SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
The faecal microbiome of forage-fed horses in New Zealand

The faecal microbiome of forage-fed horses in New Zealand is described and the dynamics is compared pre- and post-dietary change, using pyrosequencing of the 16S and 18S rRNA genes

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Changes in the Equine Fecal Microbiota Associated with the Use of Systemic Antimicrobial Drugs.

The intestinal tract is a rich and complex environment and its microbiota has been shown to have an important role in health and disease in the host. Several factors can cause disruption of the normal intestinal microbiota, including antimicrobial therapy, which is an important cause of diarrhea in horses. This study aimed to characterize changes in the fecal bacterial populations of healthy horses associated with the administration of frequently used antimicrobial drugs.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
effect of metronidazole on horse microbiota


Biome: root:Host-associated:Mammals
Human Oral, nasal microbiota and smoking

This project has two goals:1. To evaluate the effect of smoking on oral and nasal microbiota2. To compare the collection of different oral samples in microbiota profiling.

Biome: root:Host-associated:Human
Expression of immune regulatory genes correlate with the abundance of specific Clostridiales and Verrucomicrobia species in the equine ileum and cecum

Billions of bacteria inhabit the gastrointestinal tract. Immune-microbial cross talk is responsible for immunological homeostasis, and symbiotic microbial species induce regulatory immunity, which helps to control the inflammation levels. In this study we aimed to identify species within the equine intestinal microbiota with the potential to induce regulatory immunity. These could be future targets for preventing or treating low-grade chronic inflammation occurring as a result of intestinal microbial changes and disruption of the homeostasis. 16S rRNA gene amplicon sequencing was performed on samples of intestinal microbial content from ileum, cecum, and colon of 24 healthy horses obtained from an abattoir. Expression of genes coding for IL-6, IL-10, IL-12, IL-17, 18s, TNF, TGF, and Foxp3 in the ileum and mesenteric lymph nodes was measured by qPCR. Intestinal microbiota composition was significantly different in the cecum and colon compared to the ileum, which contains large abundances of Proteobacteria. Especially members of the Clostridiales order correlated positively with the regulatory T-cell transcription factor Foxp3 and so did the phylum Verrucomicrobia. We conclude that Clostridiales and Verrucomicrobia have the potential to induce regulatory immunity and are possible targets for intestinal microbial interventions aiming at regulatory immunity improvement.

Biome: root:Host-associated:Mammals:Digestive system
The bacterial microbiota in  different gastrointestinal tract compartments in Mongolian horses Raw sequence reads

This study was designed to provide a detailed microbiological profile of the Mongolian horses gastrointestinal tract, including samples collected from the lumen of the stomach, jejunum, ileum, cecum, ventral colon and dorsal colon.We characterized the microbial composition of the different parts of the Mongolian horse GIT using high throughput sequencing for the first time.

Biome: root:Host-associated:Mammals:Gastrointestinal tract
Temporal variation of the horse faecal microbiota

The study aimed at investigating temporal stability of faecal microbiota in horses managed on pasture. A group of 7 horses were sampled every 14 days for a year.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Horse faecal material Metagenome

Characterisation of the faecal microbiome of Thoroughbred racehorses.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Investigating gut microbiome in horses that had laparotomy for treatment of primary large colon disease

Horses treated surgically for colic signs associated with large colon disease are more likely to develop postoperative recurrent colic episodes. Delayed recovery of gut bacteria following surgery is one potential mechanism of this observation. The study aimed at investigating gut microbiota before and overtime following laparotomy in horses diagnosed with a primary large colon disease and to compare findings to a control group of horses undergoing emergency orthopedic treatment.

Biome: root:Host-associated:Mammals:Digestive system
Tibetan Chicken caecum feces Targeted Locus (Loci)

To reveal the bacteria community related to Tibetan Chicken caecum

Biome: root:Host-associated:Birds:Digestive system:Ceca
Molecular and Functional diversity of bacteria associated with earthworm gut


Biome: root:Host-associated:Annelida:Digestive system
Human sigmoid colon mucosal biopsy metagenomes in cohort with and without diverticula

The study''s goals were to look for associations between the microbial community and diverticulosis using a large cohort (535 patients) with and without diverticula of the sigmoid colon.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Sigmoid colon
Soil microbial diversity in the Maintenance of Exotic vs. Native Diversity experiment (depth study)

Grasslands dominated by non-native species have replaced purely native-dominated areas in many parts of the world. This replacement has led to altered plant-plant interactions aboveground, but it is poorly understood how soil microbial communities differ between native and exotic plant communities. We tested how exotic vs. native plant species and summer irrigation affect bacterial and fungal community composition and diversity in a common garden experiment, Maintenance of Exotic vs. Native Diversity. In this study, the samples were taken at various soil depth: 0-10 cm, 10-30 cm, 30-60 cm, and 60-100 cm to assess if these changes are maintained in deeper soil layers.

Biome: root:Environmental:Terrestrial:Soil
Bacterial and archaeal diversity on mammalian skin

Characterization of the microorganisms on skin is essential for understanding how a host evolves in association with its microbial symbionts, modeling immune system development, diagnosing illnesses, and exploring the origins and etiology of disease. Although many studies have characterized the human microbiome, far less is known about the skin microbiome of non-human mammals. The objective of this research was to create a baseline skin microbiome dataset for the Mammalia class, testing the effects of species, location, hygiene, body region, and biological sex. The back, torso, and inner thigh regions of 187 non-human mammals and 20 human participants were collected to include representatives from 38 species and 10 mammalian orders. Animals were collected from local farms, zoos, households, and the wild. All samples were amplified using the V3-V4 16S rRNA gene region and sequenced using a MiSeq (Illumina). Human skin was significantly less diverse than all other mammalian orders according to Shannon indices (6.54 versus 3.96, p < 0.001). The factor most strongly associated with community variation for all samples was whether the host was a human (PERMANOVA, F = 37.8, p < 0.001; Figure 2). By analyzing all samples together, random forest modelling identified that human and animal samples could be distinguished correctly 98.51.2% of the time. This study represents the largest mammalian skin microbiome project to date and is the first study to elucidate the skin microbiota for 32 distinct species. Additionally, these findings are the first to demonstrate that human skin is distinct, not only distinct from other Primates, but from all 10 mammalian orders sampled. Baseline data on the mammalian skin microbiome is crucial to make informed decisions for veterinarian research and conservation strategies, as well as providing implications for mammalian evolutionary history.

Biome: root:Host-associated:Mammals:Skin
Emergent simplicity in microbial community assembly

We established laboratory-adapted and self-assembled microbial communities to study the microbial community assembly.

Biome: root:Engineered:Lab Synthesis
Population-based study on tongue microbiota composition of Japanese elderly adults

Tongue coating samples were collected from Japanese community-dwelling elderly adults aged 70-80 years in a health examination performed as a part of the follow-up survey of the Hisayama cohort study on 2016. The V1-V2 regions of 16S rRNA gene amplicons were analyzed using Ion PGM. The project goal is to understand the variation among normal tongue microbiota observed the community-dwelling elderly adults.

Biome: root:Host-associated:Human:Digestive system:Oral:tongue dorsum
Development of outbred CD1 mouse colonies with distinct standardized gut microbiota profiles.

Outbred CD1 mouse colonies were generated to be colonized with four distinct complexgut microbiota (GM) profiles representing contemporary rodent producer profiles. Mice were maintained atthe University of Missouri for nine generations and fecal samples were analyzed using 16S rRNA gene sequencing.Additionally, ninth generation mice were shipped to collaborating institutions and fecal samples were collectedand sequenced for detection of post-shipping associated shifts in GM profile.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
16S rRNA amplicon V4 Rag1KO and WT mice infected with Clostridium difficile

16S rRNA amplicon sequencing of V4 region from mus musculus (C57B6 WT and RAG1KO) intestinal communities collected over the course of a study which sought to determine the role of adaptive immunity in clearance of Clostridium difficile colonization.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Measures of reproducibility in sampling and laboratory processing methods in high-throughput microbiome analysis

Microbial community analysis can be biased by multiple technical factors, such as storage conditions, DNA extraction, or amplification conditions. In a high-throughput laboratory that relies on samples obtained from thousands of different subjects, knowledge of the extent of subject-introduced sampling and storage variation on the outcome of the inferred microbiome, as well as the effect of laboratory-introduced variation caused by reagent batches, equipment, or operator on the consistency of these processes within the laboratory is paramount. Here, we analyzed the effect of sampling from different parts of the same stool specimen or on different consecutive days, as well as short-term storage of samples at different temperatures on microbiome profiles obtained by 16S rRNA gene amplification. Each of these factors had relatively little effect on the microbial composition. In addition, replicate amplification of 44 stool samples showed reproducible results. Finally, 363 independent replicate extractions and amplifications of a single human homogenized stool (HS) specimen showed reproducible results (average Lins correlation = 0.95), with little variation introduced by HS batch, operator, extraction equipment, or DNA sequencer. In all cases, variations between replicates were significantly smaller than those between individual samples; subject identity always was the largest determinant. We propose that homogenized stool specimens could be used as quality control to routinely monitor the laboratory process and to validate new methods.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Deciphering microbial interactions in synthetic human gut microbiome communities

The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-dimensional consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi-species community dynamics, as opposed to higher-order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological drivers and responsive recipient species were discovered in the network. Our model demonstrated that a prevalent positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop that balances disparities in monospecies fitness levels. We show that negative interactions could generate history-dependent responses of initial species proportions that frequently do not originate from bistability. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis of microbial interactions. In sum, these methods defined the ecological roles of major human-associated intestinal species and illuminated design principles of microbial communities.

Biome: root:Host-associated:Human:Digestive system
Microbial communities associated with Eurasian watermilfoil, water and sediment

Characterize microbial communities associated with Eurasian watermilfoil, water and sediment in freshwater lakes in Minnesota USA

Biome: root:Environmental:Aquatic:Freshwater:Lake
Antibiotic induced changes in the microbiota disrupt redox dynamics in the gut

Mouse and ex vivo gut microbial responses to broad spectrum antibiotic treatment.

Biome: root:Host-associated:Mammals:Gastrointestinal tract
EPICON Sorghum Drought Microbiome

##### Experimental design# The following sequence data was used as part of a DOE funded project to explore the relationship between drought and microbial recruitment in Sorghum bicolor. For detailed descriptions of experimental design, please see the associated publication. In brief, we planted two different sorghum cultivars (RTx430 and BTx642) within a randomized block design that accounted for treatments, genotypes and replication, with three replicate blocks in total. From this field experiment, we collected a variety of plant phenotypes, soil measurements, and rhizosphere, root and soil samples for microbial community analysis and metatranscriptomics. All samples were collected weekly at the same time of day (between 10am and 1pm) and the same day of the week for seventeen weeks following seedling emergence (TP1 to TP17).

Biome: root:Host-associated:Plants:Rhizosphere
Quantitative genetic analysis of the maize phyllosphere

Sequencing of bacterial populations on maize leaves to identify the community structure and how the genetics of the maize plant impact its microbial communities.

Biome: root:Host-associated:Plants:Phylloplane
Gut microbiome in German Shepherd dogs

The aim of this study was to explore the development of the gut microbiota in 168 German Shepherd dogs (30 litters) from 7 weeks to 18 months of age and furthermore, to study the effect of relatedness , maternal microbiota composition and living environment in a large and well-defined population of dogs.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Temporal variation in pesticide biodegradation

Bacterial and phototrophic sequence reads for seasonal pesticide degradation project.

Biome: root:Environmental:Aquatic:Freshwater
The impact of tampon use on the vaginal microbiota

We conducted a cohort study with crossover design to assess the impact of tampon use on the composition and dynamics of the vaginal microbiota. Women self-collected vaginal swabs twice weekly for four menstrual cycles and used tampons as assigned during each menstrual cycle. We used 16S rRNA gene amplicon sequencing to characterize vaginal microbiota composition at each time point and observed a significant trend of decreased vaginal microbiota stability during menses compared to elsewhere during the menstrual cycle.

Biome: root:Host-associated:Human:Reproductive system:Vagina
Non-target effects of Metarhizium brunneum on soil microbial communities

The aim of this project was the assessment of potential non-target effects of the entomopathogenic fungus and biological control agent Metarhizium brunneum on soil fungal and prokaryotic community structures. To our knowledge, this research question was assessed for the first time using next generation sequencing technology of ribosomal markers. Non-target effect studies are required for product registration and expand knowledge on the impact of agricultural applications to the environment. M. brunneum was applied against Agriotes spp. in potato in a pot. The presence of the applied strain and the microbial community structures were monitored in soil over 4 months (1 pre-treatment sampling and 2 post-treatment samplings). M. brunneum was applied in different formulations and as unformulated spores. Controls included an insecticide, non-fungal components of the formulations and untreated pots.

Biome: root:Environmental:Terrestrial:Soil:Contaminated
Dynamics of human gut microbiota and metabolites in response to prebiotic interventions

Human gut microbiota composition and SCFA concentrations in response to prebiotic fiber supplementation in young adults.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Root bacterial and archaeal microbiota dynamics over the life cycle of rice plants. Targeted loci environmental

We monitored how the rice root microbiota changes over the course of the plant''s life cycle. We inspected how rhizocompartment, field geography, seasonal variation, and plant development rates affect this process.Using these data we formed a model to predict plant age and tested how abiotic factors affect microbiota development.

Biome: root:Host-associated:Plants:Root
Dietary fiber-deprived gut microbiota degrades the protective mucus barrier and promotes pathogen susceptibility

Little is known about how chronic or periodic dietary fiber deprivation impacts metabolism of the human gut microbiota and potentially leads to deterioration of colonic health. Here, we elucidated the mechanistic interactions among dietary fiber, the gut microbiota and the protective colonic mucus barrier that is one of the hosts first lines of defence. We employed a tractable approach consisting of a synthetic community of fully sequenced human gut bacteria assembled in gnotobiotic mice. The members of this community were selected to represent the phylogenetic diversity in a complete microbiota, but also based on empirical knowledge of their abilities to degrade various fiber polysaccharides and mucin glycans in vitro. The responses of this synthetic microbiota, and the corresponding impact on the host colonic mucus layer, to variation of dietary fiber were monitored by multiple readouts in conditions where mice were fed constant high- or low-fiber diets or daily alternations of the two. We show that starvation of dietary fiber diminishes the colonic mucus barrier by enhancing the activities of mucin-degrading bacteria. One-day alternations of the fiber-rich and fiber-free diets or feeding of a prebiotic diet still displayed thinner mucus barriers reflecting a residual increase in mucus-degrading bacteria and their mucin glycan-degrading enzymes. The microbiota starved of dietary fiber led to low-grade intestinal inflammation and heightened susceptibility to infection by a mucosal pathogen, Citrobacter rodentium, illustrating adverse effects of diet lacking complex natural fiber.

Biome: root:Host-associated:Mammals:Digestive system
Soil bacterial communities (Hainich National Park)

This study focuses on the influence of tree species composition, soil properties and seasonality on the structure of soil bacterial communities by employing high-throughput sequencing of the 16SrRNA gene. Soil cores were collected from bulk soil (0 - 5 cm depth) within eight tree clusters containing mono-species (beech, horn, lime and oak) and mixed-species (BOH, BOL, BHL and OHL) stands during Spring, Summer and Autumn 2012.

Biome: root:Environmental:Terrestrial:Soil
Infant (COPSAC) feces microbiome Raw sequence reads

16s rRNA gene sequencing of fecal samples of infants in the COPSAC2010 cohort

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Bacterial microbiomes of individual ectomycorrhizal Pinus sylvestris roots are shaped by soil horizon and differentially sensitive to nitrogen addition

Plant roots select non-random communities of fungi and bacteria from the surrounding soil that have effects on their health and growth, but we know little about the factors influencing their composition. We profiled bacterial microbiomes associated with individual ectomycorrhizal Pinus sylvestris roots colonised by different fungi and analysed differences in microbiome structure related to soils from distinct podzol horizons and effects of short term additions of N, a growth-limiting nutrient commonly applied as a fertiliser, but known to influence patterns of carbon allocation to roots. Ectomycorrhizal roots growing in soil from different horizons harboured distinct bacterial communities. The fungi colonising individual roots had a strong effect on the associated bacterial communities. Even closely related species within the same ectomycorrhizal genus had distinct bacterial microbiomes in unfertilised soil, but fertilisation removed this specificity. Effects of N were rapid and context dependent, being influenced by both soil type and the particular ectomycorrhizal fungi involved. Fungal community composition changed in soil from all horizons, but bacteria only responded strongly to N in soil from the B horizon where community structure was different and bacterial diversity was significantly reduced, possibly reflecting changed carbon allocation patterns.

Biome: root:Host-associated:Plants:Root
Topical treatment interventions elicit personalized and site-specific shifts in human skin bacterial communities

The skin microbiome represents a significant contributor to cutaneous health and disease. This includes its roles in immune tolerance and defense against pathogenic microorganisms. Despite these critical functions, the impact of topical interventions meant to disrupt these communities remains poorly understood. In this study, we present the effects of three clinically-relevant antiseptics, alcohol, povidone-iodine (Betadine), and chlorhexidine, on cutaneous bacterial populations. We illustrate a proficiency of these treatments in altering skin bacterial communities, a result which was highly dependent on interpersonal and body site-specific signatures. We also show that the magnitude of this response can be influenced by both the identity and relative abundances of bacterial inhabitants. By comparing the effects of antiseptic regimens, we highlight the importance of antibacterial activity and mechanical clearance to treatment disruption. We also demonstrate the potential for pre-treatment communities to inform post-treatment response. In all, these results further our understanding of treatment-derived perturbations to the skin microbiota, and establish the ability of topical interventions to influence skin bacterial dynamics.

Biome: root:Host-associated:Human:Skin
Fungal internal transcribed spacer 2 amplicons of sugarcane plant compartments and soils Targeted loci environmental

Unravelling the sugarcane microbiome

Biome: root:Host-associated:Plants:Rhizoplane:Endophytes