SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
The 2014 and 2015 International Geobiology Courses took place at Little Hot Creek (LHC), California. The data shown here represents an attempt to gather information from a number of sources at LHC.

Samples were collected from a series of hot springs at the headwaters of Little Hot Creek located in the Long Valley Caldera near Mammoth Lake, CA. The springs are supersaturated for carbonate, circumneutral in pH, and range from a temperature of 50? to 80? C. Genomic DNA was isolated from biofilms and water filtered through a PES 0.22?m 13mm filter using the Zymo Xpedition Soil/Fecal kit (Zymo Research Corp., Irvine, CA). Sequencing was conducted using either MiSeq PE250, PE300, or HiSeq Rapid PE250. MiSeq runs were prepared using the Agilent SureSelect kit (Agilent Technologies, Irvine, CA) with an approximate insert size of 400bp, and HiSeq PE250 samples were prepared using the Nextera XT library preparation kit (Illumina, San Diego, CA).

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
In this study we describe some of the challenges of clinical metagenomics through benchtop sequencing of two distinct sample types, designed to highlight current application and opportunities in this field.

Availability of fast, high throughput and low cost whole genome sequencing (WGS) holds great promise within public health microbiology, with applications ranging from outbreak detection and tracking transmission events, to understanding the role played by microbial communities in health and disease. Within clinical metagenomics, identifying microorganisms from a complex and host enriched background remains a central computational challenge. In this study we sequenced two metagenomic samples, a known viral mixture of 25 human pathogens and an unknown complex biological mode using benchtop technology, highlighting the current challenges  and opportunities in this field.

Biome: root:Engineered:Modeled:Simulated communities (microbial mixture)
Analysis of the goat rumen microbial community following inhibition of methane formation by bromochloromethane (a halogenated methane analogue)

Japanese goats fed a diet of 50% Timothy grass and 50% concentrate with increasing levels of the anti-methanogenic compound, bromochloromethane (BCM) were investigated with respect to the microbial population shifts in the rumen. Microbial ecology methods identified species that exhibited positive and negative responses to the increasing levels of BCM. The methane-inhibited rumen appeared to adapt to the higher H2 levels by shifting fermentation to propionate which was mediated by an increase in the population of hydrogen-consuming Prevotella and Selenomonas spp.

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Diesel contamination of Antarctic soils and sediments

Hydrocarbon contamination is a threat resulting from human activity in Antarctica because of the low degradation rate due to the cold climate conditions and the seasonal freezing and thawing of soil in summer ice-free areas like the Antarctic Peninsula. Hydrocarbons can accidentally reach soil and sediments and distribute underground, likely affecting the biota and causing changes in bacterial communities. Monitoring and study of the distribution of hydrocarbons and the consequent response of the microbiota helps in the design of bioremediation strategies and elaboration of contingency plans, both required by the Antarcic Treaty.

Biome: root:Environmental:Terrestrial:Soil:Contaminated
The RNA metagenomes of Argentine ants (Linepithema humile) collected in New Zealand.

Argentine ants were collected from two nests located in Wellington, New Zealand. RNA was extracted from a pool of 30 ants collected from each of these nests. All RNA was then combined and subjected to de novo metagenomic analysis, using an Illumina MiSeq instrument. Multiple displacement amplification was used to increase the yield of transcribed DNA to meet the minimum input requirements of the Illumina MiSeq. The Illumina TruSeq DNA library preparation was used to prepare libraries, and produce 250 bp paired end reads.

Biome: root:Host-associated:Arthropoda
Assimilation of C by microbial populations in glacial forefields

Microbial communities and soil carbon (C) have been shown to vary in response to increasing vegetation cover during soil development after deglaciation. However, little is known about the ability of microorganisms to utilize various C sources in glacier forefield soils. We supplied ecologically relevant 13C-labelled C sources (Chlorella, Penicillium and Festuca) to three distinct environments (supraglacial sediments, barren soils and vegetated soils) of the Damma glacier area to monitor 13CO2 production. We identified prokaryotic and fungal populations able to utilize these sources by using DNA-stable isotope probing coupled with Illumina MiSeq sequencing of ribosomal markers. A high initial 13CO2 pulse indicated that 13C-labelled microbial and plant material were consumed. The 13C-enriched DNA results indicated that betaproteobacterial taxa affiliated to the families Oxalobacteraceae and Comamonadaceae were important players in C utilization from different sources and present in all environments. In contrast, different fungal taxa played different roles in C degradation depending on the soil environment. Overall, our findings reveal that C utilization  is driven by similar prokaryotic populations along a glacier forefield, while the distribution of active fungal populations are more influenced by environmental factors.

Biome: root:Environmental:Terrestrial:Soil
Effect and mode of action of chitosan and ivy fruit saponins on the microbiota, fermentation and methanogenesis in the rumen simulation technique

Manipulation of the rumen microbial ecosystem to increase the efficiency of nutrient use by the animal, or to decrease its environmental impact, has long been a goal for nutritionists and gut microbiologist. This paper investigates the effect and mode of action of chitosan (CHI) and ivy fruit saponins (IVY) when used as novel feed additives for ruminants. These compounds were supplemented at 5% inclusion rate into a control diet (CON) in a rumen simulation technique. Both, CHI and IVY had a strong and similar ability to decrease methane emissions in comparison to CON (-42% and -40%, respectively). The mode of action of these feed avidities was however remarkably different: CHI promoted a shift in the fermentation pattern towards more energetically favourable pathways (propionate) which explained about two thirds of the decrease in rumen methanogenesis. This shift was achieved by a simplification and modification of the structure in the bacterial community consisting on an increment of Bacteroidetes and Proteobacteria in detriment of Firmicutes and Fibrobacteres. This substitution of fibrolytic bacteria by amylolitic bacteria induced by CHI resulted on a 2.5-fold increase in the amylase enzymatic activity, lactate concentration (+53%) and microbial protein yield (+14%) with no detrimental effect on feed digestibility. Additionally, CHI decreased the relative abundance of methanogens respect to total bacteria which could also contribute to lower rumen methanogenesis. On the contrary, IVY promoted only minor changes on the fermentation pattern and on the structure of the bacterial community which explained only one third of the observed decrease in rumen methanogenesis. Instead, IVY had a specific effect on the methanogens population. This effect consisted on a change in the structure of the methanogens community and a decrease in its diversity. This specific effect, together with the anti-protozoal activity, can be thus considered the main anti-methanogenic property for IVY. Moreover IVY showed to have some beneficial effect to buffer the post-prandial drop in rumen pH and to decrease rumen ammonia levels (-61%), but its anti-microbial properties had a negative impact on microbial protein synthesis (-10%). Therefore, both CHI and IVY should be further investigated in vivo in order to determine the optimum doses which maintain low rumen methanogenesis but prevent negative effects on the rumen microbial ecosystem.

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Brain meta-transcriptomics from harbor seals to infer the role of the microbiome and virome in a stranding event

Marine diseases are becoming more frequent, and tools for identifying pathogens and disease reservoirs are needed to help prevent and mitigate epizootics. Meta-transcriptomics provides insights into disease etiology by cataloguing and comparing sequences from suspected pathogens. This method is a powerful approach to simultaneously evaluate both the viral and bacterial communities, but few studies have?applied this technique in marine systems.?In 2009 seven harbor seals,?Phoca vitulina,?stranded along the California coast from a similar brain disease of?unknown cause of death (UCD). We evaluated the differences between the virome and microbiome of UCDs and harbor seals with known causes of death. Here we determined that UCD stranded animals had no viruses in their brain tissue. However, in the bacterial community, we identified?Burkholderia?and?Coxiella burnetii?as important pathogens associated with this stranding event.?Burkholderia?were 100% prevalent and ~2.8 log2 fold more abundant in the UCD animals. Further, while?C. burnetii?was found in only 35.7% of all samples, it was highly abundant (~94% of the total microbial community) in a single individual. In this harbor seal, C. burnetii?showed high transcription rates of invading and translation genes, implicating it in the pathogenesis of this animal. Based on these data we propose that?Burkholderia?taxa and?C. burnetii?are potentially important opportunistic neurotropic pathogens in UCD stranded harbor seals.

Biome: root:Host-associated:Mammals:Nervous system:Brain
The oral microbiome in HIV infected individuals

The aim of this project was to compare the oral microbiome of HIV-infected individuals to that of age- and gender-matched HIV-negative individuals. A 16S rRNA gene sequencing approach by means of a Roche GS-FLX+ sequencer was used to characterise the bacterial communities of plaque and saliva from each of the study participants.The oral microbiomes of HIV-positive and -negative individuals were found to be similar overall, although there were minor but significant differences in the composition of the salivary microbiota of the two groups. In addition, the results confirmed that plaque and saliva have a differing bacterial composition.

Biome: root:Host-associated:Human:Digestive system:Oral