SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Long-term effect of the administration of two doses of formic acid on the intestinal microbiota profile of growing pigs

Thirty-four post-weaned pigs (35 day of age, of an average body weight of 7081.78 ± 956.23 g) were individually reared in cages. Based on litter and body weight, pigs were assigned to one of the three experimental diets. The diets were based on the same basal diet (C), without antibiotic supplementation, and supplemented with 1.4 kg/ton (L) and 6.4 kg/ton (H) of Ca-formate respectively. Pigs were fed with the experimental diets for 6 week and then slaughtered. Samples composed on scraped mucosa and digesta content was obtained from mid-jejunum and immediately frozen in liquid nitrogen. Total bacterial DNA was extracted using Qiamp Stool Mini Kit (Qiagen). The library formation and sequencing of 16S rRNA gene were performed with MiSeq® Reagent Kit V3-V4 on MiSeq-Illumina® platform. The letters “C”, “L” and ”H” in samples name indicate the three different diets, respectively.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine
Comparison between mouse caecal contents and faeces

Comparison between shotgun metagenomic results obtained from paired mouse caecal contents and faeces

Biome: root:Host-associated:Mammals:Digestive system
Radcliffe dental calculus

Ancient dental calculus from skeletons from the Radcliffe Hospital burial ground

Biome: root:Host-associated:Human:Digestive system:Oral
The antibiotic resistance potential of the preterm infant gut microbiome measured using shotgun metagenomics.

These samples were generated to quantify and interrogate the antibiotic resistome within a cohort of premature infants, using shotgun metagenomic sequencing.

Biome: root:Host-associated:Human:Digestive system:Large intestine
Metagenomic samples from soil

Soil consist of wide range of microbes that can be applied for various processes. This study aims to do meta-genomics analysis of the given soil sample.

Biome: root:Environmental:Terrestrial:Soil
De novo transcriptome of a novel Graphium fungal species derived from a mixed microbial composting community enriched with wheat-straw, further grown on wheat straw

A simplified mixed microbial composting community was grown under laboratory conditions. A novel fungal isolate was found to be highly abundant and culturable.  This species was further grown singly on wheat-straw as a sole carbon source.  Its transcriptome was de novo assembled and used in transcriptome informed proteomics.

Biome: root:Engineered:Solid waste:Composting
Using metagenomic approach to study the microbial community structures in drinking water system.

The tap filters (Torayvino, Toray Industries Inc., Japan) were installed at the tap ends of a residential area, and continuously filtered 2000 L drinking water within ~2 days. After that, the filters were immersed into 50% ethanol solution to fix the microorganisms collected on the surface of hollow filter membrane in the filter. Then, extract the biomass on the membrane filter and extract DNA for metagenomic sequencing.

Biome: root:Environmental:Aquatic:Freshwater:Drinking water:Delivery networks
Wheat straw mixed microbial community metatranscriptome

Metatranscriptome of a mixed microbial composting community grown on wheat straw for 1 week.

Biome: root:Engineered:Solid waste:Composting:Grass
Multiple mycorrhizal fungi connect the roots of orchid and ash in a Newfoundland fen

The observation made by naturalists in Newfoundland that Cypripedium reginae, the showy lady slipper orchid, and Fraxinus nigra, the black ash tree, regularly co-occur, and that the orchid is not seen without the ash, has led to the suggestion of a fungal connection between the two plants. A DNA sequencing analysis was done to find shared fungi between both plants. Fungal DNA was sequenced using the Ion Torrent and Illumina Next Generation sequencing systems. Several fungal associates were found shared between C. reginae and F. nigra, and differences were observed between the OTU outputs between Ion Torrent and Illumina NGS.

Biome: root:Host-associated:Plants:Rhizosphere
16S amplicon data from soils in "Soil Service" sites.

Using these 16S data as a complementary study for the captured metagenomes targeted using Sequence Capture probes.

Biome: root:Environmental:Terrestrial:Soil
Sequencing of Ammonia oxidising bacteria from FISH enriched samples

Fluorescence In-Situ Hybridization was used to label Ammonia Oxidising bacteria, which were subsequently sorted with flow cytommetry and sequenced. Two conditions (aerobic and anaerobic) are compared, with two replicates each.

Biome: root:Engineered
Metagenomic study of the eukaryotic microorganisms diversity of a pond based on an environmental DNA (eDNA) sample.

Usually, to determine the biological quality of a body of water, micro fauna and especially macroinvertebrates are determined using a binocular microscope. This study aims to compare this traditional method of species census with the analysis by metagenomic of environmental DNA (eDNA) from the same pond sample.

Biome: root:Environmental:Aquatic:Freshwater:Pond
Amplicon-based metagenomics analysis of Vitis vinifera L. cv. Corvina grapes and fresh musts

The fungal populations present in Vitis vinifera L. cv. Corvina grapes and musts were compared in two different years vintages. The comparison was carried out through ITS1-5.8S-ITS2 454-pyrosequencing. Grapes were collected from a recent vineyard located in the Italian winery region called "Valpolicella" (Sant"Ambrogio, Verona, Italy). After the harvesting, grapes were subjected to withering in a dedicated warehouse located a few kilometers far from the vineyars (<5Km). The warehouse is supplemented with automatic systems able to control and modify the internal temperature and humidity. The duration of grape withering was defined according to the regional rules for Amarone production (Paronetto and Dellaglio, 2011), which define the time in which the grapes for Amarone vinification can be mashed. The comparison of the fungal populations present in these samples sheds lights on the Amarone production, allowing the identification of the persistent fungal genera and on genera varying as suffering from seasonal environmental changes.

Biome: root:Host-associated:Plants
Metagenomic analysis of soil samples from an oil contaminated military base

Samples were taken from 3 contaminated and 1 non contaminated sites of the military base in 3 depth (1m, 5.5-5.8m and 7.5-7.8m). After DNA extraction whole metagenome sequencing was performed on Illumina MiSeq platform.

Biome: root:Environmental:Terrestrial:Soil:Sand:Oil-contaminated
Metagenomes from the marine sponge Ianthella Basta

We applied differential coverage binning of multiple metagenomes from two different microbial cell enrichments derived from the marine sponge Ianthella basta.

Biome: root:Host-associated:Invertebrates
Microbial community diversity in reactors digesting chicken manure

Microbial community diversity in reactors digesting chicken manure

Biome: root:Engineered:Bioreactor
A Catalogue of the Mouse Gut Metagenome

The importance of the gut microbiota for regulation of whole body metabolism, energy homeostasis, development of the immune system and even complex behavioural traits is well documented. The acquisition of comprehensive gene catalogues of the human gut metagenome using “next generation sequencing” has immensely advanced our insight into the complex metagenome-host genome interaction and the connection between common human diseases and the gut microbiota. Causal links are difficult to establish in humans, and therefore, mice still serve as important models for functional studies. We used HiSeq2000-based whole metagenome sequencing to establish a catalogue of 2.6 million non-redundant microbial genes from faecal samples of 184 mice representing different strains, fed different diets, obtained from different providers, and kept in different housing laboratories to secure high diversity and representation. Similar to the human gut microbiome, more than 99% of the genes in the catalogue were bacterial, suggesting that the mouse microbiota overall comprises between 800 and 900 bacterial species. A core mouse gut microbiome was defined at the genus level comprising 60 genera, 25 of which were shared with the core genera in the human gut microbiome. Although the mouse gut microbiome was functionally similar to its human counterpart, sharing 79.9% of its KEGG orthologous groups, only 4.0% of the mouse gut microbial genes were shared with those identified in human gut microbiome, emphasising the need for a specific mouse catalogue. We observed marked differences regarding provider, housing laboratory, strains, gender and feed, emphasizing the need for carefully controlled experimental conditions and caution comparing data from different laboratories.   As we have accounted for these factors in creating the catalogue, it provides a useful reference for future studies, including studies using short reads for comprehensive analyses of the mouse gut microbiome.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Bioelectrochemical BTEX removal at different voltages: assessment of the degradation and characterization of the microbial communities

BTEX compounds (Benzene, Toluene, Ethylbenzene and Xylenes) are toxic hydrocarbons that can be found in groundwater due to accidental spills. Bioelectrochemical systems (BES) are an innovative technology to stimulate the anaerobic degradation of hydrocarbons. In this work, single chamber BESs were used to assess the degradation of a BTEX mixture at different applied voltages (0.8 V, 1.0 V, 1.2 V) between the electrodes. At the end of the experiment the microbial communities were characterized by high throughput sequencing of the 16S rRNA gene. Hydrocarbon degradation was linked to current production and to sulfate reduction, at all the tested potentials. The highest current densities applied (about 200 mA/m2 with a maximum peak at 480 mA/m2) were observed when 0.8 V were. The application of an external voltage increased the removal of toluene, m-xylene and p-xylene. The highest removal rate constants at 0.8 V, calculated for toluene, m-xylene and p-xylene, were: 0.4 ± 0.1 days-1, 0.34 ± 0.09 days-1 and 0.16 ± 0.02 days-1, respectively).At the end of the experiment, the microbial communities were characterized by high throughput sequencing of the 16S rRNA gene. Microorganisms belonging to the families Desulfobulbaceae, Desulfuromonadaceae and Geobacteraceae were enriched on the anodes suggesting that both direct electron transfer and sulfur cycling occurred. The cathodic communities were dominated by the family Desulfomicrobiaceae that may be involved in hydrogen production.

Biome: root:Environmental:Terrestrial:Soil:Contaminated
Technical biases and variations on species abundances for a repetitively sequenced fecal sample 16S rRNA library.

The high throughput sequencing powered by next generation sequencing offered unprecedented resolution in delineating the composition of microbial profiles. To best evaluate the biases and artifacts entangled within the sequencing output we had repeatedly sequenced an amplicon library from the same fecal sample 10 times in 4 distinct Illumina MiSeq sequencing runs. Analysis of the observed Operational Taxonomic Units (OTUs) showed as expected a strong correlation of relative abundance with the coefficient of variation. The results are used to argue about the appropriate relative abundance exclusion cutoff used in the Rhea pipeline for the analysis of microbial profiles.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Microbiome samples derived from Buruli ulcer wounds and non-Buruli ulcer skin ulcerations

Background: Buruli ulcer (BU) is an infectious disease caused by Mycobacterium ulcerans and considered the third most prevalent mycobacterial disease in humans. This skin disease can affect the entire body surface, but primarily the lower extremities, with symptoms varying from nodules to ulcers. Secondary bacterial infections in open BU lesions are the main cause of pain, delayed healing and systemic illness, resulting in prolonged hospital stay. Thus understanding the diversity of bacteria in these open lesions is important for proper treatment. The normal skin flora is known to protect the host through commensal relationships, however, certain factors such as ulceration can shift the skin flora from being primarily commensal to potentially pathogenic. Therefore, the objective of this study was to characterize and compare the skin bacteria from BU ulcers, non-BU ulcers, and similar locations on the skin of healthy individuals. Results: Using 16S rRNA sequencing, we determined the microbial composition of 5 BU lesions, 3 non-BU lesions and 3 healthy skin samples, and compared these using a data analysis pipeline. Our results showed a lower bacterial diversity in both the BU and non-BU lesions compared to the healthy skin. However, no significant differences were found between BU and non-BU lesions. The BU lesions were characterized by an increase of Bacteroidetes compared to the non-BU wounds, which contained more (Gamma)Proteobacteria. Furthermore, the BU lesions also contained significantly more obligate anaerobes. All lesions contained a mixture of gram-positive and gram-negative bacteria, with more gram-negatives present in the BU and non-BU lesions than in healthy skin samples. With this molecular-based study, we were also able to detect bacteria, which were missed by culture-based methods in previous BU studies.Conclusions: Our study suggests that BU leads to changes in the bacterial community within the lesions. These changes are potentially detrimental and may cause a delay in the healing process. In order to determine if the alterations in Bacteroidetes were due to a specific wound environment, underlying pathophysiological conditions created by M. ulcerans, or associated with wound location on the body, further microbiome studies are necessary.

Biome: root:Host-associated:Human:Skin
Complicated Sputum Microbial Composition in the Patients of Pulmonary Tuberculosis

Background. Amount of studies have suggested the relationship between the microbiota and the onset of diseases, especially some chronic diseases. An understanding of bacterial community in the sputum from patients has deeply recognized the pulmonary tuberculosis.   Methods. We enrolled 31 patients suffering from pulmonary tuberculosis and 24 healthy persons as the normal control, and then extracted the total DNA of sputum samples of pulmonary tuberculosis patients and respiratory secretions of normal person. 16S rDNA V3 hyper-variable regions were amplified using bar-coded primiers and pyro-sequenced using  Roche 454 FLX .   Results. All the sequences we get were analysed by tools in the Ribosomal Database Project. the amplicons were classified into 24 main phyla, there are 24 phylum in the pulmonary tuberculosis samples and 17 phylum in normal person. Microbiota changed in the sputum of pulmonary tuberculosis patients, and we can separate pulmonary tuberculosis patients from normal person through the respiratory microbial community. The microbial composition in the sputum of pulmonary tuberculosis patients is much more diversity than that in normal person(p<0.05). Furthermore, lots of foreign bacteria such as Stenotrophomonas, Cupriavidus, Pseudomonas, Thermus, Sphingomonas, Methylobacterium, Diaphorobacter, Comamonas and Mobilicoccus uniquely distributed in the pulmonary tuberculosis patients.   Conclusions. The study concludes that the respiratory tract microbial composition  in pulmonary tuberculosis become much more complicated than that in normal person. Besides, amount of foreign bacteria exist in the sputum of pulmonary tuberculosis patients. The role these foreign bacteria played in the onset or processing of pulmonary tuberculosis may need pay much more attention to.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Term and preterm shotgun samples

This study was approved by the University of East Anglia (UEA) Faculty of Medical and Health Sciences Ethics Committee, and sample collection was in accordance with protocols laid out by the NRES approved UEA Biorepository (Licence no: 11208). Infants were born at the Neonatal Intensive Care Unit (NICU) of the Norfolk and Norwich University Hospital (NNUH, Norwich, UK) and The Rosie Hospital (Cambridge, UK) were recruited by doctors or nurses with informed and written consent obtained from parents.  Both NICUs have similar protocols for feeding, prescription of antibiotics, and antifungal drugs with the exception that NNUH administered a probiotic treatment containing Bifidobacterium bifidum and Lactobacillus acidophilus (i.e. Infloran®) to their infants from birth.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Metagenome analysis of oil drilling waste at a oil drilling waste recycling plant

The 1 % weight emission-limit of drill waste set by the authorities has set an end to disposal of waste containing oil-based drilling fluids into the sea. The waste mud is instead shipped on shore for cleansing and re-cycling. Several waste plants have been built along the coast of Norway for this purpose. The business of handling and recycling oil drill waste is relatively new, and there is limited documentation of any possible negative health effects for workers handling drilling mud at these plants. The on-site occupational health services report of ailments such as of odors, fatigue, headaches and sickness. These are vague descriptions that may have several causes, but exposure on the work place cannot be ruled out. It is therefore desirable to survey the risk of exposure and possible negative health effects at these work places. For this purpose the chemical and biological agents in the air generated by recycling of the oil drilling waste was characterized and the community biodiversity and function of the drilling waste was analyzed by shotgun sequencing.

Biome: root:Environmental:Aquatic:Marine:Oil-contaminated sediment
Metagenomic analysis of sediment (MNS3) of Manikaran hot springs

Bacteriophages are the most dominant predators of prokaryotic communities in thermal springs yet understanding of the phage ecology remains limited in these hydrothermal environments. Here we examine the metagenomic phage profile from hot spring sediments (n = 4, 78°C-98°C) and microbial mats (n = 2, 57°C).  Caudovirales comprised 91% of the 65 reconstructed phage genotypes, including members of the Myoviridae, Siphoviridae, Podoviridae, and Inoviridae. Siphoviridae were predominant in the sediment and Myoviridae in the microbial mats. Phage genomes were often more well-conserved across sediments compared with microbial mats, which could suggest that there are fewer hosts in the sediments, which represent an extreme environment (78°C-98°C).  A minimal phage genome (28 orthologous proteins) was maintained across both sediment and microbial mats including proteins like histidine kinase, integrase, and Clp protease suggesting a common origin over an inter-habitat distance of 500 m, which are part of survival strategy of bacterial communities at thermophillic environments. We reconstructed bacterial genomes, including Ralstonia (5 Mbp), Pseudoxanthomonas (3.5 Mbp), Dechloromonas (1.9 Mbp), Herbaspirillum (1.5 Mbp), which were predicted to be hosts based on integrated phage DNA and unique CRISPR arrays, suggesting prior phage infections. This study provides detailed insight into the genetic give-and-take between hosts and phages in the ecological niches of thermal springs.

Biome: root:Environmental:Aquatic:Thermal springs:Sediment
Artificial mix of real bacterial sequences

Artificial mix of real bacterial sequences. 15 genomes, even representation. 10X coverage

Biome: root:Engineered:Modeled:Simulated communities (sequence read mixture)
Metagenomic analysis of sediment (MNS2) of Manikaran hot springs

Bacteriophages are the most dominant predators of prokaryotic communities in thermal springs yet understanding of the phage ecology remains limited in these hydrothermal environments. Here we examine the metagenomic phage profile from hot spring sediments (n = 4, 78°C-98°C) and microbial mats (n = 2, 57°C).  Caudovirales comprised 91% of the 65 reconstructed phage genotypes, including members of the Myoviridae, Siphoviridae, Podoviridae, and Inoviridae. Siphoviridae were predominant in the sediment and Myoviridae in the microbial mats. Phage genomes were often more well-conserved across sediments compared with microbial mats, which could suggest that there are fewer hosts in the sediments, which represent an extreme environment (78°C-98°C).  A minimal phage genome (28 orthologous proteins) was maintained across both sediment and microbial mats including proteins like histidine kinase, integrase, and Clp protease suggesting a common origin over an inter-habitat distance of 500 m, which are part of survival strategy of bacterial communities at thermophillic environments. We reconstructed bacterial genomes, including Ralstonia (5 Mbp), Pseudoxanthomonas (3.5 Mbp), Dechloromonas (1.9 Mbp), Herbaspirillum (1.5 Mbp), which were predicted to be hosts based on integrated phage DNA and unique CRISPR arrays, suggesting prior phage infections. This study provides detailed insight into the genetic give-and-take between hosts and phages in the ecological niches of thermal springs.

Biome: root:Environmental:Aquatic:Thermal springs:Sediment
Freshwater shotgun metagenome from the surface of Nakdong River during algal bloom, Busan, South Korea

We monitored seasonal variation of shotgun metagenome during occurrence of algal bloom

Biome: root:Environmental:Aquatic:Freshwater
metagenomic Shotgun analysis of cecum microbiome of poultry

metagenomic Shotgun analysis of cecum microbiome of poultry from Indian sub Continent

Biome: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
Study of the changes in the metagenome of the groundwater community at

During the 1960s, assorted radioactive waste was disposed at the Little Forest Legacy Site near Sydney (Australia). Trenches were dug and filled with waste. It has been observed that after rainfall events, water overflows. The study aims to evaluate the potential community changes and relate them with expected fluctuating redox conditions.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
The initial state of the human gut microbiome determines its reshaping by antibiotics

The human gut microbiota is affected by antibiotics, but the heterogeneous response between individuals remains unexplored. To specifically address this question and examine the effect of antibiotics on selection of resistance genes, we administered the second-generation cephalosporin cefprozil to healthy volunteers. Stool samples gathered before antibiotic exposure, at the end of the treatment and three months later were analyzed using shotgun metagenomic sequencing. We show that normal antibiotic treatment can alter the gut microbiome in a specific, reproducible and predictable fashion. Strikingly, we identified a subgroup of participants that were enriched in opportunistic pathogen Enterobacter cloacae after exposure to the antibiotic, an effect linked to lower initial microbiome diversity and to the Bacteroides enterotype. Resistance genes that were not detectable before the treatment were observed after a 7-day course of antibiotic. Knowledge of the initial composition of the microbiome could assist in the prevention of the adverse effects of antibiotics.

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