SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Comparison of meta-barcoding and shotgun metagenomic analysis of fungi associated with spontaneous wine fermentation

Wine is a complex beverage, comprised of thousands of metabolites that are produced through the action of yeasts and bacteria in fermenting grape must. To ensure a robust and reliable fermentation, most commercial wines are produced via inoculation with large amounts of the major wine yeast, Saccharomyces cerevisiae. However, there is a growing trend towards the use of uninoculated or wild fermentations, in which the yeasts and bacteria that are naturally associated with the vineyard or winery perform the fermentation. The varied metabolic contributions of the numerous non-Saccharomyces species in this microbial community are thought to impart complexity and desirable taste and aroma attributes to wild ferments when compared to their inoculated counterparts.In order the map the microflora of spontaneous fermentation, metagenomic techniques were used to characterise and monitor the progression of fungal species in several wild fermentations. Both amplicon-based ITS phylotyping and shotgun metagenomics were used to assess community structure, in addition to the isolation, sequencing and de novo assembly of the first reference genomes for several dominant wine-associated species.

Biome: root:Engineered:Food production:Fermented beverages
Bioreactor inoculated with sediment Metagenome

Metagenomic contigs were binned following isolation from a continuous culture bioreactor inoculated with sediment from the German Wadden Sea.  Eight samples were taken from the bioreactor at different time points (between day 48 and day 185 of cultivation).

Biome: root:Engineered:Bioreactor:Continuous culture:Marine sediment inoculum:Wadden Sea-Germany
Canadian MetaMicrobiome Library Projects

Our studies aim to probe various environments, including the soil and gut environments, for interesting or novel microbial functions of industrial, environmental, or medical relevance. We apply sequence- and function-based metagenomic techniques to explore these environments.

Biome: root
Fungal community across a tropical forest disturbance gradient

Woody debris is an important component of forest ecosystems, forming a substantial carbon pool and habitat for a diversity of organisms, including specialist species. The decomposition of woody debris is controlled by both abiotic and biotic factors. However, much less is known about the biotic factors, such as the contribution of fungi to nutrient cycling in tropical biomes. Moreover, given the high rates of tropical deforestation and forest degradation, it is vital to better understand anthropogenic impacts on essential biotic processes, such as decomposition. Hence, we set out to link the impacts of forest degradation and the role of biotic characteristics, especially fungal diversity and composition, in determining woody debris decomposition rates in a tropical biomeSpecifically, we examined the following questions; (i) what is the effect of wood species identity on the diversity and community structure of fungi; (ii) how does fungal diversity and composition in woody debris change through time and with state of decay; (iii) how does the degree of forest disturbance affect fungal diversity and community structure and (iv) how do these factors determine the rate of wood decomposition?

Biome: root:Environmental:Terrestrial:Soil:Tropical rainforest
Distinct spatial patterns of bacterial diversity shaped by salivary flow on tooth surfaces in humans

Bacteria that inhabit the oral cavity of humans Raw sequence reads

Biome: root:Host-associated:Human:Digestive system:Oral
We sequenced the bacterial compositions of 2,882 samples from the foxtail millet rhizoplane, rhizosphere and corresponding bulk soil from two well-separated geographic locations.

The root microbes play pivotal roles in plant productivity, nutrient uptakes and disease resistance. The microbial communities were widely investigated by the 16S amplicons sequencing in crops and model plants. We sequenced the bacterial compositions of 2,882 samples from the foxtail millet rhizoplane, rhizosphere and corresponding bulk soil from two well-separated geographic locations.We revealed the root microbial composition of the foxtail millet and defined the core rhizoplane bacteria.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Two metagenomes from outflow channels of Lost Hammer ultrasaline, perennial spring from Canadian High Arctic.

Characterization of microorganisms that thrive in extreme habitats, often called extremophiles, enable us to understand how biology functions at the frontiers of life. This knowledge allows us to model the potential habitability of environments in Solar System bodies such as Mars and Jupiter's icy moon Europa, as well as understand the long-term evolution and fate of microbial life on Earth. The samples for this study were collected from immediate surroundings of a cold, hypersaline spring in the Canadian Arctic as planetary analogue for Europa.

Biome: root:Environmental:Aquatic:Sediment
Persistent gut microbiota immaturity in malnourished Bangladeshi children

Therapeutic food interventions have reduced mortality in children with severe acute malnutrition (SAM) but incomplete restoration of healthy growth remains a major problem. The relationships between the type of nutritional intervention, the gut microbiota, and therapeutic responses are unclear. In the current study, bacterial species whose proportional representation define a healthy gut microbiota as it assembles during the first two postnatal years were identified by applying a machine-learning-based approach to 16S rRNA datasets generated from monthly fecal samples obtained from a birth-cohort of children, living in an urban slum of Dhaka, Bangladesh, who exhibited consistently healthy growth. These age-discriminatory bacterial species were incorporated into a model that computes a relative microbiota maturity index and microbiota-for-age Z-score that compare development (defined here as maturation) of a childs fecal microbiota relative to healthy children of similar chronologic age. The model was applied to twins and triplets (to test for associations of these indices with genetic and environmental factors including diarrhea), children with SAM enrolled in a randomized trial of two food interventions, and children with moderate acute malnutrition. Our results indicate that SAM is associated with significant relative microbiota immaturity that is only partially ameliorated following two widely used nutritional interventions. Immaturity is also evident in less severe forms of malnutrition and correlates with anthropometric measurements. Microbiota maturity indices provide a microbial measure of human postnatal development, a way of classifying malnourished states, and a parameter for judging therapeutic efficacy. More prolonged interventions with existing or new therapeutic foods and/or addition of gut microbes may be needed to achieve enduring repair of gut microbiota immaturity in childhood malnutrition and improve clinical outcomes. (Subramanian et al., doi:10.1038/nature13421)

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Characterizing postnatal co-development of the gut microbiota and mucosal IgA responses in healthy twin pairs and a gnotobiotic mouse model

Abstract: Immunoglobulin A (IgA) is the major class of antibody secreted by the gut mucosa, where it contributes to barrier function by preventing microbial and food antigens from interacting with host tissues1,2. The lack of metrics for quantifying development of the gut microbiota and mucosal immune system has hindered the ability to dissect the effects of microbial, host and environmental factors on their co-development. Therefore, we subjected fecal samples, collected monthly during the first 3 postnatal years from 40 healthy USA twin pairs, to bacterial 16S rRNA gene sequencing and to fluorescence-activated cell sorting to distinguish IgA-targeted from non-targeted taxa. Applying a machine-learning algorithm (Random Forests), we identified a set of 25 age-discriminatory bacterial taxa whose patterns of representation define a program of microbiota assembly/maturation shared across twin pairs. Remarkably, IgA responses to 30 taxa, including a subset of the age-discriminatory organisms, converge on a pattern shared across twin pairs by the second postnatal year; the observed targeting patterns were not simple reflections of relative abundance or taxonomy. Zygosity, delivery mode, and breast versus formula feeding had small albeit statistically significant effects on targeting. In follow-up studies, young germ-free mice were colonized with fecal microbiota obtained from two twin pairs at 6 and 18 months of age, and fed a sequence of human diets designed to simulate the transition from milk feeding to complementary foods. Distinct age-associated differences in mucosal IgA responses to the transplanted human microbiota were recapitulated in both diet contexts for both twin pairs, suggesting that intrinsic properties of their community members play a dominant role in dictating IgA responses.  This approach can be used to define gut mucosal immune development in health and disease states, and help identify ways to repair or prevent perturbations in this facet of host immunity.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Metatranscriptome of an algal bloom from St Helena Bay on the west coast of South Africa

The aim of this project is to investigate changes in gene expression specifically genes linked to PCD the duration of an algal bloom event. The study was motivated by the paucity of knowledge in changes in microbial complexity in algal blooms and by the lack of empirical evidence of PCD from field and natural environments such as algal blooms. Despite the progress made, algal blooms remain poorly understood, specifically why a particular taxa proliferates to dominate the bloom remains a challenge and a call for species specific information has been made. Concomitant to documenting the changes in microbial diversity and environment conditions during an algal bloom, changes in gene expression in relation to PCD will also be assessed to provide a contextual understanding of PCD during a bloom event.

Biome: root:Environmental:Aquatic:Marine
Prunus Root and soil microbial community Targeted loci

Amplicon-based sequencing was used to examine the bacteria, fungi, and oomycetes associated with soils collected from almond orchards throughout the central valley of California. Later, peach seedlings were grown in these soils in a greenhouse, and amplicon sequencing was used to examine the root-associated microbial community.

Biome: root:Host-associated:Plants:Root
Infant nasopharyngeal bacteria microbiome

Bacterial community profiling of nasopharyngeal (NP) aspirates across a birth cohort of 234 infants. Multiple samples per child, including "healthy" NP samples collected in the absence of respiratory symptoms and "infection" NP samples collected during episodes of acute respiratory illness.

Biome: root:Host-associated:Human:Respiratory system:Nasopharyngeal
Mouse fecal microbiome after exposure to high LET radiation

Space travel is associated with continuous low-dose-rate exposure to high Linear Energy Transfer (LET) radiation. Pathophysiological manifestations after low-dose radiation exposure are strongly influenced by non-cytocidal radiation effects including microbiome and cellular gene expression. Using a mouse model for exposure to high LET radiation, we observed substantial changes in the composition and functional potential of the microbiome. These were paralleled by changes in the abundance of multiple metabolites, which were related to the enzymatic activity of the altered metagenome by means of metabolic network modeling. There was a complex dynamic in microbial and metabolic composition at different radiation doses, suggestive of transient, dose-dependent interactions between microbial ecology and signals from the hosts cellular damage repair processes. Functional shifts included features associated with dysbiosis at the onset of chronic inflammatory responses, which could pre-dispose space travelers to systemic, long-term health risks.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Analysis of dust samples from the Russian part of the ISS

Our study focuses on the hardiest microorganisms inhabiting the ISS, in order to assess their diversity, and capabilities to resist certain stresses. We specifically selected dust samples from the Russian modules that were obtained 8-10 years ago, and stored since then under sealed conditions on Earth. Targeting long-time survivors and spore-forming microorganisms, we assessed consequently the cultivable microbial community of these samples, in order to obtain model microbial strains that could help to analyze specific adaptation towards environmental stresses, such as desiccation and lack of nutrients. In this study, we analyzed these microorganisms with respect to their resistance towards thermal stress and exposure to clinically relevant antibiotics. In addition, we assessed the bacterial and archaeal community via molecular methods (NGS sequencing) and compared our new data with the previously derived information from the ISS microbiome.

Biome: root:Engineered:Built environment
Bacterial endophytes of tree species belonging to the family Pinaceae Targeted loci environmental

Bacterial endophytes of tree species belonging to the family Pinaceae. Tree species were collected along the native range of Pinus flexilis

Biome: root:Host-associated:Plants:Phylloplane:Endophytes
16S rRNA gene amplicon sequencing of patients with colorectal cancer

A collection of 16S rRNA gene amplicon sequences from patients with colorectal cancer, and technical controls. Samples come from stool, mucosa, tissue biopsies and tumor biopsies.

Biome: root:Host-associated:Human:Digestive system
Ice Wedge Polygon

Frozen soil samples were collected that represent topographically high and low areas from basins of various ages around Barrow, Alaska. All of the sites are coordinated with portable or permanent Eddy covariance towers that have been used to study gas exchange. The samples were collected from several transects that include polygon rims and centers. At each site two cores were taken from rims and three from centers. The cores were approximately 25 cm deep, and so only include the active layer. Specifically samples were obtained from matching sets of polygon rims and centers from 3 different basins. This produced 24 samples: 3 basins x 2 types (rim/center) x 4 depths (6-10, 16-20, 26-30, 36-40cm). These were supplemented with smaller cores from additional basins: 3 basins x 2 types x 2 depths (6-10, 16-20cm). For the samples high refers to polygon rims, low to polygon centers. Additional abundant biological and chemical metadata have been collected for these samples.

Biome: root:Environmental:Terrestrial:Soil:Permafrost
Flores_palm_EBI

palm samples from Flores_SMP for submission to EBI

Biome: root:Host-associated:Human:Skin
Gut and nasal microbiome in Parkinson''s disease

Amplicon sequencing and metagenomic data of nasal and stool samples of PD patients, RBD patients and healthy controls.

Biome: root:Host-associated:Human
Metagenomics of gut microbiome from diarrheal samples

Stool samples from diarrheal patients were used to study the structural and functional diversity of the gut microflora.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Gut Microbiome Alterations Drive Distinct Metabolic Expression Patterns in a Cohort of Italian Patients with Parkinson's Disease

Parkinson's disease is a neurodegenerative disorder characterized by the accumulation of intracellular aggregates of misfolded alpha-synuclein along the cerebral axis. Several studies report the association between intestinal dysbiosis and Parkinson, although a cause-effect relationship yet remains to be established. Herein, the composition of the microbiota in fecal extracts of 64 patients with Parkinson's disease and 51 controls was determined using a next generation sequencing approach. A hypothetical functional profile based on the 16S rRNA profile using a predictive metagenomic tool was also performed. A significant decrease in the abundance of taxa belonging to the phylum Firmicutes, particularly in the Lachnospiraceae family was detected in the patient group. Key members of the Lachnospiraceae family, such as the genus Blautia and some related species, were significantly reduced in patients compared to controls. Moreover, consistent with depletion of short chain fatty acids-producing bacteria, genera and species within the Lachnospiraceae family (Butyrivibrio, Pseudobutyrivibrio, Coprococcus, Roseburia and Roseburia faecis) were also decreased. Interestingly, the relative abundance of Brevibacteriaceae and Lachnospiraceae was positively associated with tremor-dominant phenotype, whereas abundance of Enterobacteriaceae and Escherichia was positively associated with non-TD phenotypes. Finally, the functional prediction of gut metagenome composition in patients, in comparison with those of healthy controls, showed the presence of 81 significantly altered metabolic pathways. In particular, there was a significant increase of most pathways of the amino acids and lipids metabolisms, of other secondary metabolites, and in the metabolism and biodegradation of xenobiotics.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Gut microbiota in Parkinson's disease: temporal stability and disease progression

Aiming to explore the temporal stability of gut microbiota in Parkinson's disease and the potential relationship of microbiota and disease progression, we characterized the gut bacterial communities of 64 Parkinson's patients and 64 control subjects from two stool samples per subject, collected on average 2.25 years apart. Microbial communities were analyzed with amplicon sequencing of the V3-V4 variable regions of the 16S rRNA gene, performed on the Illumina MiSeq platform.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Home Microbiome Metagenomes

The project identifies patterns in microbial communities associated with different home and home occupant (human and pet) surfaces.

Biome: root:Engineered:Built environment
uncultured prokaryote Metagenome

In the present study, microbial communities ofsponges, Sediments and Seawater inhabitingcoral reef ecosystems were investigated usingbarcoded pyrosequencing of 16S rRNA geneamplicons. Our main goals were to compare thebacterial and archaeal richness and composition ofsponge species, sediment and seawaterinhabiting coral reef systems. FLX 454 titanium pyrosequencingstudy.

Biome: root:Mixed
Temperate invertebrates associated prokaryotic diversity

This study compares gorgonian microbiomes to those from other surrounding fauna and seawater using partial 16S rRNA gene amplicons.

Biome: root:Mixed
Biogeography of cyanobacterial consortia from the culture collection of microorganisms from extreme environments

Very little is known about how members of the phylum cyanobacteria affect and respond to changes in complex biological systems. To fill this knowledge-gap we selected 26 photosynthetic consortia, based on their collection site and growth condition, from a total of over 1,200 environmental samples available in the Culture Collection of Microorganisms from Extreme Environments (CCMEE) for 16S rRNA sequencing to identify common community members and potential keystone species. Results from this work will help to determine the nutritional and environmental requirements of microorganisms that can currently only be grown in co-culture and to define the molecular processes that facilitate carbon and nitrogen sequestration by these phototrophic consortia and the individual organisms that contribute to them.

Biome: root:Mixed
Marine Lakes Jellyfish and water Metagenome

In the present study, microbial communities of jellyfish and water inhabiting Marine Lakes ecosystems were investigated using barcoded pyrosequencing of 16S rRNA gene amplicons. FLX 454 titanium pyrosequencing study.

Biome: root:Mixed
Coral Reef Biotopes Metagenome

In the present study, microbial communities of sponges, Sediments and Seawater inhabiting coral reef ecosystems were investigated using barcoded pyrosequencing of 16S rRNA gene amplicons. Our main goals were to compare the bacterial and archaeal richness and composition of two sponge species, sediment and seawater inhabiting coral reef systems. FLX 454 titanium pyrosequencing study. Note that the sequences submitted are raw sequences prior to any analysis and thus contain short sequences, poor quality sequences and chimera. These will need to be filtered out using, e.g., using qiime scripts such as split_libraries and pick_otus with the usearch_ref argument, which will provide a chimera check and filter out poor quality sequences.

Biome: root:Mixed
16S rRNA gene Sequencing of Ircinia felix tissue

16S rRNA gene sequencing of tissue from the Caribbean sponge, Ircinia felix, and surrounding sediment and ambient water. The goals of this study were to assess the overall bacterial community changes between the three sample types as a correlation to nutrient processing by the sponges.

Biome: root:Mixed
Design and Evaluation of Illumina MiSeq compatible 18S rRNA Primers for Improved Characterization of Mixed Phototrophic Communities.

A systematic analysis of the most commonly amplified 18S rRNA hypervariable regions and the effect that PCR/sequencing bias has on community representation. The V4 and V8-V9 hypervariable regions were amplified for seven mock communities and for freshwater, marine, and wastewater samples to compare the sequenced community structure to theoretical communities and validate these results with environmental samples.

Biome: root:Mixed
16S rRNA gene metabarcoding reveals a potential metabolic role for intracellular bacteria in a major marine planktonic calcifier (Foraminifera).

We have investigated the possibility of bacterial symbiosis in Globigerina bulloides, a palaeoceanographically important planktonic foraminifera commonly used in investigations of climatically sensitive sub-polar and temperate water masses and wind driven upwelling regions of the worlds oceans. G. bulloides is unusual, since it lacks the protist algal symbionts often found in other spinose species and has an atypical geochemical shell signature. This is suggestive of a divergent ecology, making it a good candidate for investigating potential bacterial symbiosis as a contributory factor in shell calcification. Such ecological information is essential to fully evaluate the potential response of G. bulloides to ocean acidification and climate change.

Biome: root:Host-associated:Protists
Effect of sediment smothering on the sponge holobiont

Dredging can cause increased sedimentation in marine communities and smothering of sessile benthic organisms. In order to provide pressure:response values for sponges to sedimentation and tease apart the cause:effect pathways of dredging pressures, five heterotrophic and phototrophic species were repeatedly smothered by sediments every 4 days, and cleaned after 4, 16 and 30 days. This study shows that non-continuous sediment smothering for up to 30 days does not alter the health and composition of adult sponge holobionts as most species possess either active or passive self-cleaning strategies which allow them to continue with their feeding activity. However, although those smothering conditions seem tolerable by most species, it is expected that the combined effect of all three dredging-related pressures will increase the negative effects on sponges under realistic field conditions. These experimental results will assist regulators and environmental managers in reducing risks from dredging development although experimental research combining sedimentation, SSC and light attenuation is required before final thresholds can be derived for dredging impacts on sponges.

Biome: root:Host-associated:Porifera