SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Do below-ground genotypes influence above-ground microbiomes of grafted tomatoes?

In this study, we evaluated how below-ground genotypes of plants determine bacterial and fungal community structures in leaves in field conditions. After growing grafted tomato individuals in a filed experiment, we analyzed the leaf microbial community compositions of the sampled tomatoes based on Illumina sequencing. The contributions of below-ground genotypes on the microbiome structures were then evaluated by comparing the community datasets of eight tomato rootstock strains.

Biome: root:Host-associated:Plants:Phylloplane
Honeybee bacterial community across gut compartments

The gut bacterial microbiome of honeybee (Apis mellifera) was investigated to evaluate the composition and spatial organization in different gut portions. Adult foragers were collected in the late summer from experimental apiaries located at DISAFA (University of Turin, Italy). Microbiological analyses were performed on the dissected guts compartments (i.e. crop, midgut, ileum and rectum) of honeybee workers. High-throughput sequencing of 16S rRNA gene was used to investigate the bacterial communities associated to the gut compartments of this insect.

Biome: root:Host-associated:Insecta:Digestive system
Honeybee fungal community across gut compartments

The gut fungal microbiome of honeybee (Apis mellifera) was investigated to evaluate the composition and spatial organization in different gut portions. Adult foragers were collected in the late summer from experimental apiaries located at DISAFA (University of Turin, Italy). Microbiological analyses were performed on the dissected guts compartments (i.e. crop, midgut, ileum and rectum) of honeybee workers. High-throughput sequencing of ITS2 region were used to investigate the fungal communities associated to the gut compartments of this insect.

Biome: root:Host-associated:Insecta:Digestive system
Upper respiratory microbiome during severe SARS-CoV-2 infection

Characterize the upper respiratory microbiome during severe SARS-CoV-2 infection

Biome: root:Host-associated:Human:Respiratory system:Nasopharyngeal
EMG produced TPA metagenomics assembly of PRJEB25419 data set (Breast Cancer Metagenomics).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB25419, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Skin.

Biome: root:Host-associated:Human:Skin
Microbiome in rhizosphere and endosphere of tomato

Bacterial, archaeal, fungal communities associated with the rhizosphere and endosphere of tomato

Biome: root:Host-associated:Plants:Phylloplane
The salivary microbiome of COVID-19 inpatients and outpatients

The aim of the study is to analyze the salivary microbiome of COVID-19 inpatients and outpatients using 16S rRNA gene sequencing.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
The gut microbiome 16s rDNA sequencing data of patients with COVID-19

The gut 16s rDNA sequencing data of patients with COVID-19

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Oomycete-Plant Metagenome

The goal of the analyses was to investigate the structure of the bacterial rhizospheric microbiota able to colonize the tomato root-P. parasitica pathosystem. 16S rRNA gene sequencing was used to describe the composition of the rhizospheric sub-microbiota of Solanum lycopersicum able to colonize tomato roots either axenic or partly covered with P. parasitica biofilms. Sampling was performed the 31st of May 2014, on soil supporting tomato growth (Solanum lycopersicum cv. Marmande). The experimental site was an E-W-oriented greenhouse located at the INRA Pathologie Végétale research unit in Montfavet (43.9 N 4.8 E). Thirty rhizospheric samples were grouped by 10 into three biological replicates (R1, R2, R3) on the basis of the distribution of the three samples from each area in distinct replicates. Biosamples results from the incubation and then the adhesion of microbial suspensions from R1, R2 and R3 at the root surface of tomato seedlings. M1R1, M1R2 and M1R3 correspond to the sub-microbiota adhering to axenic roots. M2R1, M2R2 and M2R3 correspond to the sub-microbiota adhering to roots partly covered with P. parasitica biofilms. An amplicon library was constructed (V3-V5 primers) for the six biosamples and sequenced using Illumina MiSeq technology. Sequence data are cleaned according to the FastQC quality parameters.

Biome: root:Host-associated:Plants:Root
Upper respiratory microbiome during SARS-CoV-2

Characterize the upper respiratory microbiome during mild-to-moderate SARS-CoV-2 infection in adult outpatients.

Biome: root:Host-associated:Human:Respiratory system:Nasopharyngeal:Nasal cavity
Gut microbiome linked to SARS-CoV-2 infection and COVID-19 severity

The gut microbiota impacts human health and contributes to regulate immune responses. Severe COVID-19 illness is characterized by a pro-inflammatory immune response. The effect of SARS-CoV-2 on altering the gut microbiome and the relevance of the gut microbiome on COVID-19 severity is unclear. This study analyses the gut microbiome associated with SARS-CoV-2 infection and COVID-19 severity.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Bacterial microbiota in roots of Arabidopsis thaliana and relative Brassicaceae species

Plants host at the contact zone with soil a distinctive root-associated bacterial microbiota believed to function in plant nutrition and health. We investigated the diversity of the root microbiota within a phylogenetic framework of hosts: three Arabidopsis thaliana ecotypes along with its sister species Arabidopsis halleri and Arabidopsis lyrata as well as Cardamine hirsuta, which diverged from the former ~35 myr ago. We surveyed their microbiota under controlled environmental conditions and of A. thaliana and C. hirsuta in two natural habitats. Deep 16S rRNA gene profiling of root and corresponding soil samples identified a total of 237 quantifiable bacterial ribotypes, of which an average of 73 community members were enriched in roots. The composition of this root microbiota depends more on interactions with the environment than with host species. Inter-host species microbiota diversity is largely quantitative and is greater between the 3 Arabidopsis species than the 3 A. thaliana ecotypes. Host species-specific microbiota were identified at the levels of individual community members, taxonomic groups and whole root communities. Most of these signatures were observed in the phylogenetically distant C. hirsuta. However, the branching order of host phylogeny is incongruent with inter-species root microbiota diversity, indicating that host phylogenetic distance alone cannot explain root microbiota diversification. Our work reveals within 35 myr of host divergence a largely conserved and taxonomically narrow root microbiota, which comprises stable community members belonging to the Actinomycetales, Burkholderiales and Flavobacteriales.

Biome: root:Host-associated:Plants:Root
microbiome analysis for patietns with COVID-19

To conduct research that contributes to the control of COVID-19 infections and to contribute to society.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
16S rRNA amplicons from Ambargasta salt flat soil

Characterization of the halophilic microbial communities of an argentinian Salt Flat by 16sRNA amplicons

Biome: root:Environmental:Terrestrial:Soil
Influence of the Herbicide Glyphosate on the bacterial community present in a sample from an Argentine salt flat

In this study, soil samples from an Argentine salt flat with added glyphosate were cultured to study halophilic strains capable of surviving and growing under these conditions.

Biome: root:Environmental:Terrestrial:Soil
Effect of crop rotation and straw addition on microbial communities in rhizosphere and bulk soil

In this study, we analysed soil microbial responses to different crop rotation systems (rice-rice (RR), maize-maize (MM), rice-maize (MR)) and rice straw mulching in the rhizosphere of Zea maize and the surrounding bulk soil. Soils were collected from different field locations subjected to the different crop rotation systems and Zea maize were planted in a microcosm experiment. The bacterial and fungal community composition was analysed by 16S rRNA gene and ITS based amplicon sequencing.

Biome: root:Host-associated:Plants:Rhizosphere
The rhizoplane/endosphere of wild Arabidopsis accessions

To investigate the role of plant genes in shaping root-associated microbial communities, we grew wild Arabidopsis thaliana accessions in a field site where the model is known to occur. Because Arabidopsis predominantly occurs as a winter annual, we grew the plants from October until late March (~156 days). At the end of the field experiment, we collected the plants using sterile technique and plants were separated at the root collar. Samples were then flash frozen in the field before being stored at -80C.To characterize the bacteria and fungi in the rhizoplane and endosphere of the roots, samples were washed in phosphate buffer. PCR amplification and sequencing of ITS1 and the hypervariable regions V5-7 of 16S rDNA was used to characterize the bacteria and fungi of these samples.

Biome: root:Host-associated:Plants:Rhizoplane:Endophytes
Human skin bacterial metagenome and Virome Metagenome

Viruses can impact microbiome structure and function through predation and genetic exchange, but little is known of cutaneous viral communities and their interactions with their hosts. To query virus-host interactions of the skin, we performed parallel metagenomic sequencing and an integrated analysis of DNA isolated from virus-like particles (VLPs) and total microbial communities. To assess spatial, interpersonal, and temporal variance, samples were collected from eight anatomical skin sites of 16 healthy individuals over two months. Skin viral communities were dominated by tailed bacteriophages--viruses replicating on human cells were comparatively rare. Similar to the skin whole metagenome, viral community composition and diversity was strongly associated with the microenvironment of the site sampled, and temporal variation within an individual was small compared to differences between individuals. Virome communities were enriched for genes indicative of a temperate phage replication style, indicating that many infections would be non-lethal to the host and provide an opportunity for gene transfer. CRISPR spacers identified in the bacterial DNA sequences provided a record of phage predation. Among these, some spacers targeted phage found at different body sites, suggesting that CRISPR spacer acquisition may provide a mechanism to explain spatial partitioning of skin phage communities. Our findings provide new insight into the skin virome, its interactions with the whole metagenome, and establish a foundation for understanding these dynamics in skin health and disease.

Biome: root:Host-associated:Human:Skin
EMG produced TPA metagenomics assembly of the Metagenome sequencing of the Hadza hunter-gatherer gut microbiota. (human gut metagenome) data set

The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA278393. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system
EMG produced TPA metagenomics assembly of the metagenome fecal microbiota, Ilumina seq reads of 12 individuals at 2 timepoints (EKmeta) data set

The EKmeta Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB6092. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system
Contrasting diversity and host association of ectomycorrhizal basidiomycetes versus root-associated ascomycetes in a dipterocarp rainforest

Ectomycorrhizal basidiomycetes and root-associated ascomycetes, including root-endophytic ascomycetes, are one of the most diverse and important belowground plant symbionts in dipterocarp rainforests. Our study aimed to compare the biodiversity, host association pattern, and community structure of ectomycorrhizal basidiomycetes with those of root-associated ascomycetes in a lowland dipterocarp rainforest in Southeast Asia. The host-plant chloroplast large-subunit of ribulose-1,5-bisphosphate caboxylase/oxygenase (rbcL) region, and fungal internal transcribed spacer 2 (ITS2) region were sequenced using a tag-encoded, massively parallel 454 pyrosequencing analysis to identify host plant and root-associated fungal taxa in root samples. In total, 1245 ascomycetous and 127 putative ectomycorrhizal basidiomycetous taxa were detected from 442 root samples. The putative ectomycorrhizal basidiomycetes  were likely to be associated with phylogenetically closely related dipterocarp taxa to greater or lesser extents, whereas host association patterns of the root-associated ascomycetes were much less distinct. The community structure of the putative ectomycorrhizal basidiomycetes was possibly more influenced by the host genetic distances than that of the root-associated ascomycetes. This study also indicated that in dipterocarp rainforests, root-associated ascomycetes were characterized by high biodiversity and indistinct host association patterns, whereas ectomycorrhizal fungi showed less biodiversity and a strong host phylogenetic preference for dipterocarp trees. Our findings suggested that root-associated ascomycetes (e.g., root-endophytic ascomycetes, may have biodiversity hotspots in the tropics, whereas biodiversity of ectomycorrhizal basidiomycetes increased with host phylogenetic diversity.

Biome: root:Host-associated:Plants:Root
EMG produced TPA metagenomics assembly of PRJEB3227 data set (Follow-up of faecal microbiota in IBS patients).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB3227, and was assembled with SPAdes v3.14.1. 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
Diversity and activity of soil bacterial communities in the rhizophere of poplars from different origins

The direct isolation of total RNA and DNA from soil samples and its analysis by sequencing with high through-put techniques (454-pyroseqencing) are useful tools for metagenomic and metatranscriptomic analyses. It provides insights into the diversity and the ecosystem function of microbial communities. Furthermore, the metatranscriptomic approach provides an opportunity to detect novel genes, which might encode key functions for important biogeochemical cycles. The aim of this study was to examine the soil structure of bacterial communities in the rhizospheres of poplars from different origins. In addition the seasonal change of the bacterial community composition was investigated. In a second experiment the influence of fertilization on total and active bacterial communities was validated.  Thsi Project was funded by the State of Lower Saxony (Ministry of Science and Culture).

Biome: root:Host-associated:Plants:Rhizosphere:Soil
EMG produced TPA metagenomics assembly of PRJEB1690 data set (This is a metagenomic study to investigate the microbial community and metabolic functions of Korean twin pairs.).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB1690, and was assembled with metaSPAdes v3.13.0. 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
Contribution of endophytic fungi to leaf litter communities

Endophytic fungi colonize healthy plant tissues without causing any signs of infection or damage to the host plant. Fungal endophytes are taxonomically diverse and inhabit all plant species analysed so far. Their ecological roles and the host-microbe interactions remain unclear; in particular for endophytes of forest trees. Composition of endophytic assemblages is unstable in time and affected by host identity, organ and tissue type, geographical location and environmental factors. Many endophytic fungi are also known as saprobes occurring in decomposing litter. They are supposed to enter a latent stage in the plant tissues and participate in nutrient cycling of forest ecosystems by decomposing plant litter.The main objective of this project is to study the contribution on litter decomposition by formerly endophytic fungi in forests dominated by Fagus sylvatica. The contribution of endophytic fungi is assessed in dependence of geographic location, spatial scale and forestry measures. Their contribution is compared against to litter-indigenous communities.In order to achieve our goals, we used Next Generation Sequencing to assess composition of the present and active communities via amplification of barcoding markers from DNA and RNA extracts, respectively.

Biome: root:Host-associated:Plants:Phylloplane:Endophytes
Characterization of the faecal microbiome of osteoporotic patients in Koreans

The main objective of this study was to discover the biomarkers of osteoporosis in human stool by comparing the gut microbiota of osteoporosis patients (OP) and normal human controls (HC). We collected 76 stool samples, 60 HC and 16 OP patients, examined using 16S ribosomal ribonucleic acid (rRNA) gene-based amplicon sequencing. The microbial communities of the two groups differed at lower taxonomical ranks. The data showed a significantly higher averaged taxonomic composition of Lachnospira in OP than HC among taxa.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Complex community structure of ectomycorrhizal, arbuscular-mycorrhizal and root-endophytic fungi in a mixed subtropical forest of ectomycorrhizal and arbuscular-mycorrhizal plants

Most terrestrial plants interact with diverse clades of mycorrhizal and root-endophytic fungi in their roots. Through the below-ground plant_fungal association, dominant plants can benefit by interacting with host-specific mutualistic fungi, while subordinate plant species may persist by sharing other sets (ecotypes) of fungal symbionts with each other. Therefore, the host preference of root-associated fungi is the key to understand plant community structure and dynamics. Based on 454-pyrosequencing, we revealed the root-associated fungal community on co-occurring 36 plant species in an oak-dominated forest in northern Japan, and statistically evaluated the host preference of diverse mycorrhizal and root-endophytic fungi. The analysis of 278 fungal taxa indicated that several taxa in the ectomycorrhizal family Russulaceae and the ecologically-diverse ascomycete order Helotiales had significant host preference for the dominant oak (Quercus) species. On the other hand, arbuscular-mycorrhizal fungi were shared mainly among subordinate plant species. While these fungi with host preference contributed to compartmentalize the below-ground plant_fungal associations, diverse clades of ectomycorrhizal fungi and possible root-endophytes associated not only with the dominant Quercus but also with the remaining plant species. Our findings suggest that dominant and subordinate plant species can host different subsets of root-associated fungi, while diverse clades of generalist fungi can counterbalance the compartmentalization of plant_fungal associations. Such insights into the overall structure of plant_root-associated fungal associations will enable us to understand the mechanisms that facilitate the co-existence of plant species in natural communities.

Biome: root:Host-associated:Plants
Bacterial Community Spatial and Temporal Variation in a North Temperate Bog Lake

Bog lakes such as Mary Lake in northern Wisconsin are ideal systems to investigate microbial communities due to easily identified spatial boundaries and well characterized seasonal ecosystem dynamics. Multiple factors are thought to influence the bacterial communities within the lake, and our goal in this study was to analyze the spatial and temporal factors causing the variations between these populations. Molecular techniques and statistical analyses were performed to gain insight into which differences caused the greatest variability. The bacterial communities were analyzed based on conserved 16S ribosomal RNA sequences as well as on short base pair sequence reads obtained from a time series in 2009 in order to determine whether the bacterial community was more variable in space or in time. We found that while the upper and lower thermal layers of the bog were composed of similar microbial communities, these communities had different temporal patterns throughout the time series.

Biome: root:Environmental:Aquatic:Freshwater:Lake
Community-scale properties of arbuscular mycorrhizal, ectomycorrhizal, and endophytic associations in temperate and subtropical forests

Based on high-throughput sequencing of root-associated fungi in forest ecosystems, we performed a comparative analysis of arbuscular mycorrhizal, ectomycorrhizal, and saprotrophic/endophytic associations across a latitudinal gradient from cool-temperate to subtropical regions.

Biome: root:Host-associated:Plants:Root
This is a test on a couple of samples from a bigger metagenomics study

In order to understand MGnify functionalities, as well as check and process its results with MGnifyR, we have decided to run a trial on a couple of samples that had its sequencing content reduced. Established methods and obtained results from this trial will guide us on a better assessment of the full dataset.

Biome: root:Environmental:Terrestrial:Soil
The daily dynamics of the vaginal microbiota before and after bacterial vaginosis

Bacterial vaginosis (BV) is a condition characterized by a dysbiotic state of the vaginal microbiota that could be accompanied with symptoms such as odor and discharge, but not always. Despite years of research, the etiology of BV is unknown, certainly due to our poor understanding of the vaginal microbiota prior to a BV event. Here we report on the characterization of the vaginal microbiota from samples collected prospectively and daily over 10 weeks in women who experience symptomatic BV (15 women) or asymptomatic BV (5 women), as well as from women who did not experience BV (4 women). This resource is unique, and we hope will contribute to a better understanding of the role that the vaginal microbiota play in the etiology of BV and ultimately to improve diagnostics and treatments.

Biome: root:Host-associated:Human:Reproductive system:Vagina
EMG produced TPA metagenomics assembly of PRJEB24129 data set (Temporal shotgun metagenomic dissection of the coffee fermentation ecosystem).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB24129, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Engineered:Food production:Fermented beverages.

Biome: root:Engineered:Food production:Fermented beverages