SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Bacterial composition and survival on Sahara dust particles transported to the European Alps

The Sahara Desert is the primary source of wind-blown biological and mineral particles (aerosols) on Earth, 10% of which arrive to Europe. Aerosols that are deposited on high alpine snowfields in freezing conditions are well preserved and facilitate downstream biological analyses. As little is known about the structure and viability of bacteria transported during Saharan dust events (SDEs), the goal of this study was to characterize SDE-associated bacteria in snow using an interdisciplinary approach. We collected samples from a snow profile at the Jungfraujoch (Swiss Alps; 3621 m asl), where the presence of distinct ochre Sahara dust layers (SD-layers) could be ascribed to two SDEs reported in February and May 2014. Backward trajectories, physicochemical analyses of the snow, and dust particle concentrations of distinct geochemical compositions permitted us to determine the origin of the SDEs. Bacterial community structures were assessed using high throughput sequencing; distinct differences in bacterial community structures and metabolic activity associated with SD-layers as compared to clean snow layers were observed. Most striking was the exclusive presence in the SD-layers of bacteria that are adapted to hostile environments, and are hence well suited to survive the harsh conditions of long-distance airborne transport.

Biome: root:Environmental:Aquatic:Freshwater:Ice
Expression of the blood-group-related gene B4galnt2 alters susceptibility to Salmonella infection

Glycans play important roles in host-microbe interactions. Tissue-specific expression patterns of the blood group glycosyltransferase β-1,4-N-acetylgalactosaminyltransferase 2 (B4galnt2) are variable in wild mouse populations, and loss of B4galnt2 expression is associated with altered intestinal microbiota. We hypothesized that variation in B4galnt2 expression alters susceptibility to intestinal pathogens. To test this, we challenged mice genetically engineered to express different B4galnt2 tissue-specific patterns with a Salmonella Typhimurium infection model. We found B4galnt2 intestinal expression was strongly associated with bacterial community composition and increased Salmonella susceptibility as evidenced by increased intestinal inflammatory cytokines and infiltrating immune cells. Fecal transfer experiments demonstrated a crucial role of the B4galnt2-dependent microbiota in conferring susceptibility to intestinal inflammation, while epithelial B4galnt2 expression facilitated epithelial invasion of S. Typhimurium. These data support a critical role for B4galnt2 in gastrointestinal infections. We speculate that B4galnt2-specific differences in host susceptibility to intestinal pathogens underlie the strong signatures of balancing selection observed at the B4galnt2 locus in wild mouse populations.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Biogeography of tropical riverine bacterioplankton communities determined by deep sequencing of 16S rRNA gene

Riverine systems are intimately coupled with and shaped by the characteristics of their watershed, yet we know little about the effect of these connections to bacterioplankton communities. Here, we characterise water samples collected on the basis of dominant watershed land-use types observed along the tropical riverine system using 16S rRNA gene Illumina MiSeq sequencing. Three types of samples were analysed with different land-use types: pristine, urban and agricultural. Bacterioplankton communities were greatly discriminated by watershed land-use types rather than environmental or climate characteristics. Watershed land-use promoted allochtonous bacterial sequences, eutrophication-linked bacterial sequences, extinction and stress to indigenous bacterioplankton taxa. Despite the considerable variation across watershed land-use types, total bacterioplankton richness was greatly contributed by among-site richness than within-site richness. Bacterioplankton taxa showed a remarkable stability over time irrespective of climatic perturbations emphasizing the possibility of being temporally predictable.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Long-term monitoring of structures of microbial communities along a vegetation gradient from alpine meadows to a glacier forefield

In a 14-months monitoring campaign, we assessed seasonal changes in soil properties and in microbial community structures at 4 locations representing an altitude and vegetation gradient (from alpine meadows at 1980 m a.s.l. to a glacier forefield at 2519 m a.s.l.). Fungal and bacterial community structures and abundances were investigated through T-RFLP profiling and qPCR of the 16S and 18S rRNA genes. In addition, Illumina sequencing was performed to identify key bacterial groups on selected samples. Seasons affected the soils and the soil microbial communities more significantly than sites (plant species, grazing). The physico-chemical properties of the soils changed greatly during the course of the year. Bacterial and fungal community structures changed during the sampling period, but didn't always complete a full seasonal cycle. Our sequence data indicates that under winter snowpack, bacterial communities were dominated by ubiquitous opportunistic groups (i.e. beta-Proteobacteria), while in the snow-free seasons, other groups (i.e. Cyanobacteria) became more abundant.

Biome: root:Environmental:Terrestrial:Soil
Deep sequencing of 16S rRNA gene reveals discrete series of microbial community succession in tropical drinking water treatment plant

Microbial community dynamics in drinking water treatment plant are remarkably understudied, despite the high demand of microbiologically safe drinking water supplies. In this study, data on coherent dynamics of taxa- and microbial community shifts along the treatment barriers of drinking water treatment plant are reported. By sequencing the 16S rRNA gene amplicon at adequate depth, a high degree of microbial diversity and overrepresentation of typical freshwater genera including Undibacterium, Novosphingobium and Cylindrospermopsis were observed. Undibacterium had a considerable contribution to the abundance of the phylum Proteobacteria and demonstrated a remarkable ability to predict microbial diversity. Shifts in community structure were due to substantial elimination of bacterial taxa by sand filtration, and significant enrichment of rare taxa following chlorination.  Coherent dynamics of taxa across treatment barriers revealed series of discrete microbial secondary successions punctuated by treatment barriers. Based on microbial community succession data, the fate of noxious bacteria  in drinking water treatment plants can be tracked.

Biome: root:Environmental:Aquatic:Freshwater:Drinking water
Diversity of particle-attached bacteria in the Baltic Sea

To evaluate if changes in salinity affecting diversity of particle-associated (PA) and free-living (FL) bacteria, we sampled both bacterial fractions in two seasons (summer and fall/winter) in surface waters of three selected stations of the Baltic Sea representing marine, mesohaline and oligohaline environments. All samples were PCR amplified with 30 cycles using the primer pair Bakt_341F (CCTACGGGNGGCWGCAG) and Bakt_805R (ACHVGGGTATCTAATCC). Primers were tailed with sample-specific 5 bp barcodes a 454-adptor region, spanning variable regions V3 and V4 of the 16S rRNA gene. PCR products were purified with Agencourt AMPure XP magnetic beads (Beckman Coulter GmbH, Krefeld, Germany), quantified with a Picogreen assay (LifeTechnologies, Carlsbad, USA), diluted and equally pooled. The bidirectional sequencing was performed on a 454 platform with Titanium Flex chemistry (Roche etc.).

Biome: root:Environmental:Aquatic:Marine
Assessment of community structures along the depth profile of an alpine snowpack in winter and at snowmelt

In this study, we assessed the hypothesis whether microbial communities in an alpine snowpack in Switzerland would change between two seasons (winter and snowmelt). We characterised physical-and chemical changes of the snowpack along the two seasons, and combined it with the assessment of the microbial community structure. Bacterial community composition was investigated through Illumina sequences of the variable regions V3 /V4 of the 16S rRNA gene. Our results showed a pronounced shift of bacterial community structures during the seasons. In winter, less diverse, but more evenly distributed communities were found throughout the entire snowpack. At snowmelt, higher diversity, and richness of bacterial OTUs was detected.  Bacterial taxa inhabiting the snow change from spore forming-psychrophilic organisms (eg. Firmicutes) in winter to a more varied composition of ubiquitous heterotrophy (i.e. Betaproteobacteria) at snowmelt.

Biome: root:Environmental:Aquatic:Freshwater:Ice
A MEMBRANE AERATED BIOFILM REACTOR (MABR) FOR SULFIDE CONTROL USING A BUBBLELESS MEMBRANE AERATION

A UASB reactor was operated combined to a membrane aerated biofilm reactor (MABR) for sulfate removal and for elemental sulfur reclamation. A commercial silicon tube was use as an oxygen delivery diffuser. The process achieved high rates of sulfide removal from liquid phase (90%). The hydrogen sulfide removal was influenced by the pH value and at pH value of 7.5, 98% of the H2S was removed. The elemental sulfur was observed in inside the membrane, with content in the biomass of 21%. 16S rRNA gene-based high throughput Illumina MiSeq sequencing was used to demonstrate the microbial community diversity and the different layers inside the silicon tube.

Biome: root:Engineered:Bioreactor
Evaluation of the bioremediation potential of Atlantic Amazon

Samples were collected from coastal area in the Amazonian basin

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Microbial ecology in polar environments

A total of 52,928 pyrosequencing reads were analyzed in order to reveal the bacterial community structures in stream and lake surface water samples from Fuglebekken and Revvatnet basins of the southern Svalbard. Depending on the sample examined, bacterial communities at higher taxonomic level consisted mainly either of Bacteroidetes, Betaproteobacteria and Microgenomates (OP11), or of Planctomycetes, Betaproteobacteria and Bacteroidetes members, whereas in two of them, a notable Microgenomates population was identified. At the lower taxonomic level, bacterial communities comprised mostly of Microgenomates, Comamonadaceae, Flavobacteriaceae, Legionellales, SM2F11, Parcubacteria (OD1) and TM7 members, although at different proportions in each sample. The abundance of OTUs shared in common among samples exceeded 70%, with the exception of samples in which the proliferation of Planctomycetaceae, Phycisphaeraceae and Candidatus Methylacidiphilum spp. lowered their relative abundance. Multi-variable analysis indicated that As, Pb and Sb were the main environmental factors influencing bacterial profiles.

Biome: root:Environmental:Aquatic:Freshwater:Ice
Analysis of gut microbiota in infants

The human gut microbiome has been demonstrated to play a vital role in health and disease. Dysbiosis may contribute significantly to adverse outcomes in child health. Using metagenomics this project seeks to identify microbiome signatures that might influence health of children.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Natural and Artificial Milk Feeding Promote Different Rumen Microbial Colonization but not Differences in Gene Expression Levels at the Rumen Epithelium of Newborn Goats

The aim of this work was to evaluate the effect of feeding management during the first month of life (natural with the mother, NAT, or artificial with milk replacer, ART) on the rumen microbial colonization and the innate immune response. Thirty pregnant goats carrying two fetuses were selected. At birth one kid was taken immediately away from the doe and fed milk replacer (ART) while the other remained with the mother (NAT). Groups of four kids (from ART and NAT experimental groups) were slaughtered at 1, 3, 7, 14, 21 and 28 days of life. On the sampling day, after slaughtering, the rumen content was sampled and epithelial rumen tissue was collected. Pyrosequencing analyses of the bacterial community structure on samples collected at 3, 7, 14 and 28 days showed that both systems promoted significantly different colonization patterns (P = 0.003). Diversity indices increased with age and were higher in NAT feeding system.

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
A method for identifying metagenomic species and variable genetic elements by exhaustive co-abundance binning

The microbial diversity of environments like the human gut extends far beyond what is covered by reference genomes. Here we present a method for exhaustive and unsupervised co-abundance gene binning across a series of highly complex metagenomic samples. As the method does not rely on previously sequenced reference genomes it allows for discovery of new species, viruses and clonal heterogeneity. We demonstrate the method on human gut microbiome data and identify 7,381 co-abundance gene groups (CAGs) ranging in size from 3 to 6,319 genes. The CAGs represent a wide variety of biological entities including microbial genomes, phages and clonal differences. We name the 741 largest of these metagenomic species (MGS), because they correspond to microbial species. In addition, we establish microbial host affiliations by dependency-associations for many small CAGs. Longitudinal sampling in the same individuals indicates that some of these dependency-associations are important for the persistence of their microbial host

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Diet assessment of European eel (Anguilla anguilla) leptocephali in the Sargasso Sea

Diet assessment of European eel (Anguilla anguilla) leptocephali in the Sargasso Sea

Biome: root:Host-associated:Fish
Geographic and host-associated variations in bacterial communities on the leaf surfaces of field-grown broccoli

This study is the first to describe bacterial community composition and diversity on broccoli leaf surfaces in-depth using 454 pyrosequencing of 16S rRNA genes. This study suggested variability of bacterial communities associated with geography of farming sites, and alterations by host growth and host health conditions. In a global view of fresh produce, this study delineated bacterial community composition specific for broccoli, which is more similar to ground vegetables than tree fruits and vegetables.

Biome: root:Host-associated:Plants:Phylloplane
The vaginal and urinary microbiota in health, during BV and after treatment

The urinary and vaginal fluid microbiota was analysed using sequencing of the rRNA gene V1-V2 regions. Vaginal fluid and urine samples were taken from women with bacterial vaginosis (BV) and analysed throughout the course of a clinical study that aimed at characterising the effect of a newly developed pessary containing an amphoteric tenside compared to a pessary containing lactic acid. Before participating women received either pessary, theywere first treated with the antibiotic metronidazole. Vaginal fluid samples were taken and analysed at five different time points thoughout the study. Urine samples were taken and analyed before and after metronidazole treatment. As healthy control groups, vaginal fluid samples were taken and analysed from healthy women and urine samples from healthy men and women.

Biome: root:Host-associated:Human:Reproductive system:Vagina
Characterization of Arabian fermented foods microbiota and interaction with gut microbiome of ‎Bedouin population

More than 2 million of Saudi population live a nomadic life and consume specific types of local ‎fermented foods and dairy products in routine diet. Microbial communities within such fermented ‎foods are often originating from environmental sources and the bacterial species in such type of ‎foods eventually reach the gut where they can interact with intestinal microbiota of the host. This ‎interaction is significant for human health, as local fermented food microbiota is considered ‎important source of probiotics and as well as of other environemtnal microorganisms that can ‎intervene in the gut microbiome composition and homeostasis. The interaction between the ‎microbiota of gut and intake food highlight the importance to investigate the microbiological ‎quality of fermented foods. In this study, we are proposing to analyze the microbiota of locally ‎fermented foods and their impact on the gut microbiome of Bedouin population of Saudi Arabia. ‎We aim to concomitantly analyse the samples via direct observation using Gram staining, electron ‎microscopy and by extensive culturomics analysis. High throughput MALDI-TOF mass ‎spectrometry system will be used for identification of isolated species. In addition, each sample ‎will be studied by 16S rRNA amplicon targeting V6 region pyrosequencing. Comperative analysis ‎will be perfomed to identifiy the impact and specific species richness in Bedouin gut's microbiome ‎due to the consumption of local fermented foods. We propose to apply these techniques on 10 ‎stool samples from Bedouin individuals compare with 7 samples of locally fermented foods ‎commonly use by those peoples.‎

Biome: root:Engineered:Food production:Dairy products
Host Transcriptomics and gut microbiome analysis in broilers with contrasting Feed Conversion Ratio

World population leading to consequent high pressure placed on animal biotechnologists/ researcher to increase the yield of current food crops and livestock, while identifying new and alternative food sources. In today's economically fast growing world poultry industry is also feeling its pace to be increased. Identification of genes associated with fatness or leanness will help in selection of individuals with better performance and thereby results in profitable poultry farming. In addition, Whole transcriptome shotgun sequencing or RNA-seq is an efficient and reliable technology for transcriptomic analysis so as to reveal genetic architecture, to identify sequence variation, and to quantify gene expression. The ultimate aim is to identify the genes which are associated with feed conversion ratio. The biomarkers identified will be useful for selection of birds with low FCR. The host genetic responses associated with weight gain and feed conversion efficiency have also played a role in changes in the physiology and gut microbial structure of birds. Therefore, shot gun and amplicon sequencing will be carrying out of each metagenomes. The ultimate aim is to detect possible association between FCR and gut microflora. The bacteria identified could be useful for feed formulation for broiler. Successful completion of project will result in identification of novel/ unigene associated with FCR in broiler. Based on identified unique/ novel gene, selection of good feed efficient birds can be done that will result in to economic production of broilers in shorter duration and profitable meat production. Also emergent microbial strains will identified by metagenome analysis and their association with good FCR birds.

Biome: root:Host-associated:Birds:Digestive system:Fecal
Biodegradable organic carbon amendments enhance attenuation of trace organic contaminants in biochar amended stormwater biofilters

Biochar-amended infiltration systems may significantly improve urban water quality by  enhancing removal of trace organic contaminants (TOrCs) from runoff. As biochar's  sorption capacity will eventually saturate, stimulation of biological TOrC attenuation may  be beneficial. The objective of this study was to determine if biodegradable organic carbon amendments can improve TOrC attenuation in biochar-amended biofilters. It was  hypothesized that microbial growth in response to dissolved organic carbon (DOC)  availability would establish more robust and diverse microbial communities, leading to  enhanced TOrC biodegradation and sorption to biological material. This hypothesis was  evaluated in TOrC-spiked microcosm and column experiments, utilizing a representative  microbial consortium from actual runoff and DOC extracted from straw and compost.  Microcosms with compost DOC exhibited broader TOrC biodegradation potential than  microcosms with raw runoff or straw DOC. 16s rRNA gene sequencing revealed  community clustering according to DOC type, suggesting that DOC availability caused  shifts in community structure that affected TOrC biodegradation. Columns exhibited  enhanced biological TOrC attenuation in presence ofbiofilms established with compost  DOC but not straw DOC. These results reveal that biodegradable organic carbon sources  stimulate biological TOrC attenuation in biochar-amended biofilters, providing insight  into the design of stormwater biofilters for improved water quality.

Biome: root:Engineered:Wastewater:Nutrient removal:Dissolved organics (aerobic)
Enrichment of anaerobic nitrate-dependent methanotrophic Candidatus Methanoperedens nitroreducens archaea from an Italian paddy field soil

Paddy fields are a significant source of methane and contribute up to 20% of total methane emissions from wetland ecosystems. These inundated, anoxic soils featuring abundant nitrogen compounds and methane are an ideal niche for nitrate-dependent anaerobic methanotrophs. After 2 years of enrichment with a continuous supply of methane and nitrate as the sole electron donor and acceptor, a stable enrichment dominated by 'Candidatus Methanoperedens nitroreducens' archaea and 'Candidatus Methylomirabilis oxyfera' NC10 phylum bacteria was achieved. The results of qPCR quantification of 16S rRNA gene copies, analysis of metagenomic 16S rRNA reads,and fluorescence in situ hybridization (FISH) correlated well and showed that, after two years, 'Candidatus Methanoperedens nitroreducens' had the highest (2.2±0.4*108) 16S rRNA copies per mL and constituted approximately 22% of the total microbial community.Metagenomic sequencing by Ion Torrent Technology was carried out after one and two years of enrichment. Phylogenetic analysis showed that the 16S rRNA genes of the dominant microorganisms clustered with previously described 'Candidatus Methanoperedens nitroreducens ANME2D' (96% identity) and 'Candidatus Methylomirabilis oxyfera' (99% identity) strains. The pooled metagenomic sequences resulted in a high-quality draft genome assembly of 'Candidatus Methanoperedens nitroreducens Vercelli' that contained all key functional genes for the reverse methanogenesis pathway and nitrate reduction. The diagnostic mcrA gene was 96% similar to 'Candidatus Methanoperedens nitroreducens ANME2D' (WP_048089615.1) at the protein level.The 'Candidatus Methylomirabilis oxyfera' draft genome contained the marker genes pmoCAB, mdh, and nirS and putative NO dismutase genes. Whole-reactor anaerobic activity measurements with methane and nitrate revealed an average methane oxidation rate of 0.012 mmol h-1 L-1, with cell-specific methane oxidation rates up to 0.57 fmol cell-1 day-1 for 'Candidatus Methanoperedens nitroreducens'. In summary, this study describes the first enrichment and draft genome of methanotrophic archaea from paddy field soil, where these organisms can contribute significantly to the mitigation of methane emissions.

Biome: root:Environmental:Aquatic:Freshwater:Wetlands