SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Gut microbial succession follows acute secretory diarrhea in humans

Disability after childhood diarrhea is an important burden on global productivity. Recent studies suggest that gut bacterial communities influence how humans recover from infectious diarrhea, but we still lack extensive data and mechanistic hypotheses for how these communities respond to diarrheal disease and its treatment. Here, we report that after V. cholerae infection, human gut microbiota undergo an orderly and reproducible succession featuring transient reversals in relative levels of enteric Bacteroides and Prevotella. Elements of this succession may be a common feature in microbiota recovery from acute secretory diarrhea, as we observed similar successional dynamics after enterotoxigenic Escherichia coli  (ETEC) infection. Our metagenomic analyses suggest multiple mechanisms driving microbial succession after cholera, including bacterial dispersal properties, changing enteric oxygen and carbohydrate levels, and phage dynamics. Thus, gut microbiota recovery after cholera may be predictable at the level of community structure, but driven by a complex set of temporally varying ecological processes. Our findings suggest opportunities for diagnostics and therapies targeting the gut microbiota in humans recovering from infectious diarrhea.

Biome: root:Host-associated:Human:Digestive system
Axial Seamount Marker 113 RNA-SIP metatranscriptomes from 2013

Hydrothermal vent systems provide access points to the extensive microbial communities of the rocky subseafloor. These subseafloor communities have the potential to influence ocean biogeochemistry and, in particular, the chemolithoautotrophic populations could potentially provide a large amount of new production to the deep sea. In this study, we used RNA-based stable isotope probing (RNA-SIP) metatranscriptomics to identify the active autotrophic players and genomic pathways present in venting fluids from Axial Seamount, a submarine volcano off the coast of Oregon, USA. Vent fluids for RNA-SIP were collected from a singular vent, Marker 113, and used in shipboard incubations with 13C labeled sodium bicarbonate at 30, 55, and 80?C. Results from RNA-SIP incubations show enrichment of RNA at all three temperatures after 18-36 hours, indicating the presence and activity of subseafloor chemolithoautotrophic microbes in vent fluids. In RNA-SIP experiments across a range of temperatures, both taxonomic and functional diversity was reduced compared to un-manipulated diffuse fluids. At 30?C and 55?C, Epsilonproteobacteria were dominant, oxidizing hydrogen and primarily reducing nitrate. Methanogenic archaea were also present at 55?C, and were the only autotrophs present at 80?C. Correspondingly, the predominant CO2 fixation pathways changed from the reductive TCA cycle to the reductive acetyl-CoA pathway with increasing temperature. This study demonstrates the presence of an active autotrophic subseafloor community across geothermal gradients, lending insight into chemolithoautotrophic communities in the subseafloor at deep-sea hydrothermal vents

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents
Metagenome analysis of Amlakhadi canal

Gauging the innate microbial community prevailing in Amlakhadi Canal, Ankleshwar

Biome: root:Environmental:Aquatic:Freshwater
Defining the core Arabidopsis thaliana root microbiome

Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota  colonizing the rhizosphere (immediately surrounding the root), and the endophytic compartment (within the root), contribute to plant growth, productivity, carbon sequestration, and phytoremediation1,2,3. Colonization of the root occurs despite a sophisticated plant immune system4,5, suggesting finely-tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. We pyrosequenced the bacterial 16S rRNA gene of >600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophyte compartment microbiota of plants grown under controlled conditions in natural soils are (i) sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and (ii) sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils, and in rhizosphere and endophyte compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophyte compartments from either soil feature overlapping low-complexity communities that are markedly enriched for Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stages and genotypes. Our work provides unprecedented rigor to define an endophyte compartment microbiome, facilitating controlled dissection of plant-microbe interactions derived from complex soil communities.

Biome: root:Host-associated:Plants
Pooled sample of human tongue scrapes from 9 healthy adults.

Human tongue scrapes were taken from 9 healthy adults at University College London, metagenomic DNA extracted and sequenced using 454 technology.

Biome: root:Host-associated:Human:Digestive system:Oral:tongue dorsum
Tongue metagenome from 9 healthy individuals.

Tongue scrapes were collected from 9 healthy individuals over a period of 3 or 4 weeks, total DNA was extracted, pooled and sequenced.

Biome: root:Host-associated:Human:Digestive system:Oral
Drain metagenome.

Hair blocking drain was removed from a bathroom shower cubicle. Liquid surrounding the hair and hair were used for the total dna extraction.

Biome: root:Environmental:Aquatic:Freshwater:Storm water:Drainage pipe biofilm
Soil sample taken from wild flower meadow for metagenome study.

Soil sample taken from wild flower meadow in Danesbury Park, Hertfordshire.

Biome: root:Environmental:Terrestrial:Soil:Grasslands
Study of the bacterial and fungal diversity in soil habitats with increased ligninocellulolytic activity

This study aims at the metagenomic analysis of ligninocellulose-degrading microbial communities of Mediterranean forest soils. For this purpose, two soil ecosystems with distinct ecophysiological characteristics were selected, and thorough spatio-seasonal sampling was undertaken. Total DNA was extracted from 48 soil samples, and PCR amplification was performed with both 16S (V3-V4) region- and ITS2-specific universal primers for the analysis of bacterial and fungal diversity, respectively. High-throughput amplicon sequencing was performed with the Illumina MiSeq technology.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Coupled metagenomic and metatransciptomic study of the Columbia River coastal margin salinity gradient

Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly influence bacterioplankton community structure, yet, a parallel shift in functional diversity has not been described. Metagenomic and metatranscriptomic analyses were conducted on five water samples spanning the salinity gradient of the Columbia River coastal margin, including river, estuary, plume, and ocean, in August 2010. Samples were pre-filtered through 3 ?m filters and collected on 0.2 ?m filters, thus results were focused on changes among free-living microbial communities. Results from metagenomic 16S rRNA sequences showed taxonomically distinct bacterial communities in river, estuary, and coastal ocean. Despite the strong salinity gradient observed over sampling locations (0 to 33), the functional gene profiles in the metagenomes were very similar from river to ocean with an average similarity of 82%. The metatranscriptomes, however, were an average of only 31% similar. We observed shifts from river to ocean in the abundance of genes encoding specific functions, such as catabolic pathways, osmoregulators, and metal transporters. Additionally, genes specifying both bacterial oxygenic and anoxygenic photosynthesis were highly abundant and expressed in the estuary and plume. Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary. Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community shifted strongly with salinity, 2) metabolic potential was highly similar across samples, with only small differences in functional gene abundance from river to ocean, and 3) gene expression was highly variable and generally was independent of changes in salinity.

Biome: root:Environmental:Aquatic:Marine:Coastal
Rumen Virome metagenome sequencing

The present study was carried out to explore the ruminal viruses and phages from buffalo

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Use of plant growth promoting rhizobacteria on the production of lettuce

Analysis of the effect of different plant growth promoting rhizobacteria on the production of lettuce plants.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Metagenomic approach to Analyze Rumen Microbiome from Gir Cows

Gir cows were fed with different diet and investigated rumen microbiome using shotgun sequencing on Ion-torrent platform

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Metagenomic profiling through 16S rRNA deep sequencing of mice strains

Comparative analysis of microbiomes from stools obtained from WT and genetically engineered mice, subjected to normal or high-fat content diet

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
The role of biogeography in shaping diversity of the intestinal microbiota in house mice

The microbial communities inhabiting the mammalian intestinal tract play an important role in diverse aspects of host biology. However, little is known regarding the forces shaping variation in these communities and their influence on host fitness. To shed light on the contributions of host genetics, transmission and geography to diversity in microbial communities between individuals, we performed a survey of intestinal microbial communities in a panel of 121 house mice derived from eight locations across western Europe using pyrosequencing of the bacterial 16S rRNA gene. The host factors studied included population structure estimated by microsatellite loci and mitochondrial DNA, genetic distance and geography. To determine whether host tissue (mucosa)-associated communities display properties distinct from those of the lumen, both the cecal mucosa and contents were examined. We identified Bacteroides, Robinsoniella and Helicobacter as the most abundant genera in both the cecal content and mucosa-associated communities of wild house mice. Overall we found geography to be the most significant factor explaining patterns of diversity in the intestinal microbiota, with a comparatively weaker influence of host population structure and genetic distance. Furthermore, the influence of host genetic distance was limited to the mucosa communities, consistent with this environment being more intimately coupled to the host.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
Gene-targeted metagenomic analysis of 1-4-?-glucan branching enzyme gene profiles among human and animal fecal microbiota

Organismal and functional aspects of the gut microbiota are of great interest in human microbiome studies. Although 16S rRNA gene sequence-based phylogenetic and whole-genome shotgun (WGS) data analysis are frequently used for assessment of genetic diversity, these techniques pose biological challenges for in-depth understanding of metabolic genes related to the gut microbiota. Phylogenetic analyses of 16S rRNA gene sequences provide limited information on their involvement in metabolic pathways. WGS data provide useful information on metabolic functions; however, this technique generates a large amount of data unrelated to the gene of interest at a high cost. In this study, we employed a metagenomic approach targeting the 1-4-?-glucan branching enzyme (gBE) gene of four host species (chicken, cow, pig, and human). Glycoside hydrolases (GHs) are key enzymes associated with the gut microbiota and its metabolic functions. The gBE gene, belonging to GH family 13, is responsible for glycogen branching and determines its solubility and subsequent catabolic metabolism. In addition to 16S rRNA gene-based phylogenetic analyses, an average of 1,200 reads of gBE were generated from fecal microbiota samples from human (n = 16), chicken (n = 18), cow (n = 15) and pig (n = 20). Each of the hosts showed distinct 16S rRNA and gBE sequence profiles. Human and pig exhibited both unique and common characteristics of operational taxonomic units (OTUs) and gBE profiles. Interestingly, the OTUs identified from the 16S rRNA and gBE gene sequences differed among the host species, suggesting the presence of different gBE genes in the same OTU in 16S rRNA sequences of different vertebrate hosts. Our data suggest that gene-targeted metagenomic analysis is useful for an in-depth understanding of the diversity of a particular gene of interest. Moreover, specific OTUs in the gut may contain metabolic genes the characteristics of which differ according to host genetic background and/or diet.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
These samples are selections from a larger cohort that were selected for the participation in the EBI metagenomics training in Sept. 2015

These samples are selections from a larger cohort that were selected for the participation in the EBI metagenomics training in Sept. 2015

Biome: root:Host-associated:Human:Skin
Study of microbial consortia of withered berries of cv. Corvina using whole metagenome sequencing approach

A whole metagenome sequencing approach was carried out, aiming at the taxonomic identification of the microbial components of berry ecosystem and to unveil whether the variations of environmental withering conditions could lead to significant modifications of microbial consortia and metabolic pathways on grape berries.

Biome: root:Host-associated:Plants
The Effect of Propidium Monoazide Treatment on Identification of Bacterial Communities of Very Low Birth Weight Preterm Infant Faeces Analysed by 16s rRNA Gene Sequencing

Next-gen sequencing technology had provided a platform for rapid advancement in the field of microbial ecology. The 11 original bacterial phyla, identified by Woese, have been expanded to over 50 following widespread use of NGS techniques. However, NGS is not without it?s flaws. This study will attempt to improve the validity of the NGS protocol by validating the use of propidium monoazide: a dsDNA chelating agent; for non-viable cell exclusion from clinical samples. This will enable researchers and clinicians to identify bacterial phyla actively affecting the biotopes of the preterm infant gut and tailor targeted therapy accordingly.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Metagenomics of TB-associated sputum

Tuberculosis remains a major global health problem. Laboratory diagnostic methods that allow effective, early detection of cases are central to management of tuberculosis in the individual patient and in the community. Since the 1880s, laboratory diagnosis of tuberculosis has relied primarily on microscopy and culture. However, microscopy fails to provide species- or lineage-level identification and culture-based workflows for diagnosis of tuberculosis remain complex, expensive, slow, technically demanding and poorly able to handle mixed infections. We therefore explored the potential of shotgun metagenomics, sequencing of DNA from samples without culture or target-specific amplification or capture, to detect and characterise strains from the Mycobacterium tuberculosis complex in smear-positive sputum samples obtained from The Gambia in West Africa. Eight smear- and culture-positive sputum samples were investigated using a differential-lysis protocol followed by a kit-based DNA extraction method, with sequencing performed on a benchtop sequencing instru- ment, the Illumina MiSeq. The number of sequence reads in each sputum-derived metagenome ranged from 989,442 to 2,818,238. The proportion of reads in each metagenome mapping against the human genome ranged from 20% to 99%. We were able to detect sequences from the M. tuberculosis complex in all eight samples, with coverage of the H37Rv reference genome ranging from 0.002X to 0.7X. By analysing the distribution of large sequence polymorphisms (deletions and the locations of the insertion element IS6110) and single nucleotide polymorphisms (SNPs), we were able to assign seven of eight metagenome-derived genomes to a species and lineage within the M. tuberculosis complex. Two metagenome-derived mycobacterial genomes were assigned to M. africanum, a species largely confined to West Africa; the others that could be assigned belonged to lineages T, H or LAM within the clade of ?modern? M. tuberculosis strains. We have provided proof of principle that shotgun metagenomics can be used to detect and characterise M. tuberculosis sequences from sputum samples without culture or target-specific amplification or capture, using an accessible benchtop-sequencing platform, the Illumina MiSeq, and relatively simple DNA extraction, sequencing and bioinformatics protocols. In our hands, sputum metagenomics does not yet deliver sufficient depth of coverage to allow sequence- based sensitivity testing; it remains to be determined whether improvements in DNA extraction protocols alone can deliver this or whether culture, capture or amplifica- tion steps will be required. Nonetheless, we can foresee a tipping point when a unified automated metagenomics-based workflow might start to compete with the plethora of methods currently in use in the diagnostic microbiology laboratory.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Influence of soil properties on Archaeal diversity and distribution in the McMurdo Dry Valleys, Antarctica

Archaea are the least studied members of the microbial community in Antarctic soils. Their occurrence in coastal mineral soils has been documented, however, less is known about their distribution in soils across the McMurdo Dry Valleys, Victoria Land. In this study, terminal-restriction fragment length polymorphism (T?RFLP) analysis and 454 pyrosequencing were coupled with a detailed analysis of physicochemical properties to characterize archaeal diversity and identify the environmental factors that might shape and maintain these archaeal communities in soils of the three most southern McMurdo Dry Valleys (Garwood, Marshall, Miers). Archaea were present, although at a low diversity (< 6 operational taxonomic units (OTUs) per sample site) in all mineral soils tested. In total, eighteen archaeal OTUs were detected which showed a predominance of Crenarchaeota belonging to Marine Group 1.1b (>?80% of all archaeal sequences recovered). Less abundant OTUs (2% of all archaeal sequences) were restricted to glacial moraines, including three OTUs (<?0.02% of all archaeal sequences) closely related to members of the phylum Euryarchaeota. Multivariate statistical analysis, ordination of T?RFLP and physicochemical data indicated that differences in moisture, carbon and nitrogen content in the soils have the greatest influence on archaeal community structure. This is the first comprehensive study showing a widespread distribution of Archaea in soils of the McMurdo Dry Valleys and verifies the worldwide distribution of Marine Group 1.1b Crenarchaeota.

Biome: root:Environmental:Terrestrial:Soil:Wetlands:Permafrost
Soil metagenome.

SoilB soil sample was collected on a rough grass terrain with the trees nearby in Danesbury Park in Hertforshire, UK.

Biome: root:Environmental:Terrestrial:Soil:Grasslands
Permafrost 454 amplicons

Study of microbial communities in permafrost, active layer and thermokarst bog in Alaska

Biome: root:Environmental:Terrestrial:Soil:Permafrost
different diet treatments

Mice of 2 genotypes followed 2 different diets.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Does dietary mitigation of enteric methane production affect rumen function and animal productivity in dairy cows?

It has been suggested that the rumen microbiome and rumen function might be disrupted if methane production in the rumen is decreased. Furthermore concerns have been voiced that geography and management might influence the underlying microbial population and hence the response of the rumen to mitigation strategies. Here we report the effect of the dietary additives: linseed oil and nitrate on methane emissions, rumen fermentation, and the rumen microbiome in two experiments from New Zealand (Dairy 1) and the UK (Dairy 2). Dairy 1 was a randomized block design with 18 multiparous lactating cows. Dairy 2 was a complete replicated 3 x 3 Latin Square using 6 rumen cannulated, lactating dairy cows. Treatments consisted of a control total mixed ration (TMR), supplementation with linseed oil (4% of feed DM) and supplementation with nitrate (2% of feed DM) in both experiments. Methane emissions were measured in open circuit respiration chambers and rumen samples were analyzed for rumen fermentation parameters and microbial population structure using qPCR and next generation sequencing (NGS). Supplementation with nitrate, but not linseed oil, decreased methane yield (g/kg DMI; P<0.02) and increased hydrogen (P<0.03) emissions in both experiments. Furthermore, the effect of nitrate on gaseous emissions was accompanied by an increased rumen acetate to propionate ratio and consistent changes in the rumen microbial populations including a decreased abundance of the main genus Prevotella and a decrease in archaeal mcrA (log10 copies/ g rumen DM content). These results demonstrate that methane emissions can be significantly decreased with nitrate supplementation with only minor, but consistent, effects on the rumen microbial population and its function, with no evidence that the response to dietary additives differed due to geography and different underlying microbial populations.

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Trans-kingdom control of microbiota diurnal oscillations promotes metabolic homeostasis

All domains of life feature diverse molecular clock machineries that synchronize physiological processes to diurnal environmental fluctuations. However, no mechanisms are known to cross-regulate prokaryotic and eukaryotic circadian rhythms in multi-kingdom ecosystems. Here, we show that the intestinal microbiota, in both mice and humans, exhibits diurnal oscillations that are influenced by feeding rhythms, leading to time-specific compositional and functional profiles over the course of a day. Ablation of host molecular clock components or induction of jet lag leads to aberrant microbiota diurnal fluctuations and dysbiosis, driven by impaired feeding rhythmicity. Consequently, jet lag-induced dysbiosis in both mice and humans promotes glucose intolerance and obesity that are transferrable to germ-free mice upon fecal transplantation. Together, these findings provide the first evidence of coordinated meta-organism diurnal rhythmicity, and offer a microbiome-dependent mechanism for common metabolic disturbances in humans with aberrant circadian rhythms, such as those documented in shift workers and frequent flyers.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Study on the microbial community of a bioleaching column test

Study on the microbial community related to de bioleaching processes of copper sulfide ore.

Biome: root:Engineered:Biotransformation