SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Associated bacterial profiles in Porites lutea tissues affected by pink pigmentation response (PPR)

This study describes the changes in associated bacteria in the coral Porites lutea showing pink pigmentation response (PPR) using Metagenomic approach. Bacterial communities were isolated from healthy tissues of P. lutea, affected by PPR and recovered from PPR. Also samples isolated from surrounding waters and sediment were analyzed. Sediment samples showed higher diversity, followed by coral tissues showing PPR signs. Unclassified bacteria, particularly the bacteria CAB-I, BB2H16SI and Alphaproteobacteria, especially Methylobacterium predominated in PPR tissues. In contrast, Gammaproteobacteria, especially Endozoicomonas predominated in healthy tissues. We propose to use Endozoicomonas, CAB-I, BB2H16S and Methylobacterium as biomarkers to explore the progress and occurrence of PPR in P. lutea.

Biome: root:Host-associated:Invertebrates:Cnidaria:Coral
16S ribosomal RNA gene sequences from fermented foods

16S ribosomal RNA gene was amplified by PCR from traditional fermented foods and was analyzed by high-throughput sequencing.

Biome: root:Engineered:Food production:Fermented beverages
Asian Microbiome Project

Asia differs substantially among and within its regions populated by diverse ethnic groups, which maintain their own respective cultures and dietary habits. On the other hand, Oriental and Western cultures are now merging at many sites in Asia and affecting our life style, especially daily diets. To inquire into diversity in gut microbiota of Asian people, which must respond to daily diets and link to host health, Asian Microbiome Project (AMP) was established in 2009. AMP aims to build a basal microbiome database of Asians covering entire region and age group and gain an insight into the link between life style and gut microbiota. By sharing information and gained knowledge obtained in this project, we hope to promote health of Asian people.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
WL Reactor published in ME

The data is the whole sequence data for the "Bacterial population dynamics in a laboratory activated sludge reactor monitored by pyrosequencing of 16S rRNA", Satoh et al. (2013), Microbes and Environments, 28(1), 65-70.  Bacterial community change in a laboratory activated sludge reactor was analyzed by NGS for around 8 months.  A sudden disappearance of a major population was observed around day 50th, and periodical increase and recessions were observed for many of the observed OTUs.

Biome: root:Engineered:Wastewater:Activated Sludge
Microbial communities associated with natural and commercially grown rooibos (Aspalathus linearis) plants

The Cape Floristic Region has an exceptionally high floral diversity and is recognized as one of the world''s biodiversity hotspots.  However, this region has a poor record of conservation and may endemic plant species are now classified as endangered.  One of the main threats to the region''s ecosystem is the overexploitation of economically valuable plant species such as rooibos (Aspalathus linearis).  The aim of this study was to determine the microbial rhizosphere community structures of rooibos plants in natural and commercial areas.  Rhizosphere soil, root samples and bulk soil were collected from natural and commercial rooibs sites located on two different farms situated in the Cederberg area, the north-western region of the fynbos biome.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Bacterial community of river sediment enriched with polycyclic aromatic hydrocarbons

16S rRNA gene amplicons (454-pyrosequencing) raw sequence reads of Chao Phraya River sediment enriched with polycyclic aromatic hydrocarbons. This study aimed to assess the biodegradation of mixed PAHs by indigenous bacteria in river sediment.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
Effect of Bifidobacterium on the intestinal microbiota in rotavirus infected mice

Human rotavirus (RV) infection is a leading cause of dehydrating diarrhea in infants and young children worldwide. We evaluated the role of microbiota in RV infected mice, and the effect of probiotics. For DNA sequencing, DNA extraction from mixture of cecum and colonic contents from suckling mice on 2-5 days old was performed by bead beating and lysozyme digestion. 16S rDNA analysis of the microbial community structure in intestinal contents was performed using a MiSeq platform. The amplicon of V3-V4 region in 16S rDNA was purified using AMPure XP magnetic beads. The Illumina Nextera XT Index kit with dual 8-base indices was used to allow for multiplexing. PCR reactions were performed to incorporate two unique indices to the 16S amplicons. After purification with AMPure XP beads, the purified barcoded library was fluorometrically quantified using a QuantIT PicoGreen ds DNA Assay Kit. Libraries were then diluted to 4 nM using 10 mM Tris-HCl (pH 8.0), followed by pooling the same volume for multiplex sequencing. The multiplexed library pool (10 pM) was spiked with 35% PhiX control DNA (10 pM) to improve base calling during sequencing. Sequencing was conducted using a 2 x? 250-bp paired-end run with MiSeq Reagent Kit v2.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine
Microbial diversity on cafeteria kitchen

we conducted a biogeographical assessment of bacteria in a cafeteria kitchen to determine the diversity of microflora on each surface and to evaluate the spatial and temporal variations of the potential cross-contamination routes. High-throughput amplicon sequencing of the 16S rRNA gene from 13 surfaces in a cafeteria kitchen was performed every quarter for one year.

Biome: root:Engineered:Built environment
Metagenome sequencing of a mock fungal community consisting of 26 fungal species

We evaluated the efficacy of mycobiome analysis strategies using three NGS techniques, Illumina MiSeq, Life Technologies IonPGM, and Pacific Biosciences PacBio RS II sequencing to characterize a mock fungal community consisting of 26 species representing 15 genera.

Biome: root:Engineered:Lab enrichment
Fermentation microbiota in kusaya gravy

Kusaya is a traditional dried fish product manufactured in the Izu Islands in Japan.  Kusaya is produced by soaking fish in a unique brine called kusaya gravy, followed by drying of the fish. This kusaya gravy is a unique fermented gravy which is used repeatedly over several hundred years. In this project, the compositions of microbiota in kusaya gravy was analysed using pyrosequencing.

Biome: root:Engineered:Food production:Fermented seafood
Metagenomic and metatranscriptomic analysis of the microbial community in drinking water distribution systems of ground and surface waterworks in Finland

The water microbiome in the drinking water distribution systems (DWDSs) of five waterworks in Finland with different raw water sources and treatment processes was explored. The sampled DWDSs were from two waterworks AB with non-disinfected, recharged groundwater as source water and from three waterworks utilizing chlorinated water (two DWDSs of surface waterworks CD and one of ground waterworks E). The water microbiome was characterized by Illumina high-throughput sequencing technology.

Biome: root:Environmental:Aquatic:Freshwater:Drinking water:Delivery networks
Oil droplet biodegradation Trondheimsfjord Metagenome

We established a novel laboratory system to investigate biodegradation of Macondo oil dispersions (10 m or 30 m median droplet sizes) at low oil concentrations (2 mg L-1) in coastal Norwegian seawater at a temperature of 4-5C. Metagenomic analyses were performed on 0.5 - 1 g whole extracted DNA using Illumina HiSeq 100 bp paired end reads.

Biome: root:Engineered:Lab enrichment:Defined media:Marine media
Gut-microbiome of Tuberculosis patients

Gut-microbiome of Tuberculosis patients

Biome: root:Host-associated:Human:Digestive system:Intestine
The Effects of Weaning Methods on Gut Microbiota Composition and Horse Physiology

Weaning has been described as one of the most stressful events in the life of horses. Given the importance of the interaction between the gut-brain axis and gut microbiota under stress, we evaluated (i) the effect of two different weaning methods on the composition of gut microbiota across time and (ii) how the shifts of gut microbiota composition after weaning affect the host. A total of 34 foals were randomly subjected to a progressive (P) or an abrupt (A) weaning method. In the P method, mares were separated from foals at progressively increasing intervals every day, starting from five min during the fourth week prior to weaning and ending with 6 h during the last week before weaning. In the A method, mares and foals were never separated prior to weaning (0 d). Different host phenotypes and gut microbiota composition were studied across 6 age strata (days 30, 0, 3, 5, 7, and 30 after weaning) by 16S rRNA gene sequencing. Results revealed that the beneficial species belonging to Prevotella, Paraprevotella, and Ruminococcus were more abundant in the A group prior to weaning compared to the P group, suggesting that the gut microbiota in the A cohort was better adapted to weaning. Streptococcus, on the other hand, showed the opposite pattern after weaning. Fungal loads, which are thought to increase the capacity for fermenting the complex polysaccharides from diet, were higher in P relative to A. Beyond the effects of weaning methods, maternal separation at weaning markedly shifted the composition of the gut microbiota in all foals, which fell into three distinct community types at 3 days post-weaning. Most genera in community type 2 (i.e., Eubacterium, Coprococcus, Clostridium XI, and Blautia spp.) were negatively correlated with salivary cortisol levels, but positively correlated with telomere length and N-butyrate production. Average daily gain was also greater in the foals harboring a community type 2 microbiota. Therefore, community type 2 is likely to confer better stress response adaptation following weaning. This study identified potential microbial biomarkers that could predict the likelihood for physiological adaptations to weaning in horses, although causality remains to be addressed.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Characterisation of the faecal bacterial community in adult and elderly horses fed a high fibre, high oil or high starch diet using 454 Pyrosequencing

Faecal samples were collected from seventeen animals fed three different diets (high fibre, high fibre supplemented with starch and high fibre supplemented with oil). DNA was extracted and the V1-V2 regions of 16SrDNA were 454-pyrosequenced to investigate the faecal microbiome of the horse. The effect of age was also considered by comparing mature (8 horses aged 5-12) versus elderly horses (9 horses aged 19-28).A reduction in diversity was found in the elderly horse group and four OTUs were identified as significantly different from the adult group (P<0.001).These OTUs were predominantly in the order Clostridiales and were decreased in the elderly group. Significant differences between diets were also found at an OTU level (36 OTUs at P<0.001). The majority of differences found for both diet and age were related to the Firmucutes phylum (28) with some Bacteroidetes (4), Proteobacteria (2), Spirochaetes (1) and Actinobacteria (1).  With a high fibre diet ,with no added starch or oil, we found 30/2934 OTUs (accounting for 15.9% of sequences) present in all horses. However the core (i.e. present in all horses)  associated with a high oil supplemented diet was somewhat smaller (25/3029 OTUs, 10.3% ) and the core associated with a high oil supplemented diet was even smaller (15/2884 OTUs, 5.4% ). The core associated with samples across all three diets was extremely small (6/5689 OTUs accounting for only 2.3% of sequences) and dominated by the order Clostridiales, with the most abundant family being Lachnospiraceae. In conclusion, addition of starch or fat to the diet produced changes in the faecal bacterial community. Further, as observed in people, ageing is associated with a reduction in bacterial diversity and a change in the bacterial community structure.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
16S rRNA gene amplicon sequencing project of gut microbiota of deep-sea fish

We report 16S rRNA gene amplicon sequence analysis of gut microbiota of deep-sea fishes (Chlorophthalmus albatrossis, Glossanodon semifasciatus, and Helicolenus hilgendorfi) collected from Suruga Bay, Japan. The analysis revealed a low taxonomic diversity of gut microbiota in these deep-sea fishes.

Biome: root:Host-associated:Fish:Digestive system
Critical Assessment of Metaproteome Investigation (CAMPI): a Multi-Lab Comparison of Established Workflows

Metaproteomics has substantially matured over the past years as a powerful tool to assess functional interactions in microbial communities. A wide variety of metaproteomic workflows is available, yet their impact on the results remains to be established.Here, we carried out the first community-driven, multi-lab comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluated the influence of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, lab-assembled human intestinal model and a human fecal sample.Although bioinformatic pipelines contributed to variability in peptide identification, wet-lab stages were the most important source of differences between analyses. Moreover, protein groups were less sensitive to those differences than peptides. Comparing taxonomic and functional profiles revealed differences between peptide- and protein-centric approaches at the taxonomic level but very similar functional profiles.These CAMPI findings present the current opportunities and challenges in metaproteomics research and provide a perspective for future benchmarking studies.

Biome: root:Engineered:Modeled:Simulated communities (microbial mixture)
Role of young olive trees in soil microbial communities after organic and mineral fertilization


Biome: root:Host-associated:Plants:Rhizoplane:Soil
EMG produced TPA metagenomics assembly of PRJNA330603 data set (Geotraces Raw sequence reads).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA330603, and was assembled with metaSPAdes v3.14.1 and MEGAHIT v1.2.9. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Marine phages from the Arctic Ocean

A combined set of 56 samples was isolated by the Suttle Laboratory from 16 different sites in the Arctic Ocean between September 1, 2002 and October 31, 2002.  The phage fraction was purified and sequenced using pyrophosphate sequencing (454 Life Sciences).    This is part of a global ocean survey of phage and virus sequences.   454 sequence data is available from the Short Read Archive (SRA): <a href="ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/SRA000410 ">SRA000410</a>.   Metagenomics SEED ID: 4440306.3  Nature paper ID: 34  The WGS project can be found using the Project data link.

Biome: N/A
EMG produced TPA metagenomics assembly of PRJNA17769 data set (Marine phages from the Arctic Ocean).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA17769, and was assembled with megahit v1.2.9. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Nitrogen fixation rates and cyanobacteria cover in a subarctic biological soil crust are enhanced by warming, wetting and light

biocrust, N-fixation, metagenomes, warming, microbAbstract textIntroduction. Areas of high latitude with volcanic andosol and winter snow cover commonly have a 3-5 mm thick biological soil crust (biocrust) characterized by the leafy liverwort Anthelia juratzkana. This biocrust can be long term or transient, especially as snow cover decreases. Although Antheliais the primary producer, the biocrust is a complex microbial community with substantial biomass and biological activities associated with bacteria and fungi. Available nitrogen is thought to bethe limiting nutrient.Methods. Acetylene reduction assays (ARA) were used as a proxy in assessing biocrust responses to temperature, moisture and light. Soil carbon and nitrogen isotopes were measured and shotgun metagenomic DNA and RNA libraries were sequenced. Decomposition rates were assessed using the tea bags index. Respiration was measured with a LI-6400 system.Results. ARA measurements yielded estimates of nitrogen fixation of 1-4 kg ha-1 yr-1. Nitrogen fixation increases with temperature up to 25 oC, with light up to ~150 moles photons m-2 s-1 as well as with moisture. In situ summer daylight is 300-3000 moles photons m-2 s-1, moisture is from 4% to saturation, and temperatures show strong diurnal cycles from 5 oC to 30 oC on sunny days. Warming effects on decomposition varied with depth and type of tea. Respiration measurements gave an estimate of ~100 kg C ha-1yr-1.There is a highly negative isotope discrimination of 15N vs. 14N in the biocrust, possibly due to fractionation between multiple compartments, from bacteria to fungi and liverworts. The microbial community is diverse, with small differences between locations and habitats. Ascomycete fungi are abundant in the surface layer, particularly the orders Heliotales and Chaetothyriales.Conclusions. Integration of in situ measurements, meteorological information and data from laboratory experiments allows us to estimate nitrogen fixation from year to year, and what effects predicted climate changes are likely to have.

Biome: root:Environmental:Terrestrial:Soil
Equine Intestinal Microbiome in Hypersensitivity Disorders

Background: Recent evidence suggests that an altered intestinal microbiome, namely a reduction of bacterial diversity or a shift in microbial composition, is associated with the development of hypersensitivity diseases in humans but this is unknown for horses.Hypothesis: We hypothesized that horses affected by either Culicoides hypersensitivity (CH) or severe equine asthma (SEA) or both show a decreased diversity of their intestinal microbiome in comparison to healthy peers.Methods: Rectal swab samples of a total of 140 horses were collected. Horses were divided into three groups. CH comprised 30 horses affected by Culicoides hypersensitivity, group SEA consisted of 30 horses suffering from severe equine asthma and group CH-SEA comprised 10 horses affected by both aforementioned diseases. For each allergic horse a healthy peer from the same stable was similarly sampled as a matched control. Microbiota in the swabs were determined by assessing the V4 region of the bacterial 16S rRNA gene by means of Illumina MiSeq. Structures of bacterial communities were investigated by means of alpha and beta diversity indices.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine
EMG produced TPA metagenomics assembly of the Ocean Sampling Day (OSD) 2014: AUTHORITY-RAW amplicon and metagenome sequencing study from the June solstice in the year 2014 (osd-2014) data set

The osd-2014 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set, PRJEB8682. This project includes samples from the following biomes : Marine

Biome: root:Environmental:Aquatic:Marine
Picoplankton 16S rRNA genes from the tropical and sub-tropical global-ocean sampled during the Malaspina-2010 expedition

Surface global ocean prokaryotic picoplankton from the Malaspina-2010 expedition: Surface waters (3m depth) from a total of 122 globally-distributed stations located in the tropical and sub-tropical global ocean were sampled from December 2010 to July 2011 as part of the Malaspina-2010 expedition (Duarte 2015). Water samples were obtained with Niskin bottles attached to a CTD profiler that included sensors for conductivity, temperature, oxygen, fluorescence and turbidity. About 12L of seawater were sequentially filtered through a 20m nylon mesh, followed by a 3m and 0.2m polycarbonate filters of 47mm diameter. Only the picoplankton size-fraction (0.2-3 m) was used for sequencing. DNA was extracted using a standard phenol-chloroform protocol (Massana, et al. 1997). The V4-V5 region of the 16S rRNA gene was amplified with the primers 515F-Y (5'-GTGYCAGCMGCCGCGGTAA) and 926R (5'-CCGYCAATTYMTTTRAGTTT)  (Parada et al. 2016) and sequenced in an Illumina MiSeq platform (2x250bp) at the Research and Testing Laboratory  (Lubbock, Texas, USA; http://www.researchandtesting.com).

Duarte CM. 2015. Seafaring in the 21St Century: The Malaspina 2010 Circumnavigation Expedition. Limnology and Oceanography Bulletin 24:11-14.

Massana R, Murray AE, Preston CM, DeLong EF. 1997. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Applied and environmental microbiology 63:50-56.

Parada AE, Needham DM, Fuhrman JA. 2016 Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol. 18: 1403-14.

Biome: root:Environmental:Aquatic:Marine
Picoplankton 18S rRNA genes from the tropical and sub-tropical global-ocean sampled during the Malaspina-2010 expedition

Surface global ocean eukaryotic picoplankton from the Malaspina-2010 expedition: Surface waters (3m depth) from a total of 122 globally-distributed stations located in the tropical and sub-tropical global ocean were sampled from December 2010 to July 2011 as a part of the Malaspina-2010 expedition (Duarte 2015; Estrada, et al. 2016). Water samples were obtained with Niskin bottles attached to a CTD profiler that included sensors for conductivity, temperature, oxygen, fluorescence and turbidity. About 12L of seawater were sequentially filtered through a 20m nylon mesh, followed by a 3m and 0.2m polycarbonate filters of 142mm diameter (Isopore, Millipore). Only the picoplankton size-fraction (0.2-3 m) was used for sequencing. DNA was extracted using a standard phenol-chloroform protocol (Massana, et al. 1997). The V4 region of the 18S (~380 bp) was amplified with the primers TAReuk454FWD1 and TAReukREV3 (Stoeck, et al. 2010). Duarte CM. 2015. Seafaring in the 21St Century: The Malaspina 2010 Circumnavigation Expedition. Limnology and Oceanography Bulletin 24:11-14.Estrada M, Delgado M, Blasco D, Latasa M, Cabello AM, Benitez-Barrios V, Fraile-Nuez E, Mozetic P, Vidal M. 2016. Phytoplankton across Tropical and Subtropical Regions of the Atlantic, Indian and Pacific Oceans. PLoS One 11:e0151699.Massana R, Murray AE, Preston CM, DeLong EF. 1997. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Applied and environmental microbiology 63:50-56.Stoeck T, Bass D, Nebel M, Christen R, Jones MD, Breiner HW, Richards TA. 2010. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Molecular ecology 19 Suppl 1:21-31.

Biome: root:Environmental:Aquatic:Marine
Picoplankton 18S rRNA gene sequences (V4 region, DNA and RNA) from Vertical Profiles (surface to 4000m depth) sampled during the Malaspina 2010 circumglobal expedition

The study here includes 182 samples (91 DNA and 91 RNA) of the 18S (V4 region) from the Malaspina-2010 expedition. The samples were sequenced using Illumina MiSeq 2x250bp.

Biome: root:Environmental:Aquatic:Marine
Picoplankton 18S rRNA gene sequences (V9 region) from Vertical Profiles (surface to 4000m depth) sampled during the Malaspina 2010 circumglobal expedition

The study here includes 40 samples (DNA) of the 18S (V9 region, DNA) from the Malaspina-2010 expedition. The samples were sequenced using Illumina MiSeq 2x250bp.

Biome: root:Environmental:Aquatic:Marine