SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Gut microbial metabolism shifts towards a more toxic profile with supplementary iron in a kinetic model of the human large intestine

Safety of oral iron administration in African children has been questioned as it is associated with an increased burden of infectious disease. However, it remains unclear to which extent oral iron administration affects the intestinal microbiome. Therefore, we here investigated the impact of multiple iron preparations and doses on the growth and metabolism of a human gut microbiota in a well-controlled in vitro model of the large intestine. Microbiome analysis showed clear iron-induced changes and prominent shifts included a decrease of Bifidobacteriaceae and Lactobacillaceae under iron-rich conditions, paralleled by an increase of  Roseburia and Prevotella. Metagenomic analyses showed a general enrichment of bacterial motility-chemotaxis systems under iron-rich conditions. Metabolome profiling showed that gut microbial activity markedly shifted from a saccharolytic to a proteolytic profile in response to iron. Levels of branched chain fatty acids and ammonia increased significantly, in particular under ferrous sulfate-rich conditions. Importantly, cell viability tests showed increased cytotoxicity of metabolite-containing effluent from iron-rich conditions. We also identified microbial metabolites with siderophoric activity that were specifically produced under low-iron conditions. Our data indicate that in the absence of host influences, iron induces a more hostile intestinal environment characterized by i) reduction of beneficial microbes and increase of certain bacterial species with pathogenic potential, ii) increased levels of bacterial metabolites that can impair the barrier function of the gut wall, and iii) increase of virulence-associated pathways of enteric pathogens. It can be envisaged that these in vitro phenomena also contribute to an increased risk for enteric infections in vivo.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Pilot study of the composition of fecal/gut metagenome of tiger populations in India

Tigers are an endangered species living in shrinking habitat. We aim to understand the impact of proximity to human settlement on gut metagenome of tigers. Here a pilot study has been conducted to designed detailed experiments to trace lineage of pathogens, track microbiome and test the presence of gut parasites.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Wisconsin, Native Prairie soil metagenome reference core Project

none provided

Biome: root:Environmental:Terrestrial:Soil
Wisconsin, Continuous corn soil metagenome reference core Project

none provided

Biome: root:Environmental:Terrestrial:Soil
Title : Biological soil crust  microbiota

Desert soil- and rock-surface communities are of crucial importance in the global biogeochemical cycles of carbon and nitrogen. In arid regions, nitrogen inputs depend on biological nitrogen fixation. Biological soil crusts contribute substantially to nitrogen fixation and act as net exporters of ammonium, nitrate and organic nitrogen to the underlying soil layers. Approximately half of the total biological nitrogen fixation on land is attributed to cryptogamic covers. Up to 70% of the fixed nitrogen can be released into the underlying soils and hence is available to other organisms. The N-cycle includes the assimilatory pathways dinitrogen fixation and nitrate assimilation. Some prokaryotes are capable of obtaining metabolic energy from nitrification and denitrification. Here, we studied the nitrogen cycling in biological soil crusts in Southern Spain.

Biome: root:Environmental:Terrestrial:Soil:Desert
Comparative metagenomics of microbial communities in gorgonian corals, marine sediments and seawater

The sustainability of coral reefs bears fundamental implications to the functioning of coastal ecosystems and the biogeochemistry of our planet. The coral-associated microbiota plays a pivotal role as a fitness-enhancing factor in the survivability and persistence of the coral holobiont in marine biomes. Nevertheless, we currently lack knowledge of the taxonomy and functional traits of the highly complex microbiome that populates most coral species. Conspicuously, symbionts inhabiting soft corals which usually thrive and dominate in temperate waters have been scarcely examined.  In this study, we employ a comparative metagenomics approach to uncover the distinct phylogenetic and functional features of the microbiome of soft corals. To this end, high-throughput, Illumina metagenome sequencing of seawater, sediments and of the symbiotic consortium from the gorgonian corals Eunicella verrucosa, Eunicella gazella and Leptogorgia sarmentosa was performed.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
Soil Targeted Locus (Loci)

Studying the effect of the erosion of microbial genetic diversity on nitrogen-cycling in soil.

Biome: root:Environmental:Terrestrial:Soil
Methanogen diversity in indigenous and introduced ruminant species on the Tibetan plateau

Host factors are regarded as important in shaping the archaeal community in the rumen but few controlled studies have been performed to demonstrate this across host species under the same environmental conditions. A study was designed to investigate the structure of the methanogen community in the rumen of two indigenous (Yak and Tibetan sheep) and two introduced domestic ruminant (cattle and crossbred sheep) species raised and fed under similar conditions on the high altitude Tibetan plateau. The methylotrophic Methanomassiliicoccaceae was the predominant archaeal group in all animals even though Methanobrevibacter are usually present in greater abundance in ruminants globally. Furthermore, within the Methanomassiliicoccaceae family members from Mmc. Group 10 and Mmc. Group 4 were dominant in Tibetan plateau ruminants compared to Mmc. Group 12 found to be highest in other ruminants studied. Small ruminants presented the highest number of sequences that belonged to Methanomassiliicoccaceae compared to the larger ruminants. Although the methanogen community structure was different among the ruminant species, there were striking similarities between the animals in this environment. This indicates that factors such as the extreme environmental conditions and diet on the Tibetan plateau might have a greater impact on rumen methanogen community than host differences.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Gut metagenomes from culturomics

The study of the human gut microbiota was relaunched by metagenomic studies.

Biome: root:Host-associated:Human:Digestive system:Hindgut:Rectum
Temperate rainforest nematodes Metagenome

A survey of nematode diversity in a temperate rainforest from soil, litter and canopy habitats - a pooled sampled of 12 MID-tagged temperate forest samples from soil (4), litter (4), and canopy (4) .

Biome: root:Environmental:Terrestrial:Soil
Mechanistic insights beyond metabolic consequences link into microbial reprogramming to poly-aromatic hydrocarbons

PAH-contaminated soil from Lugones, Asturias, Spain.

Biome: root:Environmental:Terrestrial:Soil
Soil Metagenome

A study on metagenomic soil was conducted under the long-term managements till and conventional tillage in crop rotation and succession in an experimental area of Embrapa Soja. The objective was to identify the genetic diversity and biotechnological potential of microorganisms and to compare the microbial communities of soils which may thus infer about the sustainability of different management systems.

Biome: root:Environmental:Terrestrial:Soil
Michigan switchgrass bulk soil replicate #2 soil metagenome

DNA was extracted from agricultural bulk soil for metagenomic comparison.  The goal of this project is to compare bulk and rhizosphere bacterial communities in switchgrass and Miscanthus plant treatments.  This is an ongoing study.

Biome: root:Host-associated:Plants:Rhizosphere
Rhizotron Metagenome Targeted Locus

Biodiversity Manipulation in Rhizosphere and Soil.  The purpose of this project is to analyze the influence of beech  and ash saplings on litter cycling and soil microbial communities using  rhizotrons planted with beech and ash saplings, as well as control  rhizotrons without any tree plant.

Biome: root:Environmental:Terrestrial:Soil
Geothermal soil crust Targeted Locus (Loci)

Diatomaceous samples from a geothermal biological soil crust.  Alkaline siliceous geothermal biological soil crust samples from across 1ha and subdivided by photic/depth.   <p> Soil cores were collected across a 1ha geothermal biological crusted        soil system with the goals of describing a novel microbial        environment, and investigating spatial heterogeneity in soil microbial        systems.  Soil cores were further separated into photic/depth levels,        and replicated.  18S universal primers were used for amplifications,        and individual samples were pyrosequenced (454-Ti).  

Biome: root:Environmental:Terrestrial:Soil
Antarctic Soil Microbiome Targeted Locus

High-throughput pyrosequencing analysis of amplified 16S rRNA genes from soil samples from the most prominent plant communities and soil types collected in ice-free areas of Keller Peninsula, King George Island, Antarctica.   The Antarctic soil metagenome is part of a larger project from the National     Institutes of Science and Technology - Antarctic Environmental Research     (abbreviated as INCT-APA in Brazilian Portuguese). The Institute was     created by the Brazilian Ministry of Science and Technology (Minist rio de     Ci ncia e Tecnologia (MCT) in search of excellence in scientific activities     at an international level in strategic areas defined by the Action Plan     2007-2010 of the Science Programme, Technology and Innovation for     Antarctica, by means of programmes and instruments made operational by CNPq     and by FAPERJ (Research support Foundations at different levels). The     referred initiative has the view to implement a network of atmospheric,     oceanic and cryospheric monitoring, in the Antarctic region. More details     about the Institute and its objectives can be found at     http://www.biologia.ufrj.br/inct-antartico/wp-content/uploads/2011/11/APA.pdf          Specifically, the Antarctic metagenome project aims to obtain a detailed     baseline description of the soil bacterial communities found in the     Antarctic soils against which to compare changes in the Antarctic     microbiome caused by climate changes or human activities. In addition, using     Antarctica as a simple ecosystem model with low or no human influence, to     determine the major factors responsible for the overall patterns of soil     microbial diversity in Antarctica.

Biome: root:Environmental:Terrestrial:Soil
Core Sample from Deep Subsurface Metagenome

An innovative technology to manage municipal biosolids and recycle this waste into clean energy is proposed and tested by City of Los Angeles. With appropriate geological formation selection, proper design, and monitoring, biosolids slurry can be injected into soft, porous, sand formations below the earth surface at 5000ft or more. The high temperature salinity condition in the subsurface will kill pathogens in the biosolids, and stimulate the growth of methanogens to generate methane. This research will take a metagenomic approach to understand the bacteria community structure and diversity changes following the deep-well inject of biosolids.

Biome: root:Environmental:Terrestrial:Soil:Sand
Harvard Forest soil microbial gene expression

This project sequenced the metagenome and metatranscriptome of a temperate forest soil microbial community.  Soil was collected from within a transition hardwood-white pine/hemlock forest in the Prospect Hill Tract of Harvard Forest (Massachusetts, USA; 42.54 N 72.18W; elevation: 385 m) on 27 September, 2010.  Two cores were taken from 1-10 cm below the leaf horizon using a 10 mm diameter soil corer.  These cores were homogenized, placed into 50 ml Falcon tubes, flash frozen in liquid nitrogen, and transported to the lab on dry ice.  Visible pieces of plant material were removed from soil subsamples with sterile forceps.  During plant removal, the subsamples were placed on a sterile surface, laid within a bed of dry ice.  Total microbial DNA and RNA was then extracted from these subsamples using PowerSoil Total RNA and DNA isolation kits (MoBio), according to the manufacturer's protocol.  Total DNA was quantified and used directly for pyrosequencing.  Total RNA was further processed to reduce the proportion of ribosomal RNA transcripts via a custom subtractive hybridization procedure.  Remaining total RNA was then linearly amplified, converted to cDNA, and used for pyrosequencing.  Soil DNA and cDNA were sequenced with full plate runs on a Roche Genome Sequencer FLX instrument using Titanium chemistry.

Biome: root:Host-associated:Protozoa
Vernal Pool Microcosm Soil Samples

These metagenomes were constructed to investigate taxonomic and functional diversity of the microbial community in artificial vernal pools with and without nitrate addition.  The first received nitrate addition and had a high denitrification rate, while the second was a control that received no nitrate addition and had no detectable denitrification.  

Biome: root:Environmental:Aquatic:Freshwater
Metagenomes isolated from NE Brazil

Mangroves are important and productive ecosystems found in tropical and subtropical environments, providing habitats for a variety of species. These ecosystems have been suffering from impacts through the years and consequently the activity of soil microorganisms, which are directly related to valuable processes in these environments, is affected. Understanding the diversity and function of microbial communities and their response to environmental changes is essential for the maintenance of significant functions in these ecosystems. Currently few studies in Brazil are devoted to the understanding of microbial diversity in mangrove soils. Thus it becomes essential to study the microbial diversity in these environments and to search for genes encoding for enzymes of biotechnological interest. For this reason, the aim of this study was to assess the soil microbial diversity from four mangroves in Ceara state, northeast Brazil, and its response to possible impacts, and search genes of biotechnological interest using metagenomics strategies.  The four studied mangroves are located in the state of Ceara, northeastern Brazil. Two of them are located in the extreme east (Jaguaribe Mangrove) and west (the Mangrove Timonha) coast of the state separated by 530 km and the other two are located in a central region, near the city of Fortaleza, state capital (Coco and Pacoti mangroves). Jaguaribe (JAG) mangrove is located at the largest river of the state, in a sub-urbanized region, and impacted by agriculture run-off and extensive shrimp farming. In contrast, Timonha (TIM) is an undisturbed mangrove, located in an island inside the estuary, with limited access to humans. The Coc? (COC) and Pacoti (PAC) mangroves, located in the metropolitan region of Fortaleza, suffer impacts due to water pollution, deforestation of native vegetation, especially vegetation of dunes and mangroves, extraction of sand, clay, stone and release of industrial effluents. The sampling locations TIM - S 02?56.587? W 041?19.064?; JAG - S 04?26.749? W 37?46.989?; PAC - S 03?49.226? W 038?24.286?; COC - S 03?46.482? W 38?26.552?. Sediment samples were collected in three sites inside the mangroves aiming to cover typical habitats in this ecosystems: near the river, Rhizophora mangle forest and the last one in an area covered by Avicennia schaueriana. In each habitat five sediment cores from 0-10 cm layer in an area of 10 m2, in the low tide of 0.0, were collected. The fifteen samples from each mangrove were pooled to form a single composite sample and DNA metagenomic extraction was carried out using the PowerMaxSoil DNA Extraction kit (MoBio Laboratories, Carlsbad, CA, USA) following the manufacturer's protocol. The extracted DNA was then subjected to 454 pyrosequencing.

Biome: root:Environmental:Terrestrial:Soil
Alert biopiles

Goal of this project was to identify the microorganisms and functional genes that are associated with a very efficient bioremediation experiment in the Canadian high Arctic. <p>   DNA can be obtained from Etienne Yergeau/Charles Greer at the National Research Council of Canada, Biotechnology Research Institute. 

Biome: root:Engineered:Bioremediation
WGA

Although high throughput sequencing is a powerful tool to access the composition of different microbial communities, low biomass environments often possess insufficient amounts of DNA for such analyses.  An example of such an environment is airborne dust that is limited in biomass as well as in the quantity of sample available for analysis. The interest in studying microbial population diversity in intercontinental dust from the Chad Republic, Africa, using culture-independent methods led to a search for protocols that enhance the amount of DNA without compromising the robustness of the analysis.  Whole genome amplification (WGA) is a method that has been used to amplify small amounts of DNA from a variety of samples. Little is known about the bias generated by WGA and the implication of bias in the pyrosequencing results.  To answer this question, DNA was extracted from a sandy soil and used as a model to optimize the protocol for DNA extraction and WGA analyses of the microbial communities that might be found in Chad sand samples. Ribosomal intergenic space analysis and 454 pyrosequencing of amplified 16S rRNA fragments showed that DNA submitted to whole genome amplification differed significantly after whole genome amplification. The 16S rRNA microbial community obtained from WGA had a higher Shannon diversity index and higher rarefaction curves compared with the microbial community obtained without amplification of the template DNA.  Changes observed with WGA were both qualitative and quantitative.

Biome: root:Environmental:Terrestrial:Soil:Sand
Permafrost metagenome

The fate of the carbon stocked in permafrost soils following global warming and permafrost thaw is of major concern in view of the potential for increased CH4 and CO2 emissions from these soils. Complex carbon compound degradation and greenhouse gas emissions are due to soil microbial communities, but their composition and functional potential in permafrost soils are largely unknown.   <p> A 2m deep permafrost and its overlying active layer soil were subjected to metagenome sequencing, quantitative PCR, and microarray analyses. The active layer soil and 2m permafrost soil microbial community structures were very similar, with Actinobacteria being the dominant phylum. The two soils also possessed a highly similar spectrum of functional genes, especially when compared to other already published metagenomes. Key genes related to methane generation, methane oxidation and organic matter degradation were highly diverse for both soils in the metagenomic libraries and some (e.g. pmoA) showed relatively high abundance in qPCR assays. Genes related to nitrogen fixation and ammonia oxidation, which could have important roles following climatic change in these nitrogen-limited environments, showed low diversity but high abundance. The 2m permafrost soil showed lower abundance and diversity for all the assessed genes and taxa. Experimental biases were also evaluated and showed that the whole community genome amplification technique used caused large representational biases in the metagenomic libraries.   <p> This study described for the first time the detailed functional potential of permafrost-affected soils and detected several genes and microorganisms that could have crucial importance following permafrost thaw. <p> Sequences deposited into the Sequence Read Archive can be found using the Project data link.

Biome: root:Environmental:Terrestrial:Soil:Permafrost
Microbial Saltern Metagenome HighSalternSDbayMicD0704

Microbial community collected July 1, 2004, from a 'high' salinity saltern (32.599040, -117.107356).  A water sample from the solar saltern of South Bay Salt Works (Chula Vista, CA) was collected in July 2004 from a ponds with high salinity (28-30%), as measured using a hand refractometer. The microbial fraction was isolated from the water sample by passage through a 0.2 mkm tangential flow filter (TFF, Millipore). The retentate was kept and the microbial fraction was collected from the 0.2 mkm TFF retentate by centrifugation at ~ 2000 xg for 10 min. Microbial DNA was extracted using the Ultra Clean Soil DNA Kit (Mo Bio Laboratories, CA). The microbial DNA samples was amplified using the strand-displacement 29 DNA polymerase (GenomiPhi Amersham Biosciences, NJ). The resulting metagenomic DNA was pyrosequenced on the GS20 sequencer (454 Life Sciences, CT). The raw metagenomic sequences were screened to remove duplicate sequences. The metagenome was named HighSalternSDbayMicD200407 and submitted to NCBI.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome

RNA-centered meta-transcriptomic approach to simultaneously obtain information on both structure and function of a soil community.

Biome: root:Environmental:Terrestrial:Soil
Metagenomic analysis of Pinus pinaster's forest soil in southern Spain

This study mainly consist in the analysis of the Pinus pinaster's soil metagenome. Two different soil samples were obtained corresponding totimes with different gene expression patterns in P. pinaster. The first sample was taken in March and the second one in July. The sampling was made in Los Reales de Sierra Bermeja (Estepona, Spain) with the present UTM coordinates North 30S 303095 4034618 and 1245m of altitude.Sierra Bermeja is a mountain range in the southern Spain near the coast and it is the biggest massif of peridotite all over the world. The peridotiteis a dense, coarse-grained igneous rock, consisting mostly of the minerals olivine and pyroxene. The samples were from the soil around three trees (70 cm approx. from the tree stem) and three different samples were taken from each tree(3 trees x 3 samples = 9 samples per each time). Total DNA from the soil samples were extracted by triplicate (9 x 3 = 27 DNA samples per each time) and the resulting DNA was pooled with equivalent amounts from each DNA samples. Each soil DNA pool was processed and sequenced in a Roche 454 Titanium FLX+ sequencer. Half PicoTiterPlete was used for each sample.

Biome: root:Environmental:Terrestrial:Soil
Mudflat sediments Targeted Locus (Loci)

mcrA genes recovred from a mudflat of the Yangtze estuary.

Biome: root:Environmental:Terrestrial:Soil
The fecal microbiota of free-ranging brown bears was collected during their active phase (summer) and hibernation (winter). Germfree mice were colonized with the seasonal bear microbiota.

Hibernation is an adaptation that helps many animals to conserve energy during food shortage in winter. Brown bears double their fat depots during summer and use these stored lipids during hibernation. Although bears seasonally become obese, they remain metabolically healthy. We analyzed the microbiota of free-ranging brown bears during their active phase and hibernation. Compared with the active phase, the hibernation microbiota had reduced diversity, reduced levels of Firmicutes and Actinobacteria, and increased levels of Bacteroidetes. Several metabolites involved in lipid metabolism including triglycerides, cholesterol and bile acids were also affected by hibernation. Transplantation of the bear microbiota from summer and winter to germ-free mice transferred some of the seasonal metabolic features and demonstrated that the summer microbiota promoted adiposity without impairing glucose tolerance, suggesting that seasonal variation in the microbiota may contribute to host energy metabolism in the hibernating brown bear.

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