SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Strain-Level Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis

Cystic fibrosis (CF) is a life-threatening genetic disorder accompanied by chronic lung infections and respiratory complications that arise from the accumulation of viscous mucus in the airways. In the clinic, cultures of microbes isolated from the coughed-up lung sputum are used to decide on the CF management strategy. The approach, however, frequently misses non-typical microbes and provides limited strain-level resolution. In the study, we applied an unbiased sequencing approach to lung sputum samples in order to gain a more complete picture of the lung microbiome. We explored changes in the lung microbiome composition over time, particularly during exacerbations and antibiotic treatments. Moreover, we distinguished between evolution of internal strains and introduction of external strains from the environment. To do this, we followed four CF patients displaying extreme clinical phenotypes over the course of two years. During each exacerbation or routine clinical visit, the lung sputum from these patients was taken for shotgun sequencing. Reads not mapping to the host were subjected to assembly, taxonomic profiling, strain typing, and variant analysis. Sequencing revealed the presence of several microbes missed by culture, particularly anaerobes. It allowed us to identify dominant strains of abundant microbes, and to correct mistakes in taxonomic assignment from culture. Finally, after analysing variation on the genome level, we describe multiple events such as a battle for dominance between multiple strains of Pseudomonas aeruginosa in the same patient. This study provides a first insight into the advantages of assessing the complete lung microbiome over time.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Microbiome of two predominant seagrass species of the Kenyan coast, Enhalus acoroides and Thalassodendron ciliatum

Background. Metagenomics studies have reported on the complexity of microbiomes associated with seagrass and can provide critical insights into the sustainable use and conservation of seagrasses. Recent conservation activities in Kenya focused mainly on coral reefs and mangrove forests with little direct action taken to conserve seagrass meadows. Pollution, over-exploitation of marine resources and minimal efforts towards enforcement of conservation laws of marine environments, have caused degradation and defoliation of seagrass habitats. Little is known about the microbes associated with seagrass species in Kenya and this study aimed to characterize the genetic diversity of the microbiomes of two prominent seagrass species, Enhalus acoroides and T. ciliatum, which is the most commonly occurring species.Methods. Replicate microbiome samples were collected from leaves, roots, sediment and water columns associated with two seagrass species from two sites on the Kenyan coast. The microbial communities of the samples were characterized and compared using 16S ribosomal RNA gene PCR and sequencing. Microbiome features including diversity and taxonomic composition were used to compare within and between sample types and sites.Results. Leaf samples from both E. acoroides and T. ciliatum had significantly different microbial communities comparted to root and sediment samples, revealing a diversity gradient with lowest diversity in water samples and highest in sediment. There were no significant variation in seagrass microbial composition associated with leaf and rhizosphere microbiomes of either E. acoroides or T. ciliatum. However, we did see a difference between water samples associated with each seagrass species.Discussion.This study of the microbial microbiomes associated with the sediments, roots, leaves and surrounding water of E. acoroides and T. ciliatum, included a limited number of samples from a small geographic area, providing a valuable first assessment of the microbial diversity of seagrass beds on the Kenyan coast. We found no significant differences between the plant-associated bacterial communities of the two-seagrass species investigated. Significant differences however, were observed amongst leaf-, root-, sediment- and water-associated bacterial communities. This work will contribute to understanding the dynamic environment of seagrass beds and will contribute to helping conserving and re-establishing seagrass beds degraded by due to anthropogenic activities.

Biome: root:Host-associated:Plants
Microorganisms related to Ethanol fermentation

The aim of this study is to identify, by metabarcoding approaches, the microorganisms of a ethanol fermentation industry.

Biome: root:Engineered:Industrial production
Metagenomic Analysis of the Marine Sponge, Cinachyrella keukenthali: Insights into an Emerging Model Sponge

Cinachyrella keukenthali is quickly emerging as a model sponge. Its small size makes it ideal for laboratory sized aquaria and long-term experiments. It is also on the Global Invertebrate Genome Alliance's priority list for genome sequencing. Other experiments have also included a focused amplicon sequencing experiment wherein, two subtypes of Cinachyrella keukenthali may be present in the environment based on microbiome results and some of the ongoing efforts of the global sponge microbiome project. What is poorly understood is the functional potential of the sponge microbiota. We analysed two metagenomes of C. keukenthali to determine non-PCR biased taxonomic makeup, functional potential, metabonomic analysis, and an early look into the microeukaryotes that might be present in the sponge

Biome: root:Host-associated:Porifera
Microbial diversity in four Mediterranean irciniid sponges

The examined host species, all collected from Crete, Greece, are Ircinia fasciculata, I. oros, I. variabilis, and Sarcotragus spinosulus. In this study we have tried to answer some specific questions such as: a) Is there a host species specific footprint on microbial communities, b) if there is an East versus West Mediterranean footprint, c) if there are similarities or differences on the composition of Ircinia species and non-Ircinia species (species specificity, sponge specificity) and finally whether there is a tissue specific patterning effect of the symbiotic microbial communities of sponges under study

Biome: root:Environmental:Aquatic:Marine:Coastal
Bacterial ecology of sponges from Irish Waters

The bacterial communities associated with the marine sponges Raspailia ramosa and Stelligera stuposa, collected from Irish Waters, were examined through 454 sequencing and analysis of the V1-V3 region of the 16S genes amplified from sponge metagenomic DNA

Biome: root:Environmental:Aquatic:Marine
A metagenetic approach for revealing community structure of marine planktonic copepods using Illumina MiSeq

Metagenetic approach is rapidly developing method for revealing community structure from bulk environmental samples. Marine planktonic copepods are diverse and abundant groups in the marine pelagic environments, and the metagenetic method using Roche 454 was constructed for copepods. However, Illumina MiSeq, which can produce more than ten times as many sequence reads as Roche 454, has been getting common sequencing platform. Here, we re-evaluated metagenetic method approach for revealing community structure of marine planktonic copepods using Illumina MiSeq. Because Illumina MiSeq can produce much more sequence reads, the developed method would be helpful for monitoring copepod community and dietary study in the future.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Bacteria of the genus Endozoicomonas dominate the microbial communities of the Mediterranean gorgonian soft coral Eunicella cavolini

Forming dense beds that provide the structural basis of a distinct ecosystem, the gorgonian Eunicella cavolini (Octocorallia) is an important species in the Mediterranean Sea. Despite the importance and prevalence of this temperate gorgonian, little is known about its microbial assemblage although bacteria are well known to be important to hard and soft coral functioning. Here, we used massively parallel pyrosequencing of 16S rRNA genes to determine the composition and relative abundances of bacteria associated with E. cavolini collected from different depths at a site on the French Mediterranean coast. We found that whereas the bacterial assemblages of E. cavolini were distinct and less diverse than those of the surrounding water column, the water depth did not affect the bacterial assemblages of this gorgonian. Our data show that E. cavolini's microbiome contains only a few shared species and that it is highly dominated by bacteria from the genus Endozoicomonas, a gamma-Proteobacteria that is frequently found to associate with marine invertebrates.

Biome: root:Environmental:Aquatic:Marine
Bacterial communities in sediments of a boreal stream

Here we study the  bacterial communities in sediments of a boreal stream. Bacterial communities were studied by NGS (454 pyroseq) of bacterial 16S rRNA, nirK, nirS and nosZ genes.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
Fe3+ and Mn4+ - induced changes in microbial communities of boreal lake sediments

Here we study the structure of bacterial and archaeal communities in sediments of two boreal lakes (littoral site in one lake and profundal site in another lake) . We specifically focused on community changes induced by increased availability of Fe3+ and Mn4+, which were studied by laboratory incubation of sediment samples collected from the profundal site. Microbial communities were studied by NGS (Ion Torrent) of bacterial and archaeal 16S rRNA genes as well as archaeal mcrA genes and mcrA-transcripts.

Biome: root:Environmental:Aquatic:Sediment
PCE/TCE dechlorinating microbial community and dehalogenase genes from Wonju Stream, South Korea

Groundwater at an industrial complex in Wonju remains contaminated with TCE despite several attempts at remediation over the last 15 years. Since the microbial dechlorination intermediates cis-DCE and VC were detected in the down-stream groundwater, we investigated whether the indigenous microbial communities could convert chloroethenes to ethene making bioremediation potentially feasible. Pyrosequencing of the 16S rRNA genes showed that Geobacter, Desulfuromonas, and Dehalococcoides populations grew significantly during the time PCE and TCE were converted to ethene. Most 16S rRNA sequences of Dehalococcoides spp. were phylogenetically close to known Dehalococcoides sp. strains, however about 10% of sequences were quite distant from the previously characterized Dehalococcoides sp. (97% or less sequence identity). Bellininea and Longilinea populations, which belong to Chloroflexi, also grew during the dechlorination phase.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
Marine sediment metagenome ICM_CRS

Diversity and structure of the microbial community in tropical coral reef sediments.

Biome: root:Environmental:Aquatic:Marine:Sediment
Deep sequencing of a DMSP-degrading gene (dmdA) in a coastal bacterioplankton community

Ten primer pairs targeting environmental clades of the dimethylsulfoniopropionate (DMSP) demethylase protein, DmdA, were designed using an iterative bioinformatic approach that took advantage of >1700 dmdA sequences captured in marine metagenomic datasets.  Using the bioinformatically-optimized primer pairs, dmdA genes were amplified from free-living coastal bacterioplankton samples and sequenced using 454 technology.  An average of 6,400 amplicons per primer pair represented almost 800 clusters of environmental dmdA sequences, with clusters defined conservatively at >90% nucleotide sequence identity (~95% protein identity).  Systematic comparisons of primer performance showed that degenerate and inosine-based primers did not perform better than specific primer sets in retrieving dmdA diversity, and sometimes captured a lower diversity of sequences from the same DNA sample.  The specific primer sets were used to compare dmdA diversity in free-living versus particle-associated bacteria in southeastern U.S. coastal waters.  Hundreds of different dmdA clusters were found in both size fractions, with Roseobacter-like and SAR11-like sequences dominating both. The free-living fraction had a higher diversity of dmdA clusters overall, though clusters retrieved by a given primer set were largely shared (52-88%) across the two size fractions, and most sequences were affiliated with these shared clusters (~90%). Despite evidence from 16S rRNA-based taxonomic surveys that free-living bacterioplankton are a considerably less diverse subset of particle-associated bacteria at this site, this seems not to be the case for a widespread bacterial gene mediating sulfur transformations.

Biome: root:Environmental:Aquatic:Marine
Methanogens and iron-reducing bacteria are major contributors to mercury methylation in boreal lake sediments

Methylmercury is a potent human neurotoxin easily biomagnified in aquatic food webs. Anaerobic microorganisms containing the hgcA gene potentially mediate the formation of methylmercury in natural environments, but the diversity of microbial mercury methylating communities in the environment remains largely unexplored. The diversity of mercury methylating microbial communities in boreal lake sediments, encompassing a wide range of mercury methylation rates, was characterized using barcoded amplification and high throughput sequencing of 16S rRNA and hgcA genes. Previously, most studies in aquatic ecosystems have implicated sulphate-reducing bacteria as the main mercury methylators. Here we demonstrate that Methanomicrobiales contribute significantly to the hgcA gene pool in boreal lake sediments. Experimental mercury isotope tracer incubations confirmed that, while sulphate-reducers contribute to mercury methylation, methanogens and iron reducers are also quantitatively important for the process. Our results change the way we perceive the local and global diversity of mercury methylating microbial communities in boreal lake sediments and call for further studies on the environmental factors regulating mercury methylation.

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
Intergenerational Lizard Lounges do not Explain Variation in the Gut Microbiomes of Green Iguanas

These samples represent the hindgut swabbings of 76 Green Iguanas (66 hatchlings, three subadults, seven adults), with hatchlings from nine sites (Gamboa, Panama and eight sites on or around Barro Colorado Island, Panama). We included an equal number of hatchlings from each site when possible. Hatchling social behavior (i.e., size of group, proximity to others) was observed haphazardly for individuals for about 60 days post-emergence over two years. (Adults and subadults were sampled and included whenever possible.) We primarily included samples taken about 4-6 weeks into the season for direct comparisons across sites and social levels. We have multiple samples (mean 3 per lizard) for 12 hatchlings spanning several days to several weeks between samples.

Biome: root:Host-associated:Reptile
Diamante Lake viral metagenome

Diamante Lake, located inside the Galan Volcano crater and placed at 4589m above sea level (coordinates: 26°00'51.04"S , 67°01'46.42"O), presents multiple extreme conditions that include: High UV radiation, salinity and arsenic, low oxygen pressure and a hydrothermal vent input. Red biofilm samples (mixed with sediments) from Diamante Lake were resuspended in PBS, cleared by centrifugation, and viral particles were purified using a CsCl gradient and ultracentrifugation. The total DNA of the purified viral fraction was then extracted using a Roche Viral DNA purification kit. Sequencing libraries were prepared using the Nextera library preparation kit from Promega and sequenced at 2x250bp using a Illumina MiSeq machine.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
Severino orchard metagenome

The total DNA sample from Severino orchard was extracted using a MoBio Powersoil DNA Isolation Kit and sequenced at 2x250bp using a Illumina MiSeq machine, to prepare a Metagenomic Shotgun Library.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
Yucra orchard metagenome

The total DNA sample from Yucra orchard was extracted using a MoBio Powersoil DNA Isolation Kit and sequenced at 2x250bp using a Illumina MiSeq machine, to prepare a Metagenomic Shotgun Library.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
Metagenomics of Ojo de Campo

Water samples from Ojo de Campo Lake were sequenced and analyzed

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
Metagenomics of Pozo Bravo microbial mats

Microbial mats from Pozo Bravo Lake were sequenced and analyzed

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
Diamante Lake Metagenome

Diamante Lake, located inside the Galan Volcano crater and placed at 4589m above sea level (coordinates: 26°00'51.04"S , 67°01'46.42"O), presents multiple extreme conditions that include: High UV radiation, salinity and arsenic, low oxygen pressure and a hydrothermal vent input. Total DNA from Diamante Lake Red Biofilm was extracted using a Fast Spin Kit for Soil (MP Biomedicals) and sheared by sonication with a target fragment size of ~ 400 bp. DNA fragment distribution was confirmed in a Fragment Analyzer (Advanced Analytical) and libraries were constructed using Illumina TruSeq DNA kit 2x300 bp as per manufacturer's instructions. Libraries were multiplexed and ran in a Illumina MiSeq machine.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
Metagenomics of Brava and Tebenquiche lakes microbial mats

Atacama region in Chile is one of the most arid locations in the world. Extreme conditions in the area include: high UV irradiation, hypersalinity, drastic temperature changes, and desiccation. Hypersaline lakes can be found in this environment, and therein, bacterial communities thrive in microbial mats and other structures. WGS metagenomics allows to analyze the genes in the environment and infer functional and taxonomic diversity, and also their influence in the biogeochemical setting. In the datasets from this project, two microbial mats from lakes Brava and Tebenquiche, in Atacama region in Chile, were analyzed.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Saline:Microbial mats
Methane and dissolved organic carbon fueled microbial loop supports a tropical subterranean estuary ecosystem

Here we demonstrate that a microbial loop shuttles CH4 and DOC to higher trophic levels of the anchialine food web in the Yucatan Peninsula (Mexico). Methane and DOC production and consumption within the coastal groundwater correspond with a microbial community capable of methanotrophy, heterotrophy and chemoautotrophy, based on characterization by 16S rRNA amplicon sequencing and respiratory quinone composition. This study reveals a heretofore unrecognized subterranean methane sink and contribute to our understanding of the carbon cycle and ecosystem function of karst subterranean estuaries.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Genetic potential for pentachlorophenol degradation at historically contaminated groundwater sites

Novel primers for pcpB  allowed us for the first time to investigate the genetic potential for degradation of the priority pollutant pentachlorophenol (PCP) in situ. We assessed whether pcpB is detectable at chlorophenol-polluted groundwater sediments at two sites, and if its abundance reflects differences in PCP concentration. We also sought correlations between the abundance and diversity of pcpB and sphingomonads that might indicate host specificity. pcpB was highly abundant, with copy numbers of up to 7% of bacterial 16S rRNA gene copies, and its relative abundance was linked to spatial or temporal differences in groundwater PCP concentration at two historically polluted sites, indicating ecological relevance of the pathway in situ. pcpB abundance was associated with sphingomonad abundance, but independent of sphingomonad community composition. This provides the first culture-independent support for widespread horizontal transfer of PCP degradation potential among sphingomonads in chlorophenol-polluted groundwaters.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
Microbial community response on waste water discharge in recipient freshwater sediments

In this study, we examined how nitrified wastewater affects the microbiology of boreal lakes sediments. Microbial community compositions were assessed with next generation sequencing of the 16S rRNA gene

Biome: root:Environmental:Aquatic:Sediment
Novel Biphenyl Oxidizing Bacteria and Dioxygenase Genes from a Korean Tidal Mudflat

Gene-targeted FLX titanium pyrosequencing integrated with 13C-stable isotope probing (SIP) revealed that tidal mudflat sediments harbor for novel aerobic biphenyl degradative bacteria and aromatic ring hydroxylating dioxygenases (ARHD). Known terrestrial biphenyl oxidizing bacteria and dioxygenase genes were rare in 13C-biphenyl enriched bacterial community. Instead, more than 80% of the detected ARHD genes are not in the public databases.

Biome: root:Environmental:Aquatic:Marine:Wetlands:Sediment
Stratification of anaerobic methanotrophs in cold-seep sediments

Methane seepages typically harbor communities of anaerobic methane oxidizers (ANME), however knowledge about fine-scale vertical variation of ANME in response to geochemical gradients is limited. Here we investigate microbial communities in sediments at two different locations at thge Nyegga field; (1) a push-core below a white microbial mat in the G11 pockmark, and (2) a Gravity-core at CNO3. Both experiments were analysed using 16S rRNA gene tag pyrosequencing and real time quantitative PCR.

Biome: root:Environmental:Aquatic:Marine:Sediment
MiSeq 16S rRNA gene (prokaryotic 16S rRNA gene) sequences of 33 Mai Po sediments, including 18 samples from winter and 15 samples from summer

DNA from 33 Mai Po sediments have been extracted and amplified by 515F/909R primer pairs (for prokaryotic 16S rRNA gene). The prokaryotic communities of these 33 samples were obtained.

Biome: root:Environmental:Aquatic:Marine:Wetlands:Sediment
MiSeq 16S rRNA gene (archaeal 16S rRNA gene) sequences of 33 Mai Po sediments, including 18 samples from winter and 15 samples from summer

DNA from 33 Mai Po sediments have been extracted and amplified by 21f/958r & Arch347F/Arch806R primer pairs (for archaeal 16S rRNA gene). The archaeal communities of these 33 samples were obtained.

Biome: root:Environmental:Aquatic:Marine:Wetlands:Sediment