SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Research of extracellular vesicle content from gut microbiome and its’ role in cancer development by applying gut on chip system

The gut microbiota and their products have a critical role in human health and are involved in all physiological processes. It is well now known that altered microflora can lead to the development of various diseases, including malignancies. One of the ways in which these processes in the body are potentially influenced by the microflora is through extracellular vesicles (EVs) and the RNA content in them, but currently research methods for these processes are limited. Classical in vitro methods cannot mimic the entry of the microbiome EV from the intestinal lumen into the circulatory system, but animal models do not fully reflect the processes in the human body and are ethically questionable models for these studies. One of the most promising methods currently in microflora research is the gut on chip (GoC) platform, however so far, the available solution has not been applied and designed for the study of the microbiome EV content. Therefore, the aim of this project is to study EV RNA content of cancer patient microbiome, that can enter from lumen to circulation by applying GoC devices already developed in a collaboration between BMC and ISSP. These results will provide answers to fundamental questions about human-microorganism interactions in the future, as well as give the opportunity to study and testing of clinical microflora samples from different patients for diagnostic and therapeutic purposes.

Biome: root:Host-associated:Human:Digestive system:Hindgut
Shotgun Metagenomics approach to Identify Biosynthetic Gene-Cluster from forest soil sample.

This study aims to identify biosynthetic Gene-Cluster and taxonomic classification of the microbiome within the sample.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
EMG produced TPA metagenomics assembly of PRJEB9718 data set (Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB9718, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
The impact of exercise and/or whey protein supplementation on the gut microbiome of sedentary adults: A prospective metagenomic and metabolomic analysis.

Many components of modern living exert influence on the resident intestinal microbiota of humans with resultant impact on host health. For example, exercise-associated changes in gut microbial diversity, composition, and functional profiles have been described in cross-sectional studies of habitual athletes. However, this relationship is compounded by changes in diet that coincide with exercise such as dietary and supplementary protein consumption. To determine whether increasing physical activity and/or increased protein intake modulates gut microbial composition and function, we prospectively challenged healthy but sedentary adults with a short-term exercise regime, with and without concurrent daily whey protein consumption. Metagenomic and metabolomic-based assessments demonstrated modest changes in gut microbial composition and function following increases in physical activity. Significant changes in the diversity of the gut virome were evident in participants receiving daily whey protein supplementation. Results indicate that improved body composition with exercise is not dependent on major changes in gut microbial diversity. The diverse microbial characteristics previously observed in long-term habitual athletes may be a later response to exercise and fitness improvement.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
16S-based metagenomic study of twelve French cheese varieties


Biome: root:Engineered:Food production:Dairy products
EMG produced TPA metagenomics assembly of PRJNA851847 data set (Mouse gut microbiota macrogenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA851847, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract.

Biome: root:Host-associated:Mammals:Gastrointestinal tract
EMG produced TPA metagenomics assembly of PRJNA650546 data set (Evolution of bacteria in the mouse gut through the selection of genetic variations by dietary extracellular vesicles in bovine milk).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA650546, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA694773 data set (Inhibitory effects of breast milk-derived Lactobacillus rhamnosus Probio-M9 on colitis-associated carcinogenesis by restoration of the gut microbiota in a mouse model).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA694773, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA473429 data set (Effect of Down Syndrome genotype on mouse microbiome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA473429, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA658981 data set (Whole Genome Shotgun Sequencing of Aging GOS-Fed Mouse Microbiota).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA658981, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
Metagenomics approach for taxonomic classification and identification of biosynthetic gene-clusters from soil microbiome.

This study focuses on taxonomic classification and functional analysis of Natural Agricultural farmland soil microbiome.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
HoloFood Chicken Caecum Metagenome – deeply sequenced batch

Metagenomic raw reads, assemblies, and bins derived from HoloFood chicken caecum samples. Samples selected for this batch were deeply sequenced, and were randomised among trials (feed), age, and breed to overcome batch effect. The samples in this project contributed to the chicken caecum MAG catalogue (project: PRJEB55374 [ERP140263]).

Biome: root:Host-associated:Birds:Digestive system
EMG produced TPA metagenomics assembly of PRJNA543206 data set (Chicken metagenome Raw sequence reads).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA543206, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system:Fecal.

Biome: root:Host-associated:Birds:Digestive system
HoloFood Salmon - Trial C Metagenome

HoloFood Salmon - Trial C Metagenome

Biome: root:Host-associated:Fish:Digestive system
An examination of the intestinal microbiome of pigs divergent in feed efficiency

Alterations between microbial profiles are potentially a key factor influencing feed efficiency in pigs. The objective of this study was to identify if differences in microbial diversity, relative abundance of taxa exist within the intestinal microbiota of pigs divergent in feed efficiency selected from two different farms of origin. Two populations of pigs were used in this study with piglets selected from two different farms of origin (Group A and B). In Group A, the 8 most efficient (LRFI) and 8 least efficient (HRFI) animals were selected for further analysis, while in Group B the 12 most efficient and 12 least efficient were utilised. Colonic digesta was collected from these pigs to analyse the intestinal microbiota using 16S rRNA gene sequencing. 106 of 126 identified taxa in this study differed between groups while a small number of taxa differed based on feed efficiency. Alpha diversity differed between the two groups in this study with pigs from Group A having increased alpha diversity based on Shannon and InvSimpson measures compared to pigs from Group B (P<0.05). Between HRFI and LRFI pigs across the two groups, no differences in any measures of Alpha diversity were identified (P>0.10). In agreement with these findings, beta diversity analysis established that pigs grouped based on farm of origin rather than RFI group.   Within the Bacteroidetes phylum the LRFI pigs had increased BS11 (P<0.05) and tended to have increased Bacteroidaceae (P<0.10) at family level while at genus level the LRFI pigs tended to have increased Bacteroides and CF231 (P<0.10). The increased abundance of these taxa suggest an increased capacity of the more efficient pigs to breakdown feed potentially impacting nutrient digestibility. The changes identified in this study suggest an influence of the microbiome in influencing feed efficiency. However, the differences between groups suggest that these results need to be corroborated in larger studies across multiple environments.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine
European grassland soils subjected to multiple disturbances

Sequencing microbial communities from multiple European grassland soils subjected to 4 different lab perturbation regimes- control, heat, drought, or flooding.

Biome: root:Environmental:Terrestrial:Soil:Grasslands
caecal microbiota on rat fed several protein

Ceacal microbiotas in rats fed milk-casein, soy-protein or fish-meal was determined by 16S rRNA gene-DGGE and pyrosequencing with bar-coded primer targeting the bacterial 16S rRNA gene.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
EMG produced TPA metagenomics assembly of PRJNA435487 data set (Chicken ceacal metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA435487, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum.

Biome: root:Host-associated:Birds:Digestive system:Ceca
Comparision of different commercial library preparations kits for soil metagenomics studies

In this study, we want to compare the sequencing results using different technology in library preparation in a high diversity custom soil sample. For that, we have selected four different commercial kits including different inputs.
In addition to this, we want to test the behavior of the libraries onto the sequencer in terms of clustering and data output.
It will generate the most accurate workflow to the scientific community in their metagenomic experiments.

Biome: root:Environmental:Terrestrial:Soil
HoloFood Chicken -- Prior Chicken Illeum

HoloFood Chicken -- Prior Chicken Illeum

Biome: root:Host-associated:Birds:Digestive system
Iceland Brent Goose May 2022 test metagenomics data

Test run of metagenomics sequencing on a small subset of faecal samples collected from Light-bellied Brent geese in Iceland, May 2022. DNA was extracted from the faecal samples and the NEBNEXT microbiome enrichment kit was used prior to shotgun sequencing on the NovaSeq platform.

Biome: root:Host-associated:Birds:Digestive system:Fecal
N/A

N/A

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
EMG produced TPA metagenomics assembly of PRJNA417359 data set (A catalogue of chicken gut metagenome and the microbial responses to antibiotic and plant-derived benzylisoquinoline alkaloids).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA417359, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system.

Biome: root:Host-associated:Birds:Digestive system
Bio-geochemistry of alkaline waste

This project investigates the application advanced molecular biology and bioinformatic techniques to the sustainable management of alkaline wastes. These wastes are produced globally in enormous quantities by societies’ primary industries, including iron, steel and aluminium production, and a significant proportion are dumped. “Aggressive” interventions are energy intensive and disturb a waste during treatment when the most significant risk to human health is airborne dusts. Microbes that occur naturally offer exciting potential to bring about beneficial chemical changes to prevent migration of harmful contaminants from the waste into the wider environment. However, to realise this potential requires better understanding of the occurrence and activity of the microbes in these extreme environments. Using samples from an alkaline waste site, microcosm experiments were established where the desired chemical processes were occurring. Samples from these microcosms are being interrogated using ‘omics’ techniques to understand which microbes and processes are critical to achieve the desired geochemical outcome and how these can be encouraged.

Biome: root:Environmental:Terrestrial:Soil:Contaminated
The effect of dietary bioactive on gut microbiome diversity (DIME) – a pilot study

The DIME study consists of a randomised 2x2 cross-over human intervention where healthy participants (n = 20) are subjected to a diet high in bioactive-rich food for two weeks and a diet low in bioactive-rich food. There is a four-week washout between the two interventions.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJEB33338 data set (Metagenomics of chicken cecal contents from fast and slower growing birds).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB33338, and was assembled with metaspades v3.13. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum.

Biome: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
EMG produced TPA metagenomics assembly of PRJNA385038 data set (chicken gut metagenome Raw sequence reads).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA385038, and was assembled with SPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system.

Biome: root:Host-associated:Birds:Digestive system
Sulfate-dependant microbially induced corrosion of mild steel in the deep sea: a 10-year microbiome study.

Metal corrosion in seawater has been extensively studied in surface and shallow waters. However, infrastructure is increasingly being installed in deep-sea environments, where extremes of temperature, salinity, and high hydrostatic pressure increase the costs and logistical challenges associated with monitoring corrosion. Moreover, there is currently only a rudimentary understanding of the role of microbially induced corrosion, which has rarely been studied in the deep-sea. We report here an integrative study of the biofilms growing on the surface of corroding mooring chain links that had been deployed for 10 years at ~2 km depth and developed a model of microbially induced corrosion based on flux-balance analysis.

Biome: root:Environmental:Aquatic:Marine
EMG produced TPA metagenomics assembly of PRJEB1788 data set (Shotgun Sequencing of Tara Oceans DNA samples corresponding to size fractions for  large DNA viruses).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB1788, and was assembled with SPAdes v3.14.1, metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.

Biome: root:Environmental:Aquatic:Marine
EMG produced TPA metagenomics assembly of PRJEB48889 data set (Multi-omic analysis in a metabolic syndrome porcine model implicates arachidonic acid metabolism disorder as a risk factor for atherosclerosis).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB48889, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system.

Biome: root:Host-associated:Mammals:Digestive system
EMG produced TPA metagenomics assembly of PRJNA385855 data set (Temporal sampling of marine metagenomes from Station ALOHA and BATS).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA385855, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic.

Biome: root:Environmental:Aquatic:Marine:Oceanic
EMG produced TPA metagenomics assembly of PRJNA656268 data set (Bio-GO-SHIP: Global marine 'omics studies of repeat hydrography transects).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA656268, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic.

Biome: root:Environmental:Aquatic:Marine
Study of infant stool samples in the first year of life.

Stool samples were collected from 12 Norwegian infants in the first year of life. This study has whole-genome metagenomic information of several timepoints of these infants.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJEB43687 data set (Shotgun metagenomic approch to identify the bacterial, archaeaa,virus, fungi and eukaryotes in Northern Indian Ocean).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB43687, and was assembled with metaSPAdes v3.14. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic.

Biome: root:Environmental:Aquatic:Marine:Oceanic
We fed expanded polystyrene plastic to wharf roach (Ligia exotica), then conducted metagenome sequencing of wharf roach gut to investigate microbiota alternation.

We fed expanded polystyrene plastic to wharf roach (Ligia exotica), then genomic DNA was extracted from wharf roach gut and we conducted metagenome sequencing to investigate microbiota alternation.

Biome: root:Host-associated:Arthropoda:Digestive system:Gut
EMG produced TPA metagenomics assembly of PRJEB11585 data set (Microbial metagenome sequencing from marine sponges (Spongia sp.), seawater and sediments).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB11585, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Mixed.

Biome: root:Mixed
EMG produced TPA metagenomics assembly of PRJEB34634 data set (Detailed study at the genetic level at bacteria in farm animals, human/animal sewage, sewage treatment works and rivers, to work out the complex network of transmission of important antibiotic-resistant bacteria and antibiotic resistance genes).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB34634, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Mixed.

Biome: root:Mixed
EMG produced TPA metagenomics assembly of PRJEB46254 data set (Deciphering the functional potential of a hypersaline marsh microbial mat community).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB46254, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Saline:Microbial mats.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Saline:Microbial mats
EMG produced TPA metagenomics assembly of PRJEB25171 data set (Flood seasonal changes in microbiota evidenced through metagenomes of freshwater lakes from Upper Amazon river basin).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB25171, and was assembled with metaSPAdes v3.15.3, metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Lake.

Biome: root:Environmental:Aquatic:Marine
Microbiome Signature in Natural Lakes

The crust of lateritic (canga)  is a particular environment to be a ferruginous complex that inhabiting a high species diversity, high endemism and unique species compositions generally metal-tolerant (see Jacobi et al. 2007). Lakes are formed in the top of Canga which are maintained by local rainfall patterns. Information about  the formation and dynamics of these lakes are scarce, considering that microorganisms play crucial roles in ecosystem functioning, here we aimed to understand the relationship between microbial diversity, functions and environmental parameters that sustain this peculiar amazonian environment. In this study, we compare the taxonomic and functional structure of the microbial communities from sediment in three neighboring lakes on top of the extensive lateritic crust in the southeast Amazon Basin using shotgun metagenome sequencing

Biome: root:Environmental:Aquatic:Freshwater:Lake
EMG produced TPA metagenomics assembly of PRJEB9740 data set (Shotgun Sequencing of Tara Oceans Polar Cicle 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 PRJEB9740, and was assembled with metaSPAdes v3.15.3, metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.

Biome: root:Environmental:Aquatic:Marine
EMG produced TPA metagenomics assembly of PRJNA254927 data set (Freshwater habitats river Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA254927, and was assembled with metaSPAdes v3.15.3, metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Low land river systems