SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Bacterial 16s Amplicon Sequencing of the Atlantic Ocean

Latitudinal transect of the Atlantic Ocean, depth range from 20-200m, size fractioned by filtering (0.22, 3, 8 µm). Amplicon Sequencing of the V5-V6 region of the bacterial 16s rRNA Gene.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Abyssal plane
Eco-pathogenomics of chlamydial infection: The role of the vaginal microbiota

Chlamydia trachomatis genital infection is one of the most widespread sexually transmitted infections in the United State and worldwide, its high prevalence speaks volume about the remarkable adaptability to thrive in human and to bear upon, perhaps outcompete against, indigenous vaginal microbiota. However, the roles of vaginal microbiome, particularly its relations to the varied degree of host predisposition to disease upon exposure to pathogens, are largely undetermined. In this study, we investigated vaginal microbial community composition and structure upon active Chlamydial infection and clearance of infection for 9 months after treatment, using a collection of samples from 101 young women. One striking findings is that the hallmark of healthy vagina Lactobacillus is markedly underrepresented in the investigated cohort, particularly L. crispatus, L. jensenii, L. gasseri, while the abundance of L. iners is similar to healthy or asymptomatic cohort. To make the results more comparable between different studies, we also compare 16S gene V1-V3 amplicon with V1-V2 amplicon in their taxonomic assignment. Furthermore, strong association of microbial community compositional profiling and pathological conditions is revealed. Gardnerella vaginalis is identified as the most abundant species in vaginal microbiota with active Chlamydial infection in addition to a group of other low abundant phylotypes, while Lactobacillus iners become the most prevalent species when infection is cleared. Our results provide evidences of the interactive roles of vaginal microbiota during the episode of infection and restoration of health or asymptomatic state, to facilitate further risk assessment and developing strategic plans of diagnostics and personalized treatments to promote health and quality of life.

Biome: root:Host-associated:Human:Reproductive system:Vagina
Temporal stability of the oral microbiota: A longitudinal study of the dental, tongue, and salivary bacterial consortia

Every individual harbors a distinct oral microbiome that is influenced by environmental changes and shifts dramatically during the transition to disease. Examining baseline variation within and between individuals over time is critical to understanding this disease transition. Here we examined the temporal stability of supragingival plaque, tongue dorsum, and salivary microbial communities of healthy individuals. Ten subjects were sampled over 90 days and oral bacterial communities were profiled by high-throughput 16S rRNA gene sequencing. In all cases, supragingival plaque consortia were distinct from tongue dorsum and salivary communities. Overall, 97% of bacterial operational taxonomic units (OTUs) found in saliva were also detected in tongue samples, whereas only 2% of salivary OTUs were associated with supragingival plaque. Relative to other sites, the tongue dorsum also exhibited the highest relative temporal stability in bacterial composition. Because of the temporal variability in intra-individual microbiota, pooling of data from at least three time-points was required to capture the majority of an individual?s diversity at all time points. Using machine learning, we could also identify each subject by their microbial profiles alone with 95% accuracy, owing to each individual?s distinct oral microbial profiles. We also identified a core set of bacterial OTUs from all samples that classified within six genera: Streptococcus, Fusobacterium, Haemophilus, Neisseria, Prevotella, and Rothia. A set of 14 additional core OTUs were present in the majority of subjects, sites, and time-points, affiliated with the Campylobacter, Bergeyella, and Porphyromonas genera. This study characterizing a baseline and examining temporal shifts of the healthy core microbiota provides an useful prospect to examine dysbiosis during disease. While this knowledge can be harnessed to develop novel prognostics and diagnostics for disease conditions, the intra-individual differences in oral microbiota also highlight the need for an individualized approach to bacterial surveillance in dentistry.

Biome: root:Host-associated:Human:Digestive system:Oral
New Primers for Discovering Fungal Diversity using Nuclear Large Ribosomal DNA

Identification and classification of a wide variety of organisms using DNA sequences has helped overcome many limitations of traditional morphological approaches. However, the utility of DNA as a tool to catalogue biodiversity, resolve phylogenies, or explore patterns in ecological communities depends strongly on choice or design of primers for selecting the appropriate genetic markers. Unfortunately, no primers have been developed to target the D1 region across a wide diversity of fungi, with a short amplicon suitable for the Illumina MiSeq platform.  Here we introduce and evaluate two primer sets targeting the D1 region of the large subunit of ribosomal DNA to evaluate fungal diversity in 24 environmental subarctic soil and peat samples.

Biome: N/A
What controls long-term changes in freshwater microbial community composition?

Microbial ecology came to the forefront of biological and ecological science in the 1990s with the development of high-throughput DNA sequencing and other molecular techniques.  Recently this field entered a second age of understanding that microbial diversity was organized into patterns at various scales, consistent with ecological concepts that were once thought applicable only to macro-organisms.  Evidence of these patterns in diversity contradicts the traditional microbial hypothesis from Bass-Becking (1934) that ?Everything is everywhere, but the environment selects,? and indicates that, as with larger organisms, dispersal processes influence microbial diversity even at regional and local scales.  It is clear that both dispersal and environmental conditions are related to patterns of diversity, but to date the mechanistic controls and the relative importance of these factors have not been determined.  This study aims to resolve these controls through a combination of field and lab experiments with monitoring and surveys of the phylogenetic composition and ecosystem function (metabolism) of microbial communities.  This research builds on a long-term record showing consistent spatial and temporal patterns of microbial growth and community composition in ~25 lakes and streams of the Toolik Lake Research Area in Arctic Alaska.  Using experiments coupled with established sampling protocols and routines, this research will answer 3 basic questions, and focus on the long-term aspects of dispersal events and climate change: (1) How does environment influence microbial community composition and rate of function? (2) How are distribution patterns of microbial communities in lakes, streams, and soils influenced by dispersal via down-slope water flow? (3) How are seasonal, inter-annual, and long-term shifts in microbial community composition related to temporal shifts in environmental conditions such as those caused by climate change?  Long-term investigations of microbial communities are critical for understanding patterns of diversity and their controls, especially because the most enduring dispersal events are also most rare.  Moreover, because this work is located in the Arctic it will capture the earliest biological effects of global climate change.

Biome: root:Environmental:Aquatic:Freshwater
The microbial database of activated sludge - Denmark (MiDAS-DK)

V13 16S rRNA amplicon sequencing of Danish activated sludge wastewater treatment plants.

Biome: root:Engineered:Wastewater:Activated Sludge
Metacommunity analysis of two protozoan taxa (Amoebozoa) in grassland soils

To contribute to the current understanding of free-living soil protozoan, we examined the diversity of two widespread and common groups of soil amoebae, the genus Acanthamoeba and the Myxomycetes, in the topsoil of grasslands from three German regions (Schorfheide-Chorin, Hainich-D?n, Schw?bische Alb). We choose these two taxa of Amoebozoa because of the converging evidence of their prevalence in soils and because they are overlooked by both traditional and molecular sampling methodologies: they are rarely, if ever, recovered using eukaryote-wide primers. We developed specific primers to target the variable region V2 in the first part of the small subunit of the ribosomal RNA gene, using Roche GS FLX high-throughput sequencing.

Biome: root:Environmental:Terrestrial:Soil:Grasslands
Arctic Ocean metagenomes from HLY1502

Arctic Ocean metagenomes sampled aboard CGC Healy during the 2015 GEOTRACES Arctic research cruise

Biome: root:Environmental:Aquatic:Marine:Oceanic
Minor impacts of reduced pH on bacterial biofilms on settlement tiles along natural pH gradients at two CO2 seeps in Papua New Guinea

To study the effect of reduced pH on bacterial biofilms on tropical coral reefs, settlement tiles were deployed along pH gradients in December 2011 at two reefs in Papua New Guinea which hosted hydrothermal CO2 seeps. This ENA entry contains the sequences from biofilm samples from the lower side of eight settlement tiles (4 per reef) that were sampled 5 and 13 months after deployment. These samples covered pH values between 8.0 and 7.6 and constitute a subset of a larger pool of samples from the settlement tiles that was analyzed with ARISA only. The bacterial biofilm consisted predominantly of Alpha-, Gamma- and Deltaproteobacteria, as well as Cyanobacteria, Flavobacteriia and Cytophaga. Bacterial biofilm composition was heterogeneous with approximately 20% shared operational taxonomic units between samples. Among the observed environmental parameters, pH only had a very weak effect on community composition (R? ~ 1%, based on ARISA) and did not affect community richness and evenness.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
Core genomes of cosmopolitan surface ocean plankton

The sunlight surface layer of the ocean is the largest
            contiguous biome on the planet.  The photoautotrophic microbial communities
            in the ocean fix roughly equal amounts of CO2 through photosynthesis as all
            terrestrial biomes, despite a widespread paucity of multiple nutrients.
            The accompanying bacterioplankton communities are important in recycling
            nutrients for autotrophs, providing or requiring vitamin cofactors, thereby
            influencing the biogeochemical cycles of important green house gasses
            N2O, CO2, dimethyl sulfide, and methane. The bacterioplankon communities
            contain a high level of diversity , particularly of uncultivated organisms
            with unknown genome contents. Single cell genomics and metagenomic assemblies
            have characterized the genomes of a few uncultivated organisms , yet a
            substantial portion of the community remains uncharacterized.  Here we report
            the collection, assembly, and analysis of 225 metagenomes collected from the
            euphotic zone of every ocean at temperatures from 0?C to 30?C.  A global assembly
            resulted in 3 Gbp of contiguous DNA assemblies, or approximately 100 genomes
            , representing over 80% of all metagenomic reads.  A large majority of the
            assemblies are cosmopolitan, with over 50% being found in 50% of the metagenomic
            sites, indicating a widespread genomic commonality between geographicall
            y separated communities. The emergent genome biogeography illuminates a
            temperature-driven distribution of genomes at multiple taxonomic levels from
            strain to phyla, while protein family level analyses at a global and genus level
            point to nutrient availability dictating finer scale variation.  The assemblies
            provide a genomic characterization of the so-called microbial dark matter in this
            environment at an unprecedented scale and point to lineage specific metabolic
            specialization both in core metabolism and nutrient acquisition, a potential niche
            diversification that leads to metasymbiosis within a complex community.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Photic zone
sequencing of Rubus V-118-13 for virus analysis

Blackberry Loch Ness showing virus like symptoms was analysed using RT-PCR. Further analysis was performed using HGS. Total RNA was extracted from leaves using MagMax 96 Total RNA Isolation Kit (Life Technologies). RiboMinus Plant Kit for RNA-Seq (Life Technologies) was used to eliminate rRNA from the sample. Sample was sequenced on Ion Torrent PGM and Illumina platforms.

Biome: root:Host-associated
sequencing of Rubus V-067-13 for virus analysis

Wild Rubus showing virus like symptoms was analysed using RT-PCR. Further analysis was performed using NGS. Total RNA was extracted from leaves using MagMax 96 Total RNA Isolation Kit (Life Technologies). RiboMinus Plant Kit for RNA-Seq (Life Technologies) was used to eliminate rRNA from the sample. Sample was sequenced on Ion Torrent PGM and Illumina platforms..

Biome: root:Host-associated
Bacterial diversity, community composition and potential activity in surface waters of the Gulf of Naples

Bacterioplankton are the key components of the biogeochemical cycles in marine ecosystem. Consequently, their richness and evenness are critical for the way the ecosystem functions, and need regular monitoring in order to have a proper assessment of ecosystem health and functioning. It is also important to estimate the functional potential of each bacterial population so as to understand their individual contribution to the ecosystem processes. Community structure and function of bacterial assemblages are influenced by a number of biotic and abiotic interactions which are highly dynamic in marine ecosystems, especially in the coastal areas. This study aims to investigate the diversity, community composition and functional potential of bacterial communities in a coastal area of the Mediterranean Sea.

Biome: root:Environmental:Aquatic:Marine:Coastal
16s metagenomics of dam water from 3 sources.

16s metagenomics study of dam water from 3 sources from Bulgaria. 7 samples from Miseq 2x300 PE run. The study aims to explore the natural microbiome of the fresh water from 3 different lakes.

Biome: root:Environmental:Aquatic:Lentic
Enrichment from groundwater treating sand filters

Samples collected at waterworks sand filters were enriched for specific functional groups e.g. ammonium oxidizers. These enrichment cultures were tested in column experiments. Samples were taken at experimental termination. 16S rRNA amplicon sequencing was done on the original sand filter material, the cultures and the samples.

Biome: root:Environmental:Aquatic
Bacterial and fungal core microbiomes associated with purple prairie clover during ensiling and aerobic spoilage.

Bacterial and fungal core microbiomes associated with purple prairie clover during ensiling and aerobic spoilage.

Biome: root:Environmental:Terrestrial:Agricultural field
Ecoli data

Compassion study

Biome: root:Host-associated:Human:Circulatory system:Blood
the Ecoli fastq file

a compassion study

Biome: root:Host-associated:Human:Circulatory system:Blood
Soil Genome sequencing

The microdiversity of soil

Biome: root:Environmental:Terrestrial:Soil
Rice field soil Targeted Locus (Loci)

To study the community structures after the addition of ammonium and nitrate

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Characterization of the vaginal microbiome in women with cervical intraepithelial neoplasia

Background: The healthy vaginal microbiota is typically Lactobacillus spp. dominant and it plays an important role in the prevention of urogenital diseases and infections. Persistent infection with oncogenic HPV subtypes is necessary for the development of invasive cervical cancer. Recent evidence indicates that the vaginal microbiome may play a functional role in the persistence or regression of Human Papillomavirus (HPV) infections. The vaginal microbiome in women with cervical intra-epithelial neoplasia (CIN) has yet to be investigated.  Objectives: To characterize the vaginal microbiome structure and diversity in women with different CIN grades.  Material and Methods:  Population: Reproductive age, non-pregnant women of reproductive age with CIN attending the colposcopy clinic. Setting: Imperial College Healthcare NHS Trust. Interventions: Vaginal swabs were collected from the posterior vaginal fornix and bacterial DNA extracted. The vaginal microbiome was characterised by 16S rRNA gene sequencing using an Illumina MiSeq platform. Women were categorized in to two groups on the basis of histology and cytology; women with low-grade (LSIL) and high-grade squamous intra-epithelial lesions (HSIL). Analysis: Supervised, and unsupervised multivariate modeling of sequence data was used to examine bacterial species classification data, and correlated these to the disease severity. Richness and diversity indices were calculated for patient population groups.   Results: We analysed 39 women with CIN, which were divided in to LSIL (n=11) and HSIL (n=28) grades. Hierarchical clustering analysis of bacterial species data revealed 3 distinct community state types (CST I: Lactobacillus crispatus; CST III: Lactobacillus iners; CST IV: mixed diverse Lactobacillus-depleted microbiome) in women with CIN. 26% of our predominantly Caucasian population had a high-diversity, non-Lactobacillus dominated microbiome (CST IV), which is approximately 3 times greater than the rate documented for Caucasian women without CIN in previous reports. None of the women with CIN had a Lactobacillus gasseri-dominated (CST II). The proportion of women with CST IV vaginal microbiome was similar for women with LSIL (n=3 out of 11; 27%) versus women with HSIL (8 out of 28; 28%).  Conclusions: One third of women with CIN have a more diverse Lactobacillus-depleted vaginal microbiome, higher than the rates previously reported in normal populations. This high rate of microbiome diversity may reflect lesions that are likely to progress and warrants further investigation. A Lactobacillus gasseri-dominated microbiome was not observed in this population of women with CIN. This supports previous reports indicating that Lactobacillus gasseri is correlated with rapid HPV clearance. Future therapeutic strategies may allow modulation of the vaginal microbiome toward a vaginal community structure that promotes HPV clearance.

Biome: root:Host-associated:Human:Reproductive system:Vagina
The vaginal microbiome during pregnancy and the postpartum period in a European population.

Determining the composition and structure of the vaginal microbiome during pregnancy is critical to understanding its role in maintaining reproductive health outcomes. Historically, studies on the pregnant vaginal microbiome have been limited to Northern American populations. Using MiSeq sequencing of 16S rRNA gene amplicons, we characterised the vaginal microbiota of a mixed British ethnic cohort of women (n=42) who experienced normal, uncomplicated term delivery and whom were sampled longitudinally throughout pregnancy (8-12, 20-22, 28-30 and 34-36 weeks gestation) and the postpartum period (6 weeks) in. We show that the composition of the vaginal microbiome dramatically changes postpartum to become less Lactobacillus spp. dominant with greater alpha-diversity (CST IV) irrespective of the community structure for that individual during pregnancy and independent of their ethnic background. As observed in North American populations, a British population is characterised by a vaginal microbiome during pregnancy that is dominated by Lactobacillus spp. and low alpha-diversity (community state types CST I, II and III). However, significant numbers of women in this British cohort have an L. jensenii (CST V) dominated microbiome that is characterised by low levels of alpha-diversity. CST V was predominantly observed in women with Asian and Caucasian ethnic backgrounds whereas CST II (L. gasseri) was absent in samples collected from Black women. This study reveals new insights into biogeographical and ethnic effects upon the microbial communities in the vaginal microbiome during pregnancy and in the postpartum period and has important implications for future studies designed to explore relationships between the vaginal microbiome, host health and pregnancy outcomes.

Biome: root:Host-associated:Human:Reproductive system:Vagina
We analysed the gut microbiota of rats kept in the same cage

Animal models are invaluable tools which allow us to investigate the microbiome-host dialogue. However, experimental design introduces biases in the data that we collect, potentially leading to false conclusions. With obesity at pandemic levels animal systems of this disease have been developed; we investigated the role of experimental design on one such rodent model.  We used 454 pyrosequencing to profile the faecal bacteria of obese (n = 6) and lean (homozygous n= 6; heterozygous n= 6) Zucker rats over a 10 week period, maintained in mixed-genotype cages, to further understand the relationships between the composition of the intestinal bacteria and age, obesity progression, genetic background and cage environment. Phylogenetic and taxon-based univariate and multivariate analyses (non-metric multidimensional scaling, principal component analysis) showed that age was the most significant source of variation in the composition of the faecal microbiota. Second to this, cage environment was found to clearly impact the composition of the faecal microbiota, with samples from animals from within the same cage showing high community structure concordance. Importantly, the obese phenotype was not found to impact the faecal bacterial profiles. These findings demonstrate that the age and local environmental cage variables were driving the composition of the faecal bacteria and were more deterministically important than host genotype. These findings have major implications for understanding the significance of functional metagenomic data in experimental studies and beg the question; what is being measured in animal experiments in which different strains are housed separately, nature or nurture?

Biome: root:Host-associated:Mammals:Digestive system
Chinese Poyang Lake resistant genes from soil metagenome

Chinese Poyang Lake resistant genes from soil metagenome

Biome: root:Environmental:Terrestrial:Soil
Puerto Morelos summer

Metagenome of coral rubble in Puerto Morelos, Quintana Roo. Mexico.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
Bacillus anthracis DNA in environmental metagenome

This study examined the efficacy of sequence analysis for detection of B. anthracis in an environmental background. Whole-genome sequencing was applied to titrated genome copy numbers of B. anthracis in the presence of background nucleic acid extracted from aerosol and soil samples.

Biome: root:Environmental:Terrestrial:Soil