SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Ercolini whole grain feces

Whole grains contain numerous physiologically bioactive compounds, a key group being polyphenolic compounds (such as ferulic acid). These compounds were shown to have potent antioxidant activity. Limited evidence exists regarding the bioavailability of the whole grain bioactive compounds and their physiological impact on health outcomes in humans such as the CVD risk, body weight and abdominal circumference. Evidence from animal and few human studies indicated that prebiotic dietary fibre ameliorates metabolic syndrome and controls body weight through reduction of inflammation. This study aims to evaluate the bioavailability WG polyphenols, the effect of WG on body weight, circumferences and composition, and to clarify the underlying mechanisms. A commercial WG product, having prebiotic properties and a high amount of polyphenols bound to dietary fibre, was selected. Eighty healthy overweight subjects will be enrolled. Forty volunteers will be asked to change their habitual diet only replacing equicaloric portions of specific foods with 68 g WG per day for 8 weeks; the other half will include a placebo. At baseline, and after 4 and 8 weeks, measure of body weight, waist and hip circumferences, bioimpedance analysis and blood, urine and feces collection will be performed. Markers linked to antioxidant status (serum ferulic acid, beta-carotene and FRAP), to inflammatory status (several cytokines by multiplexed immunometric assay), to lipid and glucose metabolism as well as to the overall nutritional status and appetite, will be measured.

Biome: root:Host-associated:Human:Digestive system
Brazelton LostCity chimney biofilm

The Lost City Hydrothermal Field, an ultramafic-hosted system located 15 km west of the Mid-Atlantic Ridge, has experienced at least 30,000 years of hydrothermal activity. Previous studies have shown that its carbonate chimneys form by mixing of round 90C, pH 9-11 hydrothermal fluids and cold seawater. Flow of methane and hydrogen-rich hydrothermal fluids in the porous interior chimney walls supports an archaeal biofilm dominated by a single phylotype of Methanosarcinales. We have a collection of 40 carbonate chimney samples, most of which have been dated with uranium-thorium isotopic systematics. The resulting ages range from 34 to 145,000 years. Previous 16S rRNA pyrotag sequencing of 4 of these samples revealed that rare sequences in young chimneys were often more abundant in older chimneys, indicating that species can remain rare in a chimney for &gt;100 years before blooming and becoming dominant when the environmental conditions allow. These results suggest that a long history of selection over many cycles of chimney growth has resulted in numerous closely related species at Lost City, each of which is pre-adapted to a particular set of re-occurring environmental conditions. Due to the unique characteristics of the Lost City Hydrothermal Field, these data offer an unprecedented opportunity to study the dynamics of a microbial ecosystem's rare biosphere over thousands of years.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents
Faecal microbiota of Schistosoma mansoni-infected mouse

Monitoring of changes in the gut microbiota of mouse along the infection with Schistosoma mansoni

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Microbial community in A2O or A2O-MBR

Microbial community in A2O or A2O-MBR

Biome: root:Engineered:Wastewater:Water and sludge
The commensal helminth Hymenolepis diminuta ameliorates chemically induced colitis in a rat model system

Hymenolepis diminuta infection in rats is an attractive model for a therapeutic helminthbecause the long-term and stable infection resembles the long-term associations humanshistorically had with helminths and offers the possibility of long-term treatment. Here weinvestigate the ability of H. diminuta to protect rats against colitis induced through applicationof the haptenizing agent DNBS directly to the colon. We test the ability of immature H.diminuta to ameliorate the effects of colitis during the prepatent period, when H. diminutainduces a type 2 immune response. We also test mature H. diminuta (patent period) againstboth moderate (single DNBS application) and severe (two DNBS applications) colitis, a modeldeveloped in this study to assess the effects of H. diminuta on longer-term disease. We monitorthe gut bacterial microbiota over time, as well as measures of rat health and TNFα expression.We show that mature H. diminuta results in lower inflammation, faster recovery and lesserpathology from severe colitis, but has little impact on moderate colitis. Immature H. diminutainduce elevated IL-10 expression, but do not protect against severe colitis. The gut microbiotais disrupted during colitis and does not appear to play an overt role in H. diminuta mediatedprotection.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine
Mediterranean Bathypelagic Habitat

In general, a remarkable number of similarities were found with the deep meso-pelagic Pacific and a convergence at the level of taxa found and types of metabolism with the soil microbiota is starting to be perceived. The authors use the term "invisible soil" paraphrasing the "invisible forest" coined by Paul Falkowski to refer to the hidden but gigantic primary productivity found in the photic zone. The diversity of metabolic enzymes involved in resilient organic compounds degradation was very high. However, many microbes could complement their heterotrophic metabolism with chemolithotrophic energy supplies and, specifically in the Mediterranean, the oxidation of carbon monoxide, probably released by tectonic activity, could be important. There is also evidence that the microbes rarely live isolated. The free living planktonic lifestyle is probably not very popular in this extremely depleted environment. Quorum sensing genes indicate that instead, microbes tend to aggregate in particles and they could become luminescent maybe to attract and be eaten by animals. This strategy could provide the cells with a sporadic visit to the nutritious oasis of an animal gut. Overall, this paper shows that the deep ocean possesses a rich and mostly unknown microbiota that deserves much more studies.

A recent analysis of a metagenomic library from the deep Mediterranean shows a surprising high number of quorum sensing or lux genes that are only expressed when bacteria live in colonies. The deep ocean might be too depleted in resources for microbes to live independently. Instead the association to detritus particles might give them a rich microenvironment. Now, some of the genes detected have been positively identified as luxA, directly involved in bioluminescence.

Why would deep sea bacteria be luminescent? One possible explanation is that they become attractive to animals that at these depths are very photosensitive. Being swallowed by one of these creatures would give the bacteria a temporary oasis of nutrient-rich conditions before another long dip in the abyssal black.

Biome: root:Environmental:Aquatic:Marine:Oceanic
The gut microbiota distinguishes GI-healthy and -unhealthy captive colobineprimates

Despite concerted efforts to improve the conservation status of Asian primates,conditions in their natural habitats continue to worsen. As a result, captive breeding programs may become increasingly important to ensure species survival. Nevertheless, maintaining healthy captive populations of Asian primates can be difficult, particularly for primates of the Colobinae subfamily that commonly suffer from morbidity and mortality due to gastrointestinal (GI) distress of unknown cause. While there is speculation that this GI distress may be associated with a dysbiosis of the gut microbiota, no study has directly examined the role of the gut microbiota in colobine GI health. Hi Seq data

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Temple TX native exotic precip study

Bacterial biodiversity between native and novel exotic-dominated communities exposed to irrigation treatment In many systems, novel exotic-dominated plant communities are replacing native plant communities. We experimentally compared species diversity decline between nine-species grassland communities under field conditions to test whether bacterial diversity differed between communities containing all exotic or all native plant species, using a pool of 40 plant species. Mixtures (64) were established with equal functional group proportions using a paired species approach that controlled for phylogeny and growth form between pairs of native and exotic plant species. Origin (native vs. exotic) was crossed with summer irrigation treatments. Here we examine weather changes in climate, plant biomass and plant diversity affect bacterial community composition. Aboveground biomass was greater in exotic than native plots, and this difference was larger in mixtures than in monocultures. Plant species diversity declined more in exotic than native plant communities. Using 16S rDNA, we will determine if soil microbial communities are sensitive to changes in irrigation and plant communities, or if soil microbial communities are resilient, resulting in minimal changes in soil bacterial community composition.

Biome: root:Environmental:Terrestrial:Soil
A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota, WI, USA

With an unprecedented decade-long time series from a temperate eutrophic lake, we analyzed bacterial and environmental co-occurrence networks to gain insight into seasonal dynamics at the community level. We found that (1) bacterial co-occurrence networks were non-random, (2) season explained the network complexity and (3) co-occurrence network complexity was negatively correlated with the underlying community diversity across different seasons. Network complexity was not related to the variance of associated environmental factors. Temperature and productivity may drive changes in diversity across seasons in temperate aquatic systems, much as they control diversity across latitude. While the implications of bacterioplankton network structure on ecosystem function are still largely unknown, network analysis, in conjunction with traditional multivariate techniques, continues to increase our understanding of bacterioplankton temporal dynamics.

Biome: root:Environmental:Aquatic:Freshwater:Lake
Marine CDOM accumulation during a coastal Arctic mesocosm experiment: No response to elevated pCO2 levels

Metagenome and transcriptome of filtered sea water samples from mesocosms under different CO2 partial pressure. CO2 pressures were increased in multiple mesocosms and samples within each were taken during an elongated period of time.

Biome: root:Environmental:Aquatic:Marine:Pelagic
Bergen Ocean Acidification Mesocosms

Water samples were obtained from a replicated mesocosm study (two treatments, each in triplicate) established in coastal waters of a fjord close to Bergen, Norway (60.27 N: 5.22 E). Each mesocosm contained 11,000 L of coastal water and two of the six mesocosms were sampled for this study. To induce the phytoplankton bloom, nitrate and phosphate were added. Water samples were taken at the peak and immediately following the collapse of the phytoplankton bloom from both a high CO2 and control mesocosm. Water samples were collected in May 2006. Metagenomic and Metatranscriptomics data has already been published. These data presented here are 16S rRNA V3-V4 Illumina amplicon data.

Biome: root:Environmental:Aquatic:Marine:Pelagic
Polluted Polar Coastal Sediments

With the goal of increasing our understanding of the biogeographic distribution and functional traits of microorganisms from cold, polluted coastal sediments, we are performing a comprehensive characterization of the structure and function of microbial communities from sediments of four hydrocarbon-polluted cold regions (Potter Cove, Antarctic Peninsula; Ushuaia Bay, Tierra del Fuego Island; Vertahamnen, Baltic Sea; Adventfjord, Svalbard Archipelago). At each site, replicate samples were collected from polluted sediments and from unpolluted sediments for comparison. This project is the result of an international collaboration between researchers of Argentina, USA, Sweden and Norway, and has been funded by the Community Sequencing Program of the Joint Genome Institute (JGI-DOE, USA). The project PIs are Hebe Monica Dinoisi (CENPAT-CONICET, Argentina) and Janet K. Jansson (LBNL).

Biome: root:Environmental:Aquatic:Marine:Oil-contaminated sediment
Laboratory Directed Research and Development Biological Carbon Sequestration

Californian_Grassland_soil_incubated_with_pyrolized_plant_material. LDRD biosequestration research: (1) to understand the mechanisms of soil carbon stabilization and how to influence them; (2) to understand how to enhance or influence different means of biologically capturing CO2 in ecological and industrial environments; and (3) to understand and evaluate strategies to increase sequestration of atmospheric carbon and minimize loss of already sequestered carbon. The context for this action is the understanding that sequestering carbon through biological capture of CO2 and stabilization in soils is one of the approaches being considered for reduction of atmospheric carbon loads. Soils are a promising reservoir for sequestration, because soil organic carbon residence times are up to tens of thousands of years, and soil carbon is less vulnerable to disturbance than is above ground biomass.

Biome: root:Environmental:Terrestrial:Soil
Great Lake Microbiome

Microbial diversity analysis at different depths and stations in great lakes of the US (Michigan, Superior)

Biome: root:Environmental:Aquatic:Freshwater:Lake
Rio de Janeiro Coastline

Although Brazil is well known for the great biodiversity within its flora and fauna, the microbial diversity has been poorly characterized. The geographic formation of Rio de Janeiro results in a combination of distinct environments near the coastal Atlantic Ocean, such as Atlantic rain forest, restingas, estuaries, bay areas, hypersaline lagoons and freshwater lakes. All together make the surrounding areas of Rio de Janeiro coastline a microbial diversity hotspot. These tropical regions are of enormous interest since they are considered an important source of novel and unique microorganisms for bioremediation and for biotechnological industries. However, the adjacent areas present either a deficient sewage treatment or/and a busy industrial park that can severely impact the environment. Therefore, the aim of this study is to characterize the microbial community and the functional diversity from pristine and contaminated aquatic environments from Rio de Janeiro coastline. Studying the microbial and functional distributions associated with environmental data, we will be able to identify the effect of environmental factors on the microbial community. This information will be useful to preserve the natural conditions of these tropical areas.

Biome: root:Environmental:Aquatic
Microbial communities of the deep unfrozen: Do microbes in taliks increase permafrost carbon vulnerability?

Microbial life in the nutrient-limited aThe vast frozen terrain of northern latitude ecosystems is typically thought of as being nearly biologically inert for the winter period. Yet deep within the frozen ground of northern latitude soils reside microbial communities that can remain active during the winter months. As we have shown previously, microbial communities may remain active in permafrost soils just below the freezing point of water. Though perhaps more importantly, microbial communities persist in unfrozen areas of water, soil, and sediment beneath water bodies the entire year. Microbial activity in taliks may have significant impacts on biogeochemical cycling in northern latitude ecosystems because their activity is not limited by the winter months. Here we present compositional and functional data, including long term incubation data, for microbial communities within permafrost landscapes, in permafrost and taliks, and the implications of these activities on permafrost carbon decomposition and the flux of CO2 and CH4. Our experiment was conducted at the Alaska Peatland Experiment (APEX) within the Bonanza Creek LTER in interior Alaska. Our site consists of a black spruce forest on permafrost that has degraded into thermokarst bogs at various times over the last five hundred years. We assume the parent substrate of the deep (1-1.5m) thermokarst peat was similar to the nearby forest soil and permafrost C before thaw. At this site, flux tower and autochamber data show that the thermokarst bog is a sink of CO2 , but a significant source of CH4. Yet this does not tell the whole story as these data do not fully capture microbial activity within the deep unfrozen talik layer. There is published evidence that within thermokarst bogs, relatively rapid decomposition of old forest floor material may be occurring. There are several possible mechanisms for this pattern; one possible mechanism for accelerated decomposition is the overwintering activities of microbial communities in taliks of thermokarst soils. To test this idea, we conducted anaerobic incubations of deep (1m) bog soils at two different temperatures to determine microbial temperature response functions. We also measured soil profile CO2 and CH4 concentrations and functional gene assays of the deep bog microbial community. Incubation data in combination with overwinter temperature profiles show that the talik has high potential rates of CO2 and CH4 production compared to the mass of C from forest floor and permafrost C to 1m depth. Results highlight the potential importance of taliks affecting the vulnerability of permafrost carbon to decomposition and reduction to methane.nd low-permeability continental crystalline crust is abundant but remains relatively unexplored. Using high-throughput sequencing to assess the 16S rRNA gene diversity, we found diverse bacterial and archaeal communities along a 2516-m-deep drill hole in continental crystalline crust in Outokumpu, Finland.

Biome: root:Environmental:Terrestrial:Soil
Myrold Alder Fir

Replacement Series. This well-designed experiment was established in the mid-1980s to evaluate competition between various mixtures of red alder and Douglas-fir. Experimental plots were established at two locations in Oregon: the Cascade Head Experimental Forest, a high-productivity site in the Coast Range and Site 1 of the Oregon Transect, and the H.J. Andrews Experimental Forest, a low-productivity site in the western Cascade Mountains similar to Site 3 of the Oregon Transect and an NSF LTER site. Both sites were clear-cut and burned in 1984 (Knowe and Hibbs, 1996). Cascade Head was planted the following year and the H.J.Andrews was planted in 1987. Both sites were planted with a design consisting of a replacement series of red alder and Douglas-fir planted on a 10-by-10 grid at 3-m spacing. Of the several mixtures available, we will use the 100 percent red alder and 100percent Douglas-fir plots. Each mixture is replicated three times within a site in a randomized complete block design. These sites have been studied intensively and significant metadata is available, including some information about microbial communities (Boyle et al., 2008; Boyle-Yarwood et al. 2008; Selmants et al., 2005; Vermes and Myrold, 1992; Yarwood et al., 2010). A total of 12 plots (2 sites, with 3 blocks per site, with each block containing plots of 2 tree species) will be sampled.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Spatial variation in arctic soil microbial communities in fire impacted permafrost ecosystems

Spatial variation in arctic soil microbial communities in fire impacted permafrost ecosystems

Biome: root:Environmental:Terrestrial:Soil
Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome

This is a preliminary study to examine the microbiota associated with the Cannabis plant. Soils samples from the bulk soil, soil associated with the roots, and the rhizosphere were extracted and the DNA sequenced. Roots from three independent plants of different strains were examined. These roots were obtained November 11, 2011 from plants that had been harvested in the summer. Future studies will attempt to analyze the soils and rhizospheres from the same location at different time points in the plant lifecycle.

Biome: root:Mixed
Spatial scale drives patterns in soil bacterial diversity.

Most soil processes, including microbial diversity and CO2 efflux, are extremely variable across spatial scales. The destructive and labor-intensive nature of traditional soil sampling and processing methods have hampered broad investigation of spatial heterogeneity in soil function. We collected microsamples of soil (&lt;3 g each) that provided enough material for DNA extraction to characterize the microbial community while reducing sample processing time that can result in DNA degradation and will dramatically enhance the spatial resolution of the of the diversity metrics. We collected twenty-five soil samples (0.7 cm dia X 5 cm deep) in a 10x10 cm grid at five points along a 36 m transect in each of six 36 x 20 m plots representing a low-diversity perennial grassland dominated by Panicum virgatum (fertilized and unfertilized treatments). The aim is to correlate microbial community structure with abiotic factors, which will help build a mechanistic understanding of feedbacks between soil microbes and ecosystem C fluxes.

Biome: root:Environmental:Terrestrial:Soil
Whole-grain wheat consumption reduces inflammation in a randomized controlled trial on overweight and obese subjects with unhealthy dietary and lifestyle behaviors: role of polyphenols bound to cereal dietary fiber

The study aims at characterizing the microbiota of the saliva in obese patients and in a randomly selected population of normal weight individuals. The overall scope is to explore the possibility that a peculiar microbial ecology characterizes the saliva of obese people and thus start wondering whether this can have any meaning on the pathology occurrence and development.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Viral communities associated with algal/coral interactions

Coral competition with benthic algae has been shown to alter the bacterial communities associated with the coral. Certain groups of algae lead to an increase in potential pathogens, potentially shifting the competitive advantage away from the coral and to the alga, while others do not. Here we investigate the changes in the viral communities associated with corals competing with different types of benthic algae to determine if similar changes occur in the viral component of the coral holobiont. We expect that algae that cause stress to corals will lead to the induction of eukaryotic viruses (e.g. infecting coral and/or zooxanthellae) and pathogen-associated phage, while algae that are inferior competitors to corals will not.

Biome: root:Mixed