SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria

The verrucomicrobial subdivision 2, class Spartobacteria, is one of the most abundant bacterial lineages in soil and has recently also been found ubiquitous in aquatic environments. A 16S rRNA gene study from samples spanning the entire salinity range of the Baltic Sea indicated that, in the pelagic brackish water, a phylotype of the Spartobacteria is one of the dominating bacteria during summer. Phylogenetic analyses of related 16S rRNA genes indicate that a purely aquatic lineage within the Spartobacteria exists. Since no aquatic representative from the Spartobacteria has been cultured or sequenced, the metabolic capacity and ecological role of this lineage are yet unknown. In this study, we reconstructed the genome and metabolic potential of the abundant Baltic Sea Spartobacteria phylotype by metagenomics. Binning of genome fragments by nucleotide composition and a self-organizing map recovered the near complete genome of the organism, the gene content of which suggests an aerobic heterotrophic metabolism. Notably, we found 23 glycoside hydrolases that likely allow the use of a variety of carbohydrates like cellulose, mannan, xylan, chitin, and starch as carbon sources. In addition, a complete pathway for sulfate utilization was found, indicating catabolic processing of sulfated polysaccharides, commonly found in aquatic phytoplankton. The high frequency of glycoside hydrolase genes implies an important role of this organism in the aquatic carbon cycle. Spatiotemporal data of the phylotype???s distribution within the Baltic Sea indicate a connection to Cyanobacteria that may hence be the main source of the polysaccharide substrates.

Biome: root:Environmental:Aquatic:Marine
Cow dung metagenomics

MiSeq reads from microbial community of cow dung after different treatments.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Rhizosphere-specific bacterial community structure and activity in long-term contaminated soil

In this study, soil contaminated with PCBs was vegetated by different plant species, horseradish (Armoracia rusticana), black nightshade (Solanum nigrum), and tobacco (Nicotiana tabacum). The aim was to investigate the influence of these plants on both phylogenetic and metabolic diversity of rhizosphere populations and associated decrease of PCBs in the rhizospheres. In addition to plants themselves, the influence of fertilizing on the viability of plants, richness of rhizosphere microorganisms, and decrease of PCB content in soil was determined.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Plant secondary metabolites-induced changes in bacterial diversity and activity in contaminated soil

The aim of the study was to investigate how selected natural compounds (naringin, caffeic acid, and limonene) induce shifts in both bacterial community structure and metabolic activity in long-term polychlorinated biphenyl (PCB)-contaminated soil and how these changes correlate with chlorobiphenyl-degradation effectivity. We have integrated analytical methods of determining PCB degradation with pyrosequencing of 16S rRNA gene tag-encoded amplicons amplified from total community metagenome and DNA-stable isotope probing (SIP) as a direct method which links the metabolic process with its microbial originators.

Biome: root:Environmental:Terrestrial:Soil
Metagenome from Pru Toh Daeng Peat Swamp

Metagenome samples were collected from the Pru Toh Daeng peat swamp forest in Narathiwat province, Southern Thailand, in 2007.
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 Community genomic DNA was extracted from the surface peat soil. Sequencing was carried out by 454 Life Sciences on the Genome Sequencer (GS) FLX System.  The aim of this study is to get a snapshot of the microbial community and obtain sequences encoding an interesting enzyme.
 
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 Data submitted to the Short Read Archive (SRA) is available from the Project Data button.
 
 
 

Biome: root:Environmental:Terrestrial:Soil
Microbial genome analysis of tsunami-affected soil

The 2011 Great East Japan Earthquake Tsunami changed terrestrial environment. We perform metagenome analysis of tsunami-affected soil and genome sequencing of four strains of Arthrobacter sp. living in the affected soil.

Biome: root:Environmental:Terrestrial:Soil
Metatranscriptomic Analysis for Eukaryotic Functional Genes in Forest Soil

For the extraction of environmental RNA after enrichment with wheat bran and avicel, the sample was collected from the forest humic soil in the site of AIST. A forest soil in the site of AIST Tsukuba, Japan (36.06N 140.17E). The extraction of total RNA and the purification of polyadenylated eukaryotic mRNA from the enriched soil sample were used to commercially available kit, respectively.  The synthesized cDNA sample from the purified mRNA was outsourced to Dragon Genomics Center for 454 GS FLX sequencing. The aim of this study is the exploration of the novel eukaryotic functional genes from an environmental sample using metatranscriptomic approach.  This method is widely applicable to the provision of novel eukaryotic enzymes and proteins of potential industrial or medical use.

Biome: root:Environmental:Terrestrial:Soil
Analysis of Early Microbial Communities on Recent Volcanic Deposits of Mt. Merapi, Indonesia

Due to the 2010 Mt. Merapi eruption, the land around the mountain was covered by pyroclastic materials. For the environmental rehabilitation of the volcanic eruption-affected area, it is important to know the pioneer soil microbial communities. The aim of this study was to characterize the early microbial communities in the Mt. Merapi unvegetated volcanic deposits. This investigation was designed to compare the microbial communities of the volcanic deposits with those of forest soil near the mountain by using molecular genetic approaches targeting bacterial 16S rRNA genes. Two unvegetated sites (BR and BRU) were established together with a forest site (FR) as a reference. The diversity index were 3.11, 2.25, and 2.91 on sites BR, BRU, and FR, respectively, which indicated that the bacterial diversity was relatively higher in site BR than in the other sites. Results of the PCoA analysis showed that all bacterial communities of the volcanic deposit samples clustered away from those of forest soil samples. Microbial communities in recent volcanic deposits of Mt. Merapi were phylogenetically diverse inspite of very low-carbon conditions. Proteobacteria was the most abundant phylum in the bacterial community of volcanic deposits. Inspection underlying families revealed the predominance of the family Caulobacteraceae in Alphaproteobacteria, Oxalobacteraceae in Betaproteobacteria, and Xanthomonadaceae in Gammaproteobacteria in the volcanic deposit communities.

Biome: root:Environmental:Terrestrial:Soil
Effects of NaCl concentrations on anode microbes in microbial fuel cells

The study investigated that single-chamber microbial fuel cells were inoculated with paddy-field soil and continuously supplied with acetate media containing different concentrations of NaCl (0 M, 0.05 M, 0.1 M, 0.3 M, 0.6 M and 1.8 M).

Biome: root:Environmental:Terrestrial:Soil
sewage sludge soil samples were subjected to chitosan treatment, the microbiodiversity and gene diversity were unknown.

sewage sludge soil samples were subjected to chitosan treatment, the microbiodiversity and gene diversity were unknown.

Biome: root:Engineered:Wastewater:Water and sludge
High throughput analysis of class 1 integron gene casettes in wastewater environments

We applied a novel sequencing pipeline that enable characterization of hundreds of thousands integron-associated gene in the WWTP environment

Biome: root:Engineered:Wastewater:Water and sludge
Ammonia oxidising Bacteria

Study of ammonia oxidising Bacteria in a Sequencing Batch Reactor over time

Biome: root:Engineered:Bioreactor
metagenomic study targeting N cycling processes

Sugarcane is a crop for bioenergy in Brazil and one of the main concerns in the production of this crop is the impact on the environment, in particular in greenhouse gases (GHG) emissions. Recent studies have shown that the N2O emissions related to sugarcane production are dependent on soil management practices (Carmo et al. 2013). The way to mitigate N2O emissions would be to understanding the conditions and the processes involved in the N2O production and consumption. However, no studies have linked the emissions of GHGs with soil-borne microbial communities, which are the main players in nutrient cycling.

Biome: root:Environmental:Terrestrial:Soil
WORKSHOP METAGENOMIC RUMEN STUDY

STUDY OF RUMEN MICROBIOME DIVERSITY COMPOSITION

Biome: root:Host-associated:Mammals:Digestive system:Foregut:Rumen
Microbial metagenome sequencing from marine sponges (Spongia sp.), seawater and sediments

Marine sponges host abundant and diverse associated bacteria, some of which known to produce biologically active natural products. Although much research effort has been applied to cultivate sponge-associated microorganisms, we still lack the ability to capture the full phylogenetic breadth of this symbiotic consortium in the laboratory. This study uses a cultivation-independent, shotgun metagenomics approach to unveil the taxonomic and functional features of the model sponge host Spongia sp. and its environmental surroundings (seawater and sediments). Samples were taken off the coast of Algarve, South Portugal (North-east Atlantic), and subjected to Illumina sequencing after microbial metagenomic DNA extraction. Taxonomic and functional profiles were assessed using MG-RAST with the Genbank and COG databases, respectively. Most abundant phyla in the sponge microbiome were Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Cyanobacteria, Planctomycetes and Acidobacteria, in this order, altogether comprising 84.35% of all the classifiable sequence reads. In contrast, the dominant phyla in seawater were Bacteroidetes and Proteobacteria (89.3% of all classifiable reads), whereas sediments were dominated by Proteobacteria, Bacteroidetes, Planctomycetes, Actinobacteria and Firmicutes (85%). We found significantly higher frequencies of transcription and translation termination factors in sediments and seawater, respectively, than in marine sponge microbial metagenomes. Moreover, higher abundances of motility and chemotaxis gene reads were found in the former microhabitats in comparison with the marine sponge microbiome, where a conspicuously higher frequency of Clustered Regularly Interspaced Palindromic Repeats (CRISPRs), accompanied by much lower viral abundance, was otherwise observed. These results suggest a highly distinct microbiome inhabiting Spongia sp., both in terms of taxonomy and function, characterized by the prevalence of k-strategy prokaryotes which collectively possess a sophisticated, early-branched viral defence system.

Biome: root:Mixed
Comparison between raw seawater and two-week enrichment with methanesulfonate

Coastal surface seawater from the North Atlantic ocean was filtered and its metagenome was sequenced by Illumina HiSeq 2500. In parallel, half of the sample was filtered and enriched with the addition of methanesulfonate as sole added source of carbon and energy during 16 days following which its metagenome was sequenced by the same method.

Biome: root:Environmental:Aquatic:Marine:Coastal
Human Microbiome Project (HMP) 16S rRNA Gene Diversity, the diversity of 16S ribosomal RNA genes in the human microbiome: 454 Protocol Validation - Mock

This HMP Centers' Evaluation of the standard 454 SOP represents the pyrosequencing of 16S rRNA genes amplified from HMP even Mock community distributed to each of the four HMP sequencing centers. The goal of the pilot was to test the provisional 454 sequencing protocol (v4.2) and to evaluate accuracy. This protocol does use barcodes, targets two 16S windows (V1-V3 and V3-V5), and sequences in the reverse direction. (Previously referred to as Centers' Evaluation of 454 SOP (CEFoS) Mock Pilot)

Biome: root:Engineered:Modeled:Simulated communities (sequence read mixture)
Desert varnish metagenome

Our study provides an insight into the microbial community structure associated with desert varnish, a coating found on exposed rock surfaces in arid environments. We characterize samples from the Mojave Desert, California, USA using whole-genome shotgut sequencing with a special focus on manganese-oxidizing species.

Biome: root:Environmental:Terrestrial:Soil:Desert
The POU/Oct transcription factor Pdm1/nub is necessary for a beneficial gut microbiota and normal lifespan of Drosophila

Maintenance of a stable gut microbial community relies on a delicate balance between immune defense and immune tolerance. We have used Drosophila to study how the microbial gut flora is affected by changes in host genetic factors and immunity. Flies with a constitutively active gut immune system, due to a mutation in the POU transcriptional regulator Pdm1/nubbin (nub) gene, had higher loads of bacteria and a more diverse taxonomic composition than controls. In addition, the microbial composition shifted considerably during the short life-span of the nub1 mutants. This shift was characterized by a loss of relatively few operational taxonomic units (OTUs) and a remarkable increase in a large number of Acetobacter spp. and Leuconostoc spp. Treating nub1 mutant flies with antibiotics prolonged their life-time survival with more than 100%. Immune gene expression was persistently high also in the presence of antibiotics, indicating that the early death was not a direct consequence of an over-active immune defense but rather an indirect consequence of the microbial load and composition. Thus, changes in host genotype and inability to regulate normal growth and composition of the gut microbiota, leads to a shift in the microbial community, dysbiosis and early death.

Biome: root:Host-associated:Arthropoda:Digestive system:Gut
Beyster Family Fund and Life Technologies Foundation-funded Global
Ocean Sampling Expedition, 2009-2011

Microbial communities in a range of aquatic environments
provide key ecological services while also potentially harboring dangerous
pathogens.  During 2009-2011, microbial communities from aquatic
communities in close contact with humans were collected and characterized
using shotgun metagenomic sequencing.  Sampled environments include
coastal sites in the Pacific and Atlantic Ocean, extensive surveys of the
Mediterranean and Baltic Seas, along with the Black Sea, Lake Constance,
Lake Banyoles, Lake Ciso, and Lake Redon.

Biome: root:Environmental:Aquatic:Marine
Gut barrier impairment by high-fat diet in mice depends on housing conditions.

SCOPE: Diet-induced obesity (DIO) is proposed to cause impairments in intestinal barrier integrity, but contradictory results have been published and it appears that the outcomes depend on other environmental factors. We therefore assessed whether the hygienic status of animal facilities alters the gut barrier in DIO mice.  METHODS AND RESULTS: Male C57BL/6N mice were housed in a conventional (CV) or a specific pathogen-free (SPF) animal facility and were fed identical diets represented by a high-fat (60kJ% fat) or control diet (11kJ% fat) for 12 weeks. Intestinal barrier function in small and large intestine was evaluated in Ussing chambers by electrical resistance and permeability measurements. Jejunal (p<0.01) and proximal colonic (p<0.05) barrier function was altered in CV DIO mice, but not in SPF DIO mice. Moreover, only CV DIO mice were characterized by metabolic endotoxemia and low-grade inflammation. High-throughput 16S rRNA gene sequencing revealed significant differences in fecal bacterial diversity and composition between the two animal facilities, but only in mice fed the HFD. Moreover, cecal DCA concentrations correlated positively with two yet uncultivated Clostridiales species.  CONCLUSIONS: We demonstrated that housing conditions and associated changes in gut bacterial colonization are pivotal for maintenance of gut barrier integrity in DIO mice.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Rice-straw enriched mixed microbial composting community de novo metatranscriptome

A rice straw enriched mixed microbial composting community was used to inoculate rice straw as sole carbon source under laboratory conditions.  A de novo metatranscriptome was assayed after 1 week of growth and used in transcriptome informed metaproteomics

Biome: root:Engineered:Solid waste:Composting
Shotgun metagenomics of moose rumen

The moose (Alces alces) manages to utilize energy from fiber-rich lignocellulose material through enzymes produced by the microbes in its rumen. Some of these specialized enzymes may outperform cellulases and hemicellulases that are used in bio-refinery processes today. Shotgun metagenomics offers a method to study microbial communities in detail and to capture the gene sequences coding for enzymes that can be produced in the laboratory. We applied the technique on rumen material from moose. Through a binning approach, a large number of metagenome-assembled genomes (MAGs) from single species and strains were isolated and characterized based on taxonomy and carbohydrate active enzyme (CAZY) profile. Most of the 99 MAGs were classified to the bacterial phyla Bacteriodetes and Firmicutes, which is in agreement with previous studies of rumen from moose and other herbivores. Phylogenomic analysis of MAGs revealed novel clades within Bacteriodetes with no related previously characterized genome. In addition, new genomes that were closely related to the recently described Melainabacteria, newly proposed candidate divisions SR1 and TM7 and previously uncharacterized Alphaproteobacteria were also retrieved. Putative cellulolytic  functions were observed in several clades of Bacteroidetes and for MAGs of genus Ruminococcus, Fibrobacteres, and Treponema. Cellulosome components were present in MAGs of Ruminococcus but also in certain clades of Bacteroidetes. Cellulosomes are generally described in the Firmicutes family Clostridiales. Multiple putative cellulases were identified within species from several phyla. At a general level, the most frequently occurring polysaccharide-degrading enzymes targeted hemicellulose, starch and pectin. This study describes the first shotgun-metagenomic characterization of moose rumen and the high number of reconstructed genomes provides a valuable link between phylogeny and cellulolytic role.


Biome: root:Host-associated:Mammals:Digestive system:Foregut:Rumen
Dilution methods to manipulate microbial biodiversity

Dilution methods to manipulate microbial biodiversitydilution

Biome: root:Engineered:Lab enrichment
Microbial Community of Mobilong Acid Sulfate Soil depth profile using Metagenomics

The latter part of the Australian Millenium drought in 2007-2009 caused the acidification of acid sulfate soils in wetland and former floodplain soils, which pose threats to terrestrial and coastal ecosystems even after the recovery of surface flows and ground water levels. Drying and subsequent oxidation of ASS materials caused soil pH to drop to less than 4 (forming sulfuric materials) in some areas, triggering environmental problems such as land degradation, loss of native plants and animals, and release of heavy metals and metalloids into ground water, rivers and wetlands. To understand this microbially-mediated oxidation process, microbial communities were studied within an acidified acid sulfate soil profile, to identify key microorganisms involved in soil acidification. Six soil layers were sampled from a soil profile according to soil morphology at the most acidic locationin the field. Total DNA from soil samples was extracted using MO-BIO PowerMax? Soil DNA Isolation Kit and sequenced by Illumina Miseq (250PE) by The Ramaciotti Centre, NSW, Australia, prepared with a Nextera DNA Sample Preparation Kit. There were five steps of non-specific amplification involved in Nextera-Miseq sequencing for obtaining enough DNA for sequencing.

Biome: root:Environmental:Terrestrial:Soil:Grasslands
Metagenome sequencing of DNA-SIP heavy fractions

Soil from the former coking plant in Neuves-Maisons (France) was amended with 13C-phenanthrene, in two conditions, namely bare soil or planted with ryegrass. After ten days, DNA was extracted from soil and separated on cesium chloride gradient. Fractions containing 13C-labeled DNA were sequenced using PE250 MiSeq technology.

Biome: root:Environmental:Terrestrial:Soil:Mine
Metagenomic analysis of soil microorganisms

Metagenomic analysis of soil microorganisms

Biome: root:Environmental:Terrestrial:Soil
Light-dependent microbial metabolisms drive carbon fluxes on glacier surfaces

Biological processes on glacier surfaces affect glacier reflectance, influence surface energy budget and glacier response to climate warming, and determine glacier carbon exchange with the atmosphere. Currently, carbon balance of supraglacial environment is assessed as the balance between the activity of oxygenic phototrophs and the respiration rate of heterotrophic organisms. Here we present a metagenomic analysis of tiny wind-blown supraglacial sediment (cryoconite) from Baltoro (Pakistani Karakoram) and Forni (Italian Alps) glaciers providing evidence for the occurrence in these environments of different and previously neglected metabolic pathways. Indeed, we observed high abundance of heterotrophic anoxygenic phototrophs, suggesting that light might directly supplement the energy demand of some bacterial strains allowing them to use as carbon source organic molecules which otherwise would be respired. Furthermore, data suggest that CO2 could be produced also by microbiologically mediated oxidation of CO, which is produced in snow by photodegradation of organic matter.

Biome: root:Environmental:Aquatic:Freshwater:Ice:Glacier
Mining for novel cellulase genes from different ecosystem metagenomes

The uncultivated microbes are a good resource for identifying potential novel cellulase genes, which are important industrial enzymes.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Alkaline:Sediment
Lake depth metagenomes comparison

We have sampled two depths from lake Redon (2m  (sample 21) and 60m (sample 60) during late september 2013. We plan to study community function and structure in both depths and compare the putative differences we find, regarding lake stratification.

Biome: root:Environmental:Aquatic:Freshwater:Lentic
Sequences produced using indexed (tagged, barcoded) primers in single and double PCR.

Massively parallel sequencing is rapidly emerging as an efficient way to quantify biodiversity at all levels, from genetic variation and expression to ecological community assemblage. However, the number of reads produced per sequencing run far exceeds the number required per sample for many applications, compelling researchers to sequence multiple samples per run in order to maximize efficiency. For studies that include a PCR step, this can be accomplished using primers that include an index sequence allowing sample origin to be determined after sequencing. The use of indexed primers assumes they behave no differently than standard primers; however, we found that indexed primers cause substantial template sequence-specific bias, resulting in radically different profiles of the same environmental sample. Likely the outcome of differential amplification efficiency due to primer-template mismatch, two indexed primer sets spuriously change the inferred sequence abundance from the same DNA extraction by up to 77.1\%. We demonstrate that a double PCR approach alleviates these effects in applications where indexed primers are necessary.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone
Horse Faecal Metagenome-Healthy

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

Biome: root:Host-associated
Mule Faecal Metagenome-Healthy

In arid parts of Rajasthan, the microbial diversity of the mule faecal metagenome was assessed.

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