SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Developing infant gut microbiome

The colonization process of the infant gut microbiome has been called chaotic, but this view could reflect insufficient documentation of the factors affecting the microbiome. We performed a 2.5-year case study of the assembly of the human infant gut microbiome to relate life events to microbiome composition and function. Sixty fecal samples were collected from a healthy infant along with a diary of diet and health status. Analysis of >300,000 16S rRNA genes indicated that the phylogenetic diversity of the microbiome increased gradually over time and that changes in community composition conformed to a smooth temporal gradient. In contrast, major taxonomic groups showed abrupt shifts in abundance corresponding to changes in diet or health. Community assembly was nonrandom: we observed discrete steps of bacterial succession punctuated by life events. Furthermore, analysis of ~500,000 DNA metagenomic reads from 12 fecal samples revealed that the earliest microbiome was enriched in genes facilitating lactate utilization, and that functional genes involved in plant polysaccharide metabolism were present prior to the introduction of solid food, priming the infant gut for an adult diet. However, ingestion of table foods caused a sustained increase in the abundance of Bacteroidetes, elevated fecal short chain fatty acid levels, enrichment of genes associated with carbohydrate utilization, vitamin biosynthesis and xenobiotic degradation, and a more stable community composition, all of which are characteristic of the adult microbiome. This study revealed that seemingly chaotic shifts in the microbiome could be attributed to life events.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Antarctica Aquatic Microbial Metagenome

Microbial metagenome from a lake in Antarctica.
Microbial community isolated from an aquatic lake in Antarctica. 

Biome: root:Environmental:Aquatic:Marine
MetaSoil

The soil ecosystem is critical for human health, affecting aspects of the environment from key agricultural and edaphic parameters to critical influence on climate change. Soil has more unknown biodiversity than any other ecosystem. We have applied diverse DNA extraction methods coupled with high throughput pyrosequencing to explore 4.88 x 10^9 bp of metagenomic sequence data from the longest continually studied soil environment (Park Grass experiment at Rothamsted Research in the UK). Results emphasize important DNA extraction biases and unexpectedly low seasonal and vertical soil metagenomic functional class variations. Clustering-based subsystems and carbohydrate metabolism had the largest quantity of annotated reads assigned although o50% of reads were assigned at an E value cutoff of 10^-5. In addition, with the more detailed subsystems, cAMP signaling in bacteria (3.24±0.27% of the annotated reads) and the Ton and Tol transport systems (1.69±0.11%) were relatively highly represented. The most highly represented genome from the database was that for a Bradyrhizobium species. The metagenomic variance created by integrating natural and methodological fluctuations represents a global picture of the Rothamsted soil metagenome that can be used for specific questions and future inter-environmental metagenomic comparisons. However, only 1% of annotated sequences correspond to already sequenced genomes at 96% similarity and E values of 10^-5, thus, considerable genomic reconstructions efforts still have to be performed. See http://www.genomenviron.org/Projects/METASOIL.html for additional details.

Biome: root:Environmental:Terrestrial:Soil:Grasslands
Brazos-Trinity Basin Sediment Metagenome: IODP Site 1320

This project describes a population genomic study focused on determining the evolutionary rates in natural populations, and to correlate human disturbance to major evolutionary divergence events. Biofilm samples from acid mine drainage were taken in the period 2006-2010 at four locations in the Richmond Mine (Iron Mt., CA). Community genomic DNA was extracted and sequenced by either 454 or Illumina sequencing.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
Peru Margin Subseafloor Biosphere

The subseafloor marine biosphere may be one of the largest reserviors of microbial biomass on Earth and has recently been the subject of debate in terms of the composition of its microbial inhabitants, particularly on sediments from the Peru Margin. A metagenomic analysis was made using whole genome amplification and pyrosequencing of sediments from Ocean Drilling Program Site 1229 on the Peru Margin to further explore the microbial diversity and overall community composition within this environment. A total of 61.9 Megabases of genetic material was sequenced from sediments at horizons 1, 16, 32 and 50 meters below seafloor. These depths include sediments from both primarily sulfate-reducing and also methane-generating regions of the sediment column. Many genes of the annotated genes, including those encoding ribosomal proteins, corresponded to those from the Chloroflexi and Euryarchaeota. However, analysis of the 16S small subunit ribosomal genes suggests that Crenarchaeota are the abundant microbial member. Quantitative PCR confirms that uncultivated Crenarchaeota are indeed a major microbial group in these subsurface samples. These findings show that the marine subsurface is a distinct microbial habitat and is different than environments previously studied by metagenomics, especially due to the predominance of uncultivated archaeal groups.

A metagenomic analysis was made using whole genome amplification and pyrosequencing of sediments from Ocean Drilling Program Site 1229 on the Peru Margin to further explore the microbial diversity and overall community composition within this environment.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
Viral metagenomic study of two freshwater Lakes

Viruses are known to be the most abundant biological entities in
    aquatic environment, where they are (i) important top-down regulation factors for
    microbial communities, (ii) known to interfere in major biogeochemical cycles, and
    (iii) thought to be an important source of genetic diversity. Yet, diversity and
    distribution of these viruses is still far from being understood, especially in
    freshwater ecosystems. Metagenomic analysis of two different temperate freshwater
    viral communities showed that most of the viral sequences were not similar to those
    in the current databases. A deep sequencing (1.5 billion sequences) associated to a
    large read size (400 bp) allowed us to assess, for the first time, the diversity in
    the main viral families through direct phylogenetic analysis of specific marker
    genes. The analysis of the major viral groups found in the two lakes shed light on a
    great diversity, and retrieved previously unknown clades among single-stranded DNA
    viruses (Microviridae, Circoviridae, Nanoviridae) and among Caudovirales. The
    absence of lake-specific clade indicated that the new viruses identified were
    ubiquitous, at least on a regional freshwater lake scale. Compared to the previously
    published viromes, a significant genetic similarity between viral communities of
    related environments was highlighted for the first time, despite the great
    geographical distances separating these different communities. Thus, viruses appear
    to be distributed worldwide, and are likely selected by the presence or absence of
    their hosts. Gene richness analysis assessed through rarefaction curves showed an
    extraordinary genetic diversity of viruses in each of the two lakes under study.
    Such diversity was never retrieved previously, even in the last generation of
    published viromes. The global virome is thereby a fantastic pool of unknown genes,
    which remains partially sampled and understood.

Biome: root:Environmental:Aquatic:Freshwater:Lake
Comparison of microbial communities in marinated and unmarinated broiler meat by metagenomics

We investigated the effect of marination on microbiota in modified athmosphere packaged broiler meat using metagenomics. To be able to see the differences in lactic acid bacteria communities on a strain level and to evaluate congruence between the methods, we characterized the lactic acid bacteria communities also by identification of isolates. Most raw poultry sold in Finland at the retail level is mixed with marinades containing oil, sugar, spices and acetic acid and packaged under modified atmosphere. Growth of Leuconostoc spp. has been observed to cause premature spoilage  of marinated broiler meat packages. In this study we investigated whether marinating enriched Leuconostoc spp. in meat microbiota. To obtain a complete view of the microbiota, we sequenced total DNA and 16S rRNA gene amplicons from the microbial communities. In addition, the lactic acid bacterial communities were characterized by identification of colonies. The results showed that marinade increased the proportions of the spoilage-associated Leuconostoc gasicomitatum in the communities as well as the proportions of L. gelidum and Lactobacillus spp.. The proportions of Carnobacterium, Vagococcus, Brochothrix thrermosphacta, Clostridium, Enterobacteriaceae and Vibrio were diminished. Analysis of 16S rRNA gene amplicons resulted in 312 and 284 operational taxonomical units (dissimilarity 0.03) in unmarinated and marinated meat, respectively, indicating that the meat communities were more diverse than hitherto shown. A number of bacterial taxa that have not been associated with late shelf-life meat before were detected, including Vagococcus and Vibrio that belonged to the predominating part of the microbial community in unmarinated meat. According to the functional analysis of the metagenomes, both communities were characterized by high proportions (15.6% or 17.9%) of genes involved in carbohydrate metabolism.

Biome: root:Engineered:Food production
Functional diversity of soil microbes across environmental gradients

Numerous globally distributed 16S rRNA surveys of soil bacterial communities are
    now revealing consistent trends in the main environmental drivers of
    biodiversity. Soil pH is consistently revealed as the predominant correlate of
    taxonomic diversity, with low pH soils comprising less diversity and being
    dominated by a few broad taxonomic groups such as the oligotrophic acidobacteria
    phylum. What is less clear is what these broad differences in patterns of
    taxonomic diversity mean for the functional genetic potential of soils. The low
    culturability of many taxa from low pH soils means that they are significantly
    underrepresented in genome sequence databases. Therefore, this study aims to
    provide a metagenomic comparison of geographically isolated soils of low pH with
    neutral pH soils to identify any broad functional differences between soils of
    similar taxonomic composition.

Biome: root:Environmental:Terrestrial:Soil
Global Ocean Sampling Expedition

Collection of metagenomes obtained during the Global Ocean Sampling Expedition

Biome: root:Environmental:Aquatic:Marine
Arctic Winter marine ecosystem

Polar winter waters are one of the least studied marine ecosystems with regard to microbial life and Thaumarchaeota are key microorganisms in this environment. We collected data on abundance and metabolic activity of Thaumarchaeota in Arctic and Antarctic waters in different seasons, including the wintertime. As previously observed, Arctic Thaumarchaeota grew throughout the winter, increasing their abundances one order of magnitude from January to March 2008. Yet, paradoxically, in situ single-cell measurements revealed an unexpected low metabolic activity for this group in both polar systems, i.e., less than 5% of archaeal cells taking up leucine or bicarbonate, inconsistent with known heterotrophic or autotrophic archaeal lifestyles. To resolve how archaea obtain energy and carbon for growth, we analyzed a metagenome collected during the Arctic winter, when the Thaumarchaeota population was at its maximum of abundance (18% of cell counts). Metagenomics and quantitative PCR showed that archaeal amoA genes were abundant in Arctic and Antarctic waters, indicating that polar Thaumarchaeota have the potential for ammonia oxidation.  The presence of a large number of archaeal genes involved in urea transport and degradation together with detectable uptake of 14C-labeled urea by the prokaryotic assemblage, suggest that the products of urea hydrolysis (NH3 and CO2) may be sources of both energy and carbon for polar ammonia oxidizing archaea. This hypothesis, consistent with the idea of polar archaea growing as nitrifiers but with apparent low incorporation of bicarbonate, would provide the molecular basis for the recurrent archaeal growth in polar winter waters.

Biome: root:Environmental:Aquatic:Marine
Substrate-controlled succession of distinct marine bacterioplankton populations induced by a spring phytoplankton bloom

Phytoplankton blooms characterize temperate ocean margin zones in spring and contribute substantially to their high productivity. We investigated the bacterioplankton response to a diatom bloom in the North Sea and observed an as yet unseen dynamic succession of thriving populations at genus level resolution. Taxonomically distinct expressions of carbohydrate-active enzymes, transporters (in particular TonB-dependent transporters) and phosphate acquisition systems were found, indicating that distinct populations of Bacteroidetes, Gammaproteobacteria and Alphaproteobacteria acted like guilds specialized for successive algal-derived organic matter decomposition. Our results suggest that algal substrate availability and bacterial ecological niches determined the succession. A better understanding of such couplings between bacterioplankton and phytoplankton is needed to pave the way for predictive models of bacterioplankton bloom dynamics and thus more accurate global carbon turnover balances.

Biome: root:Environmental:Aquatic:Marine
Metatranscriptomics of the marine sponge Geodia barretti: Tackling phylogeny and function of its microbial community.

Geodia barretti is a marine cold-water sponge harbouring high numbers of microorganisms. Significant rates of nitrification have been observed in this sponge, indicating a substantial contribution to nitrogen turnover in marine environments with high sponge cover. In order to get closer insights into the phylogeny and function of the active microbial community and the interaction with its host G. barretti, a metatranscriptomic approach was employed, using the simultaneous analysis of rRNA and mRNA. Of the 262,298 RNA-tags obtained by pyrosequencing, 92% were assigned to ribosomal RNA (ribo-tags). A total of 109 325 SSU rRNA ribo-tags revealed a detailed picture of the community, dominated by group SAR202 of Chloroflexi, candidate phylum Poribacteria and Acidobacteria, which was different in its composition from that obtained in clone libraries prepared form the same samples. Optimized assembly strategies allowed the reconstruction of full-length rRNA sequences from the short ribo-tags for more detailed phylogenetic studies of the dominant taxa. Cells of several phyla were visualized by FISH analyses for confirmation. Of the remaining 21,325 RNA-tags, 10,023 were assigned to mRNA-tags, based on similarities to genes in the databases. A wide range of putative functional gene transcripts from over 10 different phyla were identified among the bacterial mRNA-tags. The most abundant mRNAs were those encoding key metabolic enzymes of nitrification from ammonia-oxidizing archaea as well as candidate genes involved in related processes. Our analysis demonstrates the potential and limits of using a combined rRNA and mRNAapproach to explore the microbial community profile, phylogenetic assignments and metabolic activities of a complex, but little explored microbial community.

Biome: root:Host-associated:Porifera
HMP Mock Community samples

The HMP metagenomes mock pilot represents the shotgun sequencing of HMP even and staggered Mock communities, distributed to each of the four HMP sequencing centers. The goal of the pilot was to test the sequencing protocol and to evaluate accuracy and consistency between centers.

Biome: root:Engineered:Modeled:Simulated communities (DNA mixture)
Metagenomics of the gill chamber epibiosis of deep-sea shrimp Rimicaris exoculata and discovery of zetaproteobacterial epibionts

The shrimp Rimicaris exoculata flourishes on deep-sea hydrothermal chimneys along the Mid-Atlantic Ridge (MAR). This species harbors dense community of chemoautotrophic epibiotic bacteria associated with mineral oxide deposits in its enlarged gill chamber. We used metagenomics on specimens from the Rainbow hydrothermal vent site, to investigate the metabolism of the two main sulfur-oxidizing epibionts affiliated to the Epsilonproteobacteria and Gammaproteobacteria. Both epibionts had genes of the Sox pathway for sulfur oxidation and hydrogenases. In the epsilonproteobacterial epibiont, two distinct denitrification systems (Nas/Nir and Nap/Nrf) as well as a complete rTCA cycle for carbon dioxide fixation were found, while the gammaproteobacterial epibiont was found to fix carbon dioxide via the CBB cycle with RuBisCo form II. The shrimp gill chamber metagenome provided information on host-epibiont interactions, like on virulence gene homologues and genes for surface attachment. Likewise, genes were found that might play a role in host nutritional and detoxification processes, and thus are of major importance for the survival of the shrimp and its adaptation to the hydrothermal vent environment. Interestingly, analysis of the metagenome revealed sequences affiliated to the iron-oxidizing class Zetaproteobacteria, which would explain gill chamber iron oxyhydroxide deposits. Presence of Zetaproteobacteria was confirmed by fluorescence in situ hybridizations and thereby provided first evidence for a Zetaproteobacteria-invertebrate.

Biome: root:Host-associated:Arthropoda:Respiratory system:Gills
Beta Lactam Antibiotics and Human Gut Microbiota

Recent research has disclosed a tight connection between beta-lactam antibiotics, microbial gut metabolism and health but obtaining a complete understanding of this process remains a major goal. Here, we conducted, to the best of our knowledge, the first global comparative OMIC investigation of gut microbial communities in samples of an individual subjected to β-lactam antibiotic therapy at different time frames. Results indicated a drastic change of the total community at response to AB at the day 11thwhich correlated with changes at the level of metabolites, mRNA transcripts and production of proteins. By contrast, AB-resistant active microbiota remains constant, showing a relevant decrease three days later, which indicate an AB time-delay between total and active bacteria. Forty days after AB therapy, the total community is restored but, surprisingly, the low abundant bacteria (Proteobacteria) become the most active members. This is in agreement with unique metabolomic signatures which indicate that human-gut microbe interactions seem to be restored (or improved) as a consequence of AB therapy. It is worth to mention that as a consequence of AB a drastic under-expression of protein production and an attenuation of the metabolic status occurred irreversibly, in agreement with the biodiversity and richness decreased of the total microbiota. Most likely, at the initial stages, AB-resistant bacteria may become, albeit at lower numbers, the most active bacterial members, but their consequent instability as response to AB therapy produced a re-establishment of the overall community containing new active members that has a connection with the host. A complete reprogramming of the bacterial structure and metabolic status seems to occur most likely at day 11th. Taken together, this study suggests a tighter, more coordinated and complex evolutionary and AB ecology scenario of human gut microbial communities than has been previously assumed.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Detoxification of arsenic mediated by microbial sulphate reduction in Mediterranean marine sediments

Micro-organisms which dwell in sediments have a crucial role in biogeochemical cycles and are thus expected to have a strong influence on the cycle of arsenic, a metalloid responsible for severe water pollution and presenting a major health risk for the populations. Nowadays, environmental genomics techniques allow to study the adaptive and cooperative strategies of microbial communities thriving in polluted environments.
We sequenced the sediment metagenomes from l'Estaque marina (Marseille, France), close to a former metallurgic industrial site highly polluted with arsenic, and from St Mandrier marina, near Toulon (France). The functional and taxonomic profiles of both metagenomes, along with those from four publicly available metagenomes used as control data sets, were obtained using the RAMMCAP workflow.
The biodiversity was higher in both harbour sediment communities in comparison to the controls. The order of Desulfobacterales represented 54.7% of the observed orders in l'Estaque and 31.7% in St Mandrier. Other orders were evenly distributed though the diversity was lower in the highly polluted site of l'Estaque than in St Mandrier.  
The Gene Ontology (GO) entries describing the functional profiles were compared with the controls in order to highlight the over-represented categories in the metagenomes of interest. We observed that categories related to arsenic resistance and oxidative stress were over-represented in l'Estaque. More importantly, the integration of metagenomic and physico-chemical data showed that in l'Estaque, dissimilatory sulphate reduction in the upper layer of sediment could increase arsenic diffusion to the water column and deeper layers, resulting in local detoxification of the sediment. 

Biome: root:Environmental:Aquatic:Marine
Long insert human faecal metagenomic library.

Metagenomics allow us to screen the genic content from, virtually, any type of environment with biological content and rendering the possibility of discovering products of interest. Here we propose a method to obtain medium-insert-size (7-15 Kb) metagenomic libraries that are sequenced through a hybrid approach based on pyrosequencing of clone pools and later Sanger-end sequencing of individual clones. Sequences are then assembled and the open reading frames annotated.
We have applied this methodology to study human gut microbiota. From the 358 analysed clones from the library obtained from a faecal sample we found various ORFs annotated as enzymes with already reported industrial or medical application. Finally, forty-three ORFs were annotated as proteins of still unknown function.
This method represents a new approach to explore microbial ecosystems, particularly the human gut microbiome, providing a scalable access to clones with potentially biotechnological and biomedical applications. Thus, previous sequence knowledge will drive the choice of the correct functional screening approach.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Crohn's Disease viral and microbial metagenome

Healthy adult controls and patients affected by ileocolic Crohn’s disease from Valencia (Spain) were examined for their viral and microbial communities from feces and, in one additional case, present in the intestinal tissue. The taxonomical and functional analyses on unassembled and assembled sequence reads, following two different approaches allows as to compare the viral and microbial communities between both groups in study in several ways. For example we compared by group (controls vs patients), by entity (viruses vs bacteria), by reads assembly (assembled vs unassembled reads) and by methodology (our approach vs an existing pipeline). 

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