SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Feeding sows resistant starch during gestation and lactation impacts their faecal microbiota and milk composition but shows limited effects on their progeny

Establishment of a beneficial microbiota profile for piglets as early in life as possible is important as it will impact their future health. In the current study, we hypothesized that resistant starch (RS)  provided in the maternal diet during gestation and lactation will be fermented in their hindgut, which would favourably modify their milk and/or microbiota composition and that it would in turn affect piglets' microbiota profile and their absorptive and immune abilities. In this experiment, 33% of pea starch was used in the diet of gestating and lactating sows and compared to control sows. Their microbiota and milk composition were determined and the microbiota, short-chain fatty acids (SCFA) production and gut health related parameters of the piglets were measured two days before weaning.  In addition, their overall performances and post-weaning faecal score were also assessed. The RS diet modulated the microbiota of the sows during gestation, increasing the Firmicutes:Bacteroidetes ratio and the relative abundance of beneficial genera like Bifidobacterium but these differences disappeared during lactation and were not transmitted to the offspring. Milk protein and lactose concentrations were impacted by the diet, without an impact on piglets' bodyweight or diarrhoea frequency post-weaning.  Moreover, the intestinal morphology measured as villus height and crypt depths, and the inflammatory cytokines in the intestine of the piglets were not differentially expressed between maternal treatments.  Only ZO-1 was more expressed in the ileum of piglets born from RS sows, suggesting a better closure of the mucosa tight junctions. It is concluded that changes in the microbiota transferred from mother to piglets due to the inclusion of RS in the maternal diet are rather limited even though milk composition was affected.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
De novo whole metagenome sequencing studies

A comparative study between control and disease condition metagenome sampples.

Biome: root:Environmental:Aquatic:Freshwater:Pond
Flores_tongue_EBI

SMP - tongue samples from Flores_SMP ID:

Biome: root:Host-associated:Human:Digestive system:Oral:tongue dorsum
Human identification through analysis of the salivary microbiome

Human identification has played a prominent role in forensic science for the past two decades and will continue to do so.  The development of techniques to exploit samples, which cannot be satisfactorily analysed at present, is driving the field.  High-throughput sequencing techniques have been available for a few years however there are very few examples of their application in forensic science.   This study investigates the potential for bacteria found in the salivary microbiome to be used in a new method for human identification. Two different targets (16S RNA and rpoB) were chosen to maximise coverage of the salivary microbiome and when combined, they increase the power of identification. Paired-end Illumina high-throughput sequencing was used to analyse the bacterial composition of saliva from two different people at four different time points (t=0 and t=28 days and then one year later at t=0 and t=28 days).   Five major phyla dominate the samples: Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria. Streptococcus, a firmicute, is one of the most abundant genera found in saliva and targeting Streptococcus rpoB has enabled a deeper characterisation of the different streptococci species otherwise impossible with 16S rRNA alone. We have observed that samples from the same person group together regardless of time of sampling. However, samples taken one month apart group closer together than those taken one year apart. The results indicate that it is possible to distinguish two people using the bacteria found in their saliva.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Core function of microbiota in peri-implantitis and periodontitis

Eleven patients who have peri-implantitis and periodontitis were selected. They were evaluated based on the clinical examination and radiographic data. Sub-gingival and sub-mucosal biofilm samples were taken from the deepest pockets of each site, and we characterized bacterial community of 16S rRNA and 16S rRNA genes (rDNA) using Illumina miseq.

Biome: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood

Variation in the human oral microbial community composition in health and disease has been observed, but factors associated with this variation remain largely unstudied. We characterized inter- and intra-individual variation of microbial communities in the largest cohort to date (264 saliva samples), using culture-independent 16S rRNA pyrosequencing. We followed the temporal dynamics of their salivary microbiota over 10 years spanning adolescence, and determined the influence of human genotype, gender, age, puberty, and weight class on the microbial communities. Participants included 107 healthy individuals sampled mainly at ages 12-13, 17-18 and 22-24, with a few sampled as early as 8 years of age. In contrast to gut or skin microbiomes, there is a core genus-level salivary microbiome; individuals are more similar to themselves and their co-twins in the 12-17 and in the 17-22 cohorts than to the whole sample population, but not over the 10 years from 12 to 22; and human genotype has no significant role in the oral bacterial composition. The data are most consistent with shared environment serving as the main determinant of microbial populations. Twins resemble each other more closely than the whole population at all time-points, but become less similar to each other when they age and no longer cohabit. Several organisms have age-specific abundance profiles, including members of the genera Veillonella, Actinomyces, and Streptococcus. There is no clear effect of weight class, puberty, and gender. The results of this work will provide a basis to further study oral microbes and human health.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Oral bacterial 16S rRNA-V4 sequencing of four Japanese adults in multiple conditions of sample storage

The project contains bacterial partial 16S rRNA sequencing data of 66 supragingival plaque samples of upper molar teeth. Samples were taken from four adult Japanese males on September 7, 2013. Partial bacterial 16S rRNA V4 region (typically 259 base pairs) was amplified and sequenced based on the Illumina MiSeq paired-end read sequencing protocol. Maximum 96 combinations of dual-index tags (Illumina D-series) were used. All relevant research protocols and procedures were approved by Ethics Committee of Tohoku University School of Medicine, Sendai, Japan. All subjects provided written informed consent.

Biome: root:Host-associated:Human:Digestive system:Oral:Supragingival plaque
Population-based study on salivary microbiome of Japanese adults

We collected saliva from Japanese adults aged over 40 years inhabiting Hisayama town, Fukuoka, Japan in a health examination performed as a part of the follow-up survey of the Hisayama cohort study on 2007. The V1-V2 region of 16S amplicon sequence of human salivary microbiome were analyzed using Ion PGM. The project goal is to identify core and pan salivary microbiome in Japanese adults and to clarify the relationship with host''s health and health-related conditions.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Salivary microbiota of Japanese orally healthy adults, pool 4

V1-V2 region of 16S amplicon sequence of human salivary microbiome from 63 orally-healthy Japanese adults were analyzed using a 454 Genome sequencer FLX. The project goal is to clarify the relationship between oral microbiota and human health.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Salivary microbiota of Japanese orally healthy adults, pool 5

V1-V2 region of 16S amplicon sequence of human salivary microbiome from 66 orally-healthy Japanese adults were analyzed using a 454 Genome sequencer FLX. The project goal is to clarify the relationship between oral microbiota and human health.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Salivary microbiota of Japanese orally healthy adults, pools 1 and 2

V1-V2 region of 16S amplicon sequence of human salivary microbiome from 37 orally-healthy Japanese adults were analyzed using a 454 Genome sequencer FLX. The project goal is to clarify the relationship between oral microbiota and human health.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Salivary microbiota of Japanese orally healthy adults, pool 3

V1-V2 region of 16S amplicon sequence of human salivary microbiome from 51 orally-healthy Japanese adults were analyzed using a 454 Genome sequencer FLX. The project goal is to clarify the relationship between oral microbiota and human health.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Salivary microbiota of orally healthy adults in South Korea

V1-V2 region of 16S amplicon sequence of human salivary microbiome from 52 orally-healthy South Korean adults were analyzed using a 454 Genome sequencer FLX. The project goal is to clarify the relationship between oral microbiota and human health.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
sputum from patients with severe asthma who received either placebo or azithromycin for 48 weeks

sputum from patients with severe asthma who received either placebo or azithromycin for 48 weeks

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Simulated oral microbiome with artificial duplicates

This study includes multiple samples simulating a human oral community with 13 bacterial species and different levels of artificial duplicates. Reads have been simulated using BBmap.

Biome: root:Engineered:Modeled:Simulated communities (sequence read mixture)
Effect of OEA on gut microbiota in mice

The lipid sensor oleoylethanolamide (OEA), an endogenous high-affinity agonist of peroxisome proliferator-activated receptor-α (PPAR-α) secreted in the proximal intestine, is endowed with several distinctive homeostatic properties, such as control of appetite, anti-inflammatory activity, stimulation of lipolysis and fatty acid oxidation. When administered exogenously, OEA has beneficial effects in several cognitive paradigms; therefore, in all respects, OEA can be considered a hormone of the gut-brain axis. Here we report an unexplored modulatory effect of OEA on the intestinal microbiota and immune response.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Human endocarditis

Identification of the causative agent of infectious endocarditis

Biome: root:Host-associated:Human:Circulatory system
Genome-wide association study of Medicago truncatula rhizosphere microbial communities and plant nutritional strategies

Coming Soon

Biome: root:Host-associated:Plants:Rhizosphere
Exploring the native habitat and wild relatives of common bean (Phaseolus vulgaris) for ‘missing plant microbes'

The rhizosphere microbiome is important for plant growth and health, contributing to nutrient acquisition and (a)biotic stress tolerance. Rhizosphere microbiome composition is shaped in part by the plant genotype, but the underlying genetic basis is largely unknown. Going back to the roots, we investigated how plant domestication affected rhizosphere microbiome assembly of common bean (Phaseolus vulgaris), a key food crop worldwide. DArT genotyping and plant phenotyping showed substantial genetic diversity and root architectural differences between ancestral and modern bean accessions grown in Colombian field soil. Bean genotypes affected rhizosphere microbiome composition, with Bacteroidetes and Verrucomicrobia enriched on roots of ancestral beans and Actinobacteria more prevalent on modern beans. Genome-wide association mapping pinpointed single nucleotide polymorphisms (SNPs) in the bean genome associated with the abundance of specific rhizobacterial families. SNPs identified in chromosomes 3 and 4 were positioned at loci associated with signaling, lignin biosynthesis and pathogen resistance.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of the The microbial colonization of the intestine during the first months of life constitutes the most important process for the microbiota-induced host-homeostasis.

The Rotavirus vaccine on infants gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB6972.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Liver cirrhosis occurs as a consequence of many chronic liver diseases that are prevalent worldwide.

The Mgwas study of LC Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB6337.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Platygyra carnosa metagenome Raw sequence reads (coral metagenome) data set.

The coral metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA302351.  This project includes samples from the following biomes: Host-associated, Invertebrates, Cnidaria, Coral.

Biome: root:Host-associated:Invertebrates:Cnidaria:Coral
EMG produced TPA metagenomics assembly of the Banana aphid (Pentalonia nigronervosa) haemolymph Metagenome (insect metagenome) data set.

The insect metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA268300.  This project includes samples from the following biomes: Host-associated, Insecta.

Biome: root:Host-associated:Insecta
EMG produced TPA metagenomics assembly of the High fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice (mice obesity) data set.

The mice obesity Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB10308.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
EMG produced TPA metagenomics assembly of the Bacteria Genome sequencing and assembly (Bacteria) data set.

The Bacteria Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA326914.  This project includes samples from the following biomes: Host-associated, Arthropoda, Digestive system, Gut.

Biome: root:Host-associated:Insecta
EMG produced TPA metagenomics assembly of the Geospatial distribution of viral communities in tropical freshwater ecosystems (freshwater metagenome) data set.

The freshwater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA400853.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater.

Biome: root:Environmental:Aquatic:Freshwater
EMG produced TPA metagenomics assembly of the Compositional_dynamics_of_intestinal_spore_forming_bacteria (Compositional_dynamics_of_intestinal_spore_forming_bacteria) data set.

The Compositional_dynamics_of_intestinal_spore_forming_bacteria Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB20539.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Intestine.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Hot spring microbial streamer communities from Conch Spring, Yellowstone National Park, USA - C T=80-84 metagenome (hot springs metagenome) data set.

The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336661.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
EMG produced TPA metagenomics assembly of the Hot spring microbial communities from South Africa to study Microbial Dark Matter (Phase II) - Tshipise hot spring metaG metagenome (hot springs metagenome) data set.

The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA364997.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
EMG produced TPA metagenomics assembly of the Hot spring and microbial mat streamer communities from Octopus Spring Streamers, Yellowstone National Park, USA - T=80-84 metagenome (hot springs metagenome) data set.

The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336655.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
EMG produced TPA metagenomics assembly of the Hot spring microbial communities from Great Boiling Spring, Nevada - cellulolytic enrichment S 77C Metagenome (hot springs metagenome) data set.

The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA279023.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C):Sediment
EMG produced TPA metagenomics assembly of the Resistome of effluents of wastewater treatment plants () data set.

The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA413894.  This project includes samples from the following biomes: Engineered, Bioremediation, Terephthalate, Wastewater.

Biome: root:Engineered:Wastewater:Water and sludge
EMG produced TPA metagenomics assembly of the freshwater metagenome Raw sequence reads (freshwater metagenome) data set.

The freshwater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA335374.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Lake.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
EMG produced TPA metagenomics assembly of the freshwater sediment metagenome Raw sequence reads (freshwater sediment metagenome) data set.

The freshwater sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA320875.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Lentic, Sediment.

Biome: root:Engineered:Bioremediation:Hydrocarbon
EMG produced TPA metagenomics assembly of the Hot Lake Unicyanobacterial Consortia (microbial mat metagenome) data set.

The microbial mat metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA283228.  This project includes samples from the following biomes: Environmental, Aquatic, Non-marine Saline and Alkaline, Hypersaline, Microbial mats.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Alkaline:Microbial mats
EMG produced TPA metagenomics assembly of the Hot spring microbial communities from Grendel Spring, Yellowstone National Park, USA - T=76-80 metagenome (hypersaline lake metagenome) data set.

The hypersaline lake metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336649.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
EMG produced TPA metagenomics assembly of the Metagenome sequencing of a chitin enriched culture (Metagenome sequencing of a chitin enriched culture) data set.

The Metagenome sequencing of a chitin enriched culture Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB6317.  This project includes samples from the following biomes: Environmental, Terrestrial, Soil.

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of the Metagenomic analysis of microbial mat of hot springs (Metagenomic analysis of microbial mat of hot springs) data set.

The Metagenomic analysis of microbial mat of hot springs Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB14856.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs.

Biome: root:Environmental:Aquatic:Thermal springs
EMG produced TPA metagenomics assembly of the Manikaran hot springs water metagenome (Water metagenome) data set.

The Water metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB19501.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs.

Biome: root:Environmental:Aquatic:Thermal springs:Near-boiling (>90C)
EMG produced TPA metagenomics assembly of the Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge (Genome sequence for Ca. "Promineofilum breve" Cfx-K) data set

The Genome sequence for Ca. "Promineofilum breve" Cfx-K Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB11413. This project includes samples from the following biomes : Sludge.

Biome: root:Engineered:Wastewater:Activated Sludge
EMG produced TPA metagenomics assembly of the Metagenome sequencing of marine membrane vesicles (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA222589.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.

Biome: root:Environmental:Aquatic:Marine
EMG produced TPA metagenomics assembly of the Experimental trial using phytase in the diet for broiler (Phytase) data set.

The Phytase Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB12987.  This project includes samples from the following biomes: Birds.

Biome: root:Host-associated:Birds
EMG produced TPA metagenomics assembly of the Metagenome on soil background with high concentration of arsenic and antimon Genome sequencing (soil metagenome) data set

The soil metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA239941. This project includes samples from the following biomes : Soil.

Biome: root:Environmental:Terrestrial:Soil:Contaminated
EMG produced TPA metagenomics assembly of the Wetland samples Metagenome (soil metagenome) data set

The soil metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA227301. This project includes samples from the following biomes : Soil.

Biome: root:Environmental:Terrestrial:Soil:Wetlands
Microbiome profiling Schlöppnerbrunnen peat cores from different depths

Microbiome profiling of Schlöppnerbrunnen peat cores collected from different depths ranging from 0-30 cm.

Biome: root:Environmental:Terrestrial:Soil