SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Impact of air pollution and urbanization on the bacterial phyllosphere of Ivy (Hedera sp.)

The surface of plant leaves, also termed the phyllosphere, is a selective habitat for microbes. From this phyllosphere microbiome, the bacterial composition seems to depend on plant host species, leaf characteristics, season, climate, and geographic distance between the plant hosts. In this study, we investigated the effect of an urban environment and air pollution on the bacterial composition of phyllosphere communities. We performed a passive biomonitoring experiment in which leaves were sampled from Ivy (Hedera sp.), a common evergreen climber species in the area under study. The bacterial community composition was determined using 16S rRNA gene sequencing on the Illumina MiSeq platform. In addition, exposure to anthropogenic particulate matter was estimated using leaf biomagnetic analyses. We found that the phyllosphere microbial communities of Ivy were greatly different between urban and more rural locations, as we observed a shift in several of the dominant taxa Beijerinckia, Hymenobacter, Methylocystaceae and Methylobacterium. Interestingly, the communities also showed greater variability in the urban area than at the less urbanized locations where we measured lower levels of air pollution. These results indicate that an urban environment and local air pollution   can greatly affect the local phyllosphere community composition.

Biome: root:Host-associated:Plants:Phylloplane
Microbial community dynamics and response to plant growth-promoting organisms in the rhizosphere of four common food crops cultivated in hydroponics

As part of the European Space Agency MELiSSA project, the effects of Myco Madness, a commercial combination of plant growth-promoting organisms, on the microbial communities of four common four crops (durum wheat, bread wheat, potato, soybean) cultivated in hydroponics was assessed. Small relative amounts (<0.5%) of successful infestation of plant root zone microbiome by Myco Madness PGPOs resulted in important changes in the composition of these communities. The dynamics of root zone communities were also followed over time. These results suggest that the microbial communities associated with hydroponic nutrient solutions are affected by plant developmental stage-associated changes in root exudation patterns.

Biome: root:Host-associated:Plants:Root
Identification of the oak microbiome

Metabarcoding was used to study bacteria in oak samples. Samples were taken from oaks showing signs of acute oak decline. A general 16S rRNA gene primer was used followed by pyrosequencing.

Biome: root:Host-associated:Plants
Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes

Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes

Biome: root:Host-associated:Plants
effect of IFNg and Akkermansia muciniphila on mouse gut microbiome composition

16s rRNA V4 region is sequenced to measure the composition of gut microbiome for IFNg knockout mice, wild type mice and germ free mice that colonized with Akkermansia muciniphila then treated with IgG or Anti-IFNg

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Metagenomic analysis of an Iranian Hypersaline Lake microbial ecosystem

We studied microbial communities in three different stations of an Iranian Hypersaline Lake (Lake Meyghan). These stations are characterized by a salinity ranging from 5%, 20% to over 30% total salt and a slightly alkaline Ph range (from 7.7 to 8.8). The microbial communities are dominated by Archaea at higher salinity and by Bacteria at lower salinity.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
construction of minimal coastal microbial mats

Minimal coastal microbial mats were created with diluted coastal mat samples obtained from the Dutch barrier island of Schiermonnikoog. The MM"s were inoculated in fresh sterilized sand in glass containers contained in a MicroBox. The MicroBox has a transparent lid (allowing photosynthetic growth) and a gas exchange filter. The MM"s are propagated under laboratory conditions at a 16h light / 8h dark regime and at a constant 23 C. Serial dilutions used for this data-set are 0, 3 and 5-fold.

Biome: root:Environmental:Aquatic:Marine:Coastal
Global Rivers

Metagenomic analysis provides knowledge of the diversity and ecological function of the biota inhabiting rivers, whether or not they can be seen or cultured.  Using MinION rapid sequencing and real time analysis of DNAs obtained from rivers, we demonstrate the utility and potential of this approach for monitoring for agricultural and industrial effects on the river biota, detecting pathogen diversity and progression through river systems, judging risk associated with water uses, and ultimately enhancing water quality.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Low land river systems
A metagenomics study of two north sea communities.

A metagenomics study of two north sea communities.

Biome: root:Environmental:Aquatic:Marine
Marine sediment from Gulf of Mexico

After the Deepwater Horizon oil spill in the Gulf of Mexico changes were detected in the microbial communities. There’s a little information about the microbial communities from southern regions of the Gulf of Mexico and it important to know its structure in case of future ecological disasters. In this study we take samples from marine sediments and analyzed it using shotgun sequencing.

Biome: root:Environmental:Aquatic:Marine:Oil-contaminated sediment
16S rRNA gene sequencing of the extremelly birth weight infant gut

16S rRNA gene sequencing of the extremelly birth weight infant gut primers 530F-926R

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Global surveillance of infectious diseases and antimicrobial resistance from sewage

Adequately monitoring of large populations and their environments is essential if we want to monitor pathogens and antimicrobial resistance around the globe. Recent developments in high‐throughput sequencing allow to rapidly identify nucleic acids from various organisms in clinical and environmental samples. Sewage systems are recognized as an important source of human pathogens, especially in crowded settings with poor infrastructure. A point‐prevalence metagenomic analysis is applied to sewage samples collected globally from the main sewage system of major cities prior to treatment plants inlet. The project is a proof‐of‐concept study for applying metagenomic approaches that could initiate a global surveillance of human infectious diseases including antimicrobial resistance from sewage collected in major cities around the world to detect, control, prevent and predict human infectious diseases.

Biome: root:Engineered:Wastewater:Water and sludge
Impact of LAB supplementation in drinking water on chicken crop and ceca

Impact of LAB supplementation in drinking water on chicken crop and ceca tested at 14 and 35 days

Biome: root:Host-associated:Birds:Digestive system:Ceca
Before and after a geosequestration experiment, volumes of reservoir water were filtered in order to infer on taxonomy, structure of the underlying microbial communities.

Before and after a geosequestration experiment, volumes of reservoir water were filtered in order to infer on taxonomy, structure of the underlying microbial communities.

Biome: root:Environmental:Aquatic:Freshwater:Drinking water:Delivery networks
16S rRNA gene sequencing in extremely low birth weight infant gut

16S rRNA gene sequencing in extremely low birth weight infant gut. Primers used for amplifying 16S rRNA were 27F and 519R

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

This is only a very small subsample of metagenomic data

Biome: root:Host-associated:Plants:Rhizosphere
Diplonemids are the most diverse planktonic eukaryotes in the world ocean

Diplonemids sequence data corresponding to the V9 loop of the 18S rDNA in 850 size-fractionnated plankton communities sampled at 123 location including samples from the mesopelagic zone.

Biome: root:Environmental:Aquatic:Marine
LAB in feed

Metagenomic study of cecum contents of chickens fed with LAB

Biome: root:Host-associated:Birds:Digestive system:Ceca
Can insecticide resistance alter behaviour and fitness by modifying the gut microbiome?

Resistance to a range of insecticides is conferred by upregulation of the cytrochrome P450 gene Cyp6g1 in Drosophila melanogaster, and has been associated with sex-specific pleiotropic effects on behaviour and fitness. Cyp6g1 is primarily overexpressed in the gut in insecticide resistant individuals and metabolises a large range of molecules, and thus upregulation may alter the gut environment and the community composition of the gut microbiota. The community composition of gut microbiota can have profound effects on behaviour and fitness, and if Cyp6g1 expression can explain differences in gut microbiota then it may help explain its observed fitness effects. Comparing microbial community composition between the guts of insecticide resistant and susceptible individuals (high and low Cyp6g1 expression, respectively) via 16s rRNA sequencing would be the first necessary experiment to demonstrate that insecticide resistance can alter behaviour and fitness by modifying the gut microbiome.

Biome: root:Host-associated:Insecta:Digestive system
A plaque on both your houses. Exploring the history of urbanisation and infectious diseases through the study of archaeological dental tartar

Human health experiences throughout much of (pre-)history remain clouded by a lack of reliable data on disease exposure and transmission. Archaeological dental tartar (mineralized plaque) entraps and preserves DNA and proteins from multiple oral and systemic infectious disease pathogens. This project aims to develop pilot data on oral microbial profiles and disease exposure within the historic period through the metagenomic analysis of archaeological dental calculus.

Biome: root:Host-associated:Human:Digestive system:Oral
Experimental Metagenome on MinION

This is an artificial metagenome created by pooling various proportions of DNA from four microbe cultures to simulate a simple metagenome for analysis by Oxford nanopore MinION.  Single-species cultures of Escherichia coli, Pseudomonas fluorescens, Microcystis aeruginosa, and Synechococcus elongatus were grown to log phase then harvested for DNA extraction.  Following mechanical shearing, templates were prepared using either equimolar amounts of each species or combinations of DNAs where one species was rare (0.05%). Libraries were created using his-tag bead purification according to MinION specifications and libraries were sequenced using MinION R7.x flow cells.  For validation, a final library was prepared using a mock microbial community with 20 species included in “staggered” proportions (obtained from ATCC, the mixture had 1,000 to 1,000,000 16S rRNA operon copies per organism per μL of material supplied).  This latter library, as it was supplied at a low concentration, required pre-amplification with Phi29 prior to library preparation.

Biome: root:Engineered:Modeled:Simulated communities (DNA mixture)
Assembled contigs from rhizosphere metatranscriptome

RNA was extracted from the rhizopheres of three crop plants and unplanted soil.  rRNA was removed using Ribo-Zero and any remaining rRNA reads removed using SortMeRNA.  Remaining high quality reads were assembled using Trinity

Biome: root:Host-associated:Plants:Rhizosphere
Metagenomic recovery of phage assemblage from Manikaran hot springs

Phages are the most dominant predators of prokaryotic community at thermal springs characterized by restricted eukaryotic grazing pressures yet understanding of the phage ecology remains limited at hydrothermal environments. This study examines the metagenomic profiles of phages across Himalayan hot springs (1760 m) at Manikaran by employing the environmental data from sediment (n = 4, 78Â°C-98Â°C) and microbial mat (n = 2, 57Â°C) deposited around thermal discharges that led to de novo reconstruction of 65 phages (24-200 Kbp). 91% (60/65) of the phages belonged to the order Caudovirales including members from Myoviridae, Siphoviridae, Podoviridae and Inoviridae with distinguishing enrichment of Siphoviridae and Myoviridae across sediment and microbial mats, respectively highlighting the temperature driven shaping of phage community. Whole genome based analysis of the phages demonstrated well-conserved phages across sediments in contrast to the microbial mat owing to moderately mesophilic microbial mats (57Â°C) compared to the thermophillic sediments (78Â°C-98Â°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. In an attempt to reconstruct potential hosts for phages from the metagenome data, genomes for Ralstonia (5 Mbp), Pseudoxanthomonas (3.5 Mbp), Dechloromonas (1.9 Mbp), Herbaspirillum (1.5 Mbp) were assembled with integrated phages and unique CRISPR arrays suggesting prior phage infections and rapidly acquired immunity against future phage attacks at these hot springs. This study provides detailed insights into the genetic give-and-take between hosts and their phages in specific ecological niches of Manikaran thermal springs.

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Biological soil crusts, Southern Spain

Biological soil crusts play vital roles in dryland regions that cover over 35% of the Earth´s land mass, including 24% of Europe. They provide important ecosystem services such as limitation of soil erosion, retention of water,  improving soil fertility and nitrogen and carbon fixation.

Biome: root:Environmental:Terrestrial:Soil:Desert
Diversity and assembling processes of bacterial communities in cryoconite holes of a Karakoram glacier

Cryoconite holes are small ponds that form on the surface of glaciers that contain a dark debris, the cryoconite, at the bottom and host active ecological communities. Differences in the structure of bacterial communities have been documented among Arctic and mountain glaciers, and among glaciers in different areas of the world. In this study we investigate the structure of bacterial communities of cryoconite holes of Baltoro Glacier, a large (62 km in length and 524 km2 of surface) glacier of the Karakoram, by high throughput sequencing of the V5-V6 hypervariable regions of the 16S rRNA gene. We found that Betaproteobacteria, dominated bacterial communities, with large abundance of genera Polaromonas, probably thanks to the highly versatile metabolism of this genus, and Limnohabitans, which may have been favoured by the presence of supraglacial lakes in the area where we sampled cryoconites. In addition, cryoconites that occurred in separate areas on the surface of the glacier hosted different bacterial communities, while no spatial pattern of variation in community structure was observed within each area. This probably occurred because of variation in environmental conditions, mainly pH, of cryoconite holes in different areas of the glacier surface.

Biome: root:Environmental:Aquatic:Freshwater:Ice:Glacier
Oyster and water samples from Texas bays.

Oyster and water samples from Texas bays.

Biome: root:Environmental:Aquatic:Marine:Coastal
Lipases from Metagenomic Sources

Soil samples were collected from restaurant grease-deposit-site. An enriching step was carried out by inoculating minimal medium with soil and grown at 20°C. Olive oil was added to the medium as the only carbon source. This was done to enrich the samples for organisms having the ability to grow by metabolising oil. DNA was extracted. The acquired metagenome was sequenced at GATC (Constance, Germany). The DNA was sequenced in 300 bp paired end reads using the MiSeq platform.

Biome: root:Environmental:Terrestrial:Soil:Oil-contaminated
scs diatom

Bacteria attached to a diatom host cell are thought to operate as potential symbionts, functioning as mutualistic, parasitic, or commensal epibionts. This study investigates if similar relationships can be found at the level of the individual diatom host cell by analyzing the metagenomes of six representative Thalassiosira host cells with dissimilar associated bacteria. Diatoms were collected from the deep chlorophyll maximum in the oligotrophic waters of Station ALOHA (22° 45"N, 158° 00"W), isolated using fluorescently activated cell sorting, and DNA amplified using multiple displacement amplification. Preliminary analysis of the 16S rDNA of 32 host cells found that the composition of bacterial associations could be divided into three distinct groups; six cells from the two most common groupings were selected for further analysis. This initial metagenomic analysis explores nutrient pathways, antibiotic production, quorum sensing, motility, and other genes that may be essential to the diatom-bacterial symbiotic interaction. This work surveys the potential genetic contribution of bacteria, diatoms, as well as community-level interactions that determine the health of the diatom host cell and their bacterial consortia.

Biome: root:Host-associated:Algae:Brown Algae
Regional heterogeneity and seasonal succession in proteorhodopsin containing marine microbial assemblages

A significant proportion of the marine prokaryote community is comprised of microbes that utilise proteorhodopsin (PR), a retinal based photoreceptor used for generating ATP from light. Using an amplicon sequencing approach, we examined spatial and temporal patterns in the diversity of PR containing Bacteria and Archaea (PRBA) along the east coast of Australia, during a period of 12 month from surface samples collected at 3 oceanographic time-series sites spanning 15° of latitude. Coastal PRBA assemblages were dynamic in both space and time, with diversity linked to several environmental factors, with positive correlations to temperature, Secchi depth and Prochlorococcus cell abundance and negative correlations to phosphate concentration observed. Shifts in the taxonomic composition of the PRBA assemblage were best explained by temperature and day length. Seasonality in taxonomic structure was accompanied by temporal variability in proteorhodopsin spectral tuning characteristics. The ratio of blue absorbing proteorhodopsin proteins (BPR) to green absorbing proteorhodopsin proteins (GPR) was strongly linearly correlated with day length, with levels of GPR increasing with day length. These observations highlight the dynamic nature of proteorhodopsin containing marine assemblages, which exhibit substantial shifts in both taxonomy and spectral tuning properties in response to seasonal and spatial variability in environmental conditions.

Biome: root:Environmental:Aquatic:Marine
Metagenome of the soil from hot spring is to be studied to get better ubderstanding of its biome.

Soil is rich in microbes. Metagenomics of soil sample from extreme environment will be helpful for discovery of a new novel bacterial stain.

Biome: root:Environmental:Terrestrial:Soil
Subseafloor microbes at Mid-Cayman Rise

The Mid-Cayman Rise hosts two geochemically distinct vent fields: Von Damm, situated in ultramafic rock, and Piccard, a mafic vent field that is the deepest known vent site in the world. We have analyzed and compared taxonomic and metabolic diversity as well as strain-level variation from 11 metagenomes from Von Damm and 4 metagenomes from Piccard.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents
Metagenome from microbial community of plankton and sediment

In this work, we have characterized the microbial diversity in mesopelagic and bathypelagic zones of the water column (500, 1000 m and 1250 m depth) and bottom sediment from the Marmara Sea by amplifying, cloning and sequencing archaeal, bacterial and eukaryotic small-subunit rRNA (SSU rRNA) genes and by direct pyrosequencing of environmental DNA from 1000 m-deep plankton and sediment (approximately 35 Mbp, respectively).  The plankton sample was recovered from the water column in the Central Basin of the Marmara Sea (40° 50.3'N 28°1.4' E) at 1000m depth.  The sediment sample was recovered from the Central Basin of the Marmara Sea at 1,300 m depth (40° 46.8'N and 29°6.1' E).  A comparative metagenomics analysis of these data with that of previous studies of deep-sea and surface plankton, subsurface deep-sea sediment, whale carcasses and soil reveals interesting trends.  <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&db=Nucleotide&cmd=search&term=HM103388:HM103902[accn]">HM103388-HM103902 </a> are ribosomal RNA sequences associated with this study.

Biome: root:Environmental:Aquatic:Marine
Reduced diversity and altered composition of the gut microbiome in individuals with Myalgic Encephalomyelitis/ChronicFatigue Syndrome

Gastrointestinal disturbances are among the cluster of symptoms commonly reported by individuals diagnosed with ME/CFS (Myalgic Encephalomyelitis/Chronic Fatigue Syndrome), who are also often reported to exhibit altered plasma cytokine profiles. In plasma of ME/CFS patients (n=48) and healthy controls (n=39), we examined a set of inflammatory markers: C-reactive protein (CRP), Intestinal Fatty Acid Binding Protein (I-FABP), lipopolysaccharide (LPS), LPS binding protein (LBP), and soluble CD14 (sCD14).  Levels of LPS, LBP, and sCD14 were elevated in ME/CFS subjects.  Levels of LBP were correlated with LPS and sCD14 and LPS levels correlated with sCD14. We examined the gut microbiota by 16S rRNA sequencing. We observed that bacterial diversity was decreased in the ME/CFS specimens compared to controls, in particular a reduction in the relative abundance and diversity of Firmicutes.  The ME/CFS samples also exhibited an increase in the pro-inflammatory family Enterobacteriaceae and decrease in the anti-inflammatory Ruminococcaceae, including Faecalibacterium, and reduced amounts of beneficial Bifidobacterium species.  Using a machine learning approach, individuals were classified correctly as ME/CFS with an average success rate of 0.8928.  Our results indicate dysbiosis of the gut microbiota in this disease and further suggest an increased incidence of microbial translocation, which may play a role in inflammatory symptoms.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Microbiota composition in Anorexia Nervosa patients before and after weight gain as compared to healthy controls

The aim of this study was to study i) to what extend the microbiota of AN is perturbed in comparison to NW and ii) whether these perturbations are recovered after weight gain and/or normalisation of eating behaviour. In this study we have comprehensively analysed the gut microbiota (by sequencing of the V4 region of the 16S rRNA gene using MiSeq PE250) and short-chain fatty-acids (SCFA) profile in stool samples of AN patients ahead (n=55) and after weight gain (n=44) in comparison to normal-weight participants matched for age and gender (NW, n=55).

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