SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Impact of a major inflow event on the composition and distribution of bacterioplankton communities in the Baltic Sea

Major Baltic inflow (MBI) events carry highly saline water from the North Sea to the central Baltic Sea and thereby affect both the environmental conditions and the biota in the Baltic's deeper layers. While bacterioplankton communities in the Baltic Sea are strongly structured by its salinity, how MBIs impact the composition and distribution of those communities is unknown. However, insights into this relationship were afforded by an exceptional MBI in 2014 that brought saline and oxygenated water into the basins of the central Baltic Sea. Following this event, we analyzed bacterioplankton community composition in the inflowing water and in the uplifted former bottom water at stations in the Western and central Baltic Sea that were reached by the MBI. Bacterial diversity data were compared with data on the respective communities obtained during a previous non-inflow situation involving the same locations. In contrast to the broad taxonomic changes in bacterial community composition that are generally associated with changes in salinity, significant changes following the 2014 MBI were mainly at the genus level. The relative similarity of the bacterial communities in the inflowing and uplifted waters as well as the results from an inflow-simulating numerical model indicated that the inflowing water did not originate directly from the North Sea but mostly from adjacent areas in the Baltic Sea. These findings further suggested that the inflow event led to a series of shifts in Baltic Sea water mass among the Baltic Sea basins and a gradual mixing of the water bodies. Dramatic changes in bacterial community composition between inflowing and uplifted waters did become visible when the bottom-water inflow reached the anoxic, sulfidic deep basins, resulting in an uplifting of the former anoxic bacterial community, dominated by the Epsilonproteobacterium Sulfurimonas spp., to water depths within the oxygenated layer. Our study of the impact of MBIs on bacterioplankton communities therefore highlights two relevant underlying mechanisms that impact the distribution and possibly also the activities of planktonic bacteria in the Baltic Sea: the successive dilution of inflowing North Sea with ambient waters and the uplifting of former bottom-water communities to higher water strata.

Biome: root:Environmental:Aquatic:Marine:Marginal Sea
A comprehensive analysis of the faecal microbiome and metabolome of Strongyloides stercoralis infected volunteers from a non-endemic area

A comprehensive analysis of the faecal microbiome and metabolome of Strongyloides stercoralis infected volunteers from a non-endemic area

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Infections by human gastrointestinal helminths are associated with changes in faecal microbiota diversity and composition

Investigations of the impact that patent infections by soil-transmitted gastrointestinal nematode parasites exert on the composition of the host gut commensal flora are attracting growing interest by the scientific community. However, information collected to date varies across experiments, and further studies are needed to identify consistent relationships between parasites and commensal microbial species. Here, we explore the qualitative and quantitative differences between the microbial community profiles of cohorts of human volunteers from Sri Lanka with patent infection by one or more parasitic nematode species (H+), as well as that of uninfected subjects (H-) and of volunteers who had been subjected to regular prophylactic anthelmintic treatment (Ht). High-throughput sequencing of the bacterial 16S rRNA gene, followed by bioinformatics and biostatistical analyses of sequence data revealed no significant differences in alpha diversity (Shannon) and richness between groups (P = 0.65, P = 0.13 respectively); however, beta diversity was significantly increased in H+ and Ht when individually compared to H-volunteers (P = 0.04). Among others, bacteria of the families Verrucomicrobiaceae and Enterobacteriaceae showed a trend towards increased abundance in H+, whereas the Leuconostocaceae and Bacteroidaceae showed a relative increase in H- and Ht respectively. Our findings add valuable knowledge to the vast, and yet little explored, research field of parasite – microbiota interactions and will provide a basis for the elucidation of the role such interactions play in pathogenic and immune-modulatory properties of parasitic nematodes in both human and animal hosts.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Pilot study to compare the effects of high carbohydrate and high fat diets on gut microbiome

Diet has been shown to affect microbiome, but effects of diet composition is less clear.We have shown that the relative content of protein, fat and carbohydrate in the diet is key to modulating calorie intake and affects metabolic changes. We wanted to explore the effects on gut microbiome.In this pilot study we selected 6 patients from a larger clinical trial currently underway.Each patient had detailed biometric and dietary data collected, then was changed to a carefully designed, isocaloric diet for 4 weeks.Prior to intervention, all 6 patients were on a normal omnivorous diet.3 patients were changed to an oral high carbohydrate (OHC) diet.3 patients were changed to an oral high fat (OHF) diet.Stool was collected at baseline (BL) and then a second final sample (FL) was collected after 4 weeks of diet change.Stool was stored immediately at 4 degrees, frozen within two hours of collection and stored at -80 degrees Celsius.DNA was extracted from the stool using a QIAGEN, AllPrep PowerFecal DNA/RNA kit.Illumina Sequencing was performed.Project: CAGRF18283Sample Preparation: Illumina TruSeq DNA NanoSequencing: HiSeq Paired End Cluster Kit v4 cBotReads were trimmed for adapters using Trimmomatic v 0.36

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Metagenomic data simulated to represent a complex microbial community

Metagenomic data simulated with grinder to represent a complex microbial community composed of 22 organisms with different relative abundances

Biome: root:Engineered:Bioreactor
Global surveillance of antimicrobial resistance - Batch June 2017

Global surveillance of antimicrobial resistance June 2017

Biome: root:Engineered:Wastewater
To determine whether there are differences in the intestinal microbiome between treatment-naïve Multiple Sclerosis (MS) subjects and controls, and between Caucasian (CA), Hispanic (HA), and African American (AA) MS subjects.

In this study focused on newly diagnosed treatment-naïve MS patients, we found increased relative abundance of Clostridia in all three patient cohorts compared to controls, with consistent and more detailed findings from the metagenomic analyses.  This work provides a candidate for further study for a role in early MS, at the least as a biomarker for the disease.  In addition, we found differences between the microbiomes of ethnic subgroups of MS patients that merit further study.

Biome: root:Host-associated:Human:Digestive system:Intestine
Human_infections_with_the_whipworm__Trichuris_trichiura__are_not_associated_with_alterations_in_the_faecal_microbiota_

Materials and Methods: We carried out the study in two rural communities 
in Esmeraldas Province, Ecuador. School-age children were screened for 
the presence of STH infections and allocated to one of 3 groups: 
uninfected, T. trichiura only, and mixed infections with T. trichiura 
and Ascaris lumbricoides. A sample of uninfected children and those with 
T. trichiura infections only were treated with albendazole (800 mg/day 
for 3 days) and ivermectin (single dose of 200 ug/kg), and stool samples 
were collected 3 weeks post-treatment. Bacterial DNA was extracted using 
the FastDNA Spin kit for soil, and bacterial community profiles were 
studied by 454 pyrosequencing of 16S rRNA genes. This generated 999,796 
sequences, which were processed and analysed using mothur.

Results: Microbiota analyses were done using stool samples from 97 
children aged 8-14 years of whom 30 were not infected, 17 were infected 
with T. trichiura alone, and 50 had mixed infections with both T. 
trichiura and A. lumbricoides. Post-treatment samples were analyzed for 
14 of the 17 children initially infected with T. trichiura alone and 21 
of 30 uninfected children. Treatment resulted in 100% cure of STH 
infections. Comparisons of the microbiota at different taxonomic levels 
showed no statistically significant differences in composition between 
uninfected children and those with T. trichiura infections. A surprising 
finding was a decreased proportional abundance of a few bacterial genera 
from the clostridia class of Firmicutes, in tandem with a reduced 
overall bacterial diversity, among children with mixed infections 
compared to either uninfected children or those with T. trichiura 
infections only, indicating a specific effect of A. lumbricoides 
infection on intestinal microbiota.  Anthelmintic treatment of children 
with T. trichiura did not appear to alter composition of faecal microbiota.

Discussion: This is the first molecular study to analyse the effect of 
whipworm infection on the human intestinal microbiota. Our data indicate 
that T. trichiura infections alone have no effect on the faecal 
microbiota of children living in endemic communities, but that A. 
lumbricoides colonisation might be associated with a disturbed 
microbiota. Our results also catalogue the microbiota that is present in 
rural Ecuadorians, and indicate that there are differences between this 
cohort and individuals from more urban, industrialised societies.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Marine sediment metagenome ICM_GMS

Microbial Census of Marine Methane Seeps: Initial Results

Biome: root:Environmental:Aquatic:Marine:Cold seeps
Marine sediment metagenome ICM_NZS

Physical and Microbial Characterisation of Marine Sediment from Two Contrasting Oceanographic Areas in New Zealand.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
Marine metagenome ICM_GPS

Global Protistan Survey: Comparison of High-Throughput ''454'' Pyrosequencing vs. ''Deep'' Sanger Sequencing of 18S rRNA genes in Arctic (Chukchi Sea) and Antarctic (Ross Sea) ecosystems.

Biome: root:Environmental:Aquatic:Marine
Bacterial diversity in the South Adriatic Sea during winter of 2016

Bacteria represent the most important microorganisms in the world oceans comprising up to 75% of the total biomass at surface and playing fundamental processes for biogeochemistry. Along the water column, they are useful markers of the trophic state of water masses, therefore representing useful ecological indicators in the surveyed areas. In this study in the southern Adriatic Sea bacteria were quantified by flow cytometry and their diversity assessed by high-throughput sequencing (HTS). In addition, the most represented bacterial groups were quantified by qPCR. The samples were collected from the surface to the seabed, at a total of 16 different depths at four stations in the southern Adriatic Sea, during the late winter BIOTA (BIO-Tracing Adriatic water masses) cruise conducted in 2016. The investigated area showed an unusual circulation characterized by a mixed layer down to 200 m, which differed from the usual winter convection conditions, typical of middle-altitude ecosystems and important for the seasonal picoplankton dynamics in the South Adriatic Sea. Heterotrophic bacteria were separated into HNA (relative High Nucleic Acid content) and LNA (Low Nucleic Acid content) subpopulations with abundances up to 1.8 x 105 and 8.8 x 105 cells/mL, respectively. HNA populations dominated at offshore stations reaching their maximum at depths below the euphotic zone. The bacterial community was dominated by Alphaproteobacteria accounting for > 40% of the total, represented by the SAR11 clade (90.84%), followed by Marinimicrobia (18% of the total), mainly represented by clade SAR406 (8.44%). However, distinctive bacterial groups were found in euphotic layer (Bacteroidetes and Actinobacteria) and aphotic layer samples (Deltaproteobacteria, Marinimicrobia, Chloroflexi, Acidobacteria and Planctomycetes). qPCR assays confirmed HTC results with abundances of targeted bacterial groups found to vary between different sampling points and sampling depths and values ranging from 8.7 x 103 to 9.13 x 105 copy number/mL for Alphaproteobacteria, from 1.44 x 104 to 5.11 x 105 copy number/mL for Gammaproteobacteria and from 1.8 x 103 to 2.4 x 105 copy number/mL for Bacteriodetes. For all targeted taxa higher abundances were found in the euphotic than in the aphotic zone. Introducing of different methodological approaches to the study allowed us to get better insight into the structure of the bacterial assemblages in the South Adriatic.

Biome: root:Environmental:Aquatic:Marine:Marginal Sea
MiSeq 16S rRNA gene (prokaryotic 16S rRNA gene) sequences of 16 SCS sediments

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

Biome: root:Environmental:Aquatic:Marine:Sediment
Distribution and composition of thiotrophic mats in the hypoxic zone of the Black Sea (150-170m water depth, Crimea margin)

Distribution and composition of thiotrophic mats were analyzed using high-resolution biogeochemical and community fingerprinting at the outer shelf of the Northwestern Black Sea. Dives with the submersible JAGO showed accumulations of organic matter forming dark patches on the seafloor, which were covered by mat-forming whitish microbial filaments. Where the Black Sea chemocline met the seabed (between 150 - 170 m), these mats covered between 25 to 55 % of the seafloor, and appeared to form a belt of 3 km width. The mats were composed of Beggiatoa-like large filamentous sulfur bacteria based on 16S rRNA sequences from the mat. The microbial community under the mats was enriched with taxa affiliated with polymer degrading, fermenting and sulfate reducing microorganisms. Under the mats, higher organic matter accumulation, as well as higher remineralization and sulfate reduction rates were measured compared to outside the mat. Mat-covered and mat-free sediments showed similar degradability of the bulk organic matter pool, suggesting that the higher sulfide fluxes and subsequent development of the thiotrophic mats in the patches are consequences of the accumulation of organic matter rather than its qualitative composition. Our observations suggest that the key factors for the distribution of thiotrophic mat-forming communities near to the Crimean shelf break are (1) hypoxic conditions repressing grazers and favoring thiotrophic bacteria and (2) the specific seafloor topography that enhances the accumulation of labile organic matter.

Biome: root:Environmental:Aquatic:Marine:Sediment
16S rRNA metagenomic investigation of arsenotrophic bacteriome of ground water and soil from arsenic-prone area of Bangladesh

In order to characterize the microbial biodiversity of arsenic contaminated water and surrounding soil a metagenomic approach by sequencing six hypervariable regions of 16S rRNA gene has been performed.

Biome: root:Environmental:Terrestrial:Soil
The effect of lifetime nutrition on the rumen microbiome and how this effects the lifetime performance and meat quality of aberdeen angus cattle

Aberdeen angus cattle have been raised on diets to promote different growth speeds; concentrate only diet for fast growth, high abundance of high quality forage (perennial ryegrass) for medium growth and restricted low quality forage grazing for slow growth. Once cattle had reached pre determined fat grade they were slaughtered and the meat was analysed for factors including fatty acid content, taste and shelf life. Alongside this rumen fluid samples were taken at slaughter for metagenomic analysis using full metagenome shotgun sequencing. This metagenome data will be compared with the meat analysis and other performance data taken throughout the experiment to assess the effect of nutrition on the rumen microbiome and how that effects the phenotype of the animal.

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Diversity and composition of sediment microbial assemblages in an Atlantic port environment

Under the framework of the PORTONOVO cooperation which endeavors to enhance monitoring of environmental quality in ports along the Atlantic coast of Europe, we assessed microbial diversity and composition in a Portuguese port environment (Ria de Aveiro). Samples were collected in five locations: two within the port, two along the channel adjacent to the port and one in a relatively undisturbed reference location. Bacterial composition differed significantly among locations with the most pronounced difference being recorded between samples from the reference site versus both port locations. Samples taken from the channel adjacent to the port were intermediate in composition. The port samples were, furthermore, associated with higher values of nitrates, phosphates and total organic carbon; abundant bacterial OTU's (= 50 sequences) were also much more prevalent. Dominance as indicated by the relative abundance of the most abundant OTU was also pronounced in samples from port locations. Port and channel locations were associated with higher relative abundances of Actinobacteria, Deltaproteobacteria (particularly Desulfobacterales) whereas non-port locations had higher relative abundances of Flavobacteria and Rhodobacterales. Our results indicate that the port environment has a pronounced effect on bacterial composition, with sediment from areas under intense port activity displaying a dominance of the Desulfobacterales order.

Biome: root:Environmental:Aquatic:Marine:Sediment
Bacterial communities in sandy sediment at submarine volcanic vents off Panarea Island (Italy)

Benthic bacterial communities composition at submarine natural CO2 vents were investigated to
            assess the effect of CO2 leakage and consequent seawater acidification on benthic marine microbial
            assemblages. Sandy sediment samples were collected off Basiluzzo Islet (Panarea Island, Italy) both at CO2
            venting areas and at CO2 not impacted area, and DNA was extracted from two different sediment layers (0-2 cm
            and 4-6 cm). Bacterial communities was described using 454-Massively Parallel Tag Sequencing (454-MPTS).

Biome: root:Environmental:Aquatic:Marine:Sediment
Habitat and host related variation in sponge bacterial communities in Indonesian coral reefs and marine lakes

Marine lakes are very rare and unique global ecosystems. Isolated from the surrounding marine habitat, many now house numerous endemic species. In the present study, we compare the bacterial communities of two sponge species, Suberites diversicolor and Cinachyrella australiensis, found inside and outside the lakes. Both species housed unique bacterial assemblages, dominated by Proteobacteria and with high concentrations of Cyanobacteria (the most abundant taxon related to Synechococcus) in one of the marine lakes. Other bacterial phyla were much less prevalent or even completely absent from both species. At the class level, Alphaproteobacteria dominated the communities of Suberites whereas Gammaproteobacteria dominated communities of C. australiensis. There was no discernible difference between bacterial communities hosted by S. diversicolor inside and outside the lake. The bacterial community of this species was, furthermore, dominated by three very closely-related Alphaproteobacterial taxa that together made up 64% of all sequences. C. australiensis, in contrast, hosted markedly different bacterial communities inside and outside the lakes with very few shared abundant taxa. Dominant OTU's in C. australiensis were closely-related to taxa known to be involved in nitrogen fixation, ammonia-oxidation and sulphur-oxidation, an indication that the sponge may be an important component of nutrient cycling inside and outside of marine lakes.

Biome: root:Environmental:Aquatic:Marine:Brackish
The ecology of microbial communities associated with Macrosystis pyrifera

Bacteria control major nutrient cycles and directly influence plant, animal and human health. However, we know relatively little about the forces shaping their large-scale ecological ranges, community assembly and stability over time. As for many living surfaces in the marine environment, the epiphytic bacterial biofilm communities on macro algae such as Macrocystis pyrifera, and the mechanisms that drive their assembly are poorly understood, apart from the magnitude and diversity of their composition. This biodiversity is not lacking for possible explanations, from colonization to dispersal, succession and persistence by competition. High throughput sequencing has contributed to a variety of potential mechanisms being proposed to characterize the assembly of these microbial communities. We used 454 parallel tag pyrosequencing of the 16s rna gene to better explore the diversity, stability and specificity of the microbial communities associated with the dominant kelp species in Monterey Bay. We also compared the kelp-associated communities with those present in the surrounding seawater to assess the influence of environmental conditions. Our results reveal patterns in the distribution of individual bacterial members at multiple levels of phylogenetic resolution within and around a M. pyrifera ecosystem suggesting the lack of a proposed stable core community of species associated with marine macro algae across space and time (Tujula et al., 2010). M. pyrifera harbors species-specific and temporally adapted epiphytic bacterial biofilms on their surfaces, and the most cosmopolitan taxa are also the most abundant in individual assemblages. Since several of the kelp-specific bacteria identified were highly similar to other bacteria known to either avoid subsequent colonization by eukaryotic larvae or to exhibit antibacterial activities, host-specific bacterial associations might play an important role for M. pyrifera. This study reports on the first published in-depth assessment of the diversity and phylogenetic profile of the bacterial communities associated with M. pyrifera.

Biome: root:Host-associated:Algae:Brown Algae
CCA_pathobiome

Coralline algae are major benthic calcifiers that play crucial roles in coral reef ecosystems. In this study, we provide data from the first investigation of the bacterial communities associated with healthy and diseased corallines. We target two diseases?Coralline White Band Syndrome (CWBS) and Coralline White Patch Disease (CWPD)?and show that they are associated with different pathobiomes, which indicates different disease causations.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
Culture-enriched human gut microbiomes reveal core and accessory resistance genes

In this study, we used culture enrichment of stools to reveal lower abundance bacteria by high-throughput sequencing. We sequenced fecal bacteria growing under four culture conditions from 24 individuals, before and after use of antibiotics (day 0 and day 7). Overall, 187 species of bacteria had an assembly size greater than 1 million nucleotides, 67 species achieved it only under culture conditions and 22 only in culture-independent fecal microbiomes.The four culture conditions are : (i) MCDA maximum enrichment broth anaerobic culture (MEB-ANA)(ii) MCDA maximum enrichment broth aerobic culture (air enriched with 5% CO2) (MEB-CO2), (iii) MCDA anaerobic culture in presence of 32µg/ml cefoxitin (FOX-ANA)(iv) MCDA aerobic (with 5% CO2) culture in presence of 32µg/ml cefoxitin (FOX-CO2)

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