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"centre-name": "Helmholtz Centre for Environmental Research GmbH - UFZ",
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"study-abstract": "Investigation of the root and rhizosphere microbial community composition of forb and grass phytometer plants out planted in sites of different land-use intensity in the German Biodiversity Exploratories (Hainich-Dün) by means of 16S and ITS rDNA paired-end amplicon sequencing using Illumina MiSeq. The study focused on the effect of plant functional group (grasses vs. forbs) and land-use as well as edaphic parameters onto the bacterial and fungal community and diversity.",
"study-name": "Microbial genomic DNA was extracted from the root, rhizosphere and bulk soil compartments from grassland phytometer plant species and was then used as templates for bacterial 16S and/or fungal ITS rDNA paired-end amplicon sequencing using Illumina MiSeq",
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"id": "MGYS00006791",
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"samples-count": 330,
"bioproject": "PRJEB60029",
"accession": "MGYS00006791",
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"last-update": "2025-04-04T11:22:46",
"secondary-accession": "ERP145068",
"centre-name": "GFZ German Research Centre for Geosciences",
"public-release-date": null,
"study-abstract": "Pioneer microbial communities participate critically in soil formation processes in arid and semiarid environments. However, how its structure impacts soil formation and stabilization and how they will respond to changes in a climate still need to be better understood. Therefore, soil samples from A and B horizons of arid and semiarid climates were incubated in a four month-experiment simulating constant water availability and temperature regimes in humid climate conditions. We used 16S-rRNA sequencing to assess changes in abundance, diversity, and structure of pioneer bacterial communities and their relation to soil physicochemical properties at three-time points during the incubation. Humid conditions decreased bacterial diversity only in arid soils, while the structure changed in both soils but faster in the arid one (12 against 16 weeks). The bacterial phyla varied markedly in arid soils over time, reassembled into a community dominated by Proteobacteria, Actinobacteriota, and Gemmatimonadota, while semiarid one was led steadily by Acidobacteriota, Proteobacteria, and Planctomycetota. The bacterial community correlated with prominent soil formation indicators such as pH, electrical conductivity, carbon, nitrogen, and mean weight diameter of aggregates, suggesting that they are involved in soil formation processes. The co-occurrence network revealed a niche differentiation per soil type and a less developed soil with a bacterial community sensitive to environmental disturbances in the arid soil. Overall, we suggest that the pioneer bacterial community was sensitive to changes when exposed to climate conditions outside the range of their life history, which, in turn, influenced the stability (semiarid soil) or turnover (arid soil) of pioneer soil-forming bacteria.",
"study-name": "Unraveling the response of pioneer soil-forming bacterial communities after simulating humid climate conditions in arid and semiarid soils",
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"secondary-accession": "ERP142430",
"centre-name": "Arcadia Science",
"public-release-date": null,
"study-abstract": "Cheese rinds are a semi-complex microbial community with bacteria, fungi, and viruses. Here, we harvested cheese rinds from 11 different cheeses, and extracted DNA from the 11 microbial communities as well as the associated virome of one cheese rind.",
"study-name": "short read sequencing of distinct cheese rinds",
"data-origination": "SUBMITTED"
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"last-update": "2025-04-03T11:33:53",
"secondary-accession": "ERP169949",
"centre-name": "EMG",
"public-release-date": null,
"study-abstract": "The Third Party Annotation (TPA) assembly was derived from the primary data set PRJNA822508",
"study-name": "Metagenome assembly of PRJNA822508 data set (Metagenomic exploration of Surface waters from the Andaman and Nicobar Islands, India.)",
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"id": "MGYS00006795",
"attributes": {
"samples-count": 36,
"bioproject": "PRJNA492714",
"accession": "MGYS00006795",
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"last-update": "2025-04-03T08:38:56",
"secondary-accession": "SRP162433",
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"public-release-date": null,
"study-abstract": "The human oral & gut microbiota continues to change phenotype by many factors (e.g. environment, host's diet, stress etc.), throughout life with a major impact on human physiology, psychology, metabolism and immune system. Amongst one such is, extreme environmental condition like High Altitude (HA) - very unique, difficult and full of health risk. Visiting population such as mountaineers, bikers, visitors, pilgrims, soldiers and special task forces who reaches High Altitude are at higher risks than at low landers. However, the reason how the extreme environment, stress, oxygen saturation and diet alter the oral & gut microbiota and affect its composition remains unclear. In this study we investigated the influence of High Altitude and stay at different heights, on the health of Indian population by using metagenomic approach to determine the variation in the gut microbiota. Fecal samples were collected from individuals, at four different time points viz. before the start of the ascending, after reaching 13000ft, descending at 11000ft and at the 16000ft –19000ft. Samples were analysed for whole genome sequencing. The oral & gut microbial diversity of members was significantly altered with the abundance of several bacteria, during the days of staying at 13000ft, 11000ft and 16000ft –19000ft. The oral & gut microbiota comprised mainly of the phyla Firmicutes, Proteobacteria, Bacteroidetes Euryachaeota, Actinobacteria and Unclassified at three time points. Further, the differential analysis of microbes across all the phyla and genus at all the four time points. Most of the identified microbial sequences were unclassified microbiota. Evidently, some metabolic pathways like amino acid, lipid and carbohydrate metabolism pathways were also altered.",
"study-name": "Impact of High altitude environment of Human oral and gut microbiota",
"data-origination": "HARVESTED"
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"id": "root:Host-associated:Human:Digestive system",
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{
"type": "studies",
"id": "MGYS00006794",
"attributes": {
"samples-count": 184,
"bioproject": "PRJEB44538",
"accession": "MGYS00006794",
"is-private": false,
"last-update": "2025-03-31T17:22:33",
"secondary-accession": "ERP128598",
"centre-name": "UNIVERSITY OF KIEL",
"public-release-date": null,
"study-abstract": "Objective: To elucidate cross-sectional patterns and longitudinal changes of oral and stool microbiota in patients with multiple sclerosis (MS) and the effect of B-cell depletion.Methods: We conducted an observational, longitudinal clinical cohort study analyzing four timepoints (days 0 and 14, weeks 24 and 52) over 12 months in 37 MS patients, of whom 22 initiated B-cell depletion therapy with ocrelizumab and 15 age- and gender-matched untreated MS patients. For microbiota analysis of the oral cavity and the gut, all provided stool and oral swab samples underwent 16S rDNA sequencing and subsequent bioinformatic analyses. Clinical outcome and MRI results were registered. Results: Compared to healthy controls, MS patients showed decreased alpha-diversity, significantly increased detection of Bacteroidetes and lower abundance of butyrate-producing members of the Firmicutes in their stool. Oral microbiota-patterns also had a reduced alpha-diversity yet showed unique and differential microbiota changes compared to stool such as increased levels of Proteobacteria and decreased abundance of Actinobacteria. Remarkably, following initiation of B-cell depletion, we observed increased alpha-diversity in the gut and the oral cavity as well as a long-term sustained reduction of pro-inflammatory Gram-negative bacteria (e.g., Escherichia/Shigella).Conclusion: MS patients have altered stool and oral microbiota diversity patterns compared to healthy controls, which are most pronounced in patients with higher disease activity and disability. Therapeutic B-cell depletion is associated with persisting regression of these changes. Whether these microbial changes are unspecific side-effects of B-cell depletion or indirectly modulate multiple sclerosis disease activity and progression is currently unknown and necessitates further investigations.",
"study-name": "Longitudinal changes of stool and oral microbiota composition in patients with multiple sclerosis undergoing B-cell depletion",
"data-origination": "SUBMITTED"
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"type": "studies",
"id": "MGYS00006793",
"attributes": {
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"bioproject": "PRJNA510326",
"accession": "MGYS00006793",
"is-private": false,
"last-update": "2025-03-28T10:33:10",
"secondary-accession": "SRP179983",
"centre-name": "National Research Council Canada",
"public-release-date": null,
"study-abstract": "DNA extracted from bacteria and mixed to form a synthetic mock community.",
"study-name": "bacterial mixed DNA library Metagenome",
"data-origination": "HARVESTED"
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"type": "studies",
"id": "MGYS00006790",
"attributes": {
"samples-count": 102,
"bioproject": "PRJEB32399",
"accession": "MGYS00006790",
"is-private": false,
"last-update": "2025-03-25T11:55:14",
"secondary-accession": "ERP115080",
"centre-name": "UCL Centre for Clinical Microbiology",
"public-release-date": null,
"study-abstract": "Background: Long-term antiretroviral therapy (ART) enables people living with HIV (PLW-HIV) to be healthier and live longer; though they remain at greater risk of pneumonia and chronic lung disease than the general population. Lung microbial dysbiosis has been shown to contribute to respiratory disease. \nMethods: 16S-rRNA gene sequencing on the Miseq-platform and qPCR for typical respiratory pathogens were performed on sputum samples collected from 64 PLW-HIV (median blood CD4 count 676 cells/μL) and 38 HIV-negative participants. \nFinding: Richness and α-diversity as well as the relative-abundance (RA) of the major taxa (RA>1%) were similar between both groups. In unweighted-Unifrac ß-diversity, the samples from PLW-HIV showed greater diversity, in contrast to the HIV negative samples which clustered together. Gut bacterial taxa such as Bilophila and members of Enterobacteriaceae as well as pathogenic respiratory taxa (Staphylococcus, Pseudomonas and Klebsiella) were significantly more frequent in PLW-HIV and almost absent in the HIV-negative group. Carriage of these taxa was correlated with the length of time between HIV diagnosis and initiation of ART (Spearman-rho=0·279, p=0·028). \n\nInterpretation: Although the core airway microbiome was indistinguishable between PLW-HIV on effective ART and HIV-negative participants, PLW-HIV’s respiratory microbiome was enriched with potential respiratory pathogens and gut bacteria. The observed differences in PLW-HIV may be due to HIV infection altering the local lung microenvironment to be more permissive to harbour pathogenic bacteria that could contribute to respiratory comorbidities. Prompt start of ART for PLW-HIV may reduce this risk.",
"study-name": "Enrichment of the airway microbiome in people living with HIV with potential pathogenic bacteria despite antiretroviral therapy",
"data-origination": "SUBMITTED"
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{
"type": "studies",
"id": "MGYS00006784",
"attributes": {
"samples-count": 81,
"bioproject": "PRJEB73722",
"accession": "MGYS00006784",
"is-private": false,
"last-update": "2025-03-21T09:53:45",
"secondary-accession": "ERP158464",
"centre-name": "EMG",
"public-release-date": null,
"study-abstract": "The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB52452, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.",
"study-name": "EMG produced TPA metagenomics assembly of PRJEB52452 data set (Malaspina Expedition 2010 Microbial Vertical Profiles Metagenomes).",
"data-origination": "SUBMITTED"
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