SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Integrated Analysis of mtDNA Single Nucleotide Polymorphisms with the Vaginal and Placental Membrane Microbiome and Rendered Risk Estimation for Preterm Birth

Background: Although we and our microbial community and genomes (the human microbiome) have co-evolved over millions of years, to what extent the human host maternally inherited ancestral genome (mitochondrial genome) informs both microbial community composition and risk of human disease is unclear. We have previously demonstrated a significant association between the placental microbiome and risk of preterm birth, as well as (in non-pregnant subjects) association of mitochondrial DNA (mtDNA) variants (mtSNPs) with the vaginal and gut microbiome. In this study, we aimed to explore complex interactions between human host mtSNPs and the vaginal and placental membrane microbiome with associated risk of preterm birth.Methods: Maternal blood and placental tissue samples from 93 gravidae (n=54 with preterm deliveries between 23 and 0/7 and <37 and 0/7 weeks; n=39 term =37 and 0/7 weeks) were deep sequenced, and mtSNPs were called with high confidence. The microbial taxonomic abundance of the vagina (introitus and posterior fornix) and placental membranes (maternal and fetal side swabs) from the same subjects were obtained via 16S ribosomal RNA sequencing, and inferred metagenomics was employed for metabolic pathway analysis. Interactions among both microbial taxa and their inferred metagenomics pathways were examined for association with mtSNPs employing multiple linear regressions modeling for both genotype and clinical covariates with PLINK quantitative trait associations. Analyses were adjusted for multiple comparisons, with a q value <0.05 denoting significance.Results: Consistent with ours and others recent published observations, we observed an association between preterm birth and the composition of the placental membrane microbiome community (PERMANOVA p=0.042). In our cohort, no significant association between any mtSNP with the occurrence of preterm birth was observed. However, overall associations between mitochondrial genome variations and both the vaginal and placental membrane preterm microbial community were observed. Of note, several functional mtSNPs (within coding regions for electron transport genes) demonstrated significant and robust associations (q value <0.05) with both occurrence and abundance of certain taxa and their metagenomics pathways among preterm births.Conclusions: We have demonstrated for the first time that maternally inherited human mtSNPs are associated with variations in both placental membrane and vaginal microbial taxa membership and their inferred metabolic function during pregnancy, and consequentially linked to the occurrence of preterm birth.

Biome: root:Host-associated:Human
Paired mucosal j-pouch and afferent limb samples from postoperative ulcerative colitis and familial ademonatous polyposis patients from Mount Sinai Hospital, Toronto. Samples were collected during pouch endoscopy and 16S sequenced.


Biome: root:Host-associated:Human:Digestive system
Green alder encroachment shapes microbial diversity in subalpine soils.

Green alder encroachment shapes microbial diversity in subalpine soils.

Biome: root:Environmental:Terrestrial:Soil
Bacterial 16S rRNA and fungal ITS Metagenome

The flooding crisis in Thailand in 2011 is one of the biggest recorded floods which caused enormous scale of damages to ecological and human habitats and public health concerns. In this study, bacterial and fungal diversity in sediments and waters collected from flooded areas in Bangkok and suburban covering residential, agricultural, and industrial areas were analyzed using high-throughput 454 pyrosequencing of 16S rRNA/ internal transcribed spacer sequences (ITS). Proximate phylogeny analysis showed differences in microbial distribution in water and sediment samples with variation in diversity profiles according to sampling locations.

Biome: root:Environmental:Aquatic:Sediment
The study includes fungal genetic diversity assessment by ITS-1 next generation sequencing (NGS) analyses. The main the main experimental objects are soils of different classes, quality groups and also subjected to various agrotechnical treatments

The study included fungal genetic diversity assessment by ITS-1 next generation sequencing (NGS) analyses as well as the characterization of the catabolic potential of microbial communities (Biolog EcoPlates) in the soil under long-term monoculture of maize using different cultivation techniques. The results obtained from the ITS-1 NGS technique enabled to classify and correlate the fungi species or genus to the soil metabolome. The research methods used in this paper have contributed to a better understanding of genetic diversity and composition of the population of fungi in the soil under the influence of the changes that have occurred in the soil under long-term maize cultivation. In all cultivation techniques, thThis study has shown that: (1) fungal diversity was changed under the influence different cultivation techniques; (2) techniques of maize cultivation and season were an important factors that can influence the biochemical activity of soil. Maize cultivated in direct sowing did not cause negative changes in the fungal structure, even making it more stable  during seasonal changes; (3) full tillage and crop rotation may change fungal community and soil function. e season had a great influence on the fungal genetic structure in the soil.

Biome: root:Environmental:Terrestrial:Soil
Diamante Lake Red Biofilm Metatranscriptome

Diamante Lake Red Biofilm Metatranscriptome

Biome: root:Environmental:Aquatic:Freshwater:Lake
Raw sequence reads from soil relic DNA study

Study to assess the impact of relic (i.e. extracellular) DNA in soil on assessment of bacterial and fungal community structure.

Biome: root:Environmental:Terrestrial:Soil
Rumen and gastrointestinal tract contents Targeted Locus (Loci)

The aim of the Global Rumen Census project is to survey the diversity of microbes present in rumen samples obtained from a range of locations and farming situations.

Biome: root:Host-associated:Mammals:Digestive system
A collection of 16S reads for samples relating to pre-term infants

The NeoM (Neonatal Microbiota) Study is an ecological study investigating the microbiota of pre-term infants. Samples collected include faecal samples, skin swabs and swabs of infant incubators. Bacterial DNA was extracted from the samples using either MPBio FastDNA Spin kits or MPBio FastDNA Spin Kits for Soil and V3-V5 amplicons were generated using Bifidobacterium-optomised primers (Sim et al, 2012, PLOS ONE) and tagged with 12bp barcodes. These were then sequenced using a 454 Life Sciences GS FLX (Roche) following the Roche Amplicon Lib-L protocol. Both raw data (.sff files) and data denoised via ampliconnoise.py (as part of the Qiime pipeline) will be submitted here.

Biome: root:Mixed
Significant disparities in allergy prevalence and microbiota between the young people in Finnish and Russian Karelia.

BACKGROUND:Atopic allergy has been more common among schoolchildren in Finland, as compared to Russian Karelia. These adjacent regions show one of the most contrasting socio-economical differences in the world.OBJECTIVE:We explored changes in allergy from school age to young adulthood from 2003 to 2010/2012 in these two areas. The skin and nasal microbiota were also compared.METHODS:Randomly selected children from Finnish (n = 98) and Russian Karelia (n = 82) were examined in 2003, when the children were 7-11 years of age, and again in 2010 (Finnish Karelia) and 2012 (Russian Karelia). We analysed self-reported allergy symptoms and sensitization to common allergens by serum sIgE values. The skin (volar forearm) and nasal mucosa microbiota, collected in 2012 (aged 15-20 years), identified from DNA samples, were compared with multivariate methods.RESULTS:Asthma, hay fever, atopic eczema, self-reported rhinitis, as well as atopic sensitization, were threefold to 10-fold more common in Finland, as compared to Russian Karelia. Hay fever and peanut sensitization were almost non-existent in Russia. These patterns remained throughout the 10-year follow-up. Skin microbiota, as well as bacterial and fungal communities in nasal mucosa, was contrastingly different between the populations, best characterized by the diversity and abundance of genus Acinetobacter; more abundant and diverse in Russia. Overall, diversity was significantly higher among Russian subjects (Pskin < 0.0001, Pnasal-bacteria < 0.0001 and Pnasal-fungi < 0.01). Allergic diseases were not associated with microbial diversity in Finnish subjects.CONCLUSIONS AND CLINICAL RELEVANCE:Differences in allergic phenotype, developed in early life, remain between populations. A parallel difference in the composition of skin and nasal microbiota suggests a potential underlying mechanism. Our results also suggest that high abundance and diversity of Acinetobacter might contribute to the low allergy prevalence in Russia. Implications of early-life exposure to Acinetobacter should be further investigated.

Biome: root:Host-associated:Human
anchialine metagenome Raw sequence reads

Microbial ecology is an important and growing field that has revealed the importance of microbes in many ecosystems; however, some ecosystems have yet to receive much attention including the anchialine ecosystem (nearshore bodies of water with subsurface freshwater and seawater connections). Hawaiian anchialine habitats in the Cape Kinau region of Maui and the Kona region of Hawaii exhibit distinctive, laminated orange cyanobacterial-bacterial crusts, but little is known about their composition, the composition of microbial communities in non-crust containing sites lacking the cyanobacterial-bacterial crusts, or the degree to which environmental factors structure them. During the summer of 2010, we surveyed benthic and water column microbial communities from ten anchialine habitats on Oahu, Maui, and Hawaii using high-throughput amplicon sequencing of the V6 (prokaryotic-biased) and V9 (eukaryotic-biased) hypervariable regions of the SSU rRNA gene. A subset of six anchialine habitats were also sampled in the spring, summer, and winter of 2011 to allow elucidation of seasonal effects on the Hawaiian anchialine microbial community.

Biome: root:Environmental:Aquatic
EMG produced TPA metagenomics assembly of the FVB F Partial Co2 (FVB F Partial Co2) data set.

The FVB F Partial Co2 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB13629.  This project includes samples from the following biomes: Host-associated, Mammals.

Biome: N/A
EMG produced TPA metagenomics assembly of the FVB Partial Co1 (FVB Partial Co1) data set.

The FVB Partial Co1 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB13645.  This project includes samples from the following biomes: Host-associated, Mammals.

Biome: N/A
EMG produced TPA metagenomics assembly of the Comparison or twelve metagenomes from peat matrix, fen and bog, at two different depths in troplicates (PeatMetagenome) data set.

The PeatMetagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB11421.  This project includes samples from the following biomes: Soil.

Biome: root:Environmental:Terrestrial:Soil
Comparison or twelve metagenomes from peat matrix, fen and bog, at two different depths in troplicates

Peat matrix samples were recovered from one fen and one bog at two different depths (5-10cm and 10-15cm) in triplicates (Les Pradeaux, Massif Centrale, France). Sequences were obtained by pyrosequences.

Biome: root:Environmental:Terrestrial:Soil
Dechlorinating community

Try to identify the microorganisms responsible for dechlorination and their functional genes.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
EMG produced TPA metagenomics assembly of the Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Seattle, Washington, United States - P5a_32mM metagenome (mixed culture metagenome) data set.

The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441893.  This project includes samples from the following biomes: Environmental, Aquatic, Lentic, Brackish.

Biome: root:Environmental:Aquatic:Lentic:Brackish
EMG produced TPA metagenomics assembly of PRJEB20800 data set (Gut resistome modulates resilience and recovery of gut microbiota after broad-spectrum antibiotic treatment).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set ERP022986, and was assembled with SPAdes (v3.13.0).

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Gut resistome modulates resilience and recovery of gut microbiota after broad-spectrum antibiotic treatment

Antibiotics have profound impacts on the microbial communities living in the human gut, where bacterial species harbor and exchange antibiotic resistance genes collectively called resistome. Human population surveys have demonstrated that gut microbial resistomes reflect local antibiotics usage patterns, while previous small cohort studies based on single antibiotic exposures have shown varying degrees of antibiotic impact on the gut microbiota and their associated resistome. However, the role of resistomes of particular gut species in their ability to persist in the face of antibiotic treatment has not been systematically studied.Applying shotgun sequencing and quantitative metagenomics, we analyzed the partial eradication and subsequent regrowth of gut microbiota in 12 healthy young men over a 6 month period following a 4-day intervention with three broad-spectrum antibiotics. The gut microbial communities of the study subjects underwent profound compositional changes due to the treatment but slowly recovered to near-baseline compositions. Immediately after the treatment, the gut microbiota featured an increased relative abundance of opportunistic and proinflammatory bacterial species, and a decreased relative abundance of short chain fatty acid producers, while exhibiting an increased functional potential for multidrug efflux pumps and virulence factors. These enrichment trends were weaker after 8 days and mostly cleared out after 42 days. However, 9 common intestinal commensal species found at baseline and associated with short chain fatty production or efficient digestion of polysaccharides remained undetectable in most of the subjects even after 180 days.Carrying genes that confer resistance to the antibiotics used in this multidrug study had specific consequences for the survival and de novo colonization potential of microbial species. While species harboring beta-lactam resistance genes were positively selected during and after the intervention, those harboring glycopeptide or aminoglycoside resistance exhibited increased odds of de novo colonization but decreased odds of survival. Despite a mild long-lasting imprint following exposure to three antibiotics, the gut microbiota of healthy young adults are resilient to a broad-spectrum antibiotic intervention, and their recovery process is modulated by antibiotic resistance gene carriage.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Human Skin Microbiome Metagenome (human skin metagenome) data set.

The human skin metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA277905.  This project includes samples from the following biomes: Host-associated, Human, Skin.

Biome: root:Host-associated:Human:Skin
Bacterial community and resistome of lettuce plants

Characterization of bacterial communities of lettuce plants and their production environment including irrigation water, soil, an manure.Additional analysis of the bacterial resistome of the same systems.

Biome: root:Host-associated:Plants
Manure microbiome of dairy cows fed grass or grass silage diets

Manure samples were taken from 18 dairy cows on one farm.  Cows were Holstein-Friesian or Holstein-Friesian cross and all from the same herd but kept under two different systems.  Nine animals were from a group kept at pasture with a diet of grazed grass plus 5.5-7kg of concentrated per day.  The other nine were from a group kept in a cubicle house with a diet of ad libitum grass silage plus 10kg concentrates per day.  Samples were taken directly after defecation and transported to the laboratory on ice.  They were frozen at -20C until DNA extraction using Qiagen Powersoil Pro kit (according to manufacturer's instructions).  The v4 region of the 16s rRNA gene was sequenced on an Illumina Miseq (250bp paired end reads).

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Bermuda Atlantic Time-series Study metagenomes

Metagenome-assembled genome bins to assess the diversity and evolution of globally abundant deep-ocean bacteria.

Biome: root:Environmental:Aquatic:Marine
Geotraces Raw sequence reads

This study is aimed to explore the microbial lifestyle in ocean and interpret metabolic potentials using metagenome/metaproteome dataset. Furthermore, it is important to learn about various mode of energy consumption that may support marine microbes i.e. photoautotrophy, chemoautotrophy and heterotrophy.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Ligning valorization strategies based on the development of a specialized microbial community

There is an increasing interest in the development of biological routes for lignin depolymerization and valorization. Studies have been performed to elucidate the enzymatic routes and microorganism involved in lignin conversion. Considering that the vast majority of microorganisms are not likely to be cultivated in an isolated form, metagenomic approaches display great potential to gain further access to microorganisms, genes and metabolic pathways linked to lignin breakdown and upgrading into high value chemicals. The present work focused on the development of a lignin-degrading specialized community (CLig) and the application of a combination of metagenomics approaches, including comprehensive taxonomic characterization and binning-assembly for reconstruction of microbial genomes. All these efforts provide basis to portray the major bacterial pathways involved in lignin degradation and aromatic compounds conversion. From the analysis of massive DNA sequencing data, several microorganisms and enzymes linked to the metabolic pathways of interest were identified, thus constituting a promising resource of biological information for lignin valorization. Along with isolation and genome sequencing of lignolytic bacterial strain of potential biotechnological interest, pathways for lignin valorization was validated based on vanillin production from ferulic acid using feruloyl-CoA synthetase (fcs) and enoyl-CoA hydratase/aldolase (ech).

Biome: root:Engineered:Biotransformation
Eimeria population derived from 18s amplicon sequencing of chicken ceacal content

18s amplicon sequencing of Eimeria species in ceacum of Poultry (Gallus gallus).

Biome: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
Anaerobic microbial community enriched with amino acids

Amino acids are important monomers that are ubiquitously present in anaerobic environments after protein hydrolysis. Anaerobic digester sludge from two sources was used to inoculate batch cultures, which were fed with twenty individual amino acids. Five successive enrichments were performed with 10% v/v transfer. 16S rRNA and rRNA gene were extracted and amplified from enrichment cultures. Amplicons were sequenced using Illumina Miseq platform. Distinct community structures were observed between the first enrichment and later enrichments. Such trajectory of community evolution indicated enrichment of specific amino acids degraders that were not abundant in the early enrichments. Based on known knowledge of fermenters, syntrophs, and methanogens, four types of communities were observed.

Biome: root:Host-associated:Human:Digestive system:Oral:tongue dorsum
Microbial community structure of sediment microbiome in the pelagic zone of Gulf of Kutch, Gujarat, India.

The pelagic sediment microbiota was assessed in the three sections of the sampled core (1m) from four locations of the Gulf of Kutch.

Biome: root:Environmental:Aquatic:Marine:Sediment
Microbial community structure of sediment microbiome in the pelagic zone of Gulf of Khambhat, Gujarat, India.

The pelagic sediment microbiota was assessed in the three sections of the sampled core (1m) from four locations of the Gulf of Khambhat and one location from the open sea (Arabian Sea).

Biome: root:Environmental:Aquatic:Marine:Sediment
EMG produced TPA metagenomics assembly of the PRJNA344863 data set (Viral Metagenomics of fecal samples of fruit bats).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA344863.  This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
EMG produced TPA metagenomics assembly of the PRJNA407112 data set (Investigating the viral ecology of global bee communities with high-throughput metagenomics).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA407112.  This project includes samples from the following biomes: root:Host-associated:Insecta.

Biome: root:Host-associated:Insecta
EMG produced TPA metagenomics assembly of the PRJEB6941 data set (Evaluation of methods to purify virus-like particles for the sequencing of intestinal viromes).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB6941.  This project includes samples from the following biomes: root:Engineered:Modeled:Simulated communities (microbial mixture).

Biome: root:Engineered:Modeled:Simulated communities (microbial mixture)
EMG produced TPA metagenomics assembly of the PRJNA288501 data set (Freshwater Viruses Metagenomic assembly).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA288501.  This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Lentic.

Biome: root:Environmental:Aquatic:Freshwater:Lentic
EMG produced TPA metagenomics assembly of the PRJNA385126 data set (viral metagenome Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA385126.  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 the PRJEB22882 data set (Taxonomic and gene content analysis of the bacterial viral metagenomes from the oral cavity from healthy youngsters in Valencia).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB22882.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.

Biome: root:Host-associated:Human:Digestive system:Oral
EMG produced TPA metagenomics assembly of the PRJEB12797 data set (Shotgun metagenomics of moose rumen).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB12797.  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