SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
EMG produced TPA metagenomics assembly of the Infant fecal microbiome related to eczema (human gut metagenome) data set.

The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA272371.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Alkaline Insect Gut Metagenome Project (SRP010470) data set.

The SRP010470 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: SRP010470.  This project includes samples from the following biomes: Host-associated, Arthropoda, Digestive system.

Biome: root:Host-associated:Arthropoda:Digestive system:Gut
EMG produced TPA metagenomics assembly of the Human Faecal Samples Raw sequence reads (human gut metagenome) data set.

The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA308846.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Metagenomics analysis of donor and recepient samples from fecal transplant for Recurrent Clostridium difficile infection () data set.

The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA339012.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Biomethanization of CO2 via ex-situ application

In recent years several studies investigated a potential of biogas upgrading to high quality biomethane using biological biomethanization of CO2 approach. Resulting biomethane can be used as a substitute of a natural gas in the National Grid or serve as a gaseous biofuel for transportation. In this study, eight lab scale reactors were inoculated with waste water treatment plant sludge and acclimatised for a period of time prior H2 injection. The conversion rate of hydrogen was monitored to determine kinetics rate. Samples were also collected to establish the microbial community structure in response to hydrogen injection using metagenomic analysis.

Biome: root:Engineered:Biogas plant
16S amplicon study of compost tea, teku kana and litters

A metagenomic study, using 16S amplicon approach, has been performed to analyze bacterial communities of compost tea, teku kana and litter used to produce it.

Biome: root:Engineered:Solid waste:Composting
EMG produced TPA metagenomics assembly of the Hot spring microbial communities from South Africa to study Microbial Dark Matter (Phase II) - Sagole hot spring metaG metagenome (hot springs metagenome) data set.

The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA364998.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
EMG produced TPA metagenomics assembly of the preterm infant gut metagenomes (NIH Y4 Cohort) (human gut metagenome) data set.

The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA396794.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Dissecting effects of community context on a gut pathobiont in a model of childhood undernutrition (Host-pathobiont-microbiota interactions in undernutrition) data set.

The Host-pathobiont-microbiota interactions in undernutrition Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB9703.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Fecal.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Cotija cheese metagenome (food metagenome) data set.

The food metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA286900.  This project includes samples from the following biomes: Engineered, Food production, Dairy products.

Biome: root:Engineered:Food production:Dairy products
Convergence of gut microbiomes in myrmecophagous mammals

Mammals have diversified into many dietary niches. Specialized myrmecophagous (ant- and termite-eating) placental mammals represent a textbook example of evolutionary convergence driven by extreme diet specialization. Armadillos, anteaters, aardvarks, pangolins, and aardwolves thus provide a model system for understanding the potential role of gut microbiota in the convergent adaptation to myrmecophagy. Here, we expand upon previous mammalian gut microbiome studies by using high-throughput barcoded Illumina sequencing of the 16S rRNA gene to characterize the composition of gut microbiota in 15 species representing all placental myrmecophagous lineages and their close relatives from zoo- and field-collected samples. We confirm that both diet and phylogeny drive the evolution of mammalian gut microbiota, with cases of convergence in global composition, but also examples of phylogenetic inertia. Our results reveal specialized placental myrmecophages as a spectacular case of large-scale convergence in gut microbiome composition. Indeed, Neighbor-Net networks and beta diversity plots based on UniFrac distances show significant clustering of myrmecophagous species (anteaters, aardvarks, and aardwolves) even though they belong to phylogenetically distant lineages representing different orders. The aardwolf, which diverged from carnivorous hyenas only in the last 10 million years, experienced a convergent shift in the composition of its gut microbiome to become more similar to other myrmecophages. These results confirm diet adaptation to be a major driving factor of convergence in gut microbiome composition over evolutionary timescales. This study sets the scene for future metagenomic studies aiming at evaluating potential convergence in functional gene content in the microbiomes of specialized mammalian myrmecophages.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Biological Impacts of Ocean Acidification

Impacts of ocean acidification and warming on marine macroalgae and its microbiota

Biome: root:Environmental:Aquatic:Marine
Biomethanization of CO2 in AD plants - amplicon study

Anaerobic digestion uses a variety of organic wastes (domestic, industrial, agricultural) to produce biogas – a mixture of carbon dioxide and methane. Biogas is often used on the industrial application to generate heat and power but can also be upgraded to biomethane and injected directly into the National Grid as a substitute for natural gas. Currently, the upgrading step limits the wider use of biomethane as a gaseous biofuel. In order to increase the biomethane potential, biomethanization can be applied either by adding H2 to the reactor and converting it to methane in presence of endogenous (in-situ) or exogenous (ex-situ) CO2 by the resident microbiome.  Here, we upgraded biogas to biomethane using in-situ biomethanization. Using DNA sequencing approaches such as metagenomics and 16S amplicon sequencing the identity of microbial members of the enriched community and their functional potential was uncovered leading to better understanding on how the AD biomethanization process can be manipulated and improved.

Biome: root:Engineered:Biogas plant:Wet fermentation
Meta_Kosmos

Bacterial diversity patterns in response to ocean acidification.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Zooplankton communities in the coastal water of northeastern Hokkaido

Monitoring zooplankton communities is important to understand changes in the marine ecosystem. In this study, total 101 zooplankton samples were collected weekly in 2014 and 2015 at the Okhotsk tower in Mombetsu city, Hokkaido, Japan. A metagenetic analysis of the 18S region was conducted to reveal seasonal changes of zooplankton diversity and community in the coastal water of northeastern Hokkaido along the Okhotsk Sea.

Biome: root:Environmental:Aquatic:Marine:Coastal
Biological Impacts of Ocean Acidification

Restructuring of epibacterial communities on Fucus vesiculosus forma mytili in response to elevated pCO2 and increased temperature levels

Biome: root:Host-associated:Algae:Brown Algae
Lactobacillus dominate in the intestine of Atlantic salmon fed dietary probiotics.

Probiotics are live microbial strains incorporated as dietary supplements in feeds and are known to provide health benefits to the host. These live microbes manipulate the gut microbes by suppressing the growth and competing with other intestinal microbes. Lactic acid bacteria (LAB) are potential probiotics that have been widely studied; in this study, we have elucidated the effects of two LAB types (LAB1 & LAB2) isolated from the intestinal content of farmed healthy juveniles of rainbow trout on the distal intestinal microbial communities of Atlantic salmon (Salmo salar). We employed high-throughput 16S rRNA gene amplicon sequencing technique to investigate the intestinal bacterial communities harbouring in the distal intestinal content and mucus of the 3 groups of Atlantic salmon fed diets-devoid of or diets-containing LABs. Our results show that LAB shifts the intestinal microbial profile; LAB supplementation did not show any significant alterations in the alpha diversity of the three groups. However, LAB2 feeding increased the bacterial diversity in the distal intestinal mucus of the fish. Beta diversity analysis showed a significant difference between control and LAB-fed groups. We found intestinal Lactobacillus abundant and dominant in the LAB-fed fish. In addition, few members of the phyla Tenericutes, Actinobacteria, and Spirochaetes were also found to be abundant in the LAB-fed groups. Furthermore, the bacterial association network analysis showed that in the LAB1-fed group significantly abundant and relevant OTUs are closely linked suggesting that they may be highly interactive. We did not find any evidence on cooperation-related runaway effect. These results indicate that dietary probiotics modulate the distal intestinal microbiota of Atlantic salmon. These results are intended to improve the understanding of the modulations and interactions of gut microbiota under the influence of selected probiotic species.

Biome: root:Host-associated:Fish:Digestive system:Foregut
Diet analysis of Japanese sardine and Pacific round herring larvae

A successful feeding on preferred prey is important for survival of fish larvae; however, it is difficult to obtain high taxonomic resolutions from damaged gut contents by morphological classification. In this study, <10 mm early post-larvae of Japanese sardine (Sardinops melanostictus) and Pacific round herring (Etrumeus teres) were collected in Tosa Bay (Japan) during their major spawning period. Their diet and environmental plankton communities were  investigated using metagenetic analysis of 18S V9 region.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Diversity, Ecology and Biogeochemistry of cyst-forming acantharia (Radiolaria) in the oceans

Marine planktonic organisms that undertake active vertical migrations over their life cycle are important contributors to downward particle flux in the oceans. Acantharia, globally distributed heterotrophic protists that are unique in building skeletons of celestite (strontium sulfate), can produce reproductive cysts covered by a heavy mineral shell that sink rapidly from surface to deep waters. We combined phylogenetic and biogeochemical analyses to explore the ecological and biogeochemical significance of this reproductive strategy. Phylogenetic analysis of the 18S and 28S rRNA genes of different cyst morphotypes collected in different oceans indicated that cyst-forming Acantharia belong to three early diverging clades from the orders Chaunacanthida and Holacanthida that are mainly heterotrophic. Environmental high-throughput V9 tag sequences and clone libraries showed that the three clades are widely distributed in the Indian, Atlantic and Pacific Oceans at different latitudes, but seem more abundant in regions of higher primary productivity. Moreover, sequences of cyst-forming Acantharia were distributed evenly in both the photic and mesopelagic zone, a vertical distribution that we attribute to their life cycle where flagellated swarmers are released in deep waters from sinking cysts. Bathypelagic sediment traps in the subantarctic and oligotrophic subtropical Atlantic Ocean showed that downward flux of Acantharia was only large at high-latitudes and during a phytoplankton bloom. High organic carbon export in cold waters would be a putative nutritional source for non-symbiotic juveniles ascending in the water column. This study improves our understanding of the life cycle and biogeochemical contribution of Acantharia, and brings new insights into a remarkable reproductive strategy in marine protists

Biome: root:Environmental:Aquatic:Marine
This workpackage details only the prokaryote (Archaea and Bacteria) analyses for the MicroPolar project.

DNA and cDNA (derived from total RNA) were amplified with primers for Illumina sequencing of the 16S rDNA gene.

Biome: root:Environmental:Aquatic:Marine
Bioaccumulation and gut microbiome response in the great pond snail Lymnaea stagnalis exposed to PBDEs in the presence and absence of nylon microplastics

It is recognised that microplastics will associate with persistent organic chemicals within the environment, potentially changing their bioavailability and the interaction of organisms with these chemicals. The aims of this study were to investigate how the presence of microplastics affect PBDE bioaccumulation and the gut microbiome in the great pond snailLymnaea stagnalis. Snails were exposed to microplastics and PBDEs independently and in combination for 96 hours. Microplastic particles (13-15 µm nylon powder) were mixed with quartz sand sediment at 1% w/w. A PBDE mix (containing BDE-47, 99, 100, 153 and PBB-153) was added to the sediment-microplastic mix in glass vessels at six environmentally relevant concentrations (94, 188, 375, 750, 1500, 3000 ng g-1 each PBDE), with six replicates consisting of one snail per treatment. There was no significant mortality observed in any of the treatments after 96 hours exposure. Of the six snails per treatment, three were analysed for PBDE tissue concentration and three were analysed for gut microbiome composition. The presence of microplastics did not significantly change PBDE bioaccumulation. However, our data indicate that that the presence of microplastics did influence gut microbial community diversity. In snails exposed to microplastics only (without PBDEs), microbial diversity was lower compared to those not exposed to microplastics. In the presence of microplastics, with increasing PBDE concentration, gut microbial diversity increased. In comparison, when microplastics were absent microbial communities were less diverse at the higher concentrations. A similar trend is reflected in the community composition data. These data imply that microplastics alone can influence the gut microbial community and they can also alter the effects of PBDEs on the gut microbiome. Given the importance of the gut microbiome for nutrition, metabolic function and immunity, such perturbation to the microbial community may have implications for organism health and fitness.

Biome: root:Host-associated:Mollusca:Digestive system
Microbiome of supragingival plaque from healthy volunteers

Microbiome of supragingival plaque from healthy volunteers

Biome: root:Host-associated:Human:Digestive system:Oral:Supragingival plaque
Development and acquisition of the microbiota across multiple body sites in preterm infants at risk of NEC and sepsis

Premature infants are at a high risk of developing necrotising enterocolitis. A microbial element of the condition has been confirmed, however exact aetiology remains enigmatic and ‘typical' microbiota development remains undefined. To characterise establishment of the severely preterm infant gut microbiota we employed targeted sequencing of the bacterial 16S rRNA gene. Sample types included oral and endotracheal swabs, stool and breast milk, collected from 7 patients over the first 2 months, postnatally (n = 158 samples). Propidium monoazide treatment was combined with targeted sequencing of the V4 region of the 16S rRNA gene to identify viable bacterial communities. Significantly lower alpha diversity was observed in stool than upstream mucosae (P < .005). Homogenising dispersal of dominant taxa was identified across all body-sites within the first week of life and persisted throughout the sampling period for all infants. Beta diversity was lowest immediately following birth and between proximal sampling sites. Oral microbiota showed the greatest similarity to stool (R2 = .73, P < 0.05), however the composition of stool microbiotas diverged from upstream mucosae over time (67% at WoL 1 vs 20% at WoL 8). We suggest a temporal pattern of gut microbiota development where speciation and divergence increase over time.

Biome: root:Host-associated:Human
Bacterial communitiy compositions on natural and artificial substrates in the Spermonde Archipelago, Indonesia

Populations on small islands surrounded by coral reefs often heavily depend on these reefs. The health and recovery of reefs are strongly influenced by recruitment of coral larvae. Their settlement relies on cues such as those emitted from bacterial communities forming biofilms on reef surfaces. Environmental conditions can change these bacterial community compositions (BCC) and may in turn affect settlement of coral larvae. We investigated BCC and coral larvae settlement at three small inhabited islands with different distance from the mainland in the Spermonde Archipelago, Indonesia. BCC and recruitment were analyzed on artificial ceramic tiles after 2-8 weeks exposure time and on natural reef substrate. Environmental analysis showed a clear separation in water parameters between inshore and near-shore/mid-shelf sites, as well as distinct benthic communities at all of the three sites. No coral recruitment was observed at the inshore site with highest anthropogenic impact. At the other two sites coral recruitment occurred on natural surfaces (recruits per 100 cm2: 0.73 ± 1.75 near-shore, 0.90 ± 1.97 mid-shelf), but there was no significant difference between the two sites. On artificial substrates coral recruitment differed between these two sites, with tile orientation and with exposure time of the tiles in the reef. The most abundant bacteria on both substrates were Gammaproteobacteria, Alphaproteobacteria and Cyanobacteria. BCC was strongly correlated with water quality and significant differences in BCC between the inshore site and near-shore/mid-shelf were found. On artificial substrates there was a significant difference in BCC with exposure time in the reef. Furthermore, bacterial communities on artificial tiles showed changes in their composition after being subjected to higher water temperatures in an experimental setting. We demonstrate how changes in water quality and temperature can affect BCC in coral reefs, which in turn could affect coral recruitment. Small islands such as these investigated feature a high spatial variability, as seen e.g. in environmental gradients, differences in BCC or in coral recruitment. Our study highlights the value of taking both BCC and coral recruitment into account in addition to the environmental conditions, when considering the recovery potential of coral reefs.

Biome: root:Environmental:Aquatic:Marine
Bacterial diversity in snow from mid-latitude mountain areas: Alps, Eastern Anatolia, Karakoram and Himalaya.

Snow can be considered an independent ecosystem that hosts active microbial communities. Snow microbial assemblages have been extensively investigated in the Arctic and in the Antarctica, but rarely in mid-latitude mountain areas. In this study, we investigated the bacterial communities of snow collected in four glacierized areas (Alps, Eastern Anatolia, Karakoram and Himalaya) by high-throughput DNA sequencing. We also investigated the origin of the air masses that produced the sampled snowfalls by reconstructing back-trajectories. A standardized approach was applied to all the analyses in order to ease comparison among different communities and geographical areas. The bacterial communities hosted from 25 to 211 Operational Taxonomic Units (OTUs), and their structure differed significantly between geographical areas. This suggests that snow bacterial communities may largely derive from ‘local' air bacteria, maybe by deposition of airborne particulate of local origin that occurs during snowfall. However, some evidence suggest that a contribution of bacteria collected during air mass uplift to snow communities cannot be excluded, particularly when the air mass that originated the snow event is particularly rich in dust.

Biome: root:Environmental:Aquatic:Freshwater:Ice
A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

Massively parallel pyrosequencing of amplicons from the V6 hypervariable regions of small-subunit (SSU) ribosomal RNA (rRNA) genes is commonly used to assess diversity and richness in bacterial and archaeal populations.  Recent advances in pyrosequencing technology provide read lengths of up to 240 nucleotides. Amplicon pyrosequencing can now be applied to longer variable regions of the SSU rRNA gene including the V9 region in eukaryotes. We present a protocol for the amplicon pyrosequencing of V9 regions for eukaryotic environmental samples for biodiversity inventories and species richness estimation. The International Census of Marine Microbes (ICoMM) and the Microbial Inventory Research Across Diverse Aquatic Long Term Ecological Research Sites (MIRADA-LTERs) projects are already employing this protocol for tag sequencing of eukaryotic samples in a wide diversity of both marine and freshwater environments.

Biome: root:Environmental:Aquatic:Marine
Short-term interaction of pyrene and cadmium in prokaryotic community in coastal sediment microcosms

Acute ecological impact of co-contamination of polycyclic aromatic hydrocarbons (PAHs) and heavy metals and their short-term interaction on diversity and composition of coastal benthic prokaryotes were unclear. We took pyrene (Pyr) and cadmium (Cd) as the representatives and mimicked an eight-week exposure of moderate and high levels of Pyr, Cd and their mixtures. 16S rRNA amplicon sequencing was used to investigate interaction of the contaminants in temporal succession of prokaryotes.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Prokaryotic community response to microalgal lysates

Changes in the community structure of heterotrophic prokaryotes in the open tropical Pacific in response to dissolved organic matter derived from microalgal lysates

Biome: root:Environmental:Aquatic:Marine:Oceanic