16S rRNA amplicon sequencing data from Tengger desert

Bacterial amplicon libraries were prepared by amplifying the V3-V4 variable regions of the 16S rRNA genes with the primer pair of 341F and 805R. 23 soil samples, with or without agricultural reclamation, were collected from the Tengger desert. CON, the soil collected from the open field without agricultural management, the control; PLT, the soil collected from the site 10 cm apart from the planta; FTL, the soil collected from the site on the fertilization furrow, 50 cm apart from the planta.

Biome: root:Environmental:Terrestrial:Soil:Desert
EMG produced TPA metagenomics assembly of PRJNA772045 data set (Diversity, phylogenetic relationships and infectivity of viruses from tomato and surrounding weeds agroecosystems).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA772045, and was assembled with metaSPAdes v3.15.3, megahit v1.2.9. This project includes samples from the following biomes: root:Host-associated:Plants.

Biome: root:Host-associated:Plants
EMG produced TPA metagenomics assembly of PRJNA579886 data set (Apis Mellifera Virome raw sequence reads).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA579886, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.

Biome: root:Host-associated:Insecta
EMG produced TPA metagenomics assembly of PRJNA486916 data set (plant metagenome Raw sequence reads).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA486916, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants.

Biome: root:Host-associated:Plants
EMG produced TPA metagenomics assembly of PRJNA179134 data set (Tomato phyllosphere Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA179134, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Phylloplane.

Biome: root:Host-associated:Plants:Phylloplane
EMG produced TPA metagenomics assembly of PRJNA599270 data set (Honey bee gut virome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA599270, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.

Biome: root:Host-associated:Insecta:Digestive system