SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Large variability of bathypelagic microbial eukaryotic communities across the world's oceans

In this work we study the diversity of bathypelagic microbial eukaryotes (0.8-20 m) in the global ocean. Seawater samples from 3000-4000 m depth from 27 stations in the Atlantic, Pacific and Indian Oceans were analyzed by pyrosequencing the V4 region of the 18S rDNA. The relative abundance of the most abundant Operational Taxonomic Units (OTUs) agreed with the results of a parallel metagenomic analysis, suggesting limited PCR biases in the tag-approach. Although rarefaction curves for single stations were seldom saturated, the global analysis of all sequences together suggested an adequate recovery of bathypelagic diversity. Community composition presented a large variability among samples, which was poorly explained by linear geographic distance. In fact, the similarity between communities was better explained by water mass composition (26% of the variability) and the ratio in cell abundance between prokaryotes and microbial eukaryotes (21%). Deep diversity appeared dominated by four taxonomic groups (Collodaria, Chrysophytes, Basidiomycota and MALV-II) appearing in different proportions in each sample. Novel diversity amounted to 1% of the pyrotags and was lower than expected. Our study represents an essential step in the investigation of bathypelagic microbial eukaryotes, indicating dominating taxonomic groups and suggesting idiosyncratic assemblages in distinct oceanic regions.

Biome: root:Environmental:Aquatic:Marine
Multi-omics of the nitrate-reducing iron(II)-oxidizing culture BP

Nitrate-reducing iron(II)-oxidizing (NDFO) bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. A second NDFO culture, culture BP, was obtained with a sample taken in 2015 at the same pond and cultured in a similar way. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture BP.This dataset contains: (1) Raw sequencing data of 16S (V4 region, primers 515f and 806r) rRNA amplicon sequencing of the microbial community composition of the autotrophic NRFeOx enrichment culture BP and of environmental samples from the pond where culture BP originates from. Illumina MiSeq sequencing (Illumina, San Diego, CA, USA) using PE 250 bp MiSeq Reagent Kit v2 (500 cycles kit) were performed at Microsynth AG (Balgach, Switzerland). (2) Raw sequencing data of near full-length 16S (primers 27F and 1492R) sequenced with PacBio Sequel SMRT at the Helmholtz research institute, Munich, Germany. (3) Raw sequencing data of shotgun metagenomics. Library was prepared with TruSeq DNA PCR-Free Kit (Illumina) and sequenced with PE 150 bp on a NovaSeq 6000 totalling 91 Gbp by CeGaT, Tuebingen, Germany. (4) Short reads were assembled with MEGAHIT v1.2.7 using https://github.com/nf-core/mag v1.0.0. (5) Raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates). Library preparation including bacterial ribodepletion (Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit) and Illumina NextSeq v2.5 sequencing with PE 75 bp and 6 to 53 Mio clusters per sample were performed by Microsynth AG (Balgach, Switzerland).

Biome: root:Environmental:Aquatic:Freshwater:Pond:Sediment
Microbial consortium enriched at the cathode of a solar microbial fuel cell

The objective of this project is to study a microbial biocathode consortium enriched at the U.S. Naval Research Laboratory's Center for Bio/Molecular Science & Engineering.  The initial inoculum for the solar microbial fuel cell was seawater collected near Rutgers, NJ, and the community has subsequently been maintained electroautotrophically via serial transfers on cathodes poised at 310 mV vs. SHE. This microbial consortium contains autotrophic organisms which can use a cathode as an electron donor and O2 as an electron acceptor, and has electrochemical properties potentially useful in bioenergy applications including microbial electrosynthesis and microbial fuel cell technology. System biology approaches will be used to identify functional genes that are relevant for bioenergy production, such as fixing CO2 as sole carbon source, electrosynthesis, O2 tolerance, etc.   Several heterotrophic constituents have been isolated in pure culture, and have been sequenced by either Illumina or PacBio technologies.  Furthermore, closed genomes and methylation data were obtained from PacBio sequencing of metagenomic DNA.    Metagenomic libraries generated from eight biological replicates of an enriched biocathode microbial community were sequenced at 2x100 base pairs (bp) (paired-end reads) using an Illumina HiSeq 2000. The reads were assembled using either IDBAUD or Ray.  The ideal k-mer length and node coverage were selected based on which gave results most similar to de novo sequencing of isolated bacterial cultures from the enriched community (Marinobacter sp. strain CP1 and Labrenzia sp. strain CP4).  Metatranscriptomic libraries were generated from four reactors inoculated with the same inoculum were grown at a set potential of 310 mV SHE until current density stabilized, cyclic voltammetry was recorded, and then two of them were set at a more positive potential (470 mV) and two remained at 310 mV for 48 hours before samples were harvested for RNA extraction.  This experiment was repeated with four more reactors inoculated with a new cell suspension from the same source electrode for a total of four biological replicates at each potential.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
Moose metagenomic assembly

Moose Ohio State 2015

Biome: root:Host-associated:Mammals:Digestive system:Midgut
Impact of sulfamethoxazole on the microbial community of a riverine environment

Antimicrobial resistance (AMR) is a global health issue. The impact of sub-lethal concentrations of antibiotics on antimicrobial resistance gene (ARG) spread in the environment is still unclear. In this study we used semi-realistic flume systems to mimic the riverine environment and we monitored the effect of low concentration of sulfamethoxazole on the microbial community composition and function (i.e. ARG).

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Low land river systems
Triangulation of microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles

The anaerobic digestion microbiome has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a non-targeted holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods, i.e., amplicon sequencing, metaproteomics, metabolomics and cytomics, in their ability to characterise the full-scale anaerobic digestion microbiome. Cytometric fingerprinting through cytomics reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting by flow cytometry. Three different digester types, i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters, each reflected different operational parameters. The alpha-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, beta-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method's features i.e., operational taxonomic units, metaproteins, metabolites, and cytometric traits, yielded certain similar features, yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, cytometric fingerprinting through flow cytometry is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.

Biome: root:Engineered:Lab enrichment:Defined media:Anaerobic media
A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function

Swine are regarded as promising biomedical models, but the dynamics of their gastrointestinal microbiome have been much less investigated than that of humans or mice. The aim of this study was to establish an integrated multi-omics protocol to investigate the fecal microbiome of healthy swine. To this end, a preparation and analysis protocol including integrated sample preparation for meta-omics analyses of deep-frozen feces was developed. Subsequent data integration linked microbiome composition with function, and metabolic activity with protein inventories, i.e., 16S rRNA data and expressed proteins, and identified proteins with corresponding metabolites. 16S rRNA gene amplicon and metaproteomics analyses revealed a fecal microbiome dominated by Prevotellaceae, Lactobacillaceae, Lachnospiraceae, Ruminococcaceae and Clostridiaceae. Similar microbiome compositions in feces and colon, but not ileum samples, were observed, showing that feces can serve as minimal-invasive proxy for porcine colon microbiomes. Longitudinal dynamics in composition, e.g., temporal decreased abundance of Lactobacillaceae and Streptococcaceae during the experiment, were not reflected in microbiome function. Instead, metaproteomics and metabolomics showed a rather stable functional state, as evident from short-chain fatty acids (SCFA) profiles and associated metaproteome functions, pointing towards functional redundancy among microbiome constituents. In conclusion, our pipeline generates congruent data from different omics approaches on the taxonomy and functionality of the intestinal microbiome of swine.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
Bifidobacterium or fiber protect against diet-induced microbiota-mediated colonic mucus deterioration

Diet strongly affects gut microbiota composition and gut bacteria can influence the colonic mucus layer, a physical barrier that separates trillions of gut bacteria from the host.  However, the interplay between a Western style diet (WSD), gut microbiota composition and the intestinal mucus layer is less clear.  Here we show that mice fed a WSD have an altered colonic microbiota composition that causes increased penetrability and a reduced growth rate of the inner mucus layer. Both barrier defects can be prevented by transplanting microbiota from chow-fed mice. In addition, we found that administration of Bifidobacterium longum was sufficient to restore mucus growth whereas administration of the fiber inulin prevented increased mucus penetrability in WSD-fed mice. We hypothesize that the presence of distinct bacteria is crucial for proper mucus function.  If confirmed in humans, these findings may help to better understand diseases with an affected mucus layer, such as ulcerative colitis.

Biome: root:Host-associated:Mammals:Digestive system:Midgut
EMG produced TPA metagenomics assembly of the Microbial composition of samples from infant gut (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 PRJNA63661. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system:Large intestine
EMG produced TPA metagenomics assembly of PRJNA274897 data set (Oil droplet biodegradation Trondheimsfjord Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA274897, and was assembled with metaSPAdes v3.13.0. This project includes samples from the following biomes: root:Engineered:Lab enrichment:Defined media:Marine media.

Biome: root:Engineered:Lab enrichment:Defined media:Marine media
PMC 728.11_cyano

Microcystis aeruginosa PMC 728.11_cyano metagenome sequencing

Biome: root:Environmental:Aquatic:Freshwater
The unexplored social language of bacteria in human oral health and disease

Systematic analysis of small-molecule encoding biosynthetic gene clusters from shotgun metagenomic sequencing data reveals differentially abundant biosynthetic pathways in health and disease associated salivary microbiota

Biome: N/A
EMG produced TPA metagenomics assembly of PRJNA478018 data set (The unexplored social language of bacteria in human oral health and disease).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA478018, and was assembled with metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva,root:Host-associated:Human:Digestive system:Oral.

Biome: root:Host-associated:Arthropoda:Digestive system:Oral
EMG produced TPA metagenomics assembly of the Canadian MetaMicrobiome Library Projects (Canadian MetaMicrobiome) data set

The Canadian MetaMicrobiome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA202388. This project includes samples from the following biomes : Terrestrial, Fecal.

Biome: root
EMG produced TPA metagenomics assembly of the Library preparation methodology can influence genomic and functional predictions in human microbiome research (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 PRJNA298489. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system
Library preparation methodology can influence genomic and functional predictions in human microbiome research

This project investigates how library preparation and sequencing protocol influence the taxonomy and function analysis of microbial species in human microbiome research.

Biome: root:Host-associated:Human:Digestive system
EMG produced TPA metagenomics assembly of PRJEB8347 data set (Temporal and technical variability of human gut metagenomes).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB8347, and was assembled with SPAdes v3.14.1, metaSPAdes 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
EMG produced TPA metagenomics assembly of the Metagenomic analysis of soil samples from an oil contaminated military base (Enviro_05_10_2015) data set

The Enviro_05_10_2015 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB15034. This project includes samples from the following biomes : Soil.

Biome: root:Environmental:Terrestrial:Soil:Sand:Oil-contaminated
EMG produced TPA metagenomics assembly of the Microbial diversity and isolation of novel hydrolases from the Kudu Rumen (Kudu Metagenome) data set

The Kudu Metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB7843. This project includes samples from the following biomes : Mammal (non-human).

Biome: root:Host-associated:Mammals
EMG produced TPA metagenomics assembly of the Human Gut Microbiome in a Multiplex Family Study of Type 1 Diabetes Mellitus (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 PRJNA289586. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system
Temporal and technical variability of human gut metagenomes

Background: Metagenomics has become a prominent approach for exploring the role of the gut microbiota in human health. However, the temporal variability of the healthy gut microbiome has not yet been studied in depth using metagenomics and little is known about the effects of different sampling and preservation approaches. We performed metagenomic analysis on fecal samples from seven subjects collected over a period of up to two years to investigate temporal variability and assess preservation-induced variation, specifically, fresh frozen compared to RNALater. We also monitored short-term disturbances caused by antibiotic treatment and bowel cleansing in one subject.

Results: We find that the human gut microbiome is temporally stable and highly personalized at both taxonomic and functional levels. Over multiple time-points, samples from the same subject clustered together, even in the context of a large dataset of 888 European and American fecal metagenomes. One exception was observed in an antibiotic intervention case where, more than one year after the treatment, samples did not resemble the pre-treatment state. Clustering was not affected by preservation method. No species differed significantly in abundance, and only 0.36% of gene families were differentially abundant between preservation methods.

Conclusions: Technical variability is small compared to the temporal variability of an unperturbed gut microbiome, which in turn is much smaller than the observed between-subject variability. Thus, short-term preservation of fecal samples in RNALater is an appropriate and cost-effective alternative to freezing of fecal samples for metagenomic studies.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJEB6070 data set (Potential of fecal microbiota for early stage detection of colorectal cancer).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB6070, and was assembled with SPAdes v3.14.1, metaSPAdes 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
EMG produced TPA metagenomics assembly of PRJNA407905 data set (Human saliva Metagenomes).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA407905, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Human saliva Metagenomes

Our research focused on the uncultured human microbial community present in saliva of IgA immunodeficiency people and healthy people

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
EMG produced TPA metagenomics assembly of PRJNA216965 data set (Dental Calculus Metagenome (archaeological)).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA216965, and was assembled with SPAdes v3.14.1. 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 PRJEB19901 data set (Quantification of mock microbial communities with metagenomes, 16S rRNA gene amplicons and metaproteomics).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB19901, and was assembled with metaSPAdes v3.14.1. 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 PRJNA309322 data set (Pediatric MLI metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA309322, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine.

Biome: root:Host-associated:Human:Digestive system:Large intestine
Pediatric MLI metagenome

Metagenome sequencing and gene prediction for pediatric mucosal-luminal interface aspirates

Biome: root:Host-associated:Human:Digestive system:Large intestine
EMG produced TPA metagenomics assembly of PRJNA683594 data set (Manure metagenome from Ceftiofur-treated dairy cow).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA683594, and was assembled with Flye v2.8.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
The relationship of evergreen shrub Empetrum nigrum and soil microbial communities and functional diversity in degraded rangeland of the subarctic highland of Iceland.

Empetrum nigrum is a common species in the degraded highland rangelands of Iceland. Empetrum nigrum is well known for its ability to produce secondary metabolites (allelochemicals) that influence the germination, growth, survival, and reproduction of other plants in the community. The aim is to determine if the presence of Empetrum has an effect on soil microbial community composition and the community's main functional genes with special emphasis on genes related to carbon cycles. 4 shotgun libraries were constructed representing two soil samples from Empetrum nigrum shrub and two soil samples from vegetation cover of grasses/moss and, depths of 0-5.

Biome: root:Host-associated:Plants
This is a metagenomic study to investigate the microbial community and metabolic functions of Korean twin pairs.

This is a metagenomic study to investigate the microbial community and metabolic functions of Korean twin pairs. Fecal samples from 10 twin pairs were collected once and those of 8 pairs were collected twice with an average interval between sampling of about 2 years. Whole genome shotgun (WGS) sequencing was performed in a total of 36 fecal samples.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJEB4391 data set (Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the faecal microbiome of growing kittens).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB4391, and was assembled with metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.

Biome: root:Host-associated:Mammals:Digestive system:Fecal