SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Multigenerational influences of the Fut2 gene on the dynamics of the gut microbiome in mice

The FUT2 gene encodes an α-1,2-fucosyltransferase responsible for the expression of ABO histo-blood-group antigens on mucosal surfaces and bodily secretions. Individuals who carry at least one functional allele are known as “secretors”, whereas those homozygous for loss-of- function mutations are known as “nonsecretors”. Nonsecretor individuals are more susceptible to chronic inflammatory disorders such as Crohn Disease, which may be mediated by alterations in the microbiome. Here, we investigated the dynamics of microbial community assembly with respect to genotype using a Fut2-deficient mouse model, taking the genotype of the maternal lineage over two generations into account. We found strong differences in community assembly of microbial communities over time, depending on the Fut2 genotype of the host and that of their progenitors. By applying interaction network analyses, we further identified patterns of specialization and stabilization over time, which are influenced by the host and parental genotype during the process of community development. We also show genotype- and breeding-dependent patterns of community susceptibility to disturbance in a novel in silico approach integrating ecological- and network analysis. Our results indicate that it may be important to investigate the influence of Fut2 genotype in a familial context in order to fully understand its role in the etiology of chronic inflammatory disorders.

Biome: root:Host-associated:Mammals:Gastrointestinal tract
Antibiotic-free conventional mice were inoculated with dysbiotic gut microbiota from both genetic and nutritional obese mice.

We show that antibiotic-free conventional mice inoculated with dysbiotic gut microbiota from both genetic and nutritional obese mice show a beneficial impact on the liver and the adipose tissue. The transfer changes both the gut microbiota and the microbiome of recipient mice.

Biome: root:Host-associated:Mammals:Digestive system
TLR5 instructs intestinal B cell responses through regulation of flagellin in the gut

Levels of flagellin, the Toll-like receptor 5 (TLR5) ligand, are low and finely regulated in the healthy gut.  TLR5-deficient mice (Tlr5-/-) displays metabolic syndrome driven by pro-inflammatory gut microbiota along with over-production of flagellin by a diversity of intestinal microbes.  This excess flagellin production results in part from abnormally low levels of flagellin-specific antibodies.  The feedback between levels of flagellin, flagellin-specific antibodies and TLR5 signaling is not well understood.  Here, we show that TLR5 deficiency on non-hematopoietic cells is required and sufficient to result in greater levels of bioactive flagellin in gut that occurs without a perturbation to the microbial diversity.  TLR5 deficiency promotes the differentiation of B cells into IgA-secreting plasma cells and reshapes immunoglobulin (Ig) repertoire in the large intestine.  Our data show that modulating microbiota gene expression, instead of altering microbiota community, would be the target for the therapeutic design of regulating intestinal B cell responses.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine
EMG produced TPA metagenomics assembly of PRJEB52998 data set (Soil sample transect of Hudson Valley Farm Hub, NY, USA).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB52998, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Environmental:Terrestrial:Soil:Clay.

Biome: root:Environmental:Terrestrial:Soil
Spatial heterogeneity of gut microbial composition along the gastrointestinal tract in natural populations of house mice

There is a growing appreciation of the role of gut microbial communities in host biology. However, the nature of variation in microbial communities among different segments of the gastrointestinal (GI) tract is not well understood. Here, we describe microbial communities from ten different segments of the GI tract (mouth, esophagus, stomach, duodenum, ileum, proximal cecum, distal cecum, colon, rectum, and feces) in wild house mice using 16S rRNA gene amplicon sequencing.  We also measured carbon and nitrogen stable isotopic ratios from hair samples of individual mice as a proxy for diet.  We identified factors that may explain differences in microbial composition among gut segments, and we tested for differences among individual mice in the composition of the microbiota. Consistent with previous studies, the lower GI tract was characterized by a greater relative abundance of anaerobic bacteria and greater microbial diversity relative to the upper GI tract. The upper and lower GI tracts also differed in the relative abundances of predicted microbial gene functions, including those involved in metabolic pathways. However, when the upper and lower GI tracts were considered separately, gut microbial composition was associated with individual mice. Finally, microbial communities derived from fecal samples were similar to those derived from the lower GI tract of their respective hosts, supporting the utility of fecal sampling for studying the gut microbiota of mice. These results show that while there is substantial heterogeneity among segments of the GI tract, individual hosts play a significant role in structuring microbial communities within particular segments of the GI tract.

Biome: root:Host-associated:Mammals:Gastrointestinal tract
Gut microbiota regulate hepatic von Willebrand Factor synthesis and arterial thrombosis via Toll-like receptor-2

The symbiotic gut microbiota plays pivotal roles in host physiology and is associated with the development of cardiovascular diseases, but microbiota-triggered pattern recognition signaling mechanisms impacting thrombosis are poorly defined. Here, we show that germ-free and Toll-like receptor (Tlr) 2-deficient mice have reduced thrombus growth following carotid artery injury relative to conventionally raised controls. Germ-free Tlr2-/- and wild-type mice were indistinguishable, but colonization with microbiota restored a significant difference in thrombus growth between genotypes. We identify reduced plasma levels of von Willebrand Factor (VWF) and reduced VWF synthesis specifically in hepatic endothelial cells as a critical factor that is regulated by gut microbiota and determines thrombus growth in Tlr2-/- mice. Static platelet aggregate formation on the extracellular matrix protein laminin was similarly reduced in germ-free wild-type, Tlr2-/-, and heterozygous Vwf+/- mice with a modest reduction in plasma VWF level. Defective matrix interaction can be restored by exposure to wild-type plasma or to purified VWF involving the VWF integrin binding site. Moreover, administration of VWF rescues defective thrombus growth in Tlr2-/- mice in vivo. These experiments delineate an unexpected pathway, in which microbiota-triggered TLR2 signaling alters the synthesis of pro-adhesive VWF by the liver endothelium and favors platelet integrin-dependent thrombus formation.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine
Impact of microcins on the gut microbiota

Fecal samples were collected from mice pre-DSS administration (Day -4), post-DSS administration (Day 0), then on Day 5 post-inoculation of a mouse commensal Escherichia coli strain and either wild-type E. coli Nissle 1917 or an mchDEF mutant. DNA was extracted from each sample, cleaned of DSS, then the 16S rDNA v4 region was amplified from each sample with barcoded primers. Libraries were pooled, then sequenced on an Illumina MiSeq.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Gut microbiota regulate hepatic von Willebrand Factor synthesis and arterial thrombosis via Toll-like receptor-2

The symbiotic gut microbiota plays pivotal roles in host physiology. Despite expanding evidence of metabolic alterations contributing to the development of cardiovascular diseases, microbiota-triggered molecular pattern recognition signaling mechanisms which impacting thrombosis are poorly defined. Here, we show that germ-free (GF) mice and mice deficient in the Toll-like receptor 2 (Tlr2) 2 have reduced thrombus growth following carotid arteryafter injury relative to conventionally-raised (CONV-R) wild-type (WT) mice. Tlr2-/- mice raised under GF conditions were indistinguishable from GF WT mice, but colonization of GF WT and GF conventionalized Tlr2-/- mice with a microbiota restored the significant difference in platelet deposition. We identify reduced plasma levels of von Willebrand Factor plasma levels (VWF) and its reduced synthesis specifically in hepatic endothelial cells as the critical factor that determines defective Tlr2-/- platelet deposition in vivo. Platelets from Tlr2-/- mice displayed reduced integrin-mediated VWF binding and diminished adhesion to extracellular matrices in vitro, as seen with thrombosis-protected heterozygous Vwf+/- mice. Administration of VWF rescued defective platelet deposition in Tlr2-/- mice without affecting platelet deposition in WT mice. These experiments delineate an unexpected pathway in which microbiota-triggered TLR2 signaling alters synthesis of pro-adhesive VWF by the liver endothelium and favors platelet-dependent vascular thrombosis.

Biome: root:Host-associated:Mammals:Digestive system
Thioguanine effects on mice gut microbiota

Male and or female mice were intra-gastrically gavaged daily with either vehicle control or thiopurine drugs (TG or MP). Caecal content (CC), caecal mucosa (CM) and faeces (F) of WT, Hprt-/- and Winnie mice were collected at day 14 post-TG administration at doses of 0, 0.5 mg/kg or 2.5 mg/kg (Winnie only). DNA was extracted from faeces at day 0 and day 14; CM and CC at day 14. DNA extracts were used as the template for PCR-based amplification of the bacterial V1-V3 region of the 16S rRNA gene using a barcoded pyrotagging approach, and sequenced with a Roche 454 FLX+ with titanium chemistry.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
The Gut Microbiota of Wild Mice

The gut microbiota profoundly affects the biology of its host. The composition of the microbiota is dynamic and is affected by both host genetic and many environmental effects. The gut microbiota of laboratory mice has been studied extensively, which has uncovered many of the effects that the microbiota can have. This work has also shown that the environments of different research institutions can affect the mouse microbiota. There has been relatively limited study of the microbiota of wild mice, but this has shown that it typically differs from that of laboratory mice (and that maintaining wild caught mice in the laboratory can quite quickly alter the microbiota). There is also inter-individual variation in the microbiota of wild mice, with this principally explained by geographical location. In this study we have characterised the gut (both the caecum and rectum) microbiota of wild caught Mus musculus domesticus at three UK sites and have investigated how the microbiota varies depending on host location and host characteristics. We find that the microbiota of these mice are generally consistent with those described from other wild mice. The rectal and caecal microbiotas of individual mice are generally more similar to each other, than they are to the microbiota of other individuals. We found significant differences in the diversity of the microbiotas among mice from different sample sites. There were significant correlations of microbiota diversity and body weight, a measure of age, body-mass index, serum concentration of leptin, and virus, nematode and mite infection.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine
Metagenomic study of oil sludge contaminated soil

Soil sample has been aseptically collected from Group gathering station(GGS) at Gourisagar, Sivasagar of ONGC(Oil and Natural Gas Corporation), Assam, India. The site from which the soil sample was collected was being contaminated/dumped with crude oil sludge for a very long time(Approximately more than 5 years). The collected soil sample was subjected to metagenomic sequencing and the data obtained will be used for ascertaining how chronic exposure to hydrocarbons will affect the soil microorganisms.

Biome: root:Environmental:Terrestrial:Soil:Oil-contaminated
Long-term seasonal development in selected lakes of Northeast Germany

Longterm data (up to 9 years) of 8 lakes situated in Northeastern Germany are provided. Samples were taken monthly on average dividing particle-associated (greater than 5.0um) and free-living (less than 5.0um, greater than 0.2um) microbes in the water column and in two lakes in the sediment. The lakes are all located closely to each other but differ in many physicochemical parameters such as pH and conductivity. Thus, similarities as well as dissimilarities of microbial communities are of high interest. One lake (Lake Tiefwaren) was sampled after phosphate restoration.

Biome: root:Environmental:Aquatic:Freshwater:Lake
16S metagenomics of steppe soils in Western Transbaikalia


Biome: root:Environmental:Terrestrial:Soil:Grasslands
EMG produced TPA metagenomics assembly of PRJNA530339 data set (Shotgun Metagenomics of 361 post-menopause women reveals gut microbiome change along with the bone loss).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA530339, and was assembled with SPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system.

Biome: root:Host-associated:Human:Digestive system
Metagenomics insights into Phylogenetic and Functional Diversity of Halophilic Communities inhabiting solar saltern in North Sinai,  Egypt

In tropical and subtropical areas around the world, Solar Salterns are artificial shallow
ponds used to manufacture halite (NaCl) from seawater. Multi-pond systems are
commonly used to make them. Saline environments ranging from intermediate to
hyper-saline water (brine) and sediment, the later are characteristic of solar saltern in
North Sinai. Metagenomics by 16S rRNA Illumina amplicon sequencing and
bioinformatical analysis was used to explore the microbial diversity of Solar Saltern
and the halophilic communities were characterized. A total of 237,899 (brine) and
59,680 (sediment) reads were collected. A microbiome featuring Archaea was
discovered using 16S rRNA sequencing (20% from brine and 0.28% from sediment)
The domain Archaea (20%) comprising phylum Euryarchaeota (19.9%) was the most
abundant, followed by Crenarchaeota (0.02%) and Thaumarchaeota (0.01%), while
domain Eubacteria (13.37%) included phylum Proteobacteria (4.5%), Bacteroidetes
(3.7%), Actinobacteria (3.4%), and Firmicutes (3.3%). Eukarya was (1.68%) and
unclassified (64.23%). In sediment Bacteria and Eukarya diversity higher than those
in brine was (47.8%) and (3.38%) respectively, domain Archaea was (0.28%) and
unclassified (48.23%). The study of halophilic microorganisms in solar saltern sheds
light on species that contribute to the ecosystem's biogeochemical cycles. This study
presents a first snapshot for halophilic communities in a hypersaline environment in
north Sinai.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
In this project we would like to study immune responses to African swine fever virus in pigs. We have realized a large animal experiment using two different viruses and pigs with different immune status. We have collected paxgene blood RNA tubes in order to investigate transcriptional changes at different stages of the early immune response.

In this project we would like to study immune responses to African swine fever virus in pigs. We have realized a large animal experiment using two different viruses and pigs with different immune status. We have collected paxgene blood RNA tubes in order to investigate transcriptional changes at different stages of the early immune response.

Biome: root:Host-associated:Mammals:Circulatory system:Blood
Cattle manure compost metagenome as a source of industrially important enzymes

Compost is an aerobic self-heating environment that houses biological degraders capable of degrading wood, starch, cellulose, lignin, lipids, peptides and other carbohydrates. It has cycle of thermophilic heating and cooling phases due to oxidation of the organic matter into inorganic matter until the maturation where it will be used as a fertilizer. Compost attracts attention as it is readily accessible hotspot for thermophilic microorganisms and its enzymes. The enzymes such as amylases, cellulases, proteases and lipases are being sought in industries and are being replaced with its mesophilic counterparts. Metagenome of manure compost was isolated and sequenced. It revealed abundances of Actinobacteria, proteobacteria, fermicutes lineages

Biome: root:Engineered:Solid waste:Composting
Analyses of biofilms in drainage water during the construction phase of the Koralm railway tunnel

During the construction phase of the Koralm railway tunnel several samples from different sites were analysed for the presence of microbes. 16S rDNA amplicon sequencing and subsequent microbial profiling revealed the presence of bacterial consortia typical for the deep continental subsurface dominated by autotrophs, methanotrophs and methylotrophs.
Reference: Koraimann G.; Bischof K. (2022) Characterisation of microbial biofilms from tunnel drainage water. Geomechanics and Tunnelling. 15 (2022), No. 4

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
COVID-19 asthma microbiome

Asthma is associated with severe outcomes of respiratory viral infections. The airway and oral microbiota play important roles in mediating immune responses to viral infections. This study evaluated differences in the nasopharyngeal and salivary microbiomes between patients with and without pre-existing asthma in response to SARS-CoV-2 infection. We collected samples from coronavirus disease 2019 (COVID-19) patients with asthma and COVID-19 patients without asthma. Using 16S ribosomal RNA sequencing, we characterized the nasopharyngeal and salivary microbiomes and analyzed differences at the community and taxa levels between asthma and non-asthma groups. Our results showed that the nasopharyngeal and salivary microbiomes harbor taxa-level, but not community-level differences between COVID-19 patients with and without asthma.

Biome: root:Host-associated:Human:Respiratory system:Nasopharyngeal
using fecal microbiota composition as a non-invasive diagnostic tool to classify colorectal carcinoma and adenoma.

We profiled the microbiota of 1185 fecal samples of colorectal carcinoma and adenoma patients and normal controls from southeastern China using 16S rRNA Illumina PE sequencing. We built random forest tree based bi-class classifier of CRC and normal and multi-class classifier of cancer, adenomas, and normal, and then test them independently. Batch effects were studied and spike-in methods were proposed as an effective strategy to model such effects and improve the results of multi-class classification. Effects of confounding factors were also studied.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Olive plants bacterial microbiota

We used 16S amplicon metagenomics to characterize the taxonomical composition of bacterial microbiota associated with leaves, fruits, and soil of two olive tree genotypes (Sinopolese and Ottobratica).

Biome: root:Host-associated:Plants
EMG produced TPA metagenomics assembly of PRJEB48301 data set (Marine aquaculture microbiomes).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB48301, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.

Biome: root:Environmental:Aquatic:Marine
Exploring the microbiomes of soils associated with contrasting agricultural systems in Colombia

Soil is one of the most diverse ecosystems on the planet, with a community of interacting bacteria, archaea, viruses, fungi, and protozoa collectively referred to as the "soil microbiome". These microorganisms play a crucial role in nutrient cycling, pathogen regulation, and soil carbon sequestration, and have direct and indirect effects on the health of plants and animals in terrestrial ecosystems. Biodiversity characterization has been widely used to reliably monitor and assess the state of the environment. In the last decade, the use of high-throughput sequencing has substantially advanced our understanding of the biogeography and ecology of soil bacterial and fungal communities worldwide. However, a recent review of global publications on soil biodiversity shows that Latin America contributes only 4% of the total information, whereas 87% of soil biodiversity research comes from the Northern Hemisphere. In the present study, samples of soils used for coffee cultivation were collected from 3 geographical zones located in Colombia: Quinchia (Risaralda), El Tambo (Cauca), and Minca (Magdalena) during the year 2021. The samples were processed for DNA extraction (LIMMA Laboratory - Universidad de Los Andes, Colombia) and sequenced (INTA Argentina) to obtain the final sequences. The raw sequences were loaded into ENA/MGnify with free access and subsequently subjected to taxonomic and diversity analysis for bacteria and fungi. This research was funded by the UKRI-BBSRC "Capacity building for bioinformatics in Latin America" (CABANA) grant, on behalf of the Global Challenges Research Fund [BB/P027849/1].

Biome: root:Environmental:Terrestrial:Soil
Niche partitioning of methanotrophs in stratified lakes

A detailed sampling of the water column in proximity to the oxygen-methane interface of four stratified Swiss lakes was performed. Amplicon sequencing analysis of 16S rRNA and pmoA genes and 16S rRNA and pmoA transcripts was used to investigate the active methane-oxidizing bacteria inhabiting the oxygen-methane resource gradient.

Biome: root:Environmental:Aquatic:Freshwater:Lake
EMG produced TPA metagenomics assembly of PRJNA801070 data set (Superworm (Zophobas morio) gut microbiome metagenomics).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA801070, 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 the Making and breaking DMS by salt marsh microbes (Illumina HiSeq 100bp) (Stiffkey_Saltmarsh_Sediment_SIP_Organosulfur) data set

The Stiffkey_Saltmarsh_Sediment_SIP_Organosulfur Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB1760. This project includes samples from the following biomes : Marine.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
Municipal Solid wastes Metagenome

Following increase in population size, urbanization and human activities, there is poor solid waste management in urban and peri-urban areas, mostly in Sub Sahara Africa. Varieties of solid wastes such as medical waste, domestic waste and industrial waste along with their associated microbes are dumped at the same place. We are witnessing high interaction between wild and domestic animals as well as people in municipal dumps. We hypothesized the municipal dumps to be the driver for the emergence of new pathogens of public health importance. We wanted to know the abundance, diversity and dynamics of bacteria circulating in municipal dumpsite and the associated risks. This knowledge is key towards improved solid waste management, hence mitigation of the associated risks.

Biome: root:Engineered:Solid waste
Lifestyles and gut microbiome composition

This study contributes to the characterization of the gut microbiome of healthy humans in a Mediterranean population sample.

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