SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Effect of Yoga and low-FODMAP diet in the intestinal microbiota of patients with IBS

Background & Aims: Irritable bowel syndrome (IBS) is unlinked to a pathophysiology, but lowering stress (e.g. by yoga) or a low-carbohydrate diet (i.e. low-FODMAP diet, LFD) relief symptoms. The effects of yoga or LFD intervention on the gut microbiota in patients with irritable bowel syndrome was examined for correlations between both treatment options.Methods: Fifty-nine patients with IBS undertook a single-blind, randomized controlled trial involving a yoga or LFD intervention. Bacterial abundance was analyzed by 16S rRNA gene amplicon sequencing at baseline and after 12 weeks using operational taxonomic units (OTUs). Results: LFD resulted in reduction of the overall relative abundance of Firmicutes, especially of the genus Blautia. This was matched by an increase in the relative abundance of bacteria belonging to the phylum Bacteroidetes. This observation appears also as a weak, but not statistically significant trend in the yoga group. Few OTUs showed a similar response to yoga and LFD. The most pronounced was a decrease observed in the family Lachnospiraceae, namely Eubacterium hallii, Blautia wexlerae and Fusicatenibacter saccharivorans.Conclusions: This study suggests that both, yoga and LFD can change the microbiota for some OTUs in a similar way. The reduction in the abundance of Firmicutes in LFD might unfold its effects through a direct change in the gut bacteria composition. In constrast, yoga might indirectly act on the microbiome through the parasympathetic nervous system, which paralleled the effects of LFD for some Lachnospiraceae species. The underlying mechanism of both interventions are open for future research.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Raw sequences of mock communities sequenced by the Langille Lab.

All of the raw sequence data for the mock communities that have been sequenced by the Langille Lab.

Biome: root:Engineered:Modeled:Simulated communities (sequence read mixture)
Metagenomic Shotgun of EPS-cultivated microorganisms

Metagenomic Shotgun of Microorganisms grown in culture medium with acidobacterial EPS as sole carbon source.

Biome: root:Engineered:Lab enrichment:Defined media
Metagenomic analysis of the minke whale (Balaenoptera acutorostrata) gut microbiome

No maximum limits (ML) for e.g. PCB or Hg in whale products exists in Europe, possibly due to the embargo on whale products by the EU in the beginning of the 80's. European and Norwegian ML for PCB6 in marine oils, which may be used as a proxy indicator ML for blubber, is 0.2 mg/kg fat, and the ML for Hg is 0.5 mg/kg wet weight for fillets of most fish. Norwegian whale is legally exported to other whale hunting nations like Japan, which have ML for both Hg and total PCB, which are 0.4 mg/kg and 0.5 mg/kg, respectively. Microbes are central players in geochemical cycles, including cycling of metals and other elements, which may affect seafood safety by e.g. by mercury methylation. Microbial analyses of intestinal microbiota may reveal the potential for transformation/methylation of mercury (Hg) to methyl mercury (MeHg).

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine
Bulk and rhizosphere soil microbial communities in wheat fields

The study aims to investigate functional activities of soil microbial communities surrounding wheat crops that are associated with higher yields. Two wheat fields were sampled for bulk and rhizosphere soil at three different wheat growth and development stages (March, June and July 2017). We used 16S rRNA sequencing to identify and compare bacteria present in these soil samples.

Biome: root:Environmental:Terrestrial:Soil:Loam:Agricultural
microbiome profile of fungivorous thrips Hoplothrips carpathicus

microbiome profile of fungivorous thrips Hoplothrips carpathicus

Biome: root:Host-associated:Insecta:Digestive system
Metagenome assembly of a bacterial community from an acidogenic thermophilic anaerobic reactor

Metagenome assembly of a bacterial community from an acidogenic thermophilic anaerobic reactor

Biome: root:Engineered:Bioreactor
Effect of infection with and treatment of sensitive and resistant strains of Teladorsagia circumcincta on the ovine intestinal microbiota

The pathogenic nature of gastro-intestinal round worms has a significant effect on absorption in the gut. However, quantifying precisely the dynamics of the microbial community has not been possible until the advent of culture-independent 16S rDNA-based sequence analysis and whole genome shot gun high throughput sequencing.  In this study, Illumina MiSeq technology was used to sequence amplicons of the V4 region of the 16S rRNA gene, to determine the inherent variability of the gut microbiota between samples obtained from two different areas of the intestinal tract (rectal and terminal ileum) in six identically treated sheep.  The same approach was used to further define the effect of infection with and treatment of sensitive and resistant strains of T.circumcincta on the ovine intestinal microbiota, and rectal faecal composition.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine
Complete BK Polyomavirus genome sequences from patients with urinary tract infections.

We report BK Polyomavirus genome sequences assembled from shotgun metagenomic sequencing data of patient urine samples previously tested for urinary tract infection. Variation and phylogenetic analysis is used to characterise the virus diversity from this patient cohort from the East of England, UK.

Biome: root:Host-associated:Human:Excretory system:Urethra:Urine
Metagenomic Analysis of soil microbial community of the western high land

In this study soil was collected from the western high land of Saudi Arabia. The samples were analyzed using next generation sequencing.

Biome: root:Environmental:Terrestrial:Soil
Targeted metagenomics of perchlorate reducing bacteria

We performed microfluidic enrichment and sequencing of environmental DNA based on the presence of the chlorite dismutase gene

Biome: root:Engineered:Lab enrichment
River Ganges Microbiome Project

River Ganges Water and Soil Community Structure

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Herbal Formula-3 alleviates food allergy in mice by modulating the composition of the gut microbiota

Formula-3, an herbal medicine formula, had been demonstrated to inhibit food allergy in rats by stabilizing mast cells. However, it is not clear how Formula-3 modulates the composition of the intestinal microbiota and alleviates food allergy. We performed 16S rDNA sequencing of gut metagenome in fecal samples, and investigated the effect of Formula-3 on healthy mice and food allergy (FA) mice. We found  that Formula-3 decreased gut community richness, increased Lactobacillus and the Bacteroides-to-Prevotella ratio in mice. Additionally, it altered the functional pathways such as energy metabolism and transport system metabolism. It will provide insights into the interaction between herbal formula and gut microbiota, and the potential mechanism of TCMs for disease alleviations.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
The effect of mixed probiotics on fecal microbiota of farmed raccoon dogs

Probiotics could be used as an alternative for improving host health, in this study, mixed probiotics were used to feed farmed raccoon dogs for 12 weeks, the fecal microbiota were investigated with Illumina MiSeq sequencing.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
The effect of mixed probiotics on fecal microbiota of farmed fox

Antibiotics had potentially negative effects on host health and environment. Probiotics could be an alternative for improving host health. In this study, mixed probiotics were used to added in the diet of farmed fox. High-through put sequencing was used to investigated the 16S rRNA gene of fecal microbiota.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Impact of GOS on chicken gut

Impact of GOS on chicken gu

Biome: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
Metagenome data from DNA stable isotope probing of Stiffkey saltmarsh sediment microcosms to investigate methanogenesis from choline

Coastal saltmarsh sediments represent an important source of natural methane emissions, much of the methanogenesis originates from quaternary and methylated amines, such as choline and trimethylamine. However, the key microbes involved in choline-dependent methanogenesis remain poorly characterized and the metabolic pathways by which the saltmarsh microbes degrade choline and form methane are yet to be determined. In this study, we combined DNA stable isotope probing microcosms with high throughput sequencing of 16S rRNA genes and 13C2-choline enriched metagenomes, followed by binning of the microbial population genomes to identify the microbes responsible for methanogenesis. Microcosm incubation with 13C2-choline leads to the formation of trimethylamine and subsequent methane production, suggesting that choline-dependent methanogenesis is a two-step process involving trimethylamine as the key intermediate. Amplicon sequencing analysis identified Deltaproteobacteria, of the genera Pelobacter and Desulfuromonas were the major choline-utilizers. The methanogenic Archaea, of the genera Methanococcoides became enriched in choline-amended microcosms, indicating their role in methane formation from trimethylamine. The binning of the microbial population genomes from metagenomic DNA resulted in the identification of bins that are classified as Pelobacter, Desulfuromonas, Methanococcoides and their associated viruses. Analyses of these bins revealed that Pelobacter and Desulfuromonas have the genetic potential to degrade choline to trimethylamine using the choline-trimethylamine lyase pathway, whereas Methanococcoides are capable of methanogenesis using the pyrrolysine-containing trimethylamine methyltransferase pathway.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
Common swift feather microbiota described by high throughput DNA sequencing

We provide the first-ever investigation of feather microbiota by high throughput DNA sequencing for any bird species by describing bacteria found on the innermost tertial feather of 22 adult Common swifts (Apus apus). We found feather microbiomes with large abundance of Bacillales, Actinomycetales, Burkholderiales, Sphingobacteriales, Sphingomonadales, Rhizobiales, Pseudomonadales, Clostridiales, Rubrobacterales and Lactobacillales. Bacterial communities did not change with any feature of individuals we measured. Network and cluster analysis of feather microbiomes disclosed three clusters , characterized by bacteria typical of seawater, plants and soil, and unrelated to conditions at the breeding grounds. We hypothesized that feather microbiomes may reflect, at least partially, airborne bacterial communities of the environments where individuals spent non-breeding periods, or of those they crossed during migration, rather than breeding environment. If confirmed, this evidence may disclose the possibility to use feather bacteria as intrinsic marks for tracing non-breeding origin and routes of migratory birds.

Biome: root:Host-associated:Birds
Impact of different diets on gut microbiomes: correlation with inflammation and metabolism

Rats were fed 3 different diets (one negative control), stools were collected and 16S gene analysed by V4 region Illumina MiSeq technology

Biome: root:Host-associated:Mammals:Digestive system:Fecal
First insight into microbial communities associated with species belonging to orders Coleoptera and Thysanura inhabiting anthills of Formica rufa and F. polyctena

In the present study we used Next Generation Sequencing (NGS) in 16S rRNA gene analysis to define microbial communities of seven insect species (Atelura formicaria, Dedrophilus pygmaeus, Leptacinus formicetorum, Monotoma angusticollis, Myrmechixenus subterraneus, Ptenidium formicetorum and Thiasophila angulata) inhabiting anthills of two ant species: Formica rufa and F. polyctena. Moreover, we analyzed obtained microbiome profiles to verify the presence of known endosymbionts.

Biome: root:Host-associated:Insecta
Weaning transition microbiota and blood types in pig

The host-gut microbiota interplay is well recognized as a key factor for the homeostatic maintenance, for the pathological events control and for growth performances of the animals. The weaning transition represents a moment of drastic changes, which also have a strong impact on the gut microbial community leading to a high risk of dysbiotic events. The adhesion of bacteria on intestinal mucosa is mediated by molecules which compose the glycocalyx on epithelium surface and which act as specific receptors determining the structure of the mucosal bacterial community. Some of these receptors are the mucosal blood type antigens which are genetically determined in the host. The association between ABO blood groups and intestinal microbial profile has been tested in human with contrasting results. For the pig there are no studies on the relationship between blood groups and gut microbiota, however, in our previous study we reported some differences in the glycomic pattern of the jejunal mucosa and in the adhesion of E. coli, associated with the porcine blood groups A0. In the present study we followed the changes in faecal microbiota of piglets from the lactation to 2 weeks after weaning testing the hypothesis that the blood types may impact on its structure. No differences were reported for the A0 blood types. The metagenomic predictions revealed a shift from fatty acid degradation to fatty acid biosynthesis in bacterial community between pre- and post-weaning.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine
Bacterial communities associated with Phormidium (cyanobacteria) dominated biofilms

The aim of the study was to investigate the spatial and temporal variation of the structure of bacterial communities associated with Phormidium in river biofilms. This work was performed in one French (Tarn River) and eight New Zealand rivers, which enabled us to compare several communities from local to intercontinental scales. We used high-throughput sequencing of 16S rRNA gene fragment including the V4-V5 variable regions.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
WGS data from FMT trial for the treatment of recurrent Clostridium difficile infection

Fecal microbiota transplantation (FMT) is a treatment for microbiome-associated diseases in which gut microbiota are transferred from a healthy donor to a patient. Although the success of FMT requires donor bacteria to engraft in the patient's gut, the forces governing bacterial engraftment in humans are unknown. Here, we use a vast, ongoing clinical experiment - the treatment of recurrent Clostridium difficile infection with FMT - to uncover the rules of engraftment in humans. First, we built a machine learning model that accurately predicts which bacterial species will engraft in a given host. We then developed a maximum-likelihood strain inference method, Strain Finder, allowing us to infer the genotypes of donor strains and to track them through patients' guts over time. Surprisingly, engraftment could be predicted largely from the abundance and phylogeny of bacteria in the donor and the pre-FMT patient. We also found that donor strains within a species engraft in an all-or-nothing manner and that previously undetected strains frequently colonize the patient after FMT. We validated these findings in another disease context, metabolic syndrome, suggesting that the same principles of engraftment extend to other indications. These findings may guide the design of bacterial therapeutics that target diseases ranging from ulcerative colitis to cancer.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Faecal metagenomes of healthy pigs

Faecal samples from 16 healthy pigs were analysed using metagenomics, 16S rRNA microbiome amplicon sequencing and qPCR analysis for relative quantities of antibiotic resistance genes.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Longitudinal study of the diabetic skin and wound microbiome

Background: Type II diabetes is a chronic health condition which is associated with skin conditions including chronic foot ulcers and an increased incidence of skin infections.  The skin microbiome is thought to play important roles in skin defence and immune functioning.  Diabetes affects the skin environment, and this may perturb skin microbiome with possible implications for skin infections and wound healing.  This study examines the skin and wound microbiome in type II diabetes. Results: Ten type II diabetic subjects with chronic foot ulcers were followed over a time course of 10 weeks, sampling from both foot skin (swabs) and wounds (swabs and debrided tissue) every two weeks. A control group of 8 non-diabetic subjects was also followed over 10 weeks, and skin swabs collected from the foot skin every two weeks.  The diabetic skin microbiome was significantly less diverse than non-diabetic skin.  Community composition was also significantly different between diabetic and non-diabetic skin, however the most abundant taxa were similar between groups, with differences driven by very low abundant members of the skin communities. Chronic wounds were generally colonized by the most dominant skin Staphylococcus, along with other taxa that generally different by patient. No significant correlations were found between wound duration or healing status and the abundance of any particular taxa, while wound size was positively correlated with the dominant skin Staphylococcus.   Conclusions: The major difference observed in this study of the skin microbiome associated with diabetes was a significant reduction in diversity.  The long-term effects of reduced diversity are not yet well understood, but are often associated with disease conditions.

Biome: root:Host-associated:Human:Skin
EMG produced TPA metagenomics assembly of the ASS lime injection - injection site (ASS lime injection - injection site) data set

The ASS lime injection - injection site Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB6137. This project includes samples from the following biomes :Grassland .

Biome: root:Environmental:Terrestrial:Soil:Clay
EMG produced TPA metagenomics assembly of the Bacterial diversity in various environments such as cultivated soil, alpine soil,  semi-arid soil (Soil diversity) data set

The Soil diversity Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB14534. This project includes samples from the following biomes :Soil .

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of the Wisconsin, Continuous corn soil metagenome reference core Project (Soil 402460) data set

The 402460 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set SRP008617. This project includes samples from the following biomes :Soil .

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of the RA Metagenome (soil metagenome) data set

The soil metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA188489. This project includes samples from the following biomes :Soil .

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of the Sheep rumen microbiome (gut metagenome) data set

The gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA202380. This project includes samples from the following biomes :Mammal (non-human) .

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Rainbow trout raised in two rearing water systems

In a crossover design feeding experiment in two rearing water, trout was fed two non-aquatic alternative protein diets to understand the effect of the water systems on trout performance and gut bacterial composition.

Biome: root:Host-associated:Fish:Digestive system
16S data from FMT trial for the treatment of recurrent Clostridium difficile infection

Fecal microbiota transplantation (FMT) is a treatment for microbiome-associated diseases in which gut microbiota are transferred from a healthy donor to a patient. Although the success of FMT requires donor bacteria to engraft in the patient's gut, the forces governing bacterial engraftment in humans are unknown. Here, we use a vast, ongoing clinical experiment - the treatment of recurrent Clostridium difficile infection with FMT - to uncover the rules of engraftment in humans. First, we built a machine learning model that accurately predicts which bacterial species will engraft in a given host. We then developed a maximum-likelihood strain inference method, Strain Finder, allowing us to infer the genotypes of donor strains and to track them through patients' guts over time. Surprisingly, engraftment could be predicted largely from the abundance and phylogeny of bacteria in the donor and the pre-FMT patient. We also found that donor strains within a species engraft in an all-or-nothing manner and that previously undetected strains frequently colonize the patient after FMT. We validated these findings in another disease context, metabolic syndrome, suggesting that the same principles of engraftment extend to other indications. These findings may guide the design of bacterial therapeutics that target diseases ranging from ulcerative colitis to cancer.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the human salivary and gut microbiomes, as well as a microflora colonized on the surface of marine kelp Metagenome (terrestrial metagenome) data set

The terrestrial metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA357324. This project includes samples from the following biomes : Human gut, Human Oral.

Biome: root:Host-associated:Human
EMG produced TPA metagenomics assembly of the Human Gut Microbiome Metagenome (human gut metagenome) data set

The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA299502. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Biochar-amended soil Targeted loci environmental (soil metagenome) data set

The soil metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA297134. This project includes samples from the following biomes : Soil.

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of the Evaluation of vertical transmission between mother-infant (human gut metagenome) data set

The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA287207. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Homo sapiens fecal metagenome Raw sequence reads (human gut metagenome) data set

The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA279580. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Metagenome study of rice samples under various conditions (soil metagenome) data set

The soil metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA271842. This project includes samples from the following biomes : Plant.

Biome: root:Environmental:Terrestrial:Soil