SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Metagenomic barcode approach of the ExStream Project 2014 for eukaryotes

Freshwater fungi have a crucial role in decomposition of organic material in aquatic ecosystems. Nevertheless they remain poorly investigated compared to fungi in other habitats like soil. Especially the community response to anthropogenic stressors is addressed in a very limited number of publications only.Therefore, we created a mesocosm experiment along an artificial sidearm of a freshwater stream in Germany, to test the effects of three stressors on the community composition. 64 mesocosms were equipped with litterbags (filled with leaf litter from riparian vegetation) and former sterilized ceramic tiles, which serve as a standardized sampling area for biofilm communities. An initial period of two weeks for colonization of respective compartments was followed by two weeks with stressor exposure. As stressors we chose fine sediment, salt (NaCl) and a reduction of flow velocity and all possible combinations. Each stressor and combination was applied in eight replicates. In contrast to the majority of hitherto published fungal freshwater studies we did not use morphological criteria to assess fungal communities but used a metagenomic barcode approach of the ITS nrDNA marker.Clustering of raw reads into Operational Taxonomic Units (OTUs) with CD-HIT-OTU and usearch revealed highly identical results between the two different algorithms. However, the detected 570 OTUs exceed the number of species detected with bait- and cultivation-based methods of former studies by factor three to ten. The unique study design with two different compartments enabled the identification of three different ecological gilds according to their compartment preferences. The first gild represents aquatic fungi, the second comprises amphibious fungi, while the third contains terrestrial fungi. Each gild is characterized by a unique stressor response supporting the idea to divide the total community of freshwater fungi into specific sub-communities. While aquatic and terrestrial fungi show no significant effect caused by the applied stressors, the amphibious fungi respond significantly towards the enriched salt concentrations. However we assume this signal to be a secondary effect since the amphibious fungi are highly correlated to algal communities, which are more prone to applied stressors than the fungal communities.

Biome: root:Environmental:Aquatic:Freshwater
Microbial populations of Lascauxs Apse in relation to collembola and black stains on cave walls.

In the Apse of Lascaux Cave (France), microorganisms present on and in arthropods were identified using the 16S rRNA genes specific for bacteria and the second internal transcribed spacer (ITS2) specific for fungi.

Biome: root:Environmental:Terrestrial:Deep subsurface
Fungal diversity associated with deep-sea asphalt seep mounds

Fungal diversity in deep-sea sediments associated with asphalt seep mounds was investigated by Ion torrent ITS amplicon sequencing.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
The San Pedro Ocean time-series is a marine time-series started circa 1997. This project aims to study ecological and biogeochemical implications of global marine microbial biodiversity.

The USC Microbial Observatory (Jed Fuhrman and David Caron, PIs) focuses on exploratory investigation of prokaryotic and unicellular eukaryotic diversity in the San Pedro Channel , California, with an initial focus on time-dependent changes in community composition in relation to environmental parameters. It also includes focused studies of particular microbial groups. We are currently in 12th year of this project.  Our primary sampling site is located midway between Los Angeles and the USC Wrigley Marine Laboratory on Santa Catalina approximately 900 m of water.  This site is visited monthly by ship for sampling to 500 m depth. Additional sampling is conducted on an ad hoc basis in coastal water near the lab on Catalina Island.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Amplicon Based Metagenomic Analysis of Microbial Composition of Kombucha

The aim of this study is to gain a more accurate and detailed insight about the microbial community of Kombucha during fermentation process employing 16S rRNA and ITS sequencing. Metagenomic DNA  was isolated from pellicule and liquid phase of two Kombucha samples obtained from Turkey at the days 3, 10 and 15 of the fermentation process. Isolated DNA samples were sequenced using amplicon based next generation sequencing.

Biome: root:Engineered:Food production:Fermented beverages
Pristine and TNT contaminated (tilled and untilled) soils


Biome: root:Environmental:Terrestrial:Soil
Amplicon sequencing of Tara Oceans DNA samples corresponding to size fractions for  large DNA viruses.

Seawater was filtered from different depths to retain small cell sizes (Girus Organisms). The DNA was extracted and amplified by PCR.

Biome: root:Environmental:Aquatic:Marine
Rhizosphere microbial community manipulated by 2-year consecutive bio-fertilizer application exhibited excellent disease suppression to banana Fusarium wilt disease

2-year consecutive application of bio-fertilizer to a banana orchard with serious Fusarium wilt disease effectively controlled this soil-borne disease reported in our previous work. Deep pyrosequencing of 16S rRNA and ITS genes were performed to investigate how rhizosphere microbial community responded to application of bio-fertilizer (BIO), common pig manure compost (PM) and only chemical fertilizer (CF) and to explore the potential correlation between microbial community and Fusarium wilt disease suppression. In total 104,201 bacterial 16S and 154,953 fungal ITS sequence reads were obtained after basal quality control. Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Ascomycota were the most abundant bacterial and fungal phyla. The alpha diversity of bacteria was significantly increased while that of fungi significantly reduced after 2-year consecutive bio-fertilizer application. Acidobacteria and Firmucutes were significantly elevated while Proteobacteria and Ascomycota significantly depleted in the rhizosphere after bio-fertilizer application. Moreover, genera of Gp1, Gp3, Leptosphaeria and Phaeosphaeriopsis were also significantly enriched in BIO treatment compared to PM and CF treatments. Interestingly, Fusarium was also significantly reduced in BIO treatment compared to CF treatment and a slightly reduce without significance compared to PM treatment. Furthermore, the disease incidence was negatively correlated to the enrichment of Gp1, Gp3, Leptosphaeria and Phaeosphaeriopsis while positively correlated to depletion of Fusarium. In conclusion, the reduction of the Fusarium wilt disease incidence after a 2-year application of bio-fertilizer might be attributed to the fact that application of bio-fertilizer containing Bacillus sp. induced general suppression by modulating rhizosphere the microbial community.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Defining the oral microbiome by Whole Genome Sequencing and resistome analysis: the complexity of the healthy picture

The microbiome of the oral cavity is the second largest and diverse microbiota after the gut, harboring over 700 species of bacteria and including also fungi, viruses and protozoa. A detailed site-specific map of oral microorganisms (including also eukaryotes and viruses) and their relative abundance is still missing. The data of this study provide for the first time a comprehensive view of the healthy oral microbiome  and its resistome, contributing to a deeper understanding of the composition of oral microbiome in the healthy subject, and providing an important reference for future studies exploring functional and metabolic alterations associated with diseases, which might be useful in identifying microbial signatures for targeted therapies and precision medicine.

Biome: root:Host-associated:Human:Digestive system:Oral
Strongyle Infection and Gut Microbiota: Profiling of Resistant and Susceptible Horses Over a Grazing Season

Gastrointestinal strongyles are a major threat to horses health and welfare. Given that strongyles inhabit the same niche as the gut microbiota, they may interact with each other. These beneficial or detrimental interactions are unknown in horses and could partly explain contrasted susceptibility to infection between individuals. To address these questions, an experimental pasture trial with 20 worm-free female Welsh ponies (10 susceptible (S) and 10 resistant (R) to parasite infection) was implemented for 5 months. Fecal egg counts (FEC), hematological and biochemical data, body weight and gut microbiological composition were studied in each individual after 0, 24, 43, 92 and 132 grazing days. R and S ponies displayed divergent immunological profiles and slight differences in microbiological composition under worm-free conditions. After exposure to natural infection, the predicted R ponies exhibited lower FEC after 92 and 132 grazing days, and maintained higher levels of circulating monocytes and eosinophils, while lymphocytosis persisted in S ponies. Although the overall gut microbiota diversity and structure remained similar during the parasite infection between the two groups, S ponies exhibited a reduction of bacteria such as Ruminococcus, Clostridium XIVa and members of the Lachnospiraceae family, which may have promoted a disruption of mucosal homeostasis at day 92. In line with this hypothesis, an increase in pathobionts such as Pseudomonas and Campylobacter together with changes in several predicted immunological pathways, including pathogen sensing, lipid metabolism, and activation of signal transduction that are critical for the regulation of immune system and energy homeostasis were observed in S relative to R ponies. Moreover, S ponies displayed an increase in protozoan concentrations at day 92, suggesting that strongyles and protozoa may contribute to each others success in the equine intestines. It could also be that S individuals favor the increase of these carbohydrate-degrading microorganisms to enhance the supply of nutrients needed to fight strongyle infection. Overall, this study provides a foundation to better understand the mechanisms that underpin the relationship between equines and natural strongyle infection. The profiling of horse immune response and gut microbiota should contribute to the development of novel biomarkers for strongyle infection.

Authors: Allison Clark, Guillaume Salle, Valentine Ballan, Fabrice Reigner, Annabelle Meynadier, Jacques Cortet, Christine Koch, Mickael Riou, Alexandra Blanchard, Nuria Mach

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
The microbiome of healthy horses compared to those with antimicrobial associated diarrhea or primary Salmonellosis

This project compares the fecal microbiome of healthy horses to those who have developed colitis either from antimicrobial use or Salmonella without prior antimicrobial administration.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Metagenomic analysis of gut microbiota in sows and piglets (EBI)

We studied the intestinal microbiome in feces from sows, five days after farrowing, their piglets during suckling and two weeks after weaning, 5-day old artificially reared and formula-fed siblings, and FP infected with Clostridium difficile.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
POULTRY METAGENOMICS: DIFFERENT FEEDING PRACTICES

BROILERS MAINTAINED UNDER DIFFERENT FEEDING CONDITIONS WERE ANALYSED FOR TAXONOMIC AND FUNCTIONAL ASPECTS

Biome: root:Host-associated:Birds
EMG produced TPA metagenomics assembly of PRJEB11511 data set (Assembly of a 5300-year-old Helicobacter pylori genome from the intestine content of the tyrollean glacier mummy).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB11511, and was assembled with metaSPAdes v3.13.0. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system.

Biome: root:Host-associated:Human:Digestive system
Assembly of a 5300-year-old Helicobacter pylori genome from the intestine content of the tyrollean glacier mummy

The stomach bacterium Helicobacter pylori is one of the most prevalent human pathogens. It has dispersed globally with its host for the past 100,000 years leading in a distinct phylogeographic pattern in modern H. pylori populations. This phylogeography is used to deduce both recent and ancient human migrations (1, 2). Owing to the complex demographic history of Europe, different hypotheses about the origin of the extant European H. pylori population (hpEurope) exist (3, 4). Here, we present a 5,300-year-old high-coverage H. pylori genome from a European Copper Age glacier mummy. Comparative sequence analysis with contemporary H. pylori classifies the Iceman Helicobacter as a cagA positive vacA s1a/i1/m1 type strain, most closely resembling a strain that today is commonly found in Central and South Asia and that substantially shaped the genomes of modern European H. pylori strains.

Biome: root:Host-associated:Human:Digestive system
equine gut metagenome Targeted Locus

Microflora of the Equine Hindgut.  This project is pyrosequencing bacterial 16S rRNA amplicons from horse fecal and cecal samples to examine the microflora in the equine hindgut.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Investigation of the bacterial microbiome of drinking water for poultry

Samples of drinking water were collected from poultry houses to examine the drinking water bacterial microbiome and how this changes during the production cycle.  Samples were collected for two consecutive production cycles from each six farms during the early, middle and late parts of the cycle.  Water samples (1 litre) were transported to the laboratory on ice and filtered through a 0.22m cellulose acetate filters. These filters were then frozen until DNA was extracted from them using Qiagen Powersoil Pro kit (according to manufacturers instructions).  The v4 region of the 16s rRNA gene was sequenced using an Illumina Miseq (250bp paired end reads).

Biome: root:Environmental:Aquatic:Freshwater:Drinking water
An investigation of the microbial population in different regions of the large intestine of the horse by 454 pyrosequencing

The aim of the study was to investigate the microbial population within different regions of the large intestine of the horse for healthy animals on a fibre based diet. A further question investigated was if there is a core microbial population found in all animals. Samples of luminal gut contents were collected from the terminal ileum and seven regions of the large intestine (caecum, right ventral colon (RVC), left ventral colon (LVC), left dorsal colon (LDC), right dorsal colon (RDC), small colon (SC) and the rectum) from five thoroughbred horses) and five British native breed ponies) euthanized for non-research purposes. Samples were taken in triplicate (240 samples in total).Genomic DNA was extracted, the V1-V2 region of the 16SrRNA was amplified before being sequenced using the Roche 454 GS FLX Titanium series sequencer.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine
Effect of Road Transport on the Equine Cecal Microbiota

The effects of travel stress on the equine cecal microbiota are poorly understood. We hypothesized that travel would affect the equine cecal microbiota. Cecally-cannulated horses (n 14 6) were randomly assigned to one of two groups, travel (n 14 3) and control (n 14 3). Horses received a basal diet (Strategy, Purina Animal Nutrition) with 1.2% body weight mixed grass/alfalfa. Travel horses were transported to an unfamiliar location, stalled to simulate weekend horse show conditions, and then returned to the Southern Illinois University Equine Center. Control horses remained at the equine center for the entire study. Cecal fluid was collected on a 6-hour rotating schedule, four times daily throughout the 6-day study. Data were analyzed using mixed models in SAS with P < .05. Cecal bacterial DNA was extracted, followed by 16S RNA sequencing and then analyzed using QIIME 1.8.0. Averages of sequence data were reported by phase (baseline, transportation, post-travel). Although there were no effects of travel associated with b-diversity (P > .05), analysis of a-diversity measures indicated an effect within the travel group during the transportation phase as compared with baseline (P < .05). Interestingly, a-diversity was also affected for control horses in the return phase when compared to baseline. This may be due to the disruption of the return of the travel group. In addition, we identified multiple taxa affected by travel at both the genus and phylum level. Continued profiling of equine gastrointestinal microbiota is necessary to improve our understanding of equine microbial dysbiosis.

Authors: Erin Perry, Tzu-Wen L Cross, Jesse M Francis, Hannah D Holscher, Stephanie D Clark, Kelly S Swanson

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
The composition of the equine microbiota undergoes a stepwise change in response to increasing levels of domestication

Changes to the gut microbiota have been associated with an increased incidence of disease in many species. This is particularly important during the process of domestication, where captive animals commonly suffer from gastrointestinal (GI) pathophysiology. Horses are a prime example of a domesticated species which suffers from a high incidence of (often life-threatening) GI disease. Some of the most significant factors affecting the gut microbiota in horses are diet, stress and drug administration, all of which are associated with the process of domestication. There are no studies, to date, which describe the effect of increasing levels of domestication on the equine microbiota whilst controlling effectively for confounding variables. Here we aimed to do this by measuring the GI microbiota of adult female Exmoor ponies under 3 management conditions, representing different levels of domestication. Faecal samples were collected from 29 ponies in the South West of the UK; ponies were categorised as Feral (n=10), Semi-Feral (n=10) and Domesticated (n=9), based on their management conditions. Diet was recorded and faecal counts were egg taken from all animals to assess parasite infection status. DNA was extracted and microbial composition identified via high-throughput sequencing of bacterial 16S rRNA gene. Bacterial communities were dominated by Firmicutes (36.71%) and Bacteroidetes (30.99%). Profound stepwise changes in global microbial community structure were seen in the transition from Feral -Semi-Feral- Domesticated groups  these changes were significant in a large number of bacterial phyla and at multiple taxonomic levels. In particular increases in members of the phylum Proteobacteria and Tenericutes were associated with the domesticated group; and increases in Methanobacteria were seen in the Feral group. Faecal egg counts were significantly different between groups, and regression between FEC and individual components of the microbiome revealed that a number of taxa associated with domestication level were also associated with parasite burden. Functional predictions based on microbiome data revealed increased amino acid and lipid metabolism in domesticated group, versus increased energy metabolism in feral group. Interestingly the semi-feral group had a wide variation in FEC and microbial alpha diversity and functional predictions were associated with disease pathways. In this study we have shown significant stepwise changes to GI microbiota due to domestication standardised in one breed of equine. A number of these changes were linked to parasite burden and, based on previous studies, the remainder are likely associated with diet. If we assume that the feral population has a more natural phenotype, akin to that with which horses have evolved, the data can potentially be used to provide bacterial markers of balanced gut homeostasis in domestic Exmoor ponies, and provide candidate markers in other equine breeds.

Authors: Bull K, Davies G, Meier S, Peachey L

Biome: root:Host-associated:Mammals:Digestive system:Fecal
The effect of diet change and insulin dysregulation on the faecal microbiome of ponies

The equine microbiome can change in response to dietary alteration and may play a role in insulin dysregulation. The aim of this study was to determine the effect of adding pasture to a hay diet on the faecal bacterial microbiome of both healthy and insulin-dysregulated ponies. Faecal samples were collected from 16 ponies before and after dietary change to enable bacterial 16S rRNA sequencing of the V3V4 region. The dominant phyla in all samples were the Firmicutes and Bacteroidetes. The evenness of the bacterial populations decreased after grazing pasture, and when a pony was moderately insulin dysregulated (P=0.001). Evenness scores negatively correlated with post-prandial glucagon-like peptide-1 concentration after a hay-only diet (r2=0.7, P=0.001). A change in diet explained 3% of faecal microbiome variability. We conclude that metabolically healthy ponies have greater microbial stability when challenged with a subtle dietary change, compared with moderately insulin-dysregulated ponies.

Authors: Danielle M Fitzgerald, Robert J Spence, Zachary K Stewart, Peter J Prentis, Martin N Sillence, Melody A de Laat

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Investigation of the bacterial microbiome of poultry litter

Samples of litter were collected from poultry houses to examine the litter bacterial microbiome and how this changes during the production cycle.  Samples were collected from six farms which used a variety of bedding types.  Samples were collected for two consecutive production cycles from each farm during the early, middle and late parts of the cycle.  Litter samples were transported to the laboratory on ice and thoroughly mixed with sterile phosphate buffered saline (PBS) at a 1:1 ratio (vol:vol). Aliquots of the PBS were frozen until DNA was extracted using Qiagen Powersoil Pro kit (according to manufacturers instructions).  The v4 region of the 16s rRNA gene was sequenced using an Illumina Miseq (250bp paired end reads).

Biome: root:Host-associated:Birds:Digestive system:Fecal
trial samples of a study in the Venice Lagoon

The samples belong to a project aiming to study the Venice lagoon from funcional prespective via metagenomics

Biome: root:Environmental:Aquatic:Marine
Mapping and Predictive Variations of Soil Bacterial Richness across French National Territory

Although numerous studies have demonstrated the key role of bacterial diversity in soil functions and ecosystem services, little is known about the variations and the determinism of such diversity on a wide scale. The overall objectives of this study were i) to describe the bacterial taxonomic richness variations across French national territory, ii) to identify the ecological processes (i.e. selection by the environment and dispersal limitation) and environmental filters most influencing this distribution, and iii) to develop a statistical predictive model of soil bacterial richness. We used the French Soil Quality Monitoring Network (RMQS), which covers all of France with 2,173 sites. The soil bacterial richness (i.e. OTU number) was determined by pyrosequencing 16S rDNA genes directly amplified from DNA of all soil samples and related to the soil characteristics, climatic conditions, geomorphology, land use and space. Mapping of bacterial richness revealed a heterogeneous spatial distribution, structured into patches of about 111 km, where the main drivers were the soil physico-chemical properties, the spatial descriptors and the land use. Based on these drivers, a predictive model was developed, which allows a good prediction of the bacterial richness (R2adj of 0.56) and provides a reference value for a given pedoclimatic condition.

Biome: root:Environmental:Terrestrial:Soil