SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Microbial diversity of consumption milk during processing and storage

Bovine milk contains a complex microbial community that affects the quality and safety of the product. Detailed knowledge of this microbiota is, therefore, of importance for the dairy industry. In this study, the bacterial composition of consumption milk was assessed during different stages in the production line and throughout the storage in cartons by using culturing techniques and 16S rRNA marker gene sequencing. Monthly samples from two dairies were analyzed to capture the seasonal variations in the milk microbiota. Although there was a core microbiota present in milk samples from both dairies, the composition of the bacterial communities were significantly influenced by sampling month, processing stage and storage temperature. Overall, a higher abundance of operational taxonomic units (OTUs) within the order Bacillales was detected in samples of raw and pasteurized milk from the spring and summer months, while Pseudomonadales and Lactobacillales OTUs were predominant in the winter months. OTUs belonging to the order Lactobacillales, Pseudomonadales, Clostridiales and Bacillales were significantly more abundant in milk samples taken immediately after pasteurization compared to raw milk samples. During storage of milk in cartons at 4 C, the bacterial composition remained stable throughout the product shelf life, while storage at 8 C significantly increased the abundance of OTUs belonging to the genus Bacillus and the plate count levels of presumptive Bacillus cereus. The knowledge obtained in this work will be useful to the dairy industry during their quality assurance work and risk assessment practices.

Biome: root:Engineered:Food production:Dairy products
16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome

Changes in the relative abundances of many intestinal microorganisms, both those that naturally occur in the human gut microbiome and those that are considered pathogens, have been associated with a range of diseases. To more accurately diagnose health conditions, medical practitioners could benefit from a molecular, culture-independent assay for the quantification of these microorganisms in the context of a healthy reference range. Here we present the targeted sequencing of the microbial 16S rRNA gene of clinically relevant gut microorganisms as a method to provide a gut screening test that could assist in the clinical diagnosis of certain health conditions. We evaluated the possibility of detecting 46 clinical prokaryotic targets in the human gut, 28 of which could be identified with high precision and sensitivity by a bioinformatics pipeline that includes sequence analysis and taxonomic annotation. These targets included 20 commensal, 3 beneficial (probiotic), and 5 pathogenic intestinal microbial taxa. Using stool microbiome samples from a cohort of 897 healthy individuals, we established a reference range defining clinically relevant relative levels for each of the 28 targets. Our assay quantifies 28 targets in the context of a healthy reference range and correctly reflected 38/38 verification samples of real and synthetic stool material containing known gut pathogens. Thus, we have established a method to determine microbiome composition with a focus on clinically relevant taxa, which has the potential to contribute to patient diagnosis, treatment, and monitoring.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Succession of dairy cow microbiota from birth to lactation

Our objective was to measure the succession of gut-associated archaeal, bacterial, and fungal communities in dairy cows from birth to lactation and to correlate these communities to calf diet as well as growth and health.

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Composition and temporal stability of the gut microbiota in older persons

Goals of this study are to refine our understanding of diet-microbiota associations and differential taxon abundance, to identify microbiota configurations associated with ageing in both community and long-stay residential care elderly subjects, to determine associations of these configurations with health, to determine if particular microbiota profiles are more variable over time than others, and to assess the role of antibiotics in temporal instability, using 16S rDNA sequences from faecal gut microbiota. These data will provide improved gut microbiota profile definitions, and inform on design of dietary or antibiotic interventions that target gut microbiota.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Fecal microbiota Targeted Locus (Loci)

Quantitative Trait Locus mapping of microbiota and expressed immunoglobulin A from G10 progeny of an advanced intercross of C57Bl6 X HR

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Composition and variation of respiratory microbiota in healthy military personnel Metagenome

Certain occupational and geographical exposures have been associated with an increased risk of lung disease. As a baseline for future studies, we sought to characterize the upper respiratory microbiome of healthy military personnel in a garrison environment. Nasal, oropharyngeal and nasopharyngeal swabs were collected from 50 healthy active duty volunteers eight times over the course of one year and subjected to pyrosequencing of 16S rDNA V3 to V1 region. The study produced a large set of pyrosequencing data of bacterial 16S rDNA V3-V1 region for respiratory microbiome of healthy active duty service members. Pre-processing of sequencing reads shows good data quality. The derived microbiome profiles are consistent both internally and with previous reports, suggesting utility for further analyses and association studies using sequence and demographic data.

Biome: root:Host-associated:Human:Respiratory system:Nasopharyngeal:Nasal cavity
human nose/throat Targeted loci

The aim of this study was to investigate the relationship between the nose/throat microbiome and influenza virus infection.

Biome: root:Host-associated:Human:Respiratory system:Nasopharyngeal
Human oral microbiome of Spanish adolescents

We provide a snapshot of the adolescent oral microbiome throughout Spain and how it varies with life-style and other factors.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Human faecal 16S Raw sequence reads

16S raw reads of IBD patients and controls. The aim was to examine differences between patients in relapse and remission

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Gut microbial factors implicated in disease progression and treatment response in pediatric ulcerative colitis

This project collected and profiled stool samples and rectal biopsies from pediatric patients with new-onset ulcerative colitis (UC) to evaluate the role of the gut microbiome in the efficacy of two conventional treatments.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Impact of rainforest transformation on phylogenetic and functional diversity of soil prokaryotic communities in Sumatra (Indonesia)

This project investigates the impact of lowland rainforest transformation on diversity and ecosystem function of soil prokaryotic communities. To identify changes in indigenous prokaryotic community composition accompanying rainforest transformation, comparative phylogenetic analyses of soil samples from lowland rainforest, jungle rubber, rubber plantations, and oil palm plantations were performed.

Biome: root:Environmental:Terrestrial:Soil:Tropical rainforest
16S rRNA amplicon analysis of Pozo Bravo Lake, Catamarca, Argentina.

16S rRNA amplicon analysis of Pozo Bravo Lake, Catamarca, Argentina.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
Ultra-high throughput multiplexing and sequencing of long amplicon regions on the Illumina HiSeq 2500 platform

Amplification, sequencing and analysis of the 16S rRNA gene affords characterization of microbial community composition. As this tool has become more popular and projects have grown in size and scope, greater sample multiplexing is becoming necessary while maintaining high quality sequencing. Here, modifications to the Illumina HiSeq 2500 platform are described that afford 300 bp paired-end reads of higher quality than those produced by the current Illumina MiSeq platform. To make this method feasible and flexible to different amplicon regions, a 2-Step PCR amplification protocol is also described that allows for amplification and sequencing of different amplicon regions, and that improves amplification success from low bacterial bioburden samples.

Biome: root:Host-associated:Human:Reproductive system:Vagina
GEMS diarrheal case/control study Targeted Locus (Loci)

16S rRNA gene survey of diarrheal stool from children under 5 and matched controls.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
A simplified framework for dissecting complex host-microbiota interactions

Charachterization of the microbiome in the roots of Arabidopsis plants growing in agar plates. Plants were germinated in plates with one of two phosphate conditions (+Pi or -Pi), and then transfered to a new plate with one of two Pi concentrations (100uM or 30uM). The plate of the second phosphate treatment was also inoculated with one of 25 synthetic bacterial communities, or kept under axenic conditions. The bacterial synthetic communities were made from pairs of bacterial blocks, were each block is made of 8-9 individual bacterial strains.

Biome: root:Host-associated:Plants:Root
Microbiota of Ustekinumab-treated Crohn's subjects.

The fecal microbiota is a rich source of biomarkers that have previously been shown to be predictive of numerous disease states. Less well studied is the effect of immunomodulatory therapy on the microbiota and its role in response to therapy. This study explored associations between the fecal microbiota and therapeutic response of ustekinumab (UST; STELARA) treated Crohn's disease (CD) patients in the phase 2 CERTIFI study. Using stool samples collected over the course of 22 weeks, the composition of these subjects'' fecal bacterial communities was characterized by sequencing the 16S rRNA gene.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
16S rRNA gene amplicon sequencing of endometrial cancer-associated bacteria

16S rRNA gene amplicon sequence of tissue, stool, urine, peritoneal fluid, tumor specimens and controls from the reproductive tract from a cohort of women with endometrial cancer

Biome: root:Host-associated:Human:Reproductive system:Female
A study of the metagenome of broiler chickens

An investigation into the metagenome of broiler chickens

Biome: root:Host-associated:Birds
Biological activates of fermented Aloe arborescence juice

The efficacy of plant-based drugs have received growing attention due to minimal or no side effects. Several plant-based extracts have been shown to be effective in cancer therapy and prevention including and among these plants, Aloe arborescens. Given the several health promoting attributes to A. arborescens, the main objectives of the present study were to evaluate the anticancer efficacy, immunomodulatory and antimicrobial effect of the fermented juice as well as the safety pattern on normal human PMNCs.  Furthermore, determining the causative bacteria participating in the fermentation process.

Biome: root:Engineered:Food production:Fermented vegetables
Pelagic sediment metagenome of Gulf of Khambhat

Community structure and pollutant degradation ability of deep sediment microflora of Gulf of Khambhat using culture independent approach

Biome: root:Environmental:Aquatic:Marine:Sediment
Pelagic sediment metagenome of Gulf of Kutch

Study of microflora associated with the Pelagic Sediments of the Gulf of Kutch using metagenomics

Biome: root:Environmental:Aquatic:Marine:Sediment
Replication and Refinement of a Vaginal Microbial Signature of Preterm Birth

We conducted a longitudinal study based on weekly sampling of the vaginal microbiota during pregnancy. Analysis was based on 16S rDNA amplicon sequencing, and was performed on two study cohorts. One cohort consisted of 39 women (30 term, 9 preterm deliveries) at low risk for preterm birth enrolled at Stanford University; the other cohort consisted of 96 women (55 term, 41 preterm) at high-risk for preterm birth enrolled at the University of Alabama, Birmingham. A case-control study design was used to compare features of the microbiota in women who delivered preterm (cases) with those of women who delivered at term (controls).

Biome: root:Host-associated:Human:Reproductive system:Vagina
16S rRNA sequence of rumen microbes in dairy cattle

The 16S rRNA sequence data was generated in the project entitled "Reduction of methane emissions from dairy cows and concurrent improvement of feed efficiency obtained through host genetics and next generation sequencing of rumen microbiome" using Illumina sequencing technology.

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Association of host genome with intestinal microbial composition in a large healthy cohort

Intestinal microbiota is known to be important in health and disease. Its composition is influenced by both environmental and host factors. However, few large-scale studies have evaluated the association between host genetic variation and the composition of microbiota. We recruited a cohort of 1,561 healthy individuals, of whom 270 belong in
123 families, and found that almost one-third of fecal bacterial taxa were heritable. In addition, we identified 58 SNPs associated with the relative abundance of 33 taxa in 1 ,098 discovery subjects. Among these, four loci were replicated in a second cohort of 463 subjects: rs621711 78 (nearest gene UBR3) associated with Rikenellaceae, rs1394174 (CNTN6) associated
with Faecalibacterium, rs59846192 (DMRTB1) associated with Lachnospira, and rs28473221 (SALL3) associated with Eubacterium. After correction for multiple testing, six associations of 58 remained significant, one of which replicated. These results identify associations between specific genetic variants and the gut microbiome.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
A catalog of microbial genes from the bovine rumen reveals the determinants of herbivory

The rumen microbiome is responsible for the unique nature of ruminants. A thorough knowledge of the genetic potential of rumen symbiotic microbes is therefore crucial for the sustainability of ruminant production systems. Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen and constructed 324 high quality metagenomic species. These metagenomic species were prevalent in the rumen of 77 cattle fed various diets whereas known rumen microbial genomes were less abundant. Compared to human, pig and mouse gut metagenome catalogs, the rumen is richer in functions and microbial species associated to the degradation of lignocellulosic material and production of methane. Genes coding for enzymes that deconstruct lignocellulosic substrates showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. These data bring new insights on functions, enzymes and microbes of the rumen, critical to understand phenotypes and biological processes.

Biome: root:Host-associated:Mammals:Digestive system:Foregut:Rumen
EMG produced TPA metagenomics assembly of the Isolation and Identification of the Follicular Microbiome: Implications for Acne Research (PRJNA435265) data set.

The PRJNA435265 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA435265.  This project includes samples from the following biomes: root:Host-associated:Human:Skin.

Biome: root:Host-associated:Human:Skin
Microbial metagenomes of Spongia agaricina

This study approaches the diversity, composition and function of microbial communities associated with the marine sponge Spongia agaricina, sampled in the northeast Atlantic. Shotgun metagenome sequencing (Illumina) was employed to decipher the functional features of the S. agaricina microbiome under different methods of metagenomic DNA extraction.

Biome: root:Host-associated:Porifera
Analysis of plasmidome of high-altitude lakes from the Andean Puna

The high-altitude lakes of the Andean Puna are exposed to multiple extreme conditions including high UV radiation, high concentration of arsenic, heavy metals and dissolved salts, high thermal amplitude and low oxygen pressure. Despite inhospitable conditions, various microbial ecosystems can develop successfully through adaptation mechanisms, which can be encoded in plasmids and can thus be transmitted in the microbial community. The aim of this study was the characterization of plasmidome (overall plasmid population) of cultivable and non-cultivable organisms of lakes from the Andean Puna, analyzing their functions and ecological significance. Genetic determinants of plasmid nature essentials to survive in these environments were sought.

Biome: root:Environmental:Aquatic:Freshwater:Lake
16S rRNA gene profiling of atopic dermatitis and psoriasis patients compared to healthy volunteers

Characterization of host-microbe interactions in patients with allergic (model: atopic dermatitis) and autoimmune (model: psoriasis) disorders by 16S rRNA gene sequencing and microarray transcriptional profiling. Skin swabs were collected from the lesional skin of a large cohort of atopic dermatitis and psoriasis patients and subjected to 16S rRNA sequencing on the Roche 454 platform.

Biome: root:Host-associated:Human:Skin
Human skin bacterial and fungal microbiotas analyses

Using high-throughput 16S rDNA and ITS1 sequencing, we characterized skin bacterial and fungal microbiotas from healthy and dandruff subjects, comparing scalp and forehead (lesional and non-lesional skin sites).

Biome: root:Host-associated:Human:Skin
Tick-symbiont interactions

Obligatory hematophagous arthropods such as lice, bugs, flies and ticks harbor bacterial endosymbionts which are expected to complete missing dietary needs, and numerous genomics and some experimental evidences currently support this expectation. In hard ticks (Acari: Ixodidae) serval linages of bacterial symbionts has been documented, and very few were experimentally shown to be essential to some aspects of ticks fitness, mostly showing reduction in reproductive fitness. In order to pinpoint the nature of hard ticks-nutritional symbionts interactions, we tested the effect of antibiotic treatment and massive elimination of Coxiella-like endosymbionts (CLE) on the development and fitness of the brown dog tick (Rhipicephalus sanguineus). Administration of ofloxacin to repleted nymphs resulted in significant and acute reduction of the tick microbial community load and in CLE numbers in subsequent life stages (aposymbiotic ticks). As a result, aposymbiotic female, but not male nymphs, suffered a delayed post-feeding development. Additionally, aposymbiotic adult females needed a significantly prolonged feeding period in order to replete, and had reduced engorgement weight. Weight conversion into eggs was lower in aposymbiotic females, which resulted in reduced fecundity, as well as excessive reduced fertility. Eggs produced by aposymbiotic females were also free of CLE and resulting aposymbiotic larvae were unable to feed successfully. These results first demonstrate that the observed effects are due to CLE reduction and not due to antibiotic administration; and second, suggest that the contribution of CLE to its Rh. sanguineus host is not mandatory for oocyte development and embryogenesis, but is required under high physiological demands such as blood meal processing and tissue build up, which are more prominent in females, presumably via supplementing the host with essential micro and macronutrients. Further nutrient complementary studies are required to support this hypothesis.

Biome: N/A
Amplicon sequencing of Tara Oceans DNA samples corresponding to size fractions for  prokaryotes or protist.

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

Biome: root:Environmental:Aquatic:Marine
Swabs from the International Space Station Raw sequence reads

16S sequencing of 15 swabs from the International Space Station

Biome: root:Engineered:Built environment
An optimized model for screening colorectal cancer established using large-scale experimental sequence-based faecal microbial community data

Objective To establish methods and effective microbial biomarkers for early colorectal cancer (CRC)-specific-screening via gut microbiota detection in the clinic.Design 5,588 stool samples 16S ribosomal RNA (rRNA) gene were sequenced, and used the relative abundance of taxonomic and functional features to develop a model resembling the populations that consisted of 3 cohorts and 3 classification models (RF, XGBoost, and GBM) that distinguished the CRC group from the control group and identified potential microbial biomarkers.Results Microbiome-based classification distinguished patients with CRC from normal participants and excluded other CRC-relevant diseases. The area under the receiver operator characteristic (AUROC) curve was 92.2%. Known associations with oral pathogenic features, benefits-generated features, and functional features of CRC were confirmed by the model.Conclusions Our optimized prediction model was established using large-scale experimental population-based data and other sequence-based faecal microbial community data. This model can be used to identify high-risk groups and has the potential to become a novel screening method for CRC biomarkers due to its low 1-specificity (i.e. false-positive rate) and good stability.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Effects of forest-management practices on below-ground fungal diversity and community composition in Idaho

We studied the fungal community composition in response to forest management practices which included: biomass harvesting, fertilization, and biochar amendments. The study site was located in the inter-mountain region of Idaho.

Biome: root:Engineered:Solid waste:Composting:Wood