SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the faecal microbiome of growing kittens

Despite being obligate carnivores, cats are fed a wide range of dietary macronutrients within commercial diets. Little is known regarding the feline gastrointestinal microbiome and how it is impacted by diet. Using 16S RNA analysis, changes in diet (protein:carbohydrate ratio) do affect fecal microbiota of growing kittens. However, to investigate potential functional differences deep Illumina shotgun sequencing is required and a study of microbial structure and function in these animals is reported here.  This is the largest and most comprehensive analysis of the feline gastrointestinal microbiome to date. It provides an overview of the taxa and gene functions present and how they are impacted by the dietary protein: carbohydrate ratio. The more diverse structure of the high-protein diet might reflect a more specialized microbiome. As anticipated, our permutation approach reduced the number of pathways to a more manageable set. The reduced data set identified six pathways readily interpretable to the study design.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
EMG produced TPA metagenomics assembly of PRJEB8087 data set (Metagenomes of Danish EBPR WWTPs).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB8087, and was assembled with SPAdes v3.11.1, metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Engineered:Wastewater:Nutrient removal:Biological phosphorus removal:Activated sludge.

Biome: root:Engineered:Wastewater:Nutrient removal:Biological phosphorus removal:Activated sludge
EMG produced TPA metagenomics assembly of PRJNA275232 data set (Streptococcus thermophilus infected with lytic phage 2972).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA275232, and was assembled with metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Engineered:Food production:Dairy products.

Biome: root:Engineered:Food production:Dairy products
Streptococcus thermophilus infected with lytic phage 2972

Many bacteria rely on CRISPR-Cas systems to provide adaptive immunity against phage, predation by which can shape the ecology and functioning of microbial communities. To characterize the impact of CRISPR immunization on phage genome evolution we performed long-term bacteria-phage (Streptococcus thermophilus  phage 2972) co-evolution experiments. We show that in this species CRISPR immunity drives fixation of single nucleotide polymorphisms that accumulate exclusively in phage genome regions targeted by CRISPR. Mutation rates in phage genomes highly exceed those of the host. The presence of multiple phage increased phage persistence by enabling recombination-based formation of chimeric phage genomes in which sequences heavily targeted by CRISPR are replaced. Collectively, results establish CRISPR-Cas adaptive immunity as a key driver of phage genome evolution under the conditions studied and highlight the importance of multiple co-existing phage for persistence in natural systems.

Biome: root:Engineered:Food production:Dairy products
EMG produced TPA metagenomics assembly of PRJNA60251 data set (Metagenome isolated from cow gut).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA60251, and was assembled with metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Foregut:Rumen.

Biome: root:Host-associated:Mammals:Digestive system:Foregut:Rumen
Metagenome isolated from cow gut

The paucity of enzymes that efficiently deconstruct plant polysaccharides represents a major bottleneck for industrial-scale conversion of cellulosic biomass into biofuels. Cow rumen microbes specialize in degradation of cellulosic plant material, but most members of this complex community resist cultivation.  To characterize biomass-degrading genes and genomes, we sequenced and analyzed metagenomic DNA from microbes adherent to plant fiber incubated in cow rumen. From these data, we identified putative carbohydrate-active genes and expressed candidate proteins, of which 57% were enzymatically active against cellulosic substrates. We also assembled 15 uncultured microbial genomes, which were validated by complementary methods including single-cell genome sequencing. These data sets provide a substantially expanded catalog of genes and genomes participating in the deconstruction of cellulosic biomass.

Biome: root:Host-associated:Mammals:Digestive system:Foregut:Rumen
EMG produced TPA metagenomics assembly of PRJNA427653 data set (Comprehensive Metagenomic).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA427653, and was assembled with SPAdes v3.12.0, SPAdes v3.11.1. This project includes samples from the following biomes: root:Mixed.

Biome: root:Mixed
Comprehensive Metagenomic

Microbiota as a functional assemblage of microbes plays an important role in environment and in lives of multicellular organisms. Animal gut microbiota is strongly influenced by dietary factors while soil microbial flora can be shaped by various physical, chemical, and biological conditions.

Biome: root:Mixed
EMG produced TPA metagenomics assembly of PRJEB23524 data set (WGS data from FMT trial for the treatment of recurrent Clostridium difficile infection).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB23524, and was assembled with metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA510036 data set (Fecal transplant influence on healthy volunteers).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA510036, and was assembled with metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Fecal transplant influence on healthy volunteers

WGS metagenomics sequencing data describing fecal transplant influence on healthy voluntaries.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA385949 data set (Longitudinal Stool Study of patients with IBD and controls).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA385949, and was assembled with metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Longitudinal Stool Study of patients with IBD and controls

Longitudinal Stool Study of patients with IBD and controls. This project combines data from PRISM and STINKI cohorts to characterize the gut microbiome of individuals with IBD and controls over time.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Hot spring thermophilic microbial communities from Obsidian Pool, Yellowstone National Park, USA - site 3 B9 metagenome


Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
EMG produced TPA metagenomics assembly of PRJEB35321 data set (Cotter Lab FF study).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB35321, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Engineered:Food production:Dairy products.

Biome: root:Engineered:Food production:Dairy products
Cotter Lab FF study

Cotter Lab FF study

Biome: root:Engineered:Food production:Dairy products
EMG produced TPA metagenomics assembly of PRJNA648297 data set (Remarkably low relative abundance of several Bifidobacterium species in the altered intestinal microbiota of Helicobacter pylori infected patients with gastric ulcer and gastric cancer).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA648297, and was assembled with Flye v2.8.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Land use change effects on the soil microbiome of the rainforest of the northwest Colombian Amazon region.

This study aimed to characterize the microbiome present in both litter and the soil of rainforest in the northwest Colombian Amazon region, and the response of the microbiome to land use change. The study was conducted specifically in Belen de los Andaquies and Solano counties, in Caqueta state, the second most important hotspot of deforestation in the entire Amazon basin. Experimental study design included 4 study sites for comparing native forest to livestock pasture systems, within the main landscapes of the region, mountain and hill landscapes separately.

Biome: root:Environmental:Terrestrial:Soil:Tropical rainforest
EMG produced TPA metagenomics assembly of PRJEB43502 data set (Nitrogen fixation rates and cyanobacteria cover in a subarctic biological soil crust are enhanced by warming, wetting and light).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB43502, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Terrestrial:Soil.

Biome: root:Environmental:Terrestrial:Soil
Transcriptome analysis of Antimicrobial peptide (AMP) treatments

We investigated the differential expression of genes in rumen-derived antimicrobial peptide treatments against two strains of Staphylococcus aureus.

Biome: root:Host-associated:Mammals:Digestive system:Foregut:Rumen
EMG produced TPA metagenomics assembly of PRJNA337758 data set (Marine microbial community from Cabo Rojo, Puerto Rico - PR CR 10% Liquid 3 metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA337758, and was assembled with 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 PRJNA214436 data set (Pink berry consortia Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA214436, and was assembled with SPAdes v3.14.1, metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
Pink berry consortia Metagenome

Microbial consortia modulate biogeochemical cycles over short spatiotemporal scales that often elude detection by traditional analytical approaches. We investigate syntrophic sulfur cycling in the 'pink berry' consortia through an integrative, multidisciplinary study at the microbial scale. The pink berries are macroscopic, photosynthetic microbial aggregates composed primarily of two closely associated species: sulfide-oxidizing purple sulfur bacteria (PSB) of the family Chromatiaceae and sulfate reducing bacteria (SRB) from the Desulfobulbacaea. Metagenomic sequencing and the reconstruction of near-complete genomes for the PSB and SRB species reveals the genetic potential for sulfur cycling within the berries.    Macroscopic microbial aggregates from the Sippewissett salt marsh, dominated by anoxygenic phototrophs (purple sulfur bacteria) and sulfate reducing bacteria.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
EMG produced TPA metagenomics assembly of PRJNA337836 data set (Marine sediment microbial community from La Parguera, Puerto Rico - PR Tt Sediment 1 metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA337836, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Coastal:Sediment.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
EMG produced TPA metagenomics assembly of PRJNA559386 data set (Sequencing of mouse gut microbiome with Nanopore Sequencing for whole genome analysis of DNA methylation.).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA559386, and was assembled with Flye v2.8.3. 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
Sequencing of mouse gut microbiome with Nanopore Sequencing for whole genome analysis of DNA methylation.

Fecal pellets from a male 12-week-old NOD/shiltj mouse were collected before and after antibiotic treatment with Tylosin. DNA samples were extracted and sequenced with Nanopore sequencing. For each microbiome sample, nanopore sequencing raw signal is compared between the native and the WGA datasets to bin metagenomic contigs by genome of origin. Those information are also leverage to detect, classify, and fine-mapped DNA methylation across the genomes.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA479723 data set (Nanopore metagenomics).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA479723, and was assembled with Flye v2.8.1. This project includes samples from the following biomes: root:Engineered:Wastewater:Water and sludge.

Biome: root:Engineered:Wastewater:Water and sludge
Nanopore metagenomics

WWTPs nanopore metagenomics

Biome: root:Engineered:Wastewater:Water and sludge
Remarkably low relative abundance of several Bifidobacterium species in the altered intestinal microbiota of Helicobacter pylori infected patients with gastric ulcer and gastric cancer

Stool sample

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA588037 data set (Strain-level identification of bacterial tomato pathogens directly from metagenomic sequences).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA588037, and was assembled with Flye v2.8.3. This project includes samples from the following biomes: root:Host-associated:Plants.

Biome: root:Host-associated:Plants
Strain-level identification of bacterial tomato pathogens directly from metagenomic sequences

Strain-level identification of bacterial tomato pathogens from Metagenomic samples sequenced with the Oxford Nanopore Technologies (ONT) MinION using ONT's WIMP software and the third party tools Sourmash, MetaMaps, and LINbase.

Biome: root:Host-associated:Plants
EMG produced TPA metagenomics assembly of PRJNA508395 data set (Nanopore long read assembly of the human gut metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA508395, and was assembled with Flye v2.8.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Nanopore long read assembly of the human gut metagenome

Long read sequencing assembly of three healthy human gut microbiome samples, with multiple closed bacterial genomes including Prevotella copri.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA343503 data set (fruitshake sequence reads using Oxford Nanopore MinION).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA343503, and was assembled with Flye v2.8.3. This project includes samples from the following biomes: root:Host-associated:Plants.

Biome: root:Host-associated:Plants
fruitshake sequence reads using Oxford Nanopore MinION


Biome: root:Host-associated:Plants
EMG produced TPA metagenomics assembly of PRJNA676218 data set (Bioreactor co-culture microbial communities from Richmond, British Columbia, Canada - Phormidium sp. AB48 metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA676218, and was assembled with Flye v2.8.3. This project includes samples from the following biomes: root:Engineered:Bioreactor:Continuous culture.

Biome: root:Engineered:Bioreactor:Continuous culture
Bioreactor co-culture microbial communities from Richmond, British Columbia, Canada - Phormidium sp. AB48 metagenome

Bioreactor co-culture microbial communities from Richmond, British Columbia, Canada

Biome: root:Engineered:Bioreactor:Continuous culture
Explore the effect of grass sickness on the equine faecal microbiome.

This study aims to explore the effect of grass sickness on the equine faecal microbiome by sequencing the faecal bacterial DNA of horses diagnosed with grass sickness and matched controls. Faeces was collected on rectal examination from ill horses and collected free falling from control horses. All samples were frozen at -80 until defrosted for bacterial DNA extraction.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
This study deals with 6 metagenomes of modified Winogradsky columns, enriched at 24 C and 28C. Furthermore three enrichment cultures are analysed, which are a mixed consortia of algae and bacteria.

This study deals with the consequences of global change scenarious on stratified microbial communities of lake ecosystems

Biome: root:Environmental:Aquatic
EMG produced TPA metagenomics assembly of the Marine microbial community from Cabo Rojo, Puerto Rico - PR CR 10% Liquid 1 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336694.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.

Biome: root:Environmental:Aquatic:Marine
EMG produced TPA metagenomics assembly of the PRJNA336640 data set (Marine sediment microbial community from La Parguera, Puerto Rico - PR Tt Sediment 2 metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336640.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Sediment.

Biome: root:Environmental:Aquatic:Marine:Sediment
EMG produced TPA metagenomics assembly of the Marine subseafloor sediment microbial communities, sample from White Oak River Estuary, NC, USA 14E metagenome (marine sediment metagenome) data set.

The marine sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA337846.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary, Sediment.

Biome: root:Environmental:Aquatic:Estuary:Sediment
Microbiota composition of Parkinson's disease patients in southern Italy

In recent years, the hypothesis that gut microbiota associates with Parkinson's disease is growing, although a specific composition cannotbe taken as a predictive biomarker of this disease. Our main objective was to investigate dysbiosis of gut microbiota in a selected population of Parkinson's disease patients from center-south of Italy.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Diversity and composition of rumen microbiome  in Sika deers (Cervus nippon yakushimae) from Yakushima Island, Japan

We characterized the rumen microbiota of wild Yaku sika population by high throughput sequencing of bacterial 16S rRNA genes. Rumen microbiota play a crucial role in digesting cellulolytic biomass for ruminant diet. Deer in Yakushima Island Japan, known as Yaku sika, graze a wide range of forage types, and have caused serious reduction of forest understory vegetation in the island while increasing their population. Dietary shifts in the host, observed especially with Yaku sika at highly populated areas, are expected to influence community composition in RM. Significantly higher diversity and distinct community structure were observed in Yaku sika from high-density areas compared to those from decreasing population density areas. These features may contribute to the flexibility of Yaku sika dietary shift and to maintain nutritional status under high density conditions.

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Study on the dynamics of gastrointestinal bacteria in subadult shrimp (Litopenaeus vannamei) with acute hepatic pancreatic necrosis syndrome (AHPND)

?In order to study the response mechanism of shrimp gastrointestinal microbes to diseases, we collected the subadult shrimp with acute hepatopancreatic necrosis syndrome (AHPND). This study preliminarily discussed the gastrointestinal bacterial community structure variation and functional differentiation of subadults when AHPND outbreak, and provided a basis reference for the microbial ecological control of AHPND.

Biome: root:Host-associated:Arthropoda:Digestive system:Gut
Oral, vaginal, and intestinal microbiota analysis in pregnancy

Threatened preterm labor (TPL) and preterm birth (PTB) are significant obstetric complications during pregnancy. However, their triggers have not been fully elucidated. To identify the predisposing factors of TPL and PTB, this project analyzed the oral, vaginal, and rectal microbial profiles to identify potential inter-organ bacterial communication.

Biome: root:Host-associated:Human
Soil fungal diversity along elevation gradients

The goal of this study was to understand the diversity of soil fungi across elevational gradients and to disentangle the direct and indirect effects of climate conditions, plant communities and soil properties on soil fungal richness. This study was conducted in cool-temperate and sub-alpine forests in the University of Tokyo Chichibu Forest in central Japan. We used amplicon-based sequencing of ITS2 region (fITS7/ITS4) to characterize the soil fungal community.

Biome: root:Environmental:Terrestrial:Soil
Data of mycorrhizal fungi

Study of mycorrhizal fungi community. DNA was extracted from root tips of mycoheterotrophic plants and references.

Biome: root:Host-associated:Plants:Root
Subseafloor microbiome  project

A massive amount of microbial cells are present in the global subseafloor environment down to several kilometers below the seafloor. However, their diversity, quantity and biogeography have been largely unknown. In this project, we extracted, amplified DNA from the subseafloor microbiome by a consistent method for comparing microbial communities in different depths and sampling locations. Subsequently, we sequenced a partial sequence of 16S rRNA gene. The analyses of microbial compositions as well as correlation analysis with various environmental meta data will provide the information about the environmental factor controlling or constraining microbial composition.

Biome: root:Environmental:Aquatic:Marine:Sediment
Manure metagenome from Ceftiofur-treated dairy cow

We collected manure from a Ceftiofur treated dairy cow to investigate the abundance, mobility and host range of its antibiotic resistome using Nanopore and Pacbio technologies.

Biome: root:Host-associated:Mammals:Digestive system:Fecal