SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Follow-up of faecal microbiota in IBS patients

Irritable bowel syndrome (IBS) is the most common functional gastrointestinal disorder in western countries. The definition and treatment of IBS is challenging due to its largely unknown aetiology and the variety of symptoms it can present. Previous studies on IBS suggest subtle alterations in the composition of intestinal microbiota. However, no consensus has been reached regarding the association between specific bacteria and IBS. To overcome the confusion introduced by inter-subject variability and heterogeneity within IBS that is problematic in cross-sectional studies, we undertook a longitudinal study that allowed us to compare samples from single patients at moments with different type and/or severity of symptoms. We present results for two IBS patients with diarrhoea subtype and the healthy relative of one of them. Faecal samples collected every two days the first week and then weekly over two months were analysed through metagenomic and metatranscriptomic approaches. Overall, we detect a greater instability of faecal microbiota in IBS patients when compared to the control, and even larger instability
 associated with acute diarrheoa.
 Bacterial composition and encoded functions were fairly stable throughout. On the contrary, the fraction of active bacteria varied markedly in time. Strong and quick compositional shifts were associated with relapse, although with low reproducibility between and within patients. Similarly, changes in the global pattern of gene expression characterized days of worsening, but we could not identify genes or functions associated with relapse. Our results confirm that the association of microbiota with IBS is rather weak.

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

Rumen metagenomics feed trial shotgun sequencing

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Metagenomic analysis of Ruminal Microbes

Studying effect of various ration on functional and community profile of fiber adherent and liquid associated rumen microbes in buffalo

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Metatranscriptomes from mesocosm experiments with added organic carbon (OM[ab] samples) and controls (C[ab] samples).


Microcosm experiments was done with water from the oxygen minimum zone (around 300-500 m depth) of the subtropical North Atlantic (latitude 17.71 , longitude -41.05) to study the response of mesopelagic prokaryotic communities to pulses of nutrients. Three different treatments and a control were established after prefiltering the seawater through 0.8 µm polycarbonate filters. Microcosms were amended either with thiosulfate (Na2S2O3), ammonium (NH4Cl) or pyruvate plus acetate (C3H3NaO3 and C2H3NaO3) and the control was not supplemented with any organic or inorganic compound. The treatments and the control were established in duplicate in 20 l carboys and held in the dark at in situ temperature for 110-140 h. At the end of the incubation the remaining water was collected through 0.22 µm polycarbonate filters for metatranscriptomic analysis

Biome: root:Environmental:Aquatic:Marine
BGI Type 2 Diabetes study

A Metagenome-Wide Association Study of gut microbiota identifies markers associated with Type 2 Diabetes based on next generation sequencing technology.

Biome: root:Host-associated:Human:Digestive system:Large intestine
French Guiana forest soil metagenomic sequencing study

Soil samples have been collected at Trois-Sauts, an isolated settlement in Amazonian National Park. In order to assess anthropogenic impact on microbial communities, a 3km transect has been sampled every 600m in order to generate anthropization gradient, from the village to the forest. Each soil samples DNA has been extracted with MoBio Power Soil Max extraction kit and directly sequenced without any prior amplification with Roche 454 Titanium chemistey

Biome: root:Environmental:Terrestrial:Soil:Tropical rainforest
Rhizosphere metatranscriptomics

Plant-microbe interactions in the rhizosphere play key roles in biogeochemical cycling, and maintenance of plant health and productivity, yet remain poorly understood. Using RNA based metatranscriptomics, the global active microbiomes were analysed in soil and rhizospheres of wheat, oat, pea, and an oat mutant (sad1) deficient in production of antifungal avenacins.  Rhizosphere microbiomes differed from bulk soil and between plant species. Pea (a legume) had a much stronger effect on the rhizosphere than wheat and oat (cereals), resulting in a dramatically different rhizosphere community. The relative abundance of eukaryotes in the oat and pea rhizospheres was more than five-fold higher than in the wheat rhizosphere or bulk soil. Nematodes and bacterivorous protozoa were enriched in all rhizospheres, while the pea rhizosphere was highly enriched for fungi. Metabolic capabilities for rhizosphere colonisation were selected, including cellulose degradation (cereals), H2-oxidation (pea) and methylotrophy (all plants). Avenacins had little effect on the prokaryotic community of oat, but the eukaryotic community was strongly altered in the sad1 mutant, suggesting that avenacins have a broader role than protecting from fungal pathogens. Profiling microbial communities with metatranscriptomics allows comparison of relative abundance, from multiple samples, across all domains of life, without PCR bias. This revealed profound differences in the rhizosphere microbiome particularly at the kingdom level between plants.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Neandertal bone Vi33.16 metagenome

The Neandertal genome was recently sequenced using DNA extracted from a 38,000-year-old fossil. At the start of the project, the fraction of mammalian and bacterial DNA in the sample was estimated to < 6% and 9%, respectively. Treatment with restriction enzymes prior to sequencing increased the relative proportion of mammalian DNA to 15%, but the large majority of sequences remain uncharacterized. PRINCIPAL FINDINGS: Our taxonomic profiling based on the analyses of 3.95 Gb of Neandertal DNA isolated from the Vindija Neandertal Vi33.16 fossil showed that 90% of about 50,000 rRNA sequence reads were of bacterial origin and that actinobacteria accounted more than 75% of the bacterial rRNA sequences. Likewise, actinobacteria represented more than 80% of the PCR-amplified 16S rRNA sequences from a cave sediment sample taken from the same G layer as the Neandertal bone. We assembled all 16S rRNA sequence read assigned to Streptomycetales, and analysed the patterns of nucleotide differences in the individual sequence reads compared to assembled consensus sequences. The typical ancient nucleotide substitution pattern with a majority of C to T changes indicative of DNA damage was observed for the Neandertal rRNA sequences, but not for the Streptomyces-like rRNA sequences. SIGNIFICANCE: Our analyses suggest that actinobacteria, and especially members of the Streptomycetales, contribute the majority of sequences in the DNA extracted from the Neandertal fossil Vi33.16. The bacterial DNA showed no signs of damage, and we hypothesize that it was derived from cave sediment bacteria that have been enriched inside the bone. The bioinformatic approach used here paves the way for future studies of microbial communities and patterns of DNA damage in bacteria from archaeological bones. Such studies can help identify targeted measures, such as selective degradation of bacterial DNA with particular base composition patterns, to increase the relative amount of ancient DNA in the sample.

Biome: root:Host-associated:Human
Shifts in Human Intestinal Microbiota after Smoking Cessation

The human intestinal microbiota is a crucial factor in the pathogenesis of various diseases, such as metabolic syndrome or inflammatory bowel disease (IBD). Yet, knowledge about the role of environmental factors such as smoking (which is known to influence theses aforementioned disease states) on the complex microbial composition is sparse. We aimed to investigate the role of smoking cessation on intestinal microbial composition in 10 healthy smoking subjects undergoing controlled smoking cessation. Methods: During the observational period of 9 weeks repetitive stool samples were collected. Based on abundance of 16S rRNA genes bacterial composition was analysed and compared to 10 control subjects (5 continuing smokers and 5 non-smokers) by means of Terminal Restriction Fragment Length Polymorphism analysis and high-throughput sequencing. Results: Profound shifts in the microbial composition after smoking cessation were observed with an increase of Firmicutes and Actinobacteria and a lower proportion of Bacteroidetes and Proteobacteria on the phylum level. In addition, after smoking cessation there was an increase in microbial diversity Conclusions: These results indicate that smoking is an environmental factor modulating the composition of human gut microbiota. The observed changes after smoking cessation revealed to be similar to the previously reported differences in obese compared to lean humans and mice respectively, suggesting a potential pathogenetic link between weight gain and smoking cessation. In addition they give rise to a potential association of smoking status and the course of IBD.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Making and breaking DMS by salt marsh microbes (Illumina HiSeq 100bp)

Study of microbial populations that cycle the globally significant organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS) in coastal intertidal sediments.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
Making and breaking DMS by salt marsh microbes (Illumina MiSeq 250bp)

Study of microbial populations that cycle the globally significant organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS) in coastal intertidal sediments.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
Gut metagenome in European women with normal, impaired and diabetic glucose control

Type 2 diabetes (T2D) is a result of complex gene-environment interactions, and several risk factors have been identified, including age, family history, diet, sedentary lifestyle and obesity. Statistical models that combine known risk factors for T2D can partly identify individuals at high risk of developing the disease. However, these studies have so far indicated that human genetics contributes little to the models, whereas socio-demographic and environmental factors have greater influence. Recent evidence suggests the importance of the gut microbiota as an environmental factor, and an altered gut microbiota has been linked to metabolic diseases including obesity, diabetes and cardiovascular disease. Here we use shotgun sequencing to characterize the faecal metagenome of 145 European women with normal, impaired or diabetic glucose control. We observe compositional and functional alterations in the metagenomes of women with T2D, and develop a mathematical model based on metagenomic profiles that identified T2D with high accuracy. We applied this model to women with impaired glucose tolerance, and show that it can identify women who have a diabetes-like metabolism. Furthermore, glucose control and medication were unlikely to have major confounding effects. We also applied our model to a recently described Chinese cohort and show that the discriminant metagenomic markers for T2D differ between the European and Chinese cohorts. Therefore, metagenomic predictive tools for T2D should be specific for the age and geographical location of the populations studied.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Metagenomic study of the virome of African straw-colored fruit bats

Viral emergence as a result of zoonotic transmission constitutes a continuous public health threat. Emerging viruses such as SARS Coronavirus, Hantaviruses and Henipaviruses have a wildlife animal reservoir. Characterizing the viral flora of candidate reservoir species in geographical areas identified as hot spots for viral emergence is a sensible approach to develop tools to predict, prevent or contain emergence events. Here, we explored the viral flora of Eidolon helvum, an Old World fruit bat species widely distributed in Africa that lives in close proximity to humans. We identified a great abundance and diversity of novel herpes and papillomaviruses, described the isolation of a novel adenovirus, and detected, for the first time, sequences of a chiropteran poxvirus that are closely related to a human contagion. In sum, E. helvum display a wide variety of mammalian viruses, some of them genetically similar to known human pathogens, highlighting the possibility of zoonotic transmission.

Biome: root:Host-associated
A metagenomics transect into the deepest point of the Baltic Sea reveals clear stratification of microbial functional capacities

The Baltic Sea is characterized by hyposaline surface waters, hypoxic and anoxic deep waters and sediments. These conditions, which in turn lead to a steep oxygen gradient, are particularly evident at Landsort Deep in the Baltic Proper. Given these substantial differences in environmental parameters at Landsort Deep, we performed a metagenomic census spanning surface to sediment to establish whether the microbial communities at this site are as stratified as the physical environment. We report strong stratification across a depth transect for both functional capacity and taxonomic affiliation, with functional capacity corresponding most closely to key environmental parameters of oxygen, salinity and temperature. We report similarities in functional capacity between the hypoxic community and hadal zone communities, underscoring the substantial degree of eutrophication in the Baltic Proper. Reconstruction of the nitrogen cycle at Landsort deep shows potential for syntrophy between archaeal ammonium oxidizers and bacterial denitrification at anoxic depths, while anaerobic ammonium oxidation genes are absent, despite substantial ammonium levels below the chemocline. Our census also reveals enrichment in genetic prerequisites for a copiotrophic lifestyle and resistance mechanisms reflecting adaptation to prevalent eutrophic conditions and the accumulation of environmental pollutants resulting from ongoing anthropogenic pressures in the Baltic Sea.

Biome: root:Environmental:Aquatic:Marine
Sand scarab gut transcriptome

We hypothesized that scarab insect guts function as miniature bioreactors and are, thus, a useful model to obtain fundamental insights into the digestion of complex plant material. More than 100 Gbp of RNA-Seq (Illumina HiSeq, paired-end, 100bp, 400bp insert) were generated.

Biome: root:Host-associated:Arthropoda:Digestive system:Gut
Microbial life in snake and spider venoms

Envenomation typically involves transdermal insertion of an appendage such as a tooth into prey and venom ejection through the appendage canal. Given the lack of sterility and infrequency of envenomation events in the wild, we hypothesise that the venom glands of animals such as snakes, spiders and scorpions might be niche environments for microorganisms such as bacteria and fungi acquired during envenomation. To explore this hypothesis we have generated 16S amplicon libraries from venoms and envenomation appendage swabs of various snakes, spiders and scorpions from captivity and the wild. We have also obtained two separate envenomation samples were possible, reasoning that the second might be a truer representative of the venom gland population as opposed to e.g. an oral cavity bacterial plug forming at the tip of the tooth between envenomation events. We wish to examine if the bacterial signatures detected differ between host species and sites of sampling.

Biome: root:Host-associated
Marine microbial indicators in coastal areas: a metagenomic approach

The present project proposes to conduct a thorough investigation of the heterotrophic bacterial communities of different sites of the Gulf of Naples, encompassing different ecological conditions, in order to find microbiological indicators of ecological status.

Biome: root:Environmental:Aquatic:Marine
Synthetic sequence dataset database metagenome

A metagenomic sequencer dataset built from database sequences to compare the accuracy and performance of various metagenomic sequence dataset analysis pipelines

Biome: root:Engineered:Modeled:Simulated communities (DNA mixture)
Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States

Although soil microbes play critical roles in terrestrial ecosystems, factors controlling spatial variability in the diversity and functional capabilities of these communities remain poorly understood. Particular knowledge gaps exist for biomes severely impacted by human activities, including the native tallgrass prairie that once covered >65 million ha of the midwestern United States, but has been nearly eradicated by decades of agricultural practices. Here we have reconstructed the microbial biodiversity that once sustained this highly productive ecosystem by analyzing soils from prairie relicts via shotgun metagenomics and targeted sequencing of the 16S rRNA gene. The taxonomic and functional diversity of the microbial communities were well-correlated, demonstrating that these communities are not functionally equivalent as has often been assumed - even small changes in belowground diversity can have important impacts on soil processes. As for many plant and animal communities, we could predict the structure and functional traits of the microbial communities from climatic conditions, allowing us to build predictive maps of soil biodiversity across the historical range of the tallgrass prairie ecosystem. The biogeographical patterns were largely driven by changes in the abundance of Verrucomicrobia, a poorly-studied bacterial phylum that dominated the prairie soils. The shotgun metagenomic data suggest that these spatial patterns were associated with shifts in soil carbon and nitrogen dynamics across the tallgrass prairie ecosystem. We show that we can use metagenomic data to reconstruct the belowground biogeochemical and diversity gradients that once existed, information that could be essential to guiding ongoing efforts to restore the threatened tallgrass prairie ecosystem.

Biome: root:Environmental:Terrestrial:Soil:Grasslands
Richmond Mine AMD Biofilm Samples Metagenome

Richmond Mine acid mine drainage biofilm samples datasets (2006-2010). 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:Freshwater:Groundwater:Biofilm
Comparative freshwater metagenomics of Swedish and American lakes

Little is known about the diversity and structuring of freshwater microbial communities beyond the patterns revealed by tracing their distribution in the landscape with common taxonomic markers such as the ribosomal RNA. To address this gap in knowledge, metagenomes from temperate lakes were compared to selected marine metagenomes. Taxonomic analyses of rRNA genes in these freshwater metagenomes confirm the previously reported dominance of a limited subset of uncultured lineages of freshwater bacteria, whereas Archaea were rare. Diversification into marine and freshwater microbial lineages was also reflected in phylogenies of functional genes and there were also significant differences in functional beta-diversity. The pathways and functions that accounted for these differences are involved in osmoregulation, active transport, carbohydrate and amino acid metabolism. Moreover, predicted genes orthologous to active transporters and recalcitrant organic matter degradation were more common in microbial genomes from oligotrophic versus eutrophic lakes. This comparative metagenomic analysis allowed us to formulate a general hypothesis that oceanic- compared to freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial communities.

Biome: root:Environmental:Aquatic:Freshwater:Lake
Metagenome of a microbial consortium obtained from the Tuna oil field in the Gippsland Basin, Australia

In 2011, fluid samples were collected from the A7A oil well in the Tuna oil field (38°10' S, 148°25' E) in the Gippsland Basin, Australia. Chemical analyses of the water revealed the sample was pH 7.2, had a salinity of 2.7%, and contained 270 mg liter–1 calcium, 320 mg liter–1 magnesium, 1,200 mg liter–1 sulfate, and 1,170 mg liter–1 bicarbonate. The temperature in the reservoir was 102°C. One liter of formation water was filtered through a 0.2-M Polyvinylidene difluoride (PVDF) filter disc and subjected to genomic DNA extraction using a Meta-G-Nome DNA isolation kit (Epicenter Biotechnologies). The resultant DNA was sequenced using 100-bp paired-end Illumina HiSeq at the University of Western Sydney.

Biome: root:Environmental:Aquatic:Marine:Oil field:bore hole
Comparative metagenomic analysis of soil microbial communities varying in disease suppression potential

Microbial communities from wheat rhizosphere samples were analysed through metagenomic sequencing of environmental DNA. Samples from sites varying disease suppression potential were analysed to identify differences in community metagenomic profiles.

Biome: root:Environmental
Unraveling the stratification of an iron-oxidizing microbial mat by metatranscriptomics

A metatranscriptomic approach was used to study community gene expression in a naturally occurring iron-rich microbial mat. Total microbial community RNA was reversely transcribed and sequenced by pyrosequencing. Characterization of expressed gene sequences provided accurate and detailed information of the composition of the transcriptionally active community and revealed phylogenetic and functional stratifications within the mat. Comparison of 16S rRNA reads and delineation of OTUs showed significantly lower values of metatranscriptomic-based richness and diversity in the upper parts of the mat than in the deeper regions. Taxonomic affiliation of rRNA sequences and mRNA genome recruitments indicated that iron-oxidizing bacteria dominated the community in the upper layers of the mat. Surprisingly, type I methanothrophs contributed to the majority of the sequences in the deep layers of the mat. Analysis of mRNA expression patterns showed that genes encoding the three subunits of the particulate methane monooxygenase (pmoCAB) were the most highly expressed in our dataset. These results provide strong hints that iron-oxidation and methane-oxidation occur simultaneously in microbial mats and that both groups of microorganisms are major players in the functioning of this ecosystem.

Biome: root:Environmental:Aquatic:Freshwater
Comparative phylogenetic analysis of microbial populations in the mammalian olfactory bulb and nasal cavity

We are examining the hypothesis that white matter microbia originate specifically from the nasal cavities of mammalian species. Perfused tissues from mice, rats and pathogen-free human volunteers are analysed for microbial DNA by 16S phylogenetics.

Biome: root:Host-associated:Amphibia
Artisanal cheese metagenome 3

Metagenome from artisanal cheeses from Tucuman

Biome: root:Engineered:Food production:Dairy products
Metagenomic approach to analyze rumen microbiome from Kankrej cows

Kankrej 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