SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
marine sediment metagenome Targeted loci environmental

Difficulties in studying growth dynamics of marine sediment microbial populations in a natural setting limits the ability to identify functions in novel populations, assess competition mechanisms, and extrapolate from growth dynamics in pure cultures. We used qPCR and 16S rRNA gene tag libraries to measure relative growth rates of a microbial community from Cape Lookout Bight, NC, in a laboratory mesocosm. Homogenized sediments were incubated for 122 days, hydrogen concentrations were consistent with thermodynamic control by sulfate-reducing prokaryotes during the sulfate-reducing phase and methanogenesis commenced when hydrogen increased above the methanogen thermodynamic maintenance. Uncultured clades of Methanosarcinales and Methanomicrobiales grew during the methanogenic phase with doubling times ranging from 15-46 days, considerably slower than those grown in pure cultures. An uncultured archaeal group, Kazan-3A-21, also increased with methane production. The majority of the population were from deeply-branching uncultured groups and, like the majority of the putative sulfate reducers, were mostly unresponsive to the shift from sulfate reduction to methanogenesis. We conclude that marine sediment methanogens grow more slowly than cultures, once thermodynamic inhibition by sulfate reducers is alleviated; and the majority of the diversity present in marine sediments grow or die more slowly than could be observed in our 122 day incubation.

Biome: root:Engineered:Lab enrichment
High solid enriched microbial communities from the Joint BioEnergy Institute, USA - SP1-9-D metagenome


Biome: root:Engineered:Lab enrichment
Desalination process Targeted Locus/Loci

Water samples were collected from a desalination plant, which were seawater, pretreated seawater, brine of reverse osmosis process and fouled reverse osmosis membranes.  Microbial community differences were determined from intake to fouling communities during desalination process.   1) seawater: intake seawater which provided to desalination process.  2) filter treated seawater: after pretreatment (multimedia filter, MF, UF).  3) Biofouling1 : on reverse osmosis  membrane 1 (front located face to inflow). 4) Biofouling2 : on reverse osmosis membrane 2 (last located). 5) Brine: the concentrated water after reverse osmosis process.

Biome: root:Engineered:Industrial production
Organic and Non-Organic Wine Targeted Locus (Loci)

Samples taken during fermentation of organic and non-organic wine

Biome: root:Engineered:Food production:Fermented beverages
Pit mud of Chinese liqour fermentation reactorMetagenome

Chinese liquor is produced by a solid-state fermentation process used for hundreds of years. The process is carried out in rectangular soil pits, whose walls have been layered with a fermentation mud. The age of these this layer is believed to influence final liquor quality and the microbes resident here form the inoculum for fermentation. Microbial diversity in these layers is poorly understood. This is the first report which describes a deep metagenomic sequencing based study to reveal the microbial diversity from 24 pits of varying ages, 20, 30, 50, 140, 220, 350, 400 and 440 years.

Biome: root:Engineered:Food production:Fermented beverages
Listeria monocytogenes Genome sequencing

Quasi-metagenomics for rapid trace-back of pathogens from complex matrices: a case study with Listeria monocytogenes from ice-cream linked to an outbreak

Biome: root:Engineered:Food production:Dairy products
Cotija cheese metagenome

Cotija cheese is a Mexican dairy product of spontaneous fermentation with a particular sensorial profile and an indisputable microbiological quality. In this study we analysed bacterial Cotija cheese metagenome in order to get a complete picture of bacterial diversity as well as metabolic potential of consortium related to flavour and odour compound production as well as gene related with bacteriocins production.

Biome: root:Engineered:Food production:Dairy products
Medium-ripened pasta-filata cheese metatranscriptome Transcriptome or Gene expression

Microbial metatranscriptome (RNA-seq) during manufacturing and ripening of Caciocavallo cheese (a traditional Italian pasta-filata cheese)

Biome: root:Engineered:Food production:Dairy products
raw sequence reads from analysis of red-smear-cheese

The cheese smear of a Swiss semi-hard red-smear cheese variety was analyzed for comparison of the microbial surface smear community patterns of cheeses differing in their smear quality.

Biome: root:Engineered:Food production:Dairy products
ITS2-based metagenomic study of twelve French cheese varieties


Biome: root:Engineered:Food production:Dairy products
Medium-ripened pasta-filata cheese Targeted loci environmental

16S rRNA sequencing (cDNA) of Caciocavallo cheese during manufacturing and ripening

Biome: root:Engineered:Food production:Dairy products
food metagenome Targeted loci environmental

The aim of the experiment is to assess the microbial communities of spoiled hard cheese using Illumina MiSeq high-throughput sequencing technologies

Biome: root:Engineered:Food production:Dairy products
Mozzarella cheese Targeted Locus (Loci)

Mozzarella cheese microbiota

Biome: root:Engineered:Food production:Dairy products
Metagenome from Piedmontese cheese

After total bacterial RNA extraction directly from Piedmontese cheese and cDNA syntesis, V1-V3 region of the 16S rRNA were amplified

Biome: root:Engineered:Food production:Dairy products
Cheese Targeted Locus (Loci)

V1-V3 rRNA gene amplicons from Fontina PDO cheese

Biome: root:Engineered:Food production:Dairy products
Canestrato cheese Targeted Locus (Loci)

Canestrato Pugliese PDO cheese metagenome

Biome: root:Engineered:Food production:Dairy products
Cheese Product Targeted Locus (Loci)

The goal are to explore and study the microbial diversity in cheese samples from Herve region in Belgium.

Biome: root:Engineered:Food production:Dairy products
Mexican cheese microbiota 18S

Yeast diversity in traditional mexican cheeses

Biome: root:Engineered:Food production:Dairy products
Mexican cheese microbiota 16S

Microbial diversity of traditional mexican cheeses

Biome: root:Engineered:Food production:Dairy products
cheese whey bioreactor Metagenome

microbial community of cheese whey

Biome: root:Engineered:Food production:Dairy products
Ricotta cheese microbiome

Ricotta cheese microbial community evolution during shelf life.

Biome: root:Engineered:Food production:Dairy products
Cheese Targeted Locus (Loci)

Microbiota of curds and natural whey cultures from Grana Padano, Parmigiano Reggiano and Mozzarella cheese manufactures

Biome: root:Engineered:Food production:Dairy products
food contamination metagenome Metagenome

fresh bagged spinach spiked with STEC

Biome: root:Engineered:Food production
Viral metagenomics of US store bought beef, pork, chicken

We describe here the metagenomics-derived viral sequences found in beef, pork, chicken purchased from supermarkets in San Francisco. Meat and meat products can be the source of numerous enteric infections in humans. A library was then constructed using Nextera XT DNA Sample Preparation Kit (Illumina) and then sequenced using the Miseq Illumina platform with 250 bases paired ends with a distinct molecular tag for each pool.

Biome: root:Engineered:Food production
Metagenome of the microbiota  of wild lavender honey


Biome: root:Engineered:Food production
Metagenome of the microbiota of lavandin honey


Biome: root:Engineered:Food production
Dietary supplements Metagenome

Dietary supplements with live microbials.

Biome: root:Engineered:Food production
Beef metagemome

Exploring the sources of beef microbial contamination and study the beef microbiota evolution after aerobic storage at 4C.

Biome: root:Engineered:Food production
ISS Metagenomes

Metagenomes created from samples collected from the International Space Station

Biome: root:Engineered:Built environment
Marine Aggregates Metagenome

Analyze the bacterial community composition of artificially produced marine aggregates on a geometric time series and associate it with the surrounding water.

Biome: root:Engineered:Built environment
Sugarcane filter cake compost raw sequence reads

Amplicon and shotgun sequencing of microbiome in two sugarcane filter cake compost piles were carried out to analyse the dynamics of fungal and bacterial communities along the process and biomass degrading profile for second generation bioethanol.

Biome: root:Engineered:Biotransformation:Mixed alcohol bioreactor
Paper sludge microbial community

Recycled paper sludge microbial community as a potential source of enzymes

Biome: root:Engineered:Biotransformation
Botany Membrane bioreactor, groundwater, granular activated carbon and soil samples 16S Tag Pyrosequencing of Metagenomic DNA.

Bacterial 16S Tag Pyrosequencing of a Membrane Bioreactor and Associated Units during Adaptation to Bioremediation of 1,2-dichloroethane.

Biome: root:Engineered:Bioremediation
AOB Genome sequencing and assembly

It is able to fixed nitrogen

Biome: root:Engineered:Bioreactor:Continuous culture:Marine sediment inoculum
Continuous culture enrichments from intertidal sediment - Metagenomes, Metatranscriptomes and 16S tag sequencing

A continuous culture was inoculated with intertidal sediment from the German Wadden Sea, and introduced with artificial seawater and a mimicked tidal condition. Natural selection on the microbial community and redox processes were investigated in the culture. Three samples for DNA extraction and four samples for RNA extraction were taken from the culture during the last three weeks of the experiment. Whole DNA shotgun metagenomes were sequenced and the reads were assembled into contigs. Enriched total mRNA was used for transcriptome sequencing. Another 14 samples at different time points were taken for 16S tag sequencing.

Biome: root:Engineered:Bioreactor:Continuous culture:Marine intertidal flat sediment inoculum
Marine sediment microorganisms Raw sequence reads

Marine sediment incubations with different substrates

Biome: root:Engineered:Bioreactor:Continuous culture
Temperature controls crystalline iron(III) oxide utilization by microbial communities in ferruginous marine sediment incubations

e carried out Incubation experiments with deep ferruginous sediments from the Helgoland Mud Area, German Bight of the North Sea. Samples were collected using a gravity corer (5 m core length) during RV HEINCKE research expedition HE 443 (54 05.23'' N; 007 58.04'' E) in May 2015. In the laboratory, these sediments were stored under anoxic conditions at 4 oC until slurry incubations were. Anoxic 50-mL slurry incubations were made in 120-ml serum vials with sediment from 416  441 and 441  466 cm depths and anoxic sulphate-free artificial sea water (ASW; composition [L-1]: 26.4 g NaCl, 11.2 g MgCl2.6H2O, 1.5 g CaCl2.2H2O and 0.7 g KCl) at a ratio of 1:3 (w/v) under a headspace of N2. Incubations (n=9) were supplemented by adding iron(III) oxides (hematite or magnetite; LanXess, Germany; 30 mol l-1) and glucose (2 mM) as electron donor. Control incubations (glucose only, n = 9) were supplemented with 2 mM glucose only. The potential for reduction of amended hematite (HG) or magnetite (MG) was evaluated by comparing the amount of Fe2+ formed in crystalline iron(III)-treated incubations to those of the glucose only control (G). Triplicates of each treatment set were incubated statically in the dark at 4 oC, 10 oC, or 30 oC. Supplementary incubations were set up at 30 oC, for testing the effect of 2-bromoethanesulfonate (BES) on methanogenesis and iron reduction in the presence of crystalline iron oxides. For molecular analysis, one millilitre of slurry from individual incubations, at specific time points as stated in each sample description, was used for nucleic acid extraction following a modified protocol from Lueders et al (2004). A two-step PCR approach for Illumina amplicon sequencing described by Herbold et al (2015) was adopted for amplification of Bacteria and Archaea 16S rRNA genes. Amplicon library was sequenced using the Miseq Illumina sequencing platform at University of Bremen, Germany. Sequence analysis of forward reads was performed on the QIIME 1.8.0 platform (Caporaso et al., 2010) based on the 16S rRNA gene profiling analysis pipeline recommended by Pylro et al (2014) with modifications. A Total Sum Scaling approach was used to identify dominant members of the microbial communities in each sample. The resulting article written on the project reported relative abundance of 16S rRNA sequences of Bacteria and Archaea that dominated the microbial communities in each sample.

Biome: root:Engineered:Bioreactor:Continuous culture
High solid enriched microbial communities from the Joint BioEnergy Institute, USA - SP1-10-D metagenome


Biome: root:Engineered:Lab enrichment
High solid enriched microbial communities from the Joint BioEnergy Institute, USA - SP1-8-D metagenome


Biome: root:Engineered:Lab enrichment
Methanogenic digester communities Raw sequence reads

Studies of microbial communities and antibiotic resistance genes

Biome: root:Engineered:Bioreactor
Methanogen diversity in the rumen in vitro fermentation culture

methanogen diversity in the rumen in vitro fermentation culture

Biome: root:Engineered:Bioreactor
Substrate variations triggered the emergent of different active bacterial and archaeal assemblages during biomethane production

Biomethane has been regarded as one of the promising renewable energy supplies. However, the microbial communities involved in methane synthesis have not been fully characterized. By examining the bacterial and archaeal 16S rRNA genes in the DNA and RNA using barcoded 454 pyrosequencing, the composition of a methane-generating microbial community and the corresponding active members during the transformation of three target substrates (food waste, cellulose, xylan) were determined. By assigning sequences to their respective taxonomies, substrate-dependent variations in the composition and relative abundance of the active microbial community members were detected. Results from this study suggest that the vast diversity of the microbial community enabled adaptation and transformation of multiple amended substrates, and a subset of the populations became active and altered in relative abundance during methane production. Overall, insights gained from high-throughput sequencing of the metabolically-active populations under different conditions should facilitate the optimization of biomethane systems.

Biome: root:Engineered:Biogas plant:Wet fermentation
bioethanol fermentation Metagenome

This project investigated the bacterial contents of yeast-based bioethanol fermentation. Bacteria are known to impact the success of bioethanol fermentation, but little is known about bacterial community structure and dynamics during the course of fermentation. Here we used 16S rRNA gene amplicon sequencing to probe community structure during multiple fermentations from multiple facilities across the United States.

Biome: root:Engineered
Lonar Lake sediment Metagenome

Understanding the relevance of bacterial and archaeal diversity in the soda lake sediments by the culture independent approach using bTEFAP.  Lonar Lake is a saline soda lake located at Lonar in Buldana district, Maharashtra State, India, which was created by a meteor impact.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Alkaline:Sediment
Postnatal gut immunity and microbiota development is minimally affected by prenatal inflammation in preterm pigs

Chorioamnionitis (CA), resulting from intra-amniotic inflammation, is a frequent cause of preterm birth and exposes the immature intestine to bacterial toxins and/or inflammatory mediators before birth via fetal swallowing. This may affect intestinal immune development, interacting with the effects of enteral feeding and gut microbiota colonization just after birth. Using preterm pigs as model for preterm infants, we hypothesized that prenatal exposure to gram-negative endotoxin influences postnatal bacterial colonization and gut immune development. Pig fetuses were given intra-amniotic lipopolysaccharide (LPS) 3 d before preterm delivery by cesarean section, and were compared with litter-mate controls (CON) at birth and after 5 d of formula feeding and spontaneous bacterial colonization. Amniotic fluid was collected for analysis of leukocyte counts and cytokines, and the distal small intestine was analyzed for endotoxin level, morphology and immune cell counts. Intestinal gene expression and microbiota were analyzed by transcriptomics and metagenomics, respectively. At birth, LPS-exposed pigs showed higher intestinal endotoxin, neutrophil/macrophage density and shorter villi. About 1.0% of intestinal genes were affected at birth and DMBT1, a regulator of mucosal immune defense, was identified as the hub gene in the co-expression network. Genes related to innate immune response (TLR2, LBP, CD14, C3, SFTPD), neutrophil chemotaxis (C5AR1, CSF3R, CCL5) and antigen processing (MHC II, CD4) were also affected and expression levels correlated with intestinal neutrophil/macrophage density and amniotic fluid cytokine levels. On day 5, LPS and CON pigs showed similar necrotizing enterocolitis (NEC) lesions, endotoxin levels, morphology, immune cell counts, gene expressions and microbiota (except for difference in some low-abundant species). Our results show that CA markedly affects intestinal genes at preterm birth, including genes related to immune cell infiltration. However, a few days later, following the physiological adaptations to preterm birth, CA had limited effects on intestinal structure, function, gene expression, bacterial colonization and NEC sensitivity. We conclude that short-term, prenatal intra-amniotic inflammation is unlikely to exert marked effects on intestinal immune development in preterm neonates beyond the immediate neonatal period.

Biome: root:Host-associated:Mammals:Digestive system
Metagenomic analysis of the cervicovaginal microbiome in women with systemic lupus erythematosus: A new insight into sex and ethnic differences

Non-Lactobacillus dominant cervicovaginal microbiomes have been associated with vaginal and auto-immune diseases such as bacterial vaginosis and systemic lupus erythematosus (SLE). Using a deep sequencing approach, the microbial composition and structure of the cervicovaginal metagenomes of a group of Afro-Caribbean women (with and without SLE) asymptomatic for vaginal disease were analysed. Community state type (CST) IV predominated the metagenomes of the Afro-Caribbean women. In the healthy group Gardnerella (16.37%) and Prevotella (11.3%) species were more abundant than Lactobacillus (5.06%). Whereas, in women with SLE the most abundant species was Prevotella (17.66%) followed by Lactobacillus (13.60%) and Gardnerella (5.73%). These findings suggest that vaginal health is not strictly dependent on the relative abundance of Lactobacillus species. Additionally, some low abundant pathobionts were 5 to 23 times more common in the SLE cohort. This study offers a new postulate into sex and ethnic differences in the prevalence of SLE.

Biome: root:Host-associated:Human:Reproductive system:Vagina
Metagenomic analysis of the cervicovaginal microbiome in women with systemic lupus erythematosus: A new insight into sex and ethnic differences

Non-Lactobacillus dominant cervicovaginal microbiomes have been associated with vaginal and auto-immune diseases such as bacterial vaginosis and systemic lupus erythematosus (SLE). Using a deep sequencing approach, the microbial composition and structure of the cervicovaginal metagenomes of a group of Afro-Caribbean women (with and without SLE) asymptomatic for vaginal disease were analysed. Community state type (CST) IV predominated the metagenomes of the Afro-Caribbean women. In the healthy group Gardnerella (16.37%) and Prevotella (11.3%) species were more abundant than Lactobacillus (5.06%). Whereas, in women with SLE the most abundant species was Prevotella (17.66%) followed by Lactobacillus (13.60%) and Gardnerella (5.73%). These findings suggest that vaginal health is not strictly dependent on the relative abundance of Lactobacillus species. Additionally, some low abundant pathobionts were 5 to 23 times more common in the SLE cohort. This study offers a new insight into sex and ethnic differences in the prevalence of SLE.

Biome: root:Host-associated:Human:Reproductive system:Vagina
Ocean Sampling Day (OSD) data from North Adriatic Sea

Ocean Sampling Day (OSD) data from North Adriatic Sea

Biome: root:Environmental:Aquatic:Marine
CAECAL METAGENOMICS

CAECAL METAGENOMICS IN DIFFERENT FEEDING CONDITIONS

Biome: root:Host-associated:Birds:Digestive system
Space environmental factor impacts upon murine colon microbiota and mucosal homeostasis

We report how high and low linear energy transfer (LET) radiation, microgravity, and elevated dietary iron affect colon microbiota (determined by 16S rDNA pyrosequencing) and colon function. Three independent experiments were conducted: 1) fractionated low LET ? radiation (137Cs, 3 Gy, RAD), high Fe diet (IRON) (650 mg/kg diet), and a combination of low LET ? radiation and high Fe diet (IRON+RAD) in male Sprague-Dawley rats; 2) high LET 38Si particle exposure (0.050 Gy), 1/6 G partial weight bearing (PWB), and a combination of high LET38Si particle exposure and PWB in female BalbC/ByJ mice; and 3) 13 d spaceflight in female C57BL/6 mice. For each experiment, the colon was resected and feces removed for microbial sequencing analysis on a Roche 454 Genome Sequencer  FLX Titanium instrument (Microbiome Core Facility, Chapel Hill NC) using the GS FLX Titanium XLR70 sequencing reagents and protocols. Analysis of amplicon sequencing data was carried out using the QIIME pipeline. Low LET radiation, high iron diet, and spaceflight increased Bacteroidetes and decreased Firmicutes. Low LET radiation, high Fe diet, and spaceflight did not significantly affect diversity or richness, or elevate pathogenic genera. Spaceflight increased Clostridiales and decreased Lactobacillales, and similar trends were observed in the experiment using a ground-based model of microgravity, suggesting altered gravity may affect colonic microbiota. Microbiota characteriztion in these models is a first step in understanding the impact of the space environment on intestinal health. Overall design: Phylogenetic characterizaiton of fecal microbiota from a total of 49 mouse and rat fecal samples (18 and 31 samples, respectively, no replicates)

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Spatiotemporal dynamics in the metagenomes of biofouling microbial communities residing in district cooling basins

Metagenomic datasets for biofouling biofilm samples collected from the water cooling tower basins of two district cooling plants.

Biome: root:Environmental:Aquatic:Freshwater
The effect of viruses on the dynamics of harmful algal blooms

Surface water from areas experiencing harmful algal blooms were collected either at the beginning or during the termination of the bloom. The water was size fractionated, and metagenomes were produced for the host and viral fractions.

Biome: root:Environmental:Aquatic:Marine
Dysbiosis associated with acute helminth infections in herbivorous youngstock - observations and implications

This study investigates, for the first time, the associations between acute infections by GI helminths and the faecal microbial and metabolic profiles of a cohort of equine youngstock, prior to and following treatment with parasiticides (ivermectin).

Biome: root:Host-associated:Mammals:Digestive system:Fecal
wrasseeggs16s

wrasseeggs16s

Biome: root:Host-associated:Fish
Mussels larvea 16S

Mussels larvea 16S

Biome: root:Host-associated:Mollusca