SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Role of salt and storage packaging conditions defining the spoilage microbial diversity of raw pork sausages

Both salt concentration and packaging type can modify the nature and the dynamic of microbial ecosystems in meat products. The purpose of this work was to investigate the influence of these two parameters on the bacterial communities of raw pork sausages using a metagenomic approach and to correlate these data with sensory analysis.  Two concentrations of sodium chloride were tested: normal content (2 % w/w) vs. a 25 % reduction (1.5 % w/w) and for each, packaging was either vacuum or modified atmosphere (N2%-CO2%). Sausages were stored at 8 °C during 21 days until their use-by date. Spoilage assessment was performed by sensory and physicochemical analyses. To characterize the bacterial diversity, the 16S rDNA of five replicates per condition tested was amplified for pyrosequencing at a scale of 15,000 reads per library. Reads were then clustered into Operational Taxonomic Units (OTU).  Spoilage was characterized by an important greying of the products and a production of gas and off-odours defined as rancid, sulphurous and sour. It was more pronounced for samples under modified atmosphere and easier to be ascertained with the lowest salt content. The 20 samples taken altogether,provided 387,111 bacterial 16S rRNA sequences which were analyzed and binned into 78 OTUs (97% threshold).. Packaging atmosphere influenced the average bacterial richness with 69 OTUs (+/-?) identified in vacuum-packed meat and a lower diversity of 46 OTUs (+/-?)in modified atmosphere-packed meat. The richness was influenced mainly in the sub-dominant population whereas the core dominant bacterial species were similar in all samples and composed of Lactobacillus sakei, Lactococcus piscium, Carnobacterium divergens, Serratia proteamaculans and Brochothrix thermosphacta. However, salt reduction turned out to induce a significant drop in species diversity evenness among the core dominant species and thus led to a faster spoilage event..   This knowledge will help in defining strategies to offset salt reduction meanwhile keeping the safety of meat products.

Biome: root:Engineered:Food production
The microbes we eat: abundance and taxonomy of microbes consumed in a day's worth of meals for three diet types (USDA recommended, vegan, and “typical American”)

We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: 1) the Average American (AMERICAN): focused on convenience foods, 2) USDA recommended (USDA): emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and 3) Vegan (VEGAN): excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis.

Biome: root:Engineered:Food production
Thermus thermophilus is responsible for the pink discolouration defect in cheese

High-throughput, culture-independent DNA sequencing-based strategies have revolutionised our understanding of the composition of microbial populations, including those in foods. While many are descriptive studies, there are studies linking particular microorganisms with specific desirable/undesirable impacts being revealed. Here we apply such a strategy to study pink discolouration of cheese, a spoilage defect that affects the associated industry worldwide. Despite efforts over many decades, the basis for this phenomenon has remained elusive with traditional approaches having failed to reveal a microbial basis for this problem.  The bacterial composition problematic cheeses were assessed by DNA sequencing. This revealed the presence of bacteria from the genus Thermus, at higher levels in defect, relative to control, cheeses. This observation was particularly notable in light of the fact that, Thermus, which are non-pathogenic, thermophilic bacteria which do not readily grow on the media employed to culture dairy microorganisms, have previously been associated with pink discolouration problems in the paper industry.  Prompted by this finding, a target-specific culture-based approach was employed and Thermus thermophilus was successfully cultured from defect cheeses. Furthermore, qPCR revealed the species to be present at 103 cfu g-1 in the aforementioned defect-containing cheeses but to be absent or present at low levels only (101 cfu g-1) in the equivalent control cheeses. The link between Thermus and the pinking phenomenon was further investigated through the production and analysis of cheeses into which Thermus was spiked and of control cheeses. Crucially, the defect was reconstructed only in test cheeses containing the cheese-derived T. thermophilus.

Biome: root:Engineered:Food production:Dairy products
Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage.

This study is a large comprehensive survey of meat and seafood spoilage microbiota using 454-GS-FLX Titanium amplicon sequencing of the 16S rRNA gene V1-V3 fragment. Primer EBP-27F was used as a forward primer and EBP-534R as a reverse primer. Eight different products were analyzed including four meat products : Ground Beef (code sample = GB), Ground Veal (code sample = GV); Poultry Sausages (code sample = PS); Bacon Dices (code sample =  BD), and four seafood products : Salmon Fillets (code sample = SF); Smoked salmon (code sample = SS); Cod fillets (code sample = CF); Cooked Peeled Shrimps (code sample = CS). Ten samples were analyzed per food product (coded 01 to 10) and at two time of storage (T0 for the freshly produced food product; TS for the spoiled product obtained after a certain period of storage time at refrigerated temperature). Overall, 160 samples were analyzed (80 samples at each storage time of analysis). All samples were subject to pyrosequencing replication, one from the 27F primer A-side (EBP-XXXX-XX-F.fastQ files, where XXXX-XX denotes the sample's code) and the second from the 534R primer B-side (EBP-XXXX-XX-R.fastQ files). All samples from a given product at a given storage time and their associated replicates were pooled in a 1/4 lane of a 454 GS-FLX Titanium run yielding an average sequencing depth of 15,000 reads per sample (~7,500 reads/replicate). All FastQ files are corresponding to Quality-filtered reads (length > 250 bp).

Biome: root:Engineered:Food production
nifH defined community samples used for analysis testing

To test the pyrosequencing technology and analysis pipeline under specific conditions, we use a nifH defined community with genomic DNAs from Desulfitobacterium hafniense DCB-2,  Nostoc sp. PCC 7120 and Burkholderia xenovorans LB400 amplified separately using the same barcode.

Biome: root:Engineered:Modeled:Simulated communities (microbial mixture)
Phylogenetic identification of GO-reducing bacteria enriched from a coast

This project conducted the phylogenetic identification of bacteria capable of respiration with an extracellular electron acceptor, graphene oxide (GO). GO is the oxidized form of graphene, a 2D honeycomb lattice of carbon. GO can be reduced to the reduced GO (rGO) by bacteria via extracellular electron transferring. Ant the rGO can facilitate the recovering electricity from bacteria. A variety of microorganisms potentially ability to reduce GO, while the reduction of GO was demonstrated by only Schewanella spp. This study enriched GO respiring bacteria from a coast, and identified the enriched GO respiring bacteria by pyrosequencing targeting V4 region of 16SrRNA gene.

Biome: root:Environmental:Terrestrial:Soil:Sand
microbial community of traditional Korean alcoholic beverages

Makgeolli is a traditional Korean alcoholic beverage manufactured with a natural starter, called nuruk, and grains. Nuruk is a starchy disk or tablet formed from wheat or grist containing various fungal and bacterial strains from the surrounding environment that are allowed to incorporate naturally into the starter, each of which simultaneously participates in the makgeolli fermentation process. In the current study, changes in microbial dynamics during laboratory-scale fermentation of makgeolli inoculated with six different kinds of nuruk were evaluated by barcoded pyrosequencing using fungal- and bacterial-specific primers targeting the internal transcribed spacer 2 region and hypervariable regions V1 to V3 of the 16S rRNA gene, respectively. A total of 61,571 fungal and 68,513 bacterial sequences were used for the analysis of microbial diversity in ferment samples. During fermentation, the proportion of fungal microorganisms belonging to the family Saccharomycetaceae increased significantly, and the major bacterial phylum of the samples shifted from ?-Proteobacteria to Firmicutes. The results of quantitative PCR indicated that the bacterial content in the final ferments was higher than in commercial rice beers, while total fungi appeared similar. This is the first report of a comparative analysis of microbial dynamics during the fermentation of alcoholic beverage using barcoded pyrosequencing of bacterial and fungal rRNA genes.

Biome: root:Engineered:Food production:Fermented beverages
The Usefulness and Reproducibility of Pyrosequencing for the Analysis of a Microbial Community of a Methane-Oxidizing Biofilm

The usefulness of pyrosequencing for uncovering a methane-oxidizing biofilm community was determined in this study. Four individual DNA samples were prepared from a methanotrophic biofilm, and a multiplex pyrosequencing was performed. A complete library (sum of the 4 libraries) contained 33,639 sequences with an average length of 415 bp. It was interesting that methanotrophs were not dominant when grouped by functionality, making up only 23% of the community. Methylosinus, Methylomonas and Methylosarcina were the dominant methanotrophs. Type II methanotrophs were more abundant than type I (56 vs. 44%), but diversity and species richness of the type II community were lower. Dominant non-methanotrophic genera included Hydrogenophaga, Flavobacterium and Hyphomicrobium. For evaluation of the reproducibility, the complete library was de-multiplexed into 4 libraries, with different sequencing efforts, ranging from 3,915 to 20,133 sequences. Sørrenson abundance similarity results showed that the four libraries were almost identical (the indices > 0.97), and phylogenetic comparisons using UniFrac and P-tests revealed the same results. The 4 libraries had the same taxonomical composition, with similar relative abundances after taxonomic classification.

Biome: root:Engineered:Bioreactor
Microbial Community in High Arsenic Shallow Aquifers in Hetao Basin of Inner Mongolia, China by 454 Pyrosequencing

A comprehensive survey of microbial community with 454 Pyrosequencing was carried out in 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic boreholes and one low arsenic borehole) in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia by. A total of 233,704 reads and 12-267 species-level OTUs were detected. Richness and diversity of microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low arsenic and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four predominant populations in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter were distinctly dominated in high arsenic sediments. Acinetobacter was distinctly dominated in groundwater with the markedly high relative abundance (average 62.41%), and Thiobacillus was significantly abundant (average abundance 24.62%) in sediments. Archaeal sequences of high arsenic groundwater were mostly related to methanogens. Groundwater and sediment samples were divided into low and high arsenic groups based on geochemical parameters and microbial communities by hierarchical clustering and PCoA analyses. This suggested that arsenic is a critical environmental factor that contributes to the difference microbial community structure. BIO-ENV and co-inertia analyses showed that some other geochemical parameters including TOC, SO42-, SO42-/TS and Fe2+ were also the important factors causing the difference of the microbial community. The results of this study expand our current understanding of microbial ecology in high arsenic aquifers and emphasize the potential importance of microbes in arsenic mobilization in the shallow aquifers of Hetao Basin, Inner Mongolia.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
The effect of different loading rates of biochar on soil microbes

Biochar and its applications in soil is involved in many aspects related to soil health and quality, for instance, chemical and physical changes in soil. However, the major aspect, which is still far from being understood and has so far received less attention than any other aspects, is the impact of biochar applications on soil microbes and how microorganisms in soil interact and adjust with biochar-modified soil environments.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
16S rRNA gene sequencing of Extremelly low birth weight infant

16S rRNA gene sequencing of Extremelly low birth weight infant using primers 926F-1394R

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Fungi associated with Rhamnus cathartica in Southwestern Ontario

Common buckthorn (Rhamnus cathartica) is a competitive Eurasian woody shrub currently invading North America. Buckthorn thickets reduce native diversity and may reduce mycorrhizal diversity through the release of allelochemicals. Two aspects of buckthorn's invasional biology are explored: 1) determining buckthorn's allelochemical impacts on arbuscular mycorrhizae in mature sugar maple (Acer saccharum) stands, and 2) assessing possible changes in mycorrhizal communities in sugar maple soils in an open-greenhouse experiment. Data from invaded and uninvaded sugar maple soils revealed that arbuscular mycorrhizal fungi (AMF) diversity fluctuated as a function of season, sampling site or potting disturbance, but the presence of buckthorn had little effect on AMF development in maple roots. Buckthorn may be a mycorrhizal generalist, and changes in AMF abundance may be more influenced by underlying stochastic soil processes and aboveground plant composition than by buckthorn and its allelochemicals.

Biome: root:Host-associated:Plants
This dataset contains the output from shotgun metagenomic and genomic sequencing of the microbiota of faecal samples collected from infants prior to developing necrotising enterocolitis (NEC).

This study describes the use of shotgun metagenomic sequencing  to characterise the microbiota of faecal samples collected from infants prior to developing necrotising enterocolitis (NEC) and from matched controls. Additional genomic sequencing of select enterobacteriaceal isolates cultured from these samples was also performed.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Integrated 'omics', targeted metabolite and single-cell analyses of Arctic snow algae functionality and adaptability

Snow algae are poly-extremophilic microalgae and important primary colonisers and producers on glaciers and snow fields. Depending on their pigmentation they cause green or red mass blooms during the melt season. This decreases surface albedo and thus further enhances snow and ice melting. Although the phenomenon of snow algal blooms has been known for a long time, large aspects of their physiology and ecology sill remain cryptic. This study provides the first in-depth and multi-omics investigation of two very striking adjacent green and red snow fields on a glacier in Svalbard. We have assessed the algal community composition of green and red snow including their associated microbiota, i.e., bacteria and archaea, their metabolic profiles (targeted and non-targeted metabolites) on the bulk and single-cell level, and assessed the feedbacks between the algae and their physico-chemical environment including liquid water content, pH, albedo and nutrient availability. We demonstrate that green and red snow clearly vary in their physico-chemical environment, their microbial community composition and their metabolic profiles. For the algae this likely reflects both different stages of their life cycles and their adaptation strategies. Green snow represents a wet, carbon and nutrient rich environment and is dominated by the algae Microglena sp. with a metabolic profile that is characterized by key metabolites involved in growth and proliferation. In contrast, the dry and nutrient poor red snow habitat is colonised by various Chloromonas species with a high abundance of storage and reserve metabolites likely to face upcoming severe conditions. Combining a multitude of techniques we demonstrate the power of such complementary approaches in elucidating the function and ecology of extremophiles such as green and red snow algal blooms, which play crucial roles in glacial ecosystems.

Biome: root:Environmental:Aquatic:Freshwater:Ice:Glacier
Characterization of the bacterioplankton communities from the Ebro River

Water samples from the River Ebro (Spain) were collected in 2011 in three occasions and the bacterioplankton communities inhabiting the reaches separated by the reservoirs were characterized by 454 pyrosequencing of the 16S rRNA gene

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
study of the Ancona harbor microbial community using 16S rRNA pyrosequencing.

The sediments of the Ancona harbor (Italy) are polluted by crude oil, hence co-contaminated by different classes of molecules like hydrocarbons and heavy metals. In our study, we aimed to investigate the bacterial community composition of highly contaminated sediments and the deriving enrichment cultures established using different hydrocarbon pollutants. To depict the assemblage of bacteria populations we used 16S rRNA pyrosequencing data.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated
Sulfate reducing and methanogenic microbial community structure in Outokumpu deep bedrock fracture zones

Sulfate reducing bacterial communities and methanogenic archaeal communities were characterized by amplicon sequencing the marker gene for sulfate reduction and methanogenesis, dsrB and mcrA, respectively. Study was conducted in Outokumpu Deep Drill Hole, Finland in a depth range of 180-2300 m.

Biome: root:Environmental:Terrestrial:Rock-dwelling (subaerial biofilm)
Reduced membrane fouling in an anaerobic electrochemical membrane bioreactors using graphene-coated hollow fiber membranes as the cathode

Electrically conductive, graphene-coated hollow-fiber porous membranes were used as cathodes in anaerobic electrochemical membrane bioreactors (AnEMBRs) operated at different applied voltages (0.7 V and 0.9 V) using a new rectangular reactor configuration, compared to a previous tubular design (0.7 V). The onset of biofouling was delayed and minimized in rectangular reactors operated at 0.9 V, compared to those at 0.7 V due to higher rates of hydrogen production. Maximum transmembrane pressures for the rectangular reactor were only 0.10 bar (0.7 V) or 0.05 bar (0.9 V) after 56 days of operation, compared to 0.46 bar (0.7 V) for the tubular reactor after 52 days. The thickness of the membrane biofouling layer was approximately 0.4 ?m for rectangular reactors and 4 ?m for the tubular reactor. Pyrosequencing of 16S rRNA gene and qPCR analysis revealed that the predominant bacteria were Desulfovibrio sp., and methanogenic archaea were mainly Methanobacteriaceae in both the tubular and the rectangular AnEMBRs. The ratio of archaea-to-bacteria varied depending on applied voltage and reactor configuration with higher ratio (>0.6) at 0.7 V than at 0.9 V (~0.1).  Higher permeate quality (TSS = 0.05 mg/L) was achieved in the rectangular AnEMBR than the tubular AnEMBR (TSS = 17 mg/L), likely due to higher current densities that minimized the accumulation of cells in suspension. These results show that the new rectangular reactor design, which had increased rates of hydrogen production, successfully delayed the onset of cathode biofouling and improved reactor performance.

Biome: root:Engineered:Bioreactor
Exploring the brine pool in the Red Sea as a source of exoelectrogenic communities

One of the challenges for using microbial electrochemical technologies (METs) with highly saline or thermophilic solutions is the lack of microbes capable of forming a biofilm and generating electrical current under these conditions. Three different locations at different depths of brine pools in the Red Sea were investigated as inocula sources for exoelectrogenic biofilms that could grow at 70oC in highly saline medium: Valdivia, Atlantis II, and Kebrit. Of these, only the inoculum from the Valdivia brine pool produced high and consistent current 6.8 ? 2.1 A/m2-anode (over 60 days) in microbial electrolysis cells (MECs) operated at a set anode potential of +0.2 V vs Ag/AgCl (+0.405 V vs. SHE), with 10 mM acetate as the electron donor. Analysis of the microbial communities with the Valdivia inoculum using 16S rRNA gene pyrosequencing showed at the genus level that sequences most similar to Bacteroides were the predominant microorganisms at the anode. These results show that microorganisms capable of producing electrical current are present in at least one of these extreme environments in the Red Sea. Enriching for efficient exoelectrogenic communities from extreme environments will provide new opportunities for niche-specific applications of METs.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
Comparative analysis of twelve viromes from fen and bog peat pore water

Using pyrosequencing,12 peatland metaviromes have been produced for both fen and bog at 4 different dates. Using shotgun metagenomics we observed a shift in viral diversity between winter/spring and summer/autumn, indicating a seasonal succession of viral communities, mainly driven by weather-related environmental changes.

Biome: root:Environmental:Terrestrial:Soil:Wetlands
Natural variation of Pacific oyster hemolymph microbiota at two sites in the Wadden Sea (Texel, Netherlands, & Sylt, Germany) throughout the summer season 2012

Pacific oysters (Crassostrea gigas) from two genetically differentiated populations from the Wadden Sea - one from Texel, the other from Sylt - were reciprocally translocated between the sites at the beginning of June 2012. Half of the oysters were additionally pretreated with antibiotics to remove resident microbiota. Local controls were included as well, resulting in four groups at each site: antibiotic treated local or translocated, and control local or translocated oysters.Hemolymph samples were taken immediately after the pretreatment in the lab and then on 3 (monthly, Texel) and 5 (biweekly, Sylt) occasions in the field. Exact position of each oyster in the field was recorded, so that the data allow for study of spatial patterns of oyster hemolymph microbiota. One seawater sample is included for reference for each sampling point.

Biome: root:Host-associated:Mollusca:Digestive system
Subseafloor microbes at Mid-Cayman Rise

Two new vent-systems on the Mid-Cayman Rise each exhibit novel geologic settings and distinctively hydrogen-rich vent fluid compositions.  We have determined and compared the chemistry, energy landscape, abundance, community composition, diversity, and function of microbes in venting fluids from both sites: Piccard, the world?s deepest vent site-site, hosted in mafic rocks, and Von Damm, an adjacent, ultramafic-influenced system.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents