SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
EMG produced TPA metagenomics assembly of PRJNA415710 data set (Elucidating the dandruff and non-dandruff scalp microbiome in Indian women and assessing the effect of coconut oil on it).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA415710, and was assembled with metaSPAdes v3.13.0. This project includes samples from the following biomes: root:Host-associated:Human:Skin.

Biome: root:Host-associated:Human:Skin
Elucidating the dandruff and non-dandruff scalp microbiome in Indian women and assessing the effect of coconut oil on it

The study aimed at exploring the scalp microbiome in Indian individuals with dandruff and non-dandruff scalp. Since, coconut oil is used in many parts of the country, the effect of coconut oil was also assessed on the microbiome in a time-course of 16 weeks.

Biome: root:Host-associated:Human:Skin
Effects of organic amendments in soil affected by fire in central Chile

This study tested the effects of fire and organic amendments on the microbial communities (16S and 18S) on Mediterranean areas of Chile

Biome: root:Environmental:Terrestrial:Soil
A metagenomic approach to understanding the microbial consequences of permafrost thaw in boreal Western Canada

This study sampled 20 lakes along a north-south permafrost gradient (continuous, discontinuous, sporadic, no permafrost) in boreal western Canada (Northwest Territories and Alberta). Samples were taken from the sediments at the edges of small boreal ponds, extracted using DNeasy Powersoil and then prepared for shotgun sequencing using an NEBNext Ultra II FS kit. Controls included: negative water only, Zymo Microbial community standard.

Biome: root:Environmental:Terrestrial:Soil:Permafrost
Comparison of the Fecal Microbiota of Healthy Horses and Horses with Colitis by High Throughput Sequencing of the V3-V5 Region of the 16S rRNA Gene.

Bacterial communities present in feces of six healthy horses and 10 horses affected by colitis were analyzed by 454 high throughput sequencing of the V3-V5 region of the 16S rRNA gene.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
human oral microbiome, metagenomic assembly

We investigated phylogenetic and functional markers of niche partitioning of enigmatic members of the oral cavity, with a focus on members of the candidate phylum TM7. We used a metagenomic assembly and binning approach to recover metagenome-assembled genomes (MAGs) from the supragingival plaque and tongue dorsum of healthy individuals, and used long-read sequencing to associate TM7 MAGs with previously identified phylotypes through 16S rRNA sequence comparison. Our genomes represent prevalent and abundant lineages that lack genomic representation in the HOMD and National Center for Biotechnology Information (NCBI) genomic databases, including members of the Candidate Phyla Radiation. Using a multi-omics approach we show that oral TM7 species are split into plaque and tongue specialists, and that plaque TM7 phylogenetically and functionally associate with environmental TM7, while tongue TM7 associate with TM7 from animal guts. To assess the generality of our results we carried out read recruitment from approximately 200 tongue and 200 plaque Human Microbiome Project (HMP) samples; which confirm that the genomes we identified are prevalent, abundant, and site-specific. Our findings suggest that at least for TM7, dental plaque resembles non-host habitats, while tongue- and gut-associated TM7s are more strongly shaped by the host. In addition, our results shed light on other understudied members of the oral cavity, and allow for better genomic insight into prevalent, yet poorly understood members of the oral microbiome.

Biome: root:Host-associated:Human:Digestive system:Oral
Characterizing the gut microbiome of the last population of undomesticated horses living in the wild, the Przewalski horse

The domestication of animals is often viewed as one of the most important developments in modern human history. Although much attention has been paid to the effects of domestication on host phenotypes, the effects of domestication on the host gut microbiome is relatively understudied. Given the important role of the mammalian gut microbiome in host health, nutrition, and the immune system (McFall-Ngai et al. 2013), filling this knowledge gap has important potential health implications for livestock, pets, and for improving current management strategies. The diet of domesticated animals is often highly different and less varied than their ancestral diet (e.g. dogs eating Iams or Purina processed food vs. wolves eating caribou or bison). We propose to study equids as a model for investigating the effects of domestication in mammals. We collected fecal samples from 45 individuals in the last wild population of the highly endangered Przewalski horse (Equus przewalskii) in Mongolia. The horse population was monitered with binoculars and fecal material was collected within an hour (usually within minutes) of defecation, allowing each fecal sample to be associated with a particular horse. Extremely detailed metadata is available for the population investigated, including pedigree, age, social structure, health, reintroduction dates, whole-genome data and years of daily behavioral observations in the field. We will compare the gut microbiota of these samples to fecal samples collected from 36 wild, domesticated horses living in the same region of Mongolia, which will allow us to isolate the effects of domestication/species differences from effects of current diet. We hypothesize that the gut microbiome of domesticated horses will have lower microbial diversity than the microbiome of their undomesticated relatives.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Temporal stability of equine microbiome

Twelve mature (aged 5-16 years) horses and ponies of mixed breed and type were fed restricted quantities of one of two fibre based diets formulated to be iso-caloric. Diet 1 comprised of 0.8% body mass (BM) of chaff based complete feed plus 0.45% BM low energy grass hay (the same hay used for both diets). Diet 2 comprised 0.1% BM of a nutrient balancer plus 1.15% BM grass hay. Faecal samples were collected at week 10 and week 16.  DNA was extracted and the V1-V2 regions of 16SrDNA were 454-pyrosequenced to investigate the bacterial microbiome of the horse. The two most abundant phyla found in both diets and sampling periods were the Firmicutes and Bacteroidetes. There was a limited degree of stability within the bacterial community of the hindgut of horses over a 6 week period with between 50 -65% of the bacteria in any horse common over the period.  What is of greater interest is that the core community in the horse does not appear to be markedly more stable than the total bacterial community.  This could clearly be a factor which contributes to the horse being more susceptible to gastrointestinal challenge and warrants significant further investigation.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
The impact of fructooligosaccharide supplementation on the gastrointestinal microbiome of Thoroughbred youngstock during nutritional stress

Background: Feeding of domesticated horses with carbohydrate-rich diets is associated with a high risk of gastrointestinal (GI) diseases. Prebiotic supplements, such as fructooligosaccharides (FOS), are promoted as gut stabilizers by reducing potentially pathogenic bacteria in the GI tract in response to carbohydrate overload. However, studies supporting FOS use have had mixed results and use outdated culture-based techniques.Objectives: To evaluate the impact of FOS prebiotics on the GI microbiome of Thoroughbred yearlings by genetic profiling of the microbiome. Study Design: Randomized case-control study.Methods: 12 male Thoroughbred yearlings were recruited by random selection into 2 groups: a prebiotic group (receiving 30g/day FOS dietary supplement for 8 weeks) and a control group (no FOS supplement). Samples were taken prior to supplementation and subsequently bi-weekly and were analyzed through microbial 16S rRNA sequencing. Qiime 2 and Calypso were used for bioinformatics and statistical analysis.Results: The prebiotic and control group had statistically significant differences in microbiome composition and diversity in the baseline sample prior to prebiotic administration. There were no significant global GI microbiome changes over time following FOS supplementation compared to the control group. Some saccharolytic bacterial species showed diverging (increasing in FOS and decreasing in control) patterns of abundance over time between groups.Main Limitations: The small sample number may reduce the relevance of the results. Also, additional factors, such as social interactions and individual wellbeing, could influence the GI microbiome.Conclusions: Contrary to previous culture-based studies, this preliminary study shows limited effects of FOS administration on the GI microbiome, however, the alterations in abundance of some saccharolytic bacterial species show potential for further investigation. Furthermore, the difference in baseline microbiomes between our study groups prior to FOS supplementation highlight the importance of baseline samples in interventional microbiome research.

Biome: root:Host-associated:Mammals:Digestive system
The effect of host phenotype on faecal microbiome in the horse

Gastrointestinal microbial communities are implicated in host susceptibilities to  utritional/metabolic diseases; which are more prevalent in obese and/or older horses. This controlled study offered a platform to evaluate associations between host-phenotype and the fecal microbiome / metabolome. Thirty-five, Welsh Mountain pony mares were studied across 2 years (Controls, n = 6/year, 5-15 years, body condition score (BCS) 4.5-6/9; Obese, n = 6/year, 5-15 years, BCS >7/9; Aged, n = 6 Year 1; n = 5 Year 2, 19 years old). Animals were individually fed the same hay to maintenance (2% body mass as daily dry matter intake) for 2 (aged / obese) or 4 (control), 4-week periods in a randomized study. Outset phenotype was determined (body fat%, markers of insulin sensitivity). Feces were sampled on the final 3 days of feeding-periods and communities determined using Next Generation Sequencing of amplified V1-V2 hypervariable regions of bacterial 16S rRNA. Copy numbers for fecal bacteria, protozoa and fungi were similar across groups, whilst diversity was increased in the obese group. Dominant bacterial phyla in all groups were Bacteroidetes>Firmicutes> Fibrobacter. Significant differences in the bacterial communities of feces were detected between host-phenotype groups. Relative to controls, abundances of Proteobacteria were increased for aged animals and Bacteroidetes, Firmicutes and Actinobacteria were increased for obese animals. Over 500 bacterial operational taxonomic units (OTUs) differed significantly between host-phenotype groups. No consistent pattern changes in discriminant OTUs between groups were maintained across groups and between years. The core bacterial populations contained 21 OTUs, 6.7% of recovered sequences.Distance-based Redundancy Analyses separated fecal bacterial communities with respect to markers of obesity and insulin dysregulation, as opposed to age. Host-phenotype had no impact on the apparent digestibility of dietary GE or DM, fecal volatile fatty acid concentrations or the fecal metabolome (FT-IR).The current study demonstrates that host-phenotype has major effects on equine fecal microbial population structure. Changes were predominantly associated with the obese state, confirming an obesity-associated impact in the absence of nutritional differences. Clear biomarkers of animal-phenotype were not identified within either the fecal microbiome or metabolome, suggesting functional redundancy within the gut microbiome and/or metabolome.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Removal of adult cyathostomins alters faecal microbiota and promotes an inflammatory phenotype in horses

The interactions between parasitic helminths and gut microbiota are considered to be an important, although as yet incompletely understood, factor in the regulation of immunity, inflammation and a range of diseases. Infection with intestinal helminths is ubiquitous in grazing horses, with cyathostomins (about 50 species of which are recorded) predominating. Consequences of infection include both chronic effects, and an acute inflammatory syndrome, acute larval cyathostominosis, which sometimes follows removal of adult helminths by administration of anthelmintic drugs. The presence of cyathostomins as a resident helminth population of the equine gut (the helminthome) provides an opportunity to investigate the effect helminth infection, and its perturbation, has on both the immune system and bacterial microbiome of the gut, as well as to determine the specific mechanisms of pathophysiology involved in equine acute larval cyathostominosis. We studied changes in the faecal microbiota of two groups of horses following treatment with anthelmintics (fenbendazole or moxidectin). We found decreases in both alpha diversity and beta diversity of the faecal microbiota at Day 7 post-treatment, which were reversed by Day 14. These changes were accompanied by increases in inflammatory biomarkers. The general pattern of faecal microbiota detected was similar to that seen in the relatively few equine gut microbiome studies reported to date. We conclude that interplay between resident cyathostomin populations and the bacterial microbiota of the equine large intestine is important in maintaining homeostasis and that disturbance of this ecology can lead to gut dysbiosis and play a role in the aetiology of inflammatory conditions in the horse, including acute larval cyathostominosis.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
The relationships between faecal egg counts and gut microbial composition in UK Thoroughbreds infected by cyathostomins

A growing body of evidence, particularly in humans and rodents, supports the existence of a complex net- work of interactions occurring between gastrointestinal (GI) helminth parasites and the gut commensal bacteria, with substantial effects on both host immunity and metabolic potential. However, little is known of the fundamental biology of such interactions in other animal species; nonetheless, given the considerable economic losses associated with GI parasites, particularly in livestock and equines, as well as the global threat of emerging anthelmintic resistance, further explorations of the complexities of host- helminth-microbiota interactions in these species are needed. This study characterises the composition of the equine gut commensal flora associated with the presence, in faecal samples, of low (Clow) and high (Chigh) numbers of eggs of an important group of GI parasites (i.e. the cyathostomins), prior to and fol- lowing anthelmintic treatment. High-throughput sequencing of bacterial 16S rRNA amplicons and asso- ciated bioinformatics and statistical analyses of sequence data revealed strong clustering according to faecal egg counts (P = 0.003). A trend towards increased populations of Methanomicrobia (class) and Dehalobacterium (genus) was observed in Clow in comparison with Chigh. Anthelmintic treatment in Chigh was associated with a significant reduction of the bacterial Phylum TM7 14 days post-ivermectin administration, as well as a transient expansion of Adlercreutzia spp. at 2 days post-treatment. This study provides a first known insight into the discovery of the intimate mechanisms governing host-parasite- microbiota interactions in equines, and sets a basis for the development of novel, biology-based interven- tion strategies against equine GI helminths based on the manipulation of the commensal gut flora.

Biome: root:Host-associated:Mammals:Digestive system
Hospitalized Horse Fecal samples Targeted Locus (Loci)

This study is a rather limited survey on 30 hospitalized horses with or without diarrhea. The fecal samples were investigated for the presence of pathogenic Clostridium difficile and for a 16S metagenetic survey of the fecal microbiota.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Broodmare faecal microbiota

Changes in faecal microbiota in broodmares around the time of foaling

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Dysbiosis associated with acute helminth infections in herbivorous youngstock  observations and implications

A plethora of data points towards a role of the gastrointestinal (GI) microbiota of neonatal and young vertebrates in supporting the development and regulation of the host immune system. However, knowledge of the impact that infections by GI helminths exert on the developing microbiota of juvenile hosts is, thus far, limited. This study investigates, for the first time, the associations between acute infections by GI helminths and the faecal microbial and metabolic profiles of a cohort of equine youngstock, prior to and following treatment with parasiticides (ivermectin). We observed that high versus low parasite burdens (measured via parasite egg counts in faecal samples) were associated with specific compositional alterations of the developing microbiome; in particular, the faecal microbiota of animals with heavy worm infection burdens was characterised by lower microbial richness, and alterations to the relative abundances of bacterial taxa with immune-modulatory functions. Amino acids and glucose were increased in faecal samples from the same cohort, which indicated the likely occurrence of intestinal malabsorption. These data support the hypothesis that GI helminth infections in young livestock are associated with significant alterations to the GI microbiota, which may impact on both metabolism and development of acquired immunity. This knowledge will direct future studies aimed to identify the long-term impact of infection-induced alterations of the GI microbiota in young livestock.

Biome: root:Host-associated:Mammals:Digestive system
Intestinal microbiota present in the equine GI tract

The objective of this study was to compare the microbiota present in several compartments of the gastro-intestinal tract of horses. This data should reveal impact of different environmental conditions like low pH, low Oxygen tension and the presence of digestive enzymes on the bacterial communities present in each compartment.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine
Equine fecal microbiota Raw sequence reads

A healthy gastrointestinal (GI) tract with a properly established microbiota is necessary for a foal to develop into a healthy weanling. In this study, we hypothesized that gut establishment in the foal transitioning from a diet of milk to a diet of grain, forage, and pasture would be detectable through analyses of the fecal microbiotas. Fecal samples from 42 sets of foals and mares were collected at multiple time points ranging from birth to weaning. Bacterial DNA was isolated from the samples, and the V4 domains of bacterial 16S rRNA genes were amplified via polymerase chain reaction. Analyses were performed to characterize the microbiome as well as the relative abundance of microbiota present.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
The equine gastrointestinal microbiome: Impacts of weight-loss

Obesity is an important equine welfare issue. Dietary restriction is the most effective weight-loss tool, although individual animals range in their weight-loss propensity. Gastrointestinal-derived bacteria play a fundamental role in host-health and have been associated with obesity and weight-loss in other species. This study evaluated the faecal microbiome (next-generation sequencing of 16S rRNA genes) of 15 obese Welsh Mountain pony mares, across 2 years (n = 8 Year 1; n = 7 Year 2) before and after a 7-week period of dietary restriction (1% body mass hay as daily dry matter intake).  Losses in body mass ranged from 7.11% to 11.59%. Changes in the faecal microbiome composition following weight-loss included a reduction in the relative abundance of Firmicutes and Tenericutes and a reduction in indices of bacterial diversity. Pre-diet diversity was negatively associated with weight-loss. Pre-diet faecal acetate concentration was a strong predictor of subsequent weight-loss and negatively associated with Sphaerochaeta (Spirochaetes phyla) abundance. These data support a role for the faecal microbiome in weight-loss propensity in ponies and provide a baseline for research evaluating elements of the faecal microbiome in predicting weight-loss success in larger cohorts

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Characterization of the microbiota present in different compartments of the equine gastrointestinal tract

This study was designed to provide a detailed microbiological profile of the healthy equine gastrointestinal tract, including samples collected from both the lumen and mucosa of the dorsal and antral stomach, jejunum, ileum, cecum, ventral and dorsal colon. This study will provide the most detailed microbiological map of the healthy equine GI tract to date using culture-independent sequencing methods, and will serve as a baseline against which samples from horses with various health conditions can be compared.

Biome: root:Host-associated:Mammals:Gastrointestinal tract
Investigating the impact of anthelmintic treatment on the equine microbiome

This pilot study evaluates the hypothesis that anthelmintic drug administration will alter the equine fecal microbiome. To address this hypothesis, twelve horses were administered a single dose of a combination anthelmintic drug [active ingredients: Moxidectin and Praziquantel] on day 0; fecal samples were collected on day -3 (pre-treatment), day 2 (post-treatment 1), day 9 (post-treatment 2).

Biome: root:Host-associated:Mammals:Digestive system
Early development of the intestinal microbiota in horses, and associations with mare microbiotas

Equine rectal microbiota was sampled at birth, 24 hours later and 7 days later. The microbial DNA was analyzed by 16S rDNA amplicon sequencing using Illumina MiSeq. The foal microbiotas were compared to mare fecal, vaginal and oral microbiotas. Extensive negative controls are included.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine
Horse feces Raw sequence reads

In equids, susceptibility to disease caused by Rhodococcus equi occurs almost exclusively in foals. This distribution might be attributable to the age-dependent maturation of immunity following birth undergone by mammalian neonates that renders them especially susceptible to infectious diseases. Expansion and diversification of the neonatal microbiome contribute to development of immunity in the gut. Moreover, diminished diversity of the gastrointestinal microbiome has been associated with risk of infections and immune dysregulation. We thus hypothesized that varying composition or reduced diversity of the intestinal microbiome of neonatal foals would contribute to increased susceptibility of their developing R. equi pneumonia. The composition and diversity indices of the fecal microbiota at 3 and 5 weeks of age were compared among 3 groups of foals: 1) foals that subsequently developed R. equi pneumonia after sampling; 2) foals that subsequently developed ultrasonographic evidence of pulmonary abscess formation or consolidation but not clinical signs (subclinical group); and, 3) foals that developed neither clinical signs nor ultrasonographic evidence of pulmonary abscess formation or consolidation. No significant differences were found among groups at either sampling time, indicating absence of evidence of an influence of composition or diversity of the fecal microbiome, or predicted fecal metagenome, on susceptibility to subsequent R. equi pneumonia. A marked and significant difference identified between a relatively short interval of time appeared to reflect ongoing adaptation to transition from a milk diet to a diet including available forage (including hay) and access to concentrate fed to the mare.

Biome: root:Host-associated:Mammals:Digestive system:Fecal