SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Diversity of microbial community (bacteria, micro-eukaryotes and fungi) in the Passage of Lascaux Cave.

In the Passage of Lascaux Cave (France), the potential effect of season, mineral substrate and presence of stains was tested on present (DNA) and active (RNA) microbial community with high-throughput sequencing.Three genes markers of microbial diversity were analyzed, the 16S rRNA genes specific for bacteria, the 18S rRNA genes specific for micro-eukaryotes and the second internal transcribed spacer (ITS2) specific for fungi. Sequences corresponding to active microbial community were named with c.

Biome: root:Environmental:Terrestrial:Deep subsurface
Fungal and bacterial decomposer taxa on Arabidopsis thaliana litter

Niche differentiation among species is a key mechanism by which biodiversity may be linked to ecosystem function. We tested a set of widely invoked hypotheses about the extent of niche differentiation in one of the most diverse communities on Earth  decomposer microorganisms  by measuring their response to changes in three abundant litter resources: lignin, cellulose, and nitrogen (N). To do this, we used the model system Arabidopsis thaliana to manipulate lignin, cellulose, and N availability and then used high-throughput DNA sequencing to measure the response of microbial communities during decay. Re-sequencing the decomposer communities after incubation of decomposed litter with pure substrates showed that groups of species had unique substrate use profiles, such that species organized into functional guilds of decomposers that were associated with individual litter chemicals.

Biome: root:Host-associated:Plants
CW_brewery_waste

Horizontal subsurface flow constructed wetland (HSSF-CW) enhaced wtih brewery waste amendment to treat nitrogen-rich leachates of a plant nursery crop.

Biome: root:Engineered:Food production:Fermented beverages
Piloderma and Ramaria Ectomycorrhizal Mat Soils Targeted Locus

Microbial communities associated with ectomycorrhizal mat soils were investigated as part of the HJ Andrews LTER Microbial Observatory II project.  Amplicon pyrosequencing of Fungal ITS and Bacterial 16S was used to quantify the microbial communities from two ectomycorrhizal mat forming genera (Piloderma and Ramaria) as well as non-mat soils.  Samples were split into organic and mineral soil horizons prior to sequencing.   The project was designed to explore the chemical and biological properties of mat-forming ectomycorrhizal fungi in the HJ Andrews forest.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
The impact of long-term N addition on temperature sensitivity to decomposition in a spruce forest

TBD

Biome: N/A
Accuracy of protist diversity assessments: morphology compared to cloning
                and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous
                tintinnid ciliates as a case study

Deep-sequencing technologies are becoming nearly routine to describe
                microbial community composition in environmental samples. 18S rDNA pyrosequencing
                has revealed a vast diversity of infrequent sequences, leading to the proposition of
                the existence of an extremely diverse microbial "rare biosphere". While rare
                microbes no doubt exist, critical views suggest that many rare sequences may
                actually be artifacts. However, information about how diversity revealed by
                molecular methods relates to that revealed by classical morphology approaches is
                practically non-existent. To address this issue, we used different approaches to
                assess the diversity of tintinnid ciliates, a species-rich group in which species
                can be easily distinguished morphologically. We studied two Mediterranean marine
                samples with different patterns of tintinnid diversity. We estimated tintinnid
                diversity in these samples employing morphological observations as well as both
                classical cloning and sequencing and pyrosequencing of two different markers, the
                18S rDNA and the ITS regions, applying a variety of computational approaches
                currently used to analyze pyrosequence reads. We found that both molecular
                approaches were efficient in detecting the tintinnid species observed by microscopy
                and revealed similar phylogenetic structures of the tintinnid community at the
                species level. However, depending on the method used to analyze the pyrosequencing
                results, we observed discrepancies with the morphology-based assessments up to
                several orders of magnitude. In several cases, the inferred number of operational
                taxonomic units (OTUs) largely exceeded the total number of tintinnid cells in the
                samples. Such inflation of the OTU numbers corresponded to "rare biosphere" taxa,
                composed largely of artefacts. Our results suggest that a careful and rigorous
                analysis of pyrosequencing datasets, including data denoising and sequence
                clustering with well-adjusted parameters, is necessary to accurately describe
                microbial biodiversity using this molecular approach.

Biome: root:Environmental:Aquatic:Marine
Deciphering the pathobiome: intra-and inter-kingdom interactions involving the pathogen Erysiphe alphitoides.

Plant-inhabiting microorganisms interact directly with each other, forming complex microbial interaction networks. These networks may be disrupted by the arrival of a new species, such as a pathogen infecting the plant. Here we decipher intra-kingdom and cross-kingdom interactions involving a pathogen species, by using a Bayesian method of network inference.  We use this method to highlight the most likely interactions between Erysiphe alphitoides, the causal agent of oak powdery mildew, and other foliar microorganisms of pedunculate oak (Quercus robur L.). Our results showed that infection by E. alphitoides is accompanied by drastic changes in the foliar fungal community composition but no significant change in the bacterial community composition. Our analyses highlighted 13 fungal Operational Taxonomic Units (OTUs) and 13 bacterial OTUs that are likely to interact directly with E. alphitoides. Four of the fungal OTUs were phyllosphere yeasts. The fungal endophytes Mycosphaerella punctiformis and Monochaetia kansensis were highlighted as potential antagonists of E. alphitoides. These potential interactions will have to be validated experimentally. The study of the temporal dynamics of microbial networks during the course of infection also appears to be a promising research avenue, that will undoubtedly give deeper insights into the ecology of this disease. Overall, we showed that combining metagenomics and network ecology may improve biological control of plant diseases, by highlighting potential antagonists of pathogen species.

Biome: root:Host-associated:Plants:Phylloplane
Soil samples Targeted Locus (Loci)

We hypothesize that a certain subset of soil microorganisms, of both bacteria and fungi, is distributed across the soil-plant continuum. Such evidence would lend credibility to a hypothesis that environmentally recruited microorganisms may establish endophytically in plant tissues, including seeds, and that at least some environmentally recruited endophytes might be then available for vertical transfer via seeds.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Sediment Metagenome of River Yamuna (Faizupur Khadar  , New Delhi s3)

To understand the microbial communities found in the contaminated sediments of the river Yamuna.

Biome: N/A
EMG produced TPA metagenomics assembly of PRJNA531097 data set (Sediment Metagenome of River Yamuna (Faizupur Khadar , New Delhi s3)).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA531097, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Sediment Metagenome of River Yamuna (Okhla Barrage, New Delhi s2)

To understand the microbial communities found in the contaminated sediments of the river Yamuna.

Biome: N/A
EMG produced TPA metagenomics assembly of PRJNA531090 data set (Sediment Metagenome of River Yamuna (Okhla Barrage, New Delhi s2)).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA531090, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Sediment Metagenome of River Yamuna (Wazaribad , New Delhi s1)

To understand the microbial Profile, in the contaminated sediments of the river Yamuna.

Biome: N/A
EMG produced TPA metagenomics assembly of PRJNA531081 data set (Sediment Metagenome of River Yamuna (Wazaribad , New Delhi s1)).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA531081, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Sediment Microbiome  of  River Ganga  (Jana village , Kanpur s3)

To understand the microbial communities found in the contaminated sediments of the river Ganga.

Biome: N/A
EMG produced TPA metagenomics assembly of PRJNA529797 data set (Sediment Microbiome of River Ganga (Jana village , Kanpur s3)).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA529797, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Sediment Microbiome  of  River Ganga  (Jajmau, Kanpur s2)

To understand the microbial communities found in the contaminated sediments of the river Ganga.

Biome: N/A
EMG produced TPA metagenomics assembly of PRJNA529770 data set (Sediment Microbiome of River Ganga (Jajmau, Kanpur s2)).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA529770, and was assembled with SPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Sediment Microbiome  of  River Ganga  (Nawabganj, Kanpur s1)

To understand the microbial communities found in the contaminated sediments of the river Ganga.

Biome: N/A
EMG produced TPA metagenomics assembly of PRJNA529749 data set (Sediment Microbiome of River Ganga (Nawabganj, Kanpur s1)).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA529749, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Sediment Microbiome  of  River Ganga  (Lalbag,Murshidabad, west Bangal F3)

To understand the microbial communities found in the sediments of the river Ganga.

Biome: N/A
EMG produced TPA metagenomics assembly of PRJNA531144 data set (Sediment Microbiome of River Ganga (Lalbag,Murshidabad, west Bangal F3)).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA531144, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Sediment Microbiome  of  River Ganga  (Paharghati Dhulian, west Bengal F2)

To understand the microbial communities found in the sediments of the river Ganga.

Biome: N/A
EMG produced TPA metagenomics assembly of PRJNA531106 data set (Sediment Microbiome of River Ganga (Paharghati Dhulian, west Bengal F2)).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA531106, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Sediment Microbiome  of  River Ganga  (Below Farakka bridge, west Bengal F1)

To understand the microbial communities, found in the sediments of the river Ganga

Biome: N/A
EMG produced TPA metagenomics assembly of PRJNA531084 data set (Sediment Microbiome of River Ganga (Below Farakka bridge, west Bengal F1)).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA531084, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
EMG produced TPA metagenomics assembly of PRJEB14491 data set (metagenomic Shotgun analysis of cecum microbiome of poultry).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB14491, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum.

Biome: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
Marine metagenomes from the bioGEOTRACES project

Marine metagenomes from the bioGEOTRACES project Metagenome

Biome: root:Environmental:Aquatic:Marine
Temporal shotgun metagenomic dissection of the coffee fermentation ecosystem

The current study employed a temporal shotgun metagenomic analysis of a prolonged (64 h) coffee fermentation process (six time points) to facilitate an in-depth dissection of the structure and functions of the coffee microbiome.

Biome: root:Engineered:Food production:Fermented beverages
a take on the impact of pollution on coastal bacterial communities

Coral reefs face increased environmental threats from anthropomorphic climate change and pollution, from agriculture, industries and tourism. They are economically vital for many people worldwide, and harbour a fantastically diverse ecosystem, being the home for many species of fish and algae. Surprisingly little is known about the microbial communities living in and in the surrounding of coral reefs. The objectives of this project is to characterise the community composition and function of bacteria living in the water and the upper sediment layer in close proximity of coral reefs. In this project we sequenced 3 water samples and 3 sediment samples out of the coast of Kenya, at 3 distinct location: Mombasa, Malindi and Kisite.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
marine metagenome Metagenome

To study the effect of diesel oil spills on microbial communities in the monitored basin experiment

Biome: root:Environmental:Aquatic:Marine
The impact of helminth infection on the mucosal and luminal GI microbiota of the horse

It is well established that the gastrointestinal (GI) microbiota regulate immune responses to GI pathogens. In particular, data from our group and others demonstrate that immune-modulatory GI microbes promote both immunopathology from, and facilitate chronic infection with, GI helminths. A deeper understanding of the mechanisms which govern these interactions will pave the way to designing novel approaches to helminth control, aimed at promoting an optimal immune response to infection whilst limiting pathology. Here we systematically described the impact of helminth infection on the GI microbiota in a herbivore-helminth system by comparing GI microbiota between acutely and chronically infected equine livestock and uninfected controls; and furthermore, we triangulated this data by profiling luminal and mucosal microbiota taken from throughout the GI tract at post-mortem in infected versus uninfected horses. The results revealed similarities between acute helminth infection models in mice and equines, suggesting that helminths may employ ubiquitous mechanisms in regulating host gut microbiota. Furthermore, the microbial signature of helminth infection was distinctly different between acutely and chronically infected animals, indicating that host adaptive immunity plays an important role in helminth-microbiota interactions. At post-mortem, data supported that from chronically infected animals, and also showed that the most profound impact of infection upon the GI microbiota was a significant down-regulation of methanogen populations. The implications of this finding for helminth control in the context of climate change will be discussed.Authors: Peachey L, Bull K, Jenkins T, Cantacessi C

Biome: root:Host-associated:Mammals:Digestive system
Short-term variability in the microbial, nano- and picoplankton dynamics during post-upwelling season at a fixed sampling point in St Helena Bay

The diversity and functionality of the organisms in the 10-0.2 m size range was studied at a fixed-point sampling site in St Helena Bay during the end of upwelling season.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Assessing secoisolariciresinol diglucoside metabolism in the rumen

Secoisolariciresinol diglucoside, a lignan found in many plants, predominantly in flaxseed. The plant lignan can play active role enhancing antioxidant capacity, however, it need to be  metabolized into enterolignans, process which the gut microbiota is responsible. The rumen is a known efficient environment for lignan metabolism, which comprises the breakdown of  SDG into secoisolariciresinol, then to enterodiol and enterolactone. The product  enterolactone increases concentration in the rumen as flax is added in the diet of ruminants  and the compound can be transferred to milk, benefiting human health by the functional food  intake, preventing many oxidative-related disorders such as cardiovascular diseases,  atherosclerosis, Alzheimers disease, breast-cancer and others. Although the knowledge on lignans metabolism in the rumen, little information is available regarding the microorganisms  linked to secoisolariciresinol diglucoside breakdown. The main bottleneck is that just few species of the rumen microbiome can be cultured in laboratory conditions, and thus, metagenomic approaches are needed to access the rumen ecology by-passing the in vitro culture. Therefore, a fosmid library was constructed using rumen microbes DNA inserts from the rumen of cows fed up to 15g/100g (dry matter basis) of flax meal, resulting on an 11,520 fosmid clones library, using Escherichia coli strain EPI300 as host bacteria. The library was screened for secoisolariciresinol diglucoside breakdown capacity using high-performance liquid chromatography and positive clones followed to plasmid DNA purification, deep sequencing and bioinformatic data analysis. Two out of 30 library plates showed effective secoisolariciresinol diglucoside breakdown, however, no metabolism products were identified and no putative gene linked to direct secoisolariciresinol diglucoside breakdown was identified from clones genome. To our knowledge this is the first fosmid library constructed to prospect rumen microorganisms with active role in plant lignans metabolism, thus, more studies regarding the subject must be carried out to broaden genes and enzymes involved in the process.

Biome: root:Host-associated:Mammals:Digestive system:Foregut:Rumen
We investigated the presence of electroactive bacteria associated with the ennoblement, an increase of the open circuit potential of stainless steel in seawater. Metagenomic result confirmed the presence of electroactive bacteria, and an associated metatranscriptomic analysis was carried out to study the gene expression and activity of the bacteria associated with ennoblement.

Stainless steel immersed in seawater have an increased risk of localized corrosion due an increase of the Open Circuit Potential (OCP), also referred as ennoblement. That increase of potential occurs during the first days of exposure and correlates to the presence and development of microorganisms naturally found in the seawater. In a previous study about the effect of temperature on ennoblement and stainless steel microbial communities, we identified an electroactive bacteria based on 16S rRNA gene sequencing and proposed a new model to explain how microorganisms could be able to change the OCP of stainless steel. In order to investigate the role of electroactive bacteria, we used normal and applied potential conditions with a metagenomic and metatranscriptomic approach. We confirmed the presence of electroactive bacteria associated with the ennoblement and investigated the gene expression associated with the different conditions.

Biome: root:Engineered
Assembly and activity of microbial communities in the Pacific temperate rainforest

Dataset includes 16S rRNA sequences from soil RNA and DNA extractions, metatranscriptomes and geochemical data related to ecological gradients and climactic variability in the Pacific temperate rainforest.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Identification of Intestinal Bacterial Taxa with a Potential Role in Parkinsons Disease using Illumina MiSeq and Ion Torrent Next Generation Sequencing

Parkinsons disease (PD) is one of the most common neurodegenerative disorders. It has been repeatedly reported that most patients with PD suffer from gastrointestinal dysfunctions and alterations of the autonomous nervous system in the gut wall called the enteric nervous system (ENS). Such alterations and functional gastrointestinal deficits might occur years before the classical clinical symptoms of PD appear. Until now, only little is known about PD-associated changes in gut microbiota composition and their implication in PD development. Due to variance in previously published reports about the differences between community composition in PD and non-PD patients, our intention is to increase knowledge in this field with the use of two next generation sequencing (NGS) methods (Illumina MiSeq and Ion Torrent PGM) on the same set of samples. The V4 and V5 hypervariable region of bacterial 16S rRNA genes was PCR-amplified from stool samples of 39 PD patients and 25 healthy, age-matched control persons, respectively. Illumina- and Ion Torrent- based sequencing yielded divergent as well as congruent results regarding the bacterial microbiota composition of PD and control samples.Bacterial taxa with differences in relative abundance between PD and control samples that were traceable with both sequencing techniques might play a role for supporting PD diagnosis and therapy.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
We investigated the presence of electroactive bacteria associated with the ennoblement, an increase of the open circuit potential of stainless steel in seawater. Metagenomic result confirmed the presence of electroactive bacteria.

Stainless steel immersed in seawater have an increased risk of localized corrosion due an increase of the Open Circuit Potential (OCP), also referred as ennoblement. That increase of potential occurs during the first days of exposure and correlates to the presence and development of microorganisms naturally found in the seawater. In a previous study about the effect of temperature on ennoblement and stainless steel microbial communities, we identified an electroactive bacteria based on 16S rRNA gene sequencing and proposed a new model to explain how microorganisms could be able to change the OCP of stainless steel. In order to investigate the role of electroactive bacteria, we used normal and applied potential conditions with a metagenomic approach.

Biome: root:Engineered