SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Metagenomic analysis of the upper bronchial tract microbiome in patients with chronic obstructive pulmonary disease and 'healthy' smoker controls

Chronic Obstructive Pulmonary Disease (COPD) may worsen with microbial changes in the respiratory tract but studies into taxonomic structure of the COPD lung microbiome have yielded equivocal results. This may reflect the poor resolving power of taxonomic classification when only based 16S rRNA amplicon sequencing. We here report the metagenomic characterisation of COPD microbiome to more accurately reveal its species-level structure and functional capacity. The bacterial metagenomes within sputum samples from eight COPD patients and ten ?healthy? smokers (Controls) were sequenced and suggested increases in the abundance of bacterial species, particularly within Streptococcus in COPD. The functional capacity of the COPD lung microbiome indicated an increased capacity for bacterial growth, which could be an important feature in bacterial-associated acute exacerbations. Regression analyses correlated COPD severity (FEV1 % of predicted) with differences in the abundance of Streptococcus pneumonia and functional classifications related to a reduced capacity for bacterial sialic acid metabolism. Neither of these lung microbiome characteristics correlated with patient age or smoking pack history, further suggesting an association with COPD pathology. This study suggests that the COPD lung microbiome could be used in patient risk stratification and in identifying novel monitoring and treatment methods.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Prokaryotic responses to ammonium and organic carbon reveal alternative CO2 fixation pathways and importance of alkaline phosphatase in the mesopelagic North Atlantic

To decipher the response of mesopelagic prokaryotic communities to input of nutrients, we tracked changes in prokaryoticabundance, extracellular enzymatic activities, heterotrophic production, dark dissolved inorganic carbon (DIC) fixation, communitycomposition (16S rRNA sequencing) and community gene expression (metatranscriptomics) in 3 microcosm experiments withwater from the mesopelagic North Atlantic. Responses in 3 different treatments amended with thiosulfate, ammonium or organicmatter (i.e. pyruvate plus acetate) were compared to unamended controls. The strongest stimulation was found in the organicmatter enrichments, where all measured rates increased >10-fold. Strikingly, in the organic matter treatment, the dark DICfixation rates —assumed to be related to autotrophic metabolisms— were equally stimulated as all the other heterotrophic-relatedparameters. This increase in DIC fixation rates was paralleled by an up-regulation of genes involved in DIC assimilation viaanaplerotic pathways. Alkaline phosphatase was the metabolic rate most strongly stimulated and its activity seemed to be relatedto cross-activation by nonpartner histidine kinases, and/or the activation of genes involved in the regulation of elemental balanceduring catabolic processes. These findings suggest that episodic events such as strong sedimentation of organic matter into themesopelagic might trigger rapid increases of originally rare members of the prokaryotic community, enhancing heterotrophic andautotrophic carbon uptake rates, ultimately affecting carbon cycling. Our experiments highlight a number of fairly unstudiedmicrobial processes of potential importance in mesopelagic waters that require future attention.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Hot stream metagenomic analysis

The examination of microbial diversity and distribution is one of the key concern in environmental microbiology. Identification of the microorganism exist in a particular environment is critical for understanding the function of organisms in that environment and the processes influencing the diversity of those organisms.  The hot springs are one of the most unique and diverse geothermal ecosystems on Earth, that host a collection of deeply-rooted and under studied prokaryotes. The combination of stringent chemical condition and extreme temperature encountered in geothermal system offers a vital opportunity for studying the diversity and function of indigenous microbiota. The unique microbial ecosystems of the hot springs from Saudi Arabia have never been studied in detail before. The purpose of this project is to examine the chemical and metabolic profile and to identify the bacterial and archaeal communities of the hot springs located at the southwestern region of the Saudi Arabia. This study will be conducted at five terrestrial hot springs for a period of two years. Culture-dependent and culture-independent metagenomic microbiological techniques will be used to investigate the microbial community composition and metabolic properties of the hot-springs microbial ecosystem.

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Bioelectrochemical phenol degradation

The use of bielectrochemical technologies for the remediation of hydrocarbon contaminated environments is gaining interest as an innovative approach for the stimulation of the microbial metabolism in anaerobic conditions. A lab-scale bieoelectrochemical reactor for groundwater treatment was operated under continuous flow conditions with phenol (25 mg/L) as a model contaminant. When the anode was poised at +200 mV (vs SHE) phenol was removed with a rate of 77±4 mg/(L d) and a current of 5.3±0.2 mA was produced. At the end of the experiment the bacterial and archaeal communities in the microbial inoculum (i.e. refinery wastewater), on the anode (i.e. graphite granules) and in the effluent were characterized by Next Generation Sequencing (NGS) of the 16S rRNA gene. NGS results showed the enrichment of the genus Geobacter on the graphite, suggesting its potential role in the bioelectrochemical removal of phenol.

Biome: root:Engineered:Bioreactor:Continuous culture
Temporal dynamics and diversity of Legionella community in cooling tower water

The persistence and abundance of Legionella species in man-made freshwater systems constitutes a public health concern. Cooling towers are the main source of legionellosis outbreaks. These outbreaks are mostly associated with L. pneumophila and its monitoring in freshwater environments is of high relevance. In this study, a developed Legionella genus-specific Illumina-based approach targeting the 16S rRNA gene was applied to a set of cooling tower water samples monthly sampled from January 2013 to December 2014 in order to provide accurate identification and precise detection and quantification of Legionella species, including the most clinically relevant L. pneumophila

Biome: root:Environmental:Aquatic
By taking three metagenomic approaches to reveal the microplankton communities from composition to functional properties in this study.

The Three Gorges Dam has significantly altered ecological and environmental conditions within the reservoir region, but how these changes affect bacterioplankton structure and function is unknown. Here, three widely accepted metagenomic tools were employed to study the impact of damming on the bacterioplankton community in the Xiangxi River. Our results indicated that bacterioplankton communities were both taxonomically and functionally different between backwater and riverine sites, which represent communities with and without direct dam effects, respectively. There were many more nitrogen cycling Betaproteobacteria (e.g., Limnohabitans), and a higher abundance of functional genes and KEGG orthology (KO) groups involved in nitrogen cycling in the riverine sites, suggesting a higher level of bacterial activity involved in generating more nitrogenous nutrients for the growth of phytoplankton. Additionally, the KO categories involved in carbon and sulfur metabolism, as well as most of the detected functional genes also showed clear backwater and riverine patterns. As expected, these diversity patterns all significantly correlated with environmental characteristics, confirming that the bacterioplankton communities in the Xiangxi River were really affected by environmental changes from the Three Gorges Dam. This study provides a first comparative metagenomic insight for evaluating the impacts of the large dam on microbial function.

Biome: root:Environmental:Aquatic:Freshwater:Lentic
BACTERIAL DIVERSITY AND SULFIDE REMOVAL IN AN INTERNAL SILICON MEMBRANE REACTOR

The objective of this study was to assess the feasibility of using an Internal Silicon Membrane Reactor (ISMR) to treat dissolved sulfide and to characterize its microbial community. The Internal Silicon Membrane Reactor (ISMR) has shown to be an effective system to eliminate sulfide produced in anaerobic reactors. Removal efficiencies of sulfide reached 96% in a combined anaerobic/micro-aerobic reactor and significant sulfate production did not occur. The oxygen transfer was strongly influenced by air pressure and flow. Pirosequencing analysis indicated different sulfide-oxidizing bacteria attached on to the membrane. The results also indicates a high similarity between the biomass deposited in the membrane wall and the biomass drawn from of the material support, that demonstrate the development of sulfide oxidizing bacteria in an anaerobic sludge under micro aerobic condition.

Biome: root:Engineered:Bioremediation:Persistent organic pollutants (POP)
Set Anode Potentials Affect the Electron Fluxes and Microbial Community Structure in Propionate-Fed Microbial Electrolysis Cells

The anode potentials in microbial electrolysis cells (MECs) influence the energy availability for the microbial growth, the microbial community structure and also the reactor performance. However, the stimulus of set anode potentials (SAPs) on the performances of MECs fed with a high concentration of propionate have not been demonstrated. Here, we examined the impact of various SAPs (-0.25, 0, and 0.25 V vs. SHE) on the reactors performance, electrons flux to various sinks, and the microbial community structure in a double chamber MECs fed with propionate (36mM). Electron balances and microbial fingerprinting showed that SAPs modulate the electron fluxes between the electrical current and CH4 and also affected the microbial community structure of a propionate fed MECs. Electrical current (49-71%) and CH4 (22.9-41%) was the largest electron sinks regardless of the potentials tested. However, 0 V indicated that higher electron fluxes to the electrical current (71±5%) and lower fraction to CH4 (22.9±1.2%). In contrast, more negative SAP (-0.25 V) had a lower percentage of the electrical current and there was a greater fraction of electron loss to CH4 (41.1±2%). Furthermore, open circuit (O.C) reactors had significantly higher CH4 (73±4%) than the SAP-MECs. A complete degradation of propionate (36mM) with no accumulation of it intermediates was observed in all the tested SAPs. Analysis of 16S r RNA gene indicated that more negative SAP (-0.25 V) showed a highly diverse communities the other potentials tested. Interestingly, in all the anode of SAPs dominated by G. sulfurreducens followed by Smithella spp. and Syntrophobacter sulfatereducens. While, the suspensions were predominated by the classic propionate fermenters namely S. sulfatereducens, Smithella spp. and Methanobacterium formicicum. Overall, these results provide new insights on the influence of SAPs of MECs fed with a high concentration of propionate.

Biome: root:Engineered:Bioreactor:Continuous culture
Daily cycle of bacterial active community structure

Microbial communities at high altitude ecosystem spring sites, are subjected along the day to extreme changes in irradiation and temperature. Herein, we determined the composition of actively transcribing bacteria from spring waters through 16S rRNA gene tag pyrosequencing (cDNA) experimentally exposed along the day (morning, noon and afternoon) to variable solar radiation and light quality, and evaluated their influence on nutrients recycling. Irradiation, temperature and nutrients rates of change were associated with changes in the active bacterial community structure, predominantly conformed by Cyanobacteria, Verrucomicrobia, Proteobacteria, and other 35 Phyla including also the recently described Candidate Phyla Radiation (e.g., Parcubacteria, Gracilibacteria, OP3, TM6, SR1). An increase of diversity was observed at noon when the highest irradiances were measured (3.3 -3.9 H', 1125 W m-2) compared to morning and afternoon (0.6-2.8 H'). These increase was associated with a decrease of Cyanobacteria and an enhancement of Proteobacteria and initially low frequently and rare bacteria phyla (<0.5% sequences contribution). UV radiation compared to full sun radiation indicates the presence of a higher number of stimulatory compared to inhibitory effects, including contrasting responses of some Orders, e.g., positive effects were found for Cyanobacteria, Rhodobacterales, Rhodospirillales, Bacteroidales; whereas negative effects for the orders Oceanospirillales, Fibrobacterales, Alteromonadales and Sphingobacteriales. Nutrient recycling was influenced by microbial composition changes, particularly for Cyanobacteria, nitrifying bacteria and Chlorobi. In total, our results indicate that phototrophic bacteria from high altitude aquatic ecosystems were affected but potentially resilient to the negative effect of high solar radiation influencing nutrient recycling in these ecosystems.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Molecular diversity patterns among various phytoplankton size-fractions in West Greenland in late summer

Arctic regions to date experience the most pronounced transformations due to global change. Current hypotheses propose an elevated impact of those environmental changes on the biodiversity, community composition and metabolic processes of species. Influence on ecosystem function and services, particular when invasive or toxigenic harmful species become dominant, can alter processes on smaller and larger scales. Our study focused on the comparison of molecular biodiversity of three planktonic size-fractions (micro-, nano-, picoplankton) in coastal waters of West Greenland and the correlation with environmental parameters. Molecular diversity was assessed via sequencing the 28S rRNA hypervariable D1/D2 region by parallel amplicon sequencing. We showed that biodiversity distribution within the area of Uummannaq Fjord, Vaigat Strait and Disko Bay differed markedly within and among size-fractions. In general, we observed a higher diversity within the picoplankton size fraction compared to the nano- and microplankton. Community composition of all three size fractions correlated to size, silicate and phosphate, chlorophyll a (chl a) and dinophysistoxin (DTX), but each size fraction community also correlated with other and different environmental parameters. We observed a more homogeneous community of the picoplankton across all stations compared to the bigger size classes, despite different environmental conditions of the sampling areas. This might suggest habitat occupation for larger organisms over plasticity, while smaller organisms compensate a lower potential plasticity with higher diversity. The presence of potential harmful algal bloom (HAB) species (such as Alexandrium fundyense, A. ostenfeldii) in the area points out the risk for this vulnerable ecosystem in a changing world.

Biome: root:Environmental:Aquatic:Marine:Coastal
Microbialite and microbial mats systems in lagoons, salt flats and Volcanoes of Andean South America Altiplane

High Andean Mountain lakes are a unique extreme environment all over the world since their locations are in high altitude saline deserts, largely influenced by volcanic activity. UV radiation, arsenic content, high salinity, and low dissolved oxygen content, together with extreme daily temperature fluctuations and oligotrophic conditions, shape up an environment that recreates the early earth and, even more, the extraterrestrial conditions. The discovery of living microbialites and microbial mats in 2009 has increased the interest in this area as an early earth counterpart. Since then, and up to now, we have started a prospection for this kind of environments in Argentina, Chile and Bolivia. In this study, we report our metagenomic WGS results from several of these unique environments

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Saline:Microbial mats
Comparison between metagenome sequencing using 16S spiking or MDA amplification

Bioinformatical research on viruses is still limited because of the low amounts of viral DNA that can be obtained for analysis. To overcome this limitation, DNA is often amplified with multiple displacement amplification (MDA), which causes an unavoidable bias. Here, we describe a DNA-spiking method to avoid the bias that is created when using amplification of DNA before metagenome sequencing. To obtain sufficient DNA for sequencing, a bacterial 16S rRNA gene was amplified and the obtained DNA was spiked to a DNA sample containing DNA from a bacteriophage population before sequencing using Ion Torrent technology. After sequencing, the 16S rRNA gene reads DNA was removed by mapping to the Silva database. The new DNA-spiking method was compared with the MDA technique.The new method provides a simple and inexpensive protocol with very low bias in sequencing of metagenomes for which low amounts of DNA are available.

Biome: root:Engineered:Modeled:Simulated communities (DNA mixture)
Genetic determinants of the gut microbiome in the TwinsUK cohort

Recent genetic studies in mice and humans have revealed intriguing genetic associations with the gut microbiome. Here we report a 16S rRNA-based analysis of the gut microbiome in 1,126 twin pairs, a subset of which we previously analyzed. Tripling the sample reduced the confidence intervals around heritability estimates and uncovered newly heritable taxa, many of which are validated in other studies. Repeat sampling of subjects showed heritable taxa to be temporally stable. A candidate gene approach uncovered associations between heritable taxa and genes related to diet, metabolism and olfaction. We replicate an association between Bifidobacterium and the lactase (LCT) gene region and identify an association between ALDH1L1 and SHA-98, suggesting a link between formate production and blood pressure. Additional genes detected are involved in barrier defense and self/non-self recognition. Our results indicate that diet sensing, metabolism, and immune defense are important drivers of human-microbiome co-evolution.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Bacterial Communiy Structures are Unique and Resilient in Full-Scale Bioenergy Systems

Anaerobic digestion is the most successful bioenergy technology worldwide with, at its core, undefined microbial communities that have poorly understood dynamics. Here, we investigated the relationships of bacterial community structure (>400,000 16S rRNA gene sequences for 112 samples) with function (i.e., bioreactor performance) and environment (i.e., operating conditions) in a yearlong monthly time series of nine full-scale bioreactor facilities treating brewery wastewater (>20,000 measurements). Each of the nine facilities had a unique community structure with an unprecedented level of stability. Using machine learning, we identified a small subset of operational taxonomic units (OTUs; 145 out of 4,962), which predicted the location of the facility of origin for almost every sample (96.4% accuracy). Of these 145 OTUs, syntrophic bacteria were systematically overrepresented, demonstrating that syntrophs rebounded following disturbances. This indicates that resilience, rather than dynamic competition, played an important role in maintaining the necessary syntrophic populations. In addition, we explained the observed phylogenetic differences between all samples based on a subset of environmental gradients (using constrained ordination), and found stronger relationships between community structure and its function rather than its environment. These relationships were strongest for two performance variables - methanogenic activity and substrate removal efficiency - both of which were also affected by microbial ecology because these variables were correlated with community evenness (at any given time) and variability in phylogenetic structure (over time), respectively. Thus, we quantified relationships between community structure and function, which opens the door to engineer communities with superior functions.

Biome: root:Engineered:Bioreactor:Continuous culture
Detection and quantification of Pseudomonas species, including P. aeruginosa, in cooling tower water using a genus-specific Illumina-based approach

Pseudomonas species are frequent inhabitants of freshwater environments and often colonisers of water supply networks via bioadhesion and biofilm formation. P. aeruginosa is the most characterized species of the genus and the most commonly associated to human disease, causing a wide variety of infections that have causality links with their presence in freshwater systems. Though several other Pseudomonas species are of ecological and health importance, little knowledge regarding environmental Pseudomonas species still exists. In the present study, an Illumina-based approach using Pseudomonas genus-specific primers and targeting the 16S rRNA gene was validated and applied to a set of freshwater samples, collected from a cooling tower system during two years.

Biome: root:Environmental:Aquatic:Freshwater
Bacterial community characterisation and pathogen profiling in a cooling tower system using an Illumina-based approach

The increasing level of human exposure to freshwater systems requires effective water quality monitoring and surveillance to reduce health risks linked to contaminated environments with pathogenic waterborne and water-based bacteria. Despite the considerable advantages of sequence-based molecular techniques, the usefulness and potential for implementation of next-generation sequencing in environmental research and routine environmental diagnostics has not be thoroughly evaluated and assessed. In this study, a Illumina MiSeq-based approach, targeting the 16S rRNA gene V4-V5 regions was applied to cooling tower water samples monthly collected from January 2013 to December 2014, in order to characterise the temporal dynamics and structure of the bacterial community as well as to detect the main potentially pathogenic bacterial genera.

Biome: root:Environmental:Aquatic:Freshwater
Bacterial Diversity of Activated Sludge from 14 Sewage Treatment Plants Revealed by 454 Pyrosequencing

Massively parallel 454 sequencing of hypervariable regions in rRNA genes was used to profile microbial communities from 15 activated sludge samples of 14 wastewater treatment plants (WWTP) from 4 countries.  Totally, 355641 effective reads were generated from these 15 samples. These reads were assigned into different taxonomies by using RDP classifier. Besides, Cluster analysis, PCA, colinearity analysis was also used to assess the beta-diversity among all these sludge samples.

Biome: root:Engineered:Wastewater:Activated Sludge
metagenome of the anaerobic digested sludge before and after long-term oxytetracycline exposure

Metagenome of the anaerobic digested sludge before and after long-term oxytetracycline exposure was revealed by high throughput illumina sequenceing. And, the mobilome of the anaerobic digested sludge before antibiotic exposure was compared with that after exposure.

Biome: root:Engineered:Wastewater:Water and sludge