SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Horse Faecal Metagenome-Clinical disorders

Assessing the microbial diversity in GI disorders of horse in the faecal samples

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Donkey Faecal Metagenome

In the arid parts of Rajasthan, the microbial diversity of donkey faecal metagenome is assessed

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Dromedary Faecal Metagenome-GI disorder

In arid parts of Rajasthan, camel is an important source of livelihood for the rural farmers. the present study aimed to study the microbial diversity of faeces in various GI disorders.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Dromedary Faecal Metagenomes-Healthy

In the arid parts of Rajasthan, camel forms an important livestock reared by rural farmers and contributing to the agricultural economy.  Assessing the faecal microbial diversity in various management practices and various districts of Rajasthan was done.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Dromedary C1 Fluid Analysis-Feed Formulations

Microbial diversity of C1 compartmemnt fluid on different feed formulations

Biome: root:Host-associated
Metagenomes of intestinal samples were obtained from wild type mice to determine the functional and taxonomic coverage by available cultivable bacteria isolated from mouse.

The important role of mice as a model in research of microbe host interactions increased the need for determining the limits of such experiments due to host specificity and adaptation of several microbes. We collected a broad collection of bacteria isolated from mice covering the whole taxonomic range of common gut bacteria. Based on the functional coverage by this collection of several metagenomic samples obtained from mice we can use it to simulate several microbial profiles using minimal consortia of bacteria, facilitating the better understanding of the systems.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine
DNA barcoding the flora of Kuwait

This project is a combined ecological and molecular investigation into the diversity of the Kuwaiti Flora and the soil seed bank. It is aimed at extracting DNA barcode regions from plant leaves to build a DNA reference library. Also, to investigate the diversity of species present in the soil by DNA extracting soil samples and using tools such as metagenomics and metabarcoding to verify the utility of the database.

Biome: root:Host-associated:Plants
Circadian rhythms in plant roots

Circadian rhythms in plant roots.

Biome: root:Host-associated
Reconstructing the ecosystem functions of the active microbial community within Baltic Sea oxygen depleted sediments

In the present study, we sought to establish whether and to what extent the functional capacities were actually expressed in the Landsort Deep anoxic sediment, using a metatranscriptomic approach. Specifically, given the global extension of anoxic ?dead zones? and the global importance of marine sediment as carbon sink, we were interested to investigate if, and how, the sediment community of the anoxic Landsort Deep sediment mineralized the accumulating carbon. Results reveal the extent of what ecosystem functions, and which nutrient recycling processes, the anoxic sediment microbial communities contribute to. This is knowledge which is important to the decision support tools underlying the Helsinki Commission Baltic Sea Action Plan.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
Analysis of metagenomes from oak wood taken from healthy and diseased trees.

The aim is to comparatively analyze the microbiome found in oak trees using metagenomics. Field samples have been taken from healthy oak trees and trees suffering from the disease acute oak decline. Acute oak decline is a spreading disease in Europe and North America, causing wilting and potentially death of oaks.

Biome: root:Host-associated:Plants
Experimental Metagenome on MinION

This is an artificial metagenome created by pooling various proportions of DNA from four microbe cultures to simulate a simple metagenome for analysis by Oxford nanopore MinION.  Single-species cultures of Escherichia coli, Paracoccus denitrificans, Microcystis aeruginosa, and Synechococcus elongatus were grown to log phase then harvested for DNA extraction.  Following mechanical shearing, templates were prepared using either equimolar amounts of each species or combinations of DNAs where one species was rare (0.05%). Libraries were created using his-tag bead purification according to MinION specifications and libraries were sequenced using MinION R7.x flow cells.

Biome: root:Engineered:Modeled:Simulated communities (DNA mixture)
Artic fresh water viromes (2)

Recent metagenomic studies have shown that our knowledge about viruses in nature is very scarce. We aimed to augment such knowledge by analyzing newly sequenced polar freshwater viral metagenomes (both arctic and antarctic..)Previously unexplored arctic viromes were dominated by ssDNA viruses with no known relatives in the databases. Arctic and antarctic viromes were shown to differ at the fine grain level, yet we were able to find a circular contig in both environments with very high similarity.

Biome: root:Environmental:Aquatic:Freshwater:Lake
A Comprehensive survey of Microbial Diversity in Hot Spring of Unai

In the present study, a high-throughput metagenomic sequencing of metagenomic DNA was performed on an Ion Torrent PGM platform for assessment of microbial diversity. Metagenome composed of 688,059 sequences with size 98,567,305 bps with an average length of 182 bps and 45% G+C content. MG-RAST community analysis revealed dominating Bacillus genus in bacterial domain. Remarkably, 20.5% sequences in a poorly characterized group, with versatile presence of commercial enzymes were marked in a functional metagenome analysis.

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Metagenomic analysis of microbial diversity of Tuva hot water spring

Molecular approaches used to analyze the microbial diversity allow the study of uncultivable microorganisms and contribute towards our understanding of the microbial world. In our study, total community DNA was isolated from environmental water sample by manual and kit based methods. Here, we use Ion-torrent PGM platform to sequence metagenome. Analysis of the community DNA revealed that the phyla Firmicutes and Proteobacteria were the most abundant. Moreover, unclassified sequences also found in this metagenome indicate there are possibilities of getting novel organisms.

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Study of early life microbiota in preterm baby

Study of early life microbiota in preterm baby using 16S rRNA sequencing

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

Human faeces Metagenome

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Rumen microbiome

Study of rumen microbiome diversity composition

Biome: root:Host-associated:Mammals:Digestive system:Foregut:Rumen
Nitrifying reactor with FNA treatment

Nitrifying reactor with FNA treatment and varying concentrations

Biome: root:Engineered:Wastewater:Nutrient removal:Nitrogen removal
Gene-Environment Interactions at the Skin Surface

16S rRNA gene sequences amplified from subjects with eczema and age-matched healthy controls.  Microbes living in and on humans are ten times more numerous than human cells. Culture-based methods have been the primary techniques used to study microbes inhabiting humans; however, many species are not successfully grown in culture. The NIH Roadmap for Medical Research Human Microbiome Project (HMP) aims to investigate the microbes in the gastrointestinal tract, oral cavity, skin, vagina, and nares. The goal of the HMP is to comprehensively characterize the human microbiota and analyze its role in human health and disease.   The skin serves not only as a barrier against invading pathogens and moisture loss, but also as a host to microbial communities. The skin of an adult is an approximately 2 square meter surface with a myriad of microenvironments.  Atopic dermatitis (AD), more commonly known as eczema, is a common skin disorder that is exacerbated by Staphylococcus aureus colonization.  This study aims to investigate the skin microbiota of AD patients at specific timepoints (quiescence, disease flares, and post-treatment) to examine how disease state correlates with changes in the skin microflora.     The 16S small subunit ribosomal (rRNA) gene is present in every bacterial cell, serving as a universal marker. The gene is sufficiently conserved to allow accurate alignment but adequately varied to enable phylogenetic analyses. Sequencing via 16S rRNA-based phylotyping has been used to survey the bacterial microbes on the skin.  Initially, we will examine the bacterial diversity associated with AD using a 16S rRNA survey and later broadening to include fungi, viruses, archaea and mites. In addition, bacteria will be cultured on a wide variety of media and isolates representing both abundant and novel species will be selected for whole genome sequencing.  To characterize fungal diversity, we utilize two phylogenetic markers within the rDNA region: 18S rRNA and the Intervening Internal Transcribed Spacer (ITS) region.  Full microbial diversity will be explored with shotgun metagenomic sequencing.

Biome: root:Host-associated:Human:Skin
Rumen microbiome

Mocrobiome study of rumen

Biome: N/A
Metagenomic workshop submission

sequence submission to EBI metagenomics

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Soil metagenome sampled from a chitin-amended agricultural field

Sampling took place on 21 st November 2010. Soil cores were taken from agricultural (pasture) fields located within Northern Ireland amended with Nephrops carapaces. Carapaces were apllied to the field biannually from 2007 (~1.236 kg m-2). Total DNA was extracted using MPBio Fast DNA Kit for soil and sequenced using an Illumina MiSeq platform - paired end reads. The soil is slightly acidic.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
NeoM

NeoM

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Kankrej cow metagenome

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Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
A metagenomics approach to evaluate the impact of Ascophyllum nodosum and Laminaria digitata on the rumen function

There is an increasing need to identify alternative feeds for livestock that do not compete with feeds for human consumption. Seaweed might provide such a resource, but there is limited information available on its value as an animal feed. Here we use a multi-omics approach to investigate the value of two brown seaweeds, Ascophyllum nodosum (ASC) and Laminaria digitata (LAM), as alternative feeds for ruminants. These seaweeds were supplemented at 5% inclusion rate into a control diet (CON) in a rumen simulation fermenter. Seaweeds had no substantial effect on rumen fermentation pattern, feed digestibility or methane emissions in vitro. Concentrations of total bacteria and anaerobic fungi, as well as biodiversity indices, and abundance of the main bacterial and methanogens genera were also unaffected by brown seaweed supplementation. However, specie-specific effects of brown seaweed on the rumen function were noted: ASC promoted a substantial decrease in the N digestibility (-24%) as a result of its high phlorotannins content. Canonical correspondence analysis of the bacterial community revealed that the low N availability led to a change in the structure of the bacterial community. ASC also decreased the concentration of Escherichia coli O157:H7 post-inoculation. On the contrary, LAM which has a much lower phlorotannins content did not cause detrimental effects on N digestibility nor modified the structure of the bacterial community in comparison to CON diets. This adaptation of the microbial community to LAM diets led to a greater microbial ability to digest xylan (+70%) and carboxy-methyl-cellulose (+41%). These differences among brown seaweeds resulted in greater microbial protein synthesis (+15%) and non-ammonia N flow (+11%) in LAM than in ASC diets and thus should led to a greater amino acid supply to the intestine of the animal. In conclusion, it was demonstrated that incorporation of 5% brown seaweed into the diet can be considered as a suitable nutritional strategy for ruminants; however special care must be taken with those seaweeds with high phlorotannins content to prevent detrimental effects on N metabolism. This study demonstrates the value of combining fermentation data with molecular characterisation of the rumen microbiome in evaluating novel feeds for ruminants.

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
metagenomic amplicon sequensing from soils for novel natural products (16S_PKS)

The final aim of this study is to identify different soil environments potentially rich in novel natural compounds correlating microbial community diversity and biosynthetic genes for polyketide synthesis. The identification of interesting environments for novel natural products will be useful for further drug discovery pipeline development.

Biome: root:Environmental:Terrestrial:Soil
Haloalkaline thiosulfate reducing bioreactor

Haloalkaline thiosulfate reducing bioreactor community analysis

Biome: root:Engineered:Bioremediation:Hydrocarbon:Benzene:Bioreactor
Illumina RNA-Seq on Olavius algarvensis worms

Olavius algarvensis is a shallow-water annelid worm that lives in obligate symbiosis with chemosynthetic bacteria. We sequenced batches of o. algarvensis worms incubated under oxic and anoxic conditions, respectively, and performed Illumina transcriptome sequencing on each for host gene discovery.

Biome: root:Host-associated:Annelida
Metagenomes and metatranscriptomes from the diffuse hydrothermal vents of Axial Seamount from 2014

This projects explores the functional diversity and activity of rocky subseafloor microbial communities in hydrothermal vent systems. Samples were collected in 2014 from three low temperature diffuse fluid vents at Axial seamount, located in the northeast Pacific Ocean. We also collected a sample using a CTD within the Axial Caldera, at 1200m depth. Shotgun metagenomics and metatranscriptomics were performed on four diffuse vent samples. This study helps to determine the genetic potential and expression patterns of the largely uncharacterized subseafloor microbial community and shows how these patterns change across the complicated biogeochemical gradients of hydrothermal vent systems.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents
Acropora aspera virome from Heron island, Australia

Previous studies of coral viruses have employed either microscopy or metagenomics, but few have attempted to comprehensively link the presence of a virus-like particle (VLP) to a genomic sequence. We conducted transmission electron microscopy imaging and virome analysis in tandem to characterize the most conspicuous viral types found within the dominant Pacific reef-building coral genus Acropora. Three of the dominant VLPs identified were observed in all tissue layers and budding out from the epidermis, including viruses that were ~70 nm, ~120 nm, and ~165 nm in diameter; these VLPs all contained electron dense cores. These morphological traits are reminiscent of retroviruses, herpesviruses, and nucleocytoplasmic large DNA viruses (NCLDVs), respectively. Some 300-500 nm Megavirus-like VLPs also were observed within and associated with dinoflagellate algal endosymbiont (Symbiodinium) cells. Abundant sequence similarities to a gammaretrovirus, herpesviruses, and members of the NCLDVs corroborated these morphology-based identifications. Additionally sequence similarities to two diagnostic genes, a MutS and a DNA polymerase B gene, were recovered and most closely resembled Pyramimonas orientalis virus, demonstrating the association of a cosmopolitan Megavirus with Symbiodinium. We also identified several other viral particles in host tissues, along with sequences phylogenetically similar to circoviruses, phages, and filamentous viruses. Given that all corals in this study had high titers of viral particles and that aerial exposure of coral colonies during extreme low tides induced bleaching on the reef flat in the weeks during this work, we hypothesize that our collections and experiment coincided with a natural outbreak of viral infection.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
Microbial diversity in a cave ecosystem

Characterisation of microbial communities in microbial mat and sediment from Movile Cave, Romania

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Cave water
Antimicrobial resistance gene monitoring in aquatic environments (Metatranscriptomes).

This dissertation documents the development of an environmental framework for monitoring antimicrobial resistance gene (ARG) dissemination in the aquatic environment. The work opens with a review of the relevant literature and outlines the importance of an environmental framework for monitoring ARG dissemination as part of antimicrobial resistance risk assessments.  The ability to interrogate sequencing data quickly and easily for the presence of ARGs is crucial in order to facilitate their monitoring in the environment. As current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria in the environment were limited in their effectiveness and scope, the dissertation begins by describing the design and implementation of a Search Engine for Antimicrobial Resistance (SEAR), a pipeline and web interface for detection of horizontally-acquired ARGs in raw sequencing data. The suitability of metagenomic methods for monitoring the ARG content of effluents from faecal sources was then assessed via a pilot study of a river catchment. Novel metagenomes generated from effluents entering the catchment were interrogated for ARGs. The relative abundance of ARGs in effluents were determined to be higher relative to the background environment, as were sequences relating to human and animal pathogens and mobile genetic elements. Thus, effluents were implicated in the dissemination of ARGs throughout the aquatic environment. To determine if ARGs were potentially in use in the environment, the expression of ARGs within effluents was then evaluated across a series of longitudinal samples through the use of metatranscriptomics, and the presence of potential environmental antimicrobial selection pressures was examined. This demonstrated that the abundance of ARGs, as well as antimicrobial usage at the effluent source, was correlated with the transcription of ARGs in aquatic environments.  The work described in this dissertation has also found that horizontally transmitted ARGs were present in pathogenic endospore-forming bacteria commonly found across the aquatic environment, potentially providing a mechanism for ARG persistence in the environment.  Finally, these findings were integrated into a universal framework for monitoring ARG dissemination in aquatic environments and used to highlight the developments required to incorporate this framework into future environmental ARG research and to facilitate antimicrobial resistance risk assessments.

Biome: root:Environmental:Aquatic
Antimicrobial resistance gene monitoring in aquatic environments

This dissertation documents the development of an environmental framework for monitoring antimicrobial resistance gene (ARG) dissemination in the aquatic environment. The work opens with a review of the relevant literature and outlines the importance of an environmental framework for monitoring ARG dissemination as part of antimicrobial resistance risk assessments.  The ability to interrogate sequencing data quickly and easily for the presence of ARGs is crucial in order to facilitate their monitoring in the environment. As current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria in the environment were limited in their effectiveness and scope, the dissertation begins by describing the design and implementation of a Search Engine for Antimicrobial Resistance (SEAR), a pipeline and web interface for detection of horizontally-acquired ARGs in raw sequencing data. The suitability of metagenomic methods for monitoring the ARG content of effluents from faecal sources was then assessed via a pilot study of a river catchment. Novel metagenomes generated from effluents entering the catchment were interrogated for ARGs. The relative abundance of ARGs in effluents were determined to be higher relative to the background environment, as were sequences relating to human and animal pathogens and mobile genetic elements. Thus, effluents were implicated in the dissemination of ARGs throughout the aquatic environment. To determine if ARGs were potentially in use in the environment, the expression of ARGs within effluents was then evaluated across a series of longitudinal samples through the use of metatranscriptomics, and the presence of potential environmental antimicrobial selection pressures was examined. This demonstrated that the abundance of ARGs, as well as antimicrobial usage at the effluent source, was correlated with the transcription of ARGs in aquatic environments.  The work described in this dissertation has also found that horizontally transmitted ARGs were present in pathogenic endospore-forming bacteria commonly found across the aquatic environment, potentially providing a mechanism for ARG persistence in the environment.  Finally, these findings were integrated into a universal framework for monitoring ARG dissemination in aquatic environments and used to highlight the developments required to incorporate this framework into future environmental ARG research and to facilitate antimicrobial resistance risk assessments.

Biome: root:Environmental:Aquatic
Pekin duck health with water troughs compared to pin-metered water lines using a US management system

Controversy has developed over the last few years as to whether or not water nipple lines or water troughs are more appropriate for Pekin ducks in grow-out commercial barns. We hypothesized that water troughs would show improved duck body conditions and environmental quality compared to pin-metered water lines.   To test this hypothesis, we housed ducks in two barns, one with water lines and one with water troughs.   Water troughs were constructed to meet RSPCA guidelines for number and density of ducks and with recently described verandas.  Ducks were divided into 4 pens per barn (n = 1000 ducks/pen).  The study was then repeated (n = 8 pens per water source). Ducks were scored for physical traits and assessed for microbial cecal content changes through 16S amplicon sequencing. Water samples were assessed for culturable microbial loads and for microbial community through 16S amplicon sequencing.

Biome: root:Engineered:Wastewater:Industrial wastewater:Agricultural wastewater
Assessment of Bacterial DNA Extraction Procedures for Metagenomic Sequencing Evaluated on Different Environmental Matrices.

Will follow later.

Biome: root:Engineered:Modeled
16S V3-V4 metagenome from four Danube water samples

Water samples have been collected at four sites in Croatia/Serbia onthe Danube river. Analysis of the samples' 16S metagenomes should provide an indication how the bacterial community changes going from a relatively clean site to more pulluted sites close to industrial areas.

Biome: root:Environmental:Aquatic:Freshwater:Lotic