SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Clinical study of saliva metabolomics and microbiomics in respiratory diseases

Chronic and acute respiratory diseases represent major challenges for clinicians with incidence rates continuing to rise throughout the world.  It is important to develop approaches to accurately and rapidly diagnose the types and stages of respiratory disease.  Many approaches are focusing on such as serum or sputum as the basis of a screening programme. Many biomolecules found within human saliva have their origins in the circulatory system and thus, saliva offers a non-invasive diagnostic tool for a number of diseases.  In this study, we assessed how far saliva could be used to reveal key changes. In particular, we have used metabolomics whereby the chemical components of a sample (1000s of biochemicals) can be accurately quantified in a matter of minutes – to assess salvia samples from 93 samples. Saliva has also been used as a biofluid for metabolomics previously used to identify specific oral, breast and pancreatic cancer profilesThe sampled population encompassed 53 COPD patients from Prince Phillip, Gwangli and Bronglais Hospitals in the Hywel Dda Health Board Area. These consisted of 38 age-matched volunteer controls, 8 lung cancer patients and 18 with a range of respiratory diseases.  The samples consisting of 50 L of saliva were analysed using metabolomic approaches involving the use of Electrospray Ionisation Mass Spectrometry (FIE-MS) to produce a large dataset 169 samples x 6500 metabolites.  Application of “multivariate” statistical approaches allowed the identification of metabolites that are different in particular sample classes.   Using statistically approaches such as Principal Component Analysis (PCA) we demonstrate that saliva could distinguish between samples from each clinical classification compared to controls.  These results were validated using a cross-validated Receiver operating characteristic (ROC) curve which indicated a diagnostic accuracy of > 0.70. Individual chemicals which are the sources of variation between the sample sets have been identified. Further, we have discovered clear differences in the saliva metabolome of COPD patients at different disease severity as defined by Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage classification.  Therefore, this innovative application of “big-data” based analyses has yield potential biomarkers that could be exploited to inform future clinical practice.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Bacterial community composition in coking wastewater treatment bioreactor sludge

This study aims to illustrate the microbial community in bioreactors of coking wastewater treatment by pyrosequencing.

Biome: root:Engineered:Wastewater:Industrial wastewater
bacterial community of chinese soybean pastes

Fermented soybean foods contain high nutritious and health beneficial component including easily digestible peptide, cholesterol-free oils, minerals, and vitamins. Various types of fermented soybean foods have been developed and largely consumed as a flavoring condiment in wide Asian regions. While the quality of fermented soybean foods is largely affected by microorganisms participated in the fermentation process, our knowledge about microorganisms of soybean pastes manufactured in the Northeast area of China is still limited.    In the current study using culture-independent massive sequencing analysis, 6,3399 high quality sequences were derived from sixteen soybean paste samples collected from Northeast area of China by a barcoded pyrosequencing method targeting hyper-variable regions V1/V2 of the 16S rRNA gene. Soybean pastes of Korean minority of china (SPKM), Hun Chinese (SPHC) and Korean doenjang showed largely different shape of bacterial community. Overall compositions of bacterial community between groups were clearly separated in Clustering analysis. In addition, each soybean pastes contained representative bacterial species significantly different between each other as follows: Bacillus subtilis in SPKM, Tetragenococcus halophilus in SPHC, and Enterococcus durans in Korean doenjang. In this study, a massive sequencing approach was applied for the first time to analyze the microbial communities of soybean pastes manufactured in Northeast area of China and clearly revealed that different shapes of microbial communities in soybean pastes were affected by manufacturing process along with manufacturing regions.

Biome: root:Engineered:Food production:Fermented vegetables
Metatranscriptomics analysis of a benzene-degrading enrichment culture under denitrifying conditions

Benzene is the risk-determining compound in oxygen-depleted subsurface environments contaminated by fuel hydrocarbons. Although anaerobic benzene degradation from benzoyl-CoA as a key aromatic central intermediate is well-known, the initial steps of benzene activation in absence of oxygen and its funneling towards benzoyl-CoA remains ill-defined. Here we conducted a metatranscriptomics analysis on biofilm and effluent samples obtained from a chemostat with an anaerobic benzene-degrading and nitrate-reducing culture that has been running for more than 14 years. The transcripts associated with strict anaerobic Firmicutes dominated all samples with 36.2-58.7% relative abundance. Among Firmicutes, members of Peptococcaceae comprised 21.5-36.3% relative abundance of the samples. A gene cluster containing genes encoding the proposed anaerobic benzene carboxylase (abcA and abcD) and a benzoate-coenzyme A ligase (bzlA) was found in the metatranscriptomic dataset that showed extraordinary similarity (> 96% at the amino acid level) and gene synteny to the proposed cluster encoding putative enzymes for direct benzene carboxylation to benzoate. Moreover, compared to the genes involved in downstream benzoyl-CoA degradation, the abcA and abcD and bzlA were among the highest transcripts with the abcA as the most transcribed gene. These results provide compelling evidence that benzene is directly carboxylated to benzoate by the products of abcAD genes and then ligated with CoA by the product of bzlA gene.

Biome: root:Environmental:Terrestrial:Soil:Oil-contaminated
NGEE Arctic Microbial Communities of Polygonal Grounds

Arctic soils contain an estimated 12-42% of the global soil C and much of this carbon is trapped in permafrost. With increasing global temperatures, thawing permafrost is becoming a potential source of greenhouse gas (GHG) emissions. On the Alaskan North Slope the collapse and rise of soil due to formation of ice wedges and permafrost thaw create distinct features called polygons. As part of the U.S. Department of Energy (DOE) Next Generation Ecosystem Experiment (NGEE) in the Arctic, we collected seasonally thawed active layer soils across a transect of polygon features at the Barrow Environmental Observatory (BEO). We used Illumina HiSeq technology to sequence metagenomes. The sequence data was accompanied by GHG flux measurements, geophysical and geochemical soil characteristics.

Biome: root:Environmental:Terrestrial:Soil:Permafrost
Effects of Western diets based on lean seafood or lean meat on energy intake, diet-induced obesity and gut microbiota in C57BL/6J mice

Male C57BL/6J mice were fed a casein-based low fat (LF) diet or Western diets (WDs) containing a mixture of lean seafood (seafood WD) or lean meat (meat WD). Glucose and insulin tolerance tests were performed after 10 and 11 weeks, respectively. After 12 weeks, mice were euthanized. Blood and tissues were sampled, and cecum content was collected. We tested meal preference and performed meal response tests to evaluate changes in postprandial glucose and C-peptide levels. We measured energy metabolism by indirect calorimetry, and spontaneous locomotor activity was recorded.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
Environmental samples from Yellowstone Lake

DNA was extracted from various water and streamer sites in Yellowstone Lake.


Biome: root:Environmental:Aquatic:Lentic
Bacterial diversity in home and personal care products

Bacterial contamination of home and personal care products is not well documented in scientific literature despite it being a major cause of product recalls and a health risk to consumers. This study aimed to survey the types and relative abundances of bacterial genera responsible for the contamination of selected home and personal care products.

Biome: root:Engineered
Effects of Leuconostoc mesenteroides starter culture on microbial communities and metabolites during kimchi fermentation

Kimchi fermentations usually rely upon the growth of naturally occurring various heterofermentative lactic acid bacteria (LAB), which sometimes makes difficult to produce kimchi with uniform quality. The use of Leuconostoc mesenteroides as a starter has been considered to produce commercial fermented kimchi with uniform and good quality in Korea. In this study, a combination of a barcoded pyrosequencing strategy and a 1H-NMR technique was used to investigate the effects of Leu. mesenteroides strain B1 as a starter culture on kimchi fermentation. Baechu (Chinese cabbage) and Chonggak (radish) kimchi with/without Leu. mesenteroides inoculation were prepared, respectively, and their characteristics including pH, cell numbers, bacterial community, and metabolites were monitored periodically for 40 days. The barcoded pyrosequencing analysis showed that numbers of bacterial operational taxonomic unit (OTU) in starter kimchi decreased more quickly than non-starter kimchi. Members of the genera, Leuconostoc, Lactobacillus, and Weissella were dominant LAB regardless of kimchi type and starter inoculation. Among three the genus Leuconostoc was most abundant, followed by Lactobacillus and Weissella. The use of Leu. mesenteroides as a starter increased Leuconsotoc proportions and decreased Lactobacillus proportions in both kimchi over the kimchi fermentations. However, interestingly, the use of the kimchi starter maintained Weissella proportions of starter kimchi more highly than non-starter kimchi until fermentations finished. The metabolite analysis using the 1H-NMR technique showed that both Baechu and Chonggak kimchi with the starter culture consumed more free sugars more rapidly with more productions of lactic and acetic acids and mannitol, which were well in accordance with the decreases of pH values and the increase of bacterial cell numbers. The PCA strategy using all kimchi componemts including carbohydrates, amino acids, and organic acids also showed that starter kimchi was fermented faster and more. In conclusion, this study showed that kimchi fermentations with the use of Leu. mesenteroides as a starter were completed more rapidly with the more production of kimchi metabolites, which may contribute to produce commercial kimchi with more uniformity and functional properties. And the combination of the barcoded pyrosequencing strategy and the 1H-NMR technique used in this study can monitor microbial succession and their metabolites effectively and will help to understand the relationships between microbial community and metabolite production (taste and function) in diverse fermented foods including kimchi.

Biome: root:Engineered:Food production:Fermented vegetables
Biomass-Adapted Thermophilic Consortia

Microbial consortia adapted to biomass at elevated temperature were enriched from compost inocula. These adapted consortia were simplified bacterial communities that secreted glycoside hydrolase enzymes with significant activity on purified substrates and pretreated biomass.

Biome: root:Engineered:Solid waste:Composting
16S rDNA analysis of antibiotic-treated mice mutant for interferon-lambda pathway genes

Wild-type (B6) mice or mice mutant for Stat1, Irf3, or Ifnlr1 were left untreated or treated for 14 days with an antibiotic cocktail of vancomycin, neomycin, ampicillin, and metronidazole in their drinking water. Stool was collected after the treatment and DNA was extracted and purified. Amplification of the V4 region of 16S rDNA was performed with individual barcodes for each sample, followed by pooling and sequencing on an Illumina MiSeq.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Identification of microbial differences between IgA-High and IgA-Low wild-type mice in two facilities

Wild-type mice from specific-pathogen-free facilities were distinguished phenotypically by fecal IgA levels. Fecal samples were collected from IgA-High and IgA-Low mice from two separate facilities. Amplification of the V4 region of 16S rDNA was performed with individual barcodes for each sample, followed by pooling and sequencing on an Illumina MiSeq.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Effects of cholera on the human gut microbiota, and interactions between human gut microbes and Vibrio cholerae.

Given the global burden of diarrheal diseases, it is important to understand how members of the gut microbiota affect the risk for, the course of, and recovery from disease.  This is true for young children when the gut microbiota is being assembled, as well as for adults.  Recent culture-independent analyses of the fecal microbiota of healthy Bangladeshi infants and children, sampled monthly from birth through the second year of life, have identified a group of age-discriminatory bacterial taxa that together define a normal program of postnatal development (maturation) of the gut microbiota. The acute voluminous diarrhea caused by Vibrio cholerae represents a dramatic example of enteropathogen invasion and gut microbial community disruption.  We have conducted a detailed time-series metagenomic study of the fecal microbiota during the acute diarrheal and recovery phases of cholera in a cohort of Bangladeshi adults living in an area with a very high burden of disease. Recovery is characterized by a pattern of accumulation of bacterial taxa that mirrors the normal pattern of assembly/maturation of the microbiota in healthy Bangladeshi children. To define underlying mechanisms, we created an artificial community of 14 sequenced human gut bacterial species in gnotobiotic mice, composed of taxa that directly correlate with recovery from cholera and that are indicative of normal microbiota maturation in healthy Bangladeshi children. One of these age-discriminatory species, Ruminococcus obeum, exhibited consistent increases in its relative abundance upon V. cholerae infection of the mice. Follow-up mono- and bi-colonization studies established that R. obeum restricts V. cholerae colonization. RNA-Seq of the community's meta-transcriptome, combined with assays of autoinducer-2 (AI-2) production and function, revealed that expression of R. obeum luxS (AI-2 synthase) and AI-2 production increase significantly with V. cholerae invasion, and that R. obeum AI-2 causes quorum-sensing mediated repression of toxin co-regulated pilus, a primary V. cholerae colonization factor. Co-colonization experiments in gnotobiotic mice established that R. obeum AI-2 reduces Vibrio colonization/pathogenicity through a novel pathway that does not depend on the canonical V. cholerae AI-2 sensor, LuxP.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
impact of diet on gene expression in bovine rumen microbiomes

impact of diet on gene expression in bovine rumen microbiomes

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Ventilator-associated pneumonia

We explored bacterial community diversity of supraglottic secretions, endotracheal apirate and broncho-alveolar lavage from intubated patients hospitalised in the intensive care unit.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system
The microbiota of developing cod larvae

The submitted dataset consists of pyrosequenced barcoded v4 16S rDNA amplicons representing bacterial communities associated with developing cod larvae, rearing water, and live feed samples. Cod larvae were reared with two different feeding regimes (copepods or rotifers).  Sampling of larvae and rearing water was carried out at 8, 17, 32, and 61 dph for two rearing tanks; one for each feeding regime. Each live feed culture was sampled once; the copepods at 8 dph, the rotifers at 17 dph, and Artemia culture at 32 dph. Total DNA from individual larvae, water and live feed samples were used as templates in PCR reactions. The V4 region of the 16S rRNA gene was amplified using a nested PCR protocol as described in Bakke et al. 2013, Environmental Microbiology Reports 5(4), 537-548. Two pooled amplicon libraries were generated (one for each rearing tank/feeding regime) and each of them was sequenced on one half of a 454 plate with a GS FLX instrument at the Norwegian Sequencing Centre.

Biome: root:Host-associated:Fish
mucosal microbiota

Changes in mucosal microbiota during healing.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine
River Sediment metagenomes of textile dye degrading communities collected from Ankleshwar, India

Samples were collected from Indian (Ankleshwar) river sediment heavily polluted with textile dyes. A control site was also used. 1-2 g of river sediment was inoculated (in triplicate) in to Bushnell Hass Broth either supplemented with or without various textile dyes. 1-2 g of sediment form the control site was also inoculate (in triplicate) into Bushnell Hass Broth without addition of textiles dyes. Cultures were incubated at 37oC  until decolourisation of the dyes occurred (usually within 24-48 hours). Two rounds of subculturing occurred where 1-2 ml of culture medium was inoculated into fresh Bushnell Hass Medium with or without dye. After these round of subculturing, all 9 cultures were sampled for metagenomics and metaproteomics.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
Analysis of variations in the microbiota of chickens fed diets supplemented with different feed additives

Conventional rearing of broiler chickens is based on routine supplementation of the feed with anticoccidials which are approved for use against intestinal coccidiosis. A sub-group of anticoccidials, which functions as ionophores, is also effective against some gram-positive bacteria, including Clostridium perfringens. This is an intestinal bacterium associated with growth depression and important gastrointestinal health problems such as necrotic enteritis and the gizzard erosion syndrome. The dual function of ionophores is part of the explanation to their widespread use in broiler feeds. The ionophore narasin has been the predominant anticoccidial used in broiler rearing in the Nordic countries. Research suggests that although narasin is not used in human medicine, its  use in broiler rearing might promote persistence of vancomycin resistant enterococci. This has led to an expressed concern that use of narasin may stimulate occurrence and spread of bacteria resistant to clinically relevant antibiotics. Dissemination of antibiotic resistant bacteria is a world-wide problem, and there is an increasing pressure to reduce the use of antimicrobial agents in animal production. The purpose of this project was to test non-antibiotic feed additives and identify characteristics of the intestinal microbiota in chickens fed diets supplemented with these alternatives to in-feed anticoccidials.The samples originate from four different feeding trials with Ross 308 broiler chickens reared under similar conditions. The chickens were divided into 6 groups, which were fed similar commercial pelleted diets formulated to meet the Ross 308 nutrition specifications with group specific supplements.Trial 1: group 1, narasin; group 2, no additive; group 3, acid product-A; group 4, acid product-B; group 5, acid product-C; group 6, acid product-D.Trial 2: group 1, narasin; group 2, no additive; group 3, acid product-E; group 4, acid product-F, group 5; yeast product-A, group 6; plant/acid product-A.Trial 3: group 1, narasin; group 2, no additive; group 3; yeast product-B + synbiotic-A, group 4; yeast product-B + plant product-A; group 5, yeast product-A + acid product-B; group 6, yeast product-A + acid product-D.Trial 4: group 1, narasin; group 2, no additive

Biome: root:Host-associated:Birds:Digestive system:Fecal
Surveillance for prevalence of drug resistance bacteria in Ugandan animal agriculture

Surveillance for prevalence of drug resistance bacteria in Ugandan animal agriculture

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Chronic Trichuris muris Infection Decreases Diversity of the Intestinal Microbiota and Concomitantly Increases the Abundance of Lactobacilli

A longituinal study looking at changes in the colon and cecum microbiota of parasite infected male C57BL/6 mice. 16s rDNA sequencing was used.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
16S pyrosequencing of the microbiota in Anopheles gambiae mosquitoes after bloodfeeding on blood treated or not with penicillin-streptomycin antibiotic cocktail.

16S pyrosequencing of the microbiota in Anopheles gambiae mosquitoes after bloodfeeding on blood treated or not with therapeutic concentrations of penicillin-streptomycin antibiotic cocktail.

Biome: root:Host-associated:Insecta
Computational integration of genomic traits into 16S rDNA microbiota sequencing studies

Molecular sequencing techniques help to understand microbial biodiversity with regard to species richness, assembly structure and function. In this context, available methods are barcoding, metabarcoding, genomics and metagenomics. The first two are restricted to taxonomic assignments, while genomics only refers to functional capabilities of a single organism. Metagenomics by contrast yields information about organismal and functional diversity of a community. However currently it is very demanding regarding labour and costs and thus not applicable to most laboratories. Here, we show in a proof-of-concept that computational approaches are able to retain functional information about microbial communities assessed through 16S rDNA (meta)barcoding by referring to reference genomes. We developed an automatic pipeline to show that such integration may infer preliminary or supplementary genomic content of a community. We applied it to two biological data sets and delineate significantly overrepresented protein families between communities. The script alongside supporting data is available at http://bioapps.biozentrum.uni-wuerzburg.de.

Biome: root:Host-associated:Plants
A case of hepatic brucelloma studied by next generation sequencing

A clinical examination of a patient pointed to a hepatic brucelloma. However, the presence of Brucella was not confirmed by culture and PCR experiments. We aimed at identifying the bacterium by whole metagenome shotgun sequencing of DNA extracted from the hepatic biopsy.

Biome: root:Host-associated:Human:Digestive system
In-depth diversity analysis of the bacterial community resident in camel rumen

We applied amplicon barcoded pyrosequencing to study bacterial community resident in the camel rumen. we generated 145043 raw reads with average read length of 382.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Bombus terrestris gut microbiome

TODO

Biome: root:Host-associated:Insecta
pigs gut microbiota

diet divers for analysis of pigs gut section microbiota

Biome: root:Host-associated:Mammals:Excretory system
Metagenomic analysis of chicken cecal feces

Metagenomic analysis of chicken cecal feces obtained from chicken farm in Japan were carried out to know microbiota composition.

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