SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
M'thermobacter and ex situ biogas upgrading

Ex situ biomethanation is a cost-effective modification of anaerobic digestion, in which hydrogenotrophic methanogens are provided excess hydrogen (H2) and carbon dioxide (CO2) in the absence of a solid biogas feedstock, placing both the process and metabolic emphasis on near-total conversion of CO2 and H2 to biomethane. The concept can be applied ex situ as ‘biological upgrading' to biogas from anaerobic digestion, and is usually carried out at thermophilic temperatures (>50°C) in order to accelerate methanogenesis. The ex situ methanogenic community responsible for this upgrading is currently poorly characterised but is expected to feature abundant methanogens specialising in fixation of CO2 and H2 to CH4. Given the lack of a digestion feedstock, the importance of bacteria in an upgrading community is less clear. In this study, the methanogenic and microbial communities involved in thermophilic ex situ upgrading of a 1 CO2 : 4 H2 mix were characterised during disruption and restoration of biogas production due to a process shift to higher temperatures (55°C to 65°C). Although DGGE, 16S clone library and 16S pyrosequencing approaches showed Methanothermobacter to be the dominant methanogen throughout operation, no relationship was evident between decreased upgrading function and Methanothermobacter abundance. Instead, it is possible that biogas production was restored through addition of organic and/or inorganic substrate in a re-inoculation event. This implies a role for the ex situ bacterial community, the majority of which (>50% reads) belong to uncharacterised Firmicutes taxa, in particular the MBA03 group.

Biome: root:Engineered:Biogas plant
Microbial structure of intermittently aerated sequencing batch reactor (IASBR) treating dairy processing wastewater.

This study investigated the application of an intermittently aerated sequencing batch reactor (IASBR) to the biorremediation of synthetic dairy processing wastewater. Aeration rates conditions were varied in the bioreactor to determine the impacts on IASBR microbial community structure and orthophosphate (PO4-P) and ammonium (NH4-N) removal efficiencies. Bacterial communities of the IASBR were described through 16S rRNA metagenomic analyses by high-throughput pyrosequencing procedure (454 pyrosequencing, Roche) using V5-V9 primers. Sequencing data were analysed by using Quantitative Insights Into Microbial Ecology (QIIME) pipeline.

Biome: root:Engineered:Wastewater
TE supplementing Grass silage Anaerobic Digestion (TE-GAD)

Wall et al. (2014) attempted to determine the optimal mix of silage/slurry in biomethane based AD. Trials showed that although BioMethane Potential (BMP) was highest in 100% silage tests, generation of biomethane was more stable with a 20% inclusion of dairy slurry (by VS%). At higher loading rates BM output in 100% silage (R-G) and 80%silage:20% slurry (R-SG) reached parity, possibly an effect of incomplete degradation of solids within the retention time, but may also be imformed by the microbial community created by increased rate of feedstock addition.Another trend documented both in the original study  and more broadly  is the decline in reactor stability with increased organic loading rate (OLR), as measured by the FOSTAC ratio (effectively the reactor's buffering capability and frequently an indicator for process stability). Increases in OLR from 2.5 to 3 kgVS/m3/d led to rapid accumulation of VFAs (AcO, PrO) in R-G, while no issue was observed over the course of R-SG operation. Due to the constant turnover of organic material and active biology of the reactor community, issues with reactor operation are frequently linked to limiting concentrations of trace elements such as Fe, Co, Ni, etc.. However it is not externally apparent which portions of the community are restricted by the lack of trace elements (TE) - this study aims to characterise the communities stressed by Wall et al., 2014, and determine which populations relate to bottlenecking of (TE).The two reactors characterised in this study (R-G,R- SG) were sampled over 68 and 65 weeks respectively after being seeded from the same sludge inoculum, fed 100% silage and 80:20% silage:slurry, and operated along the same design principles. R-G was sampled at week 1, 20, 37, 40, 43, 49, 54, 64, 65, 68. R-GS was sampled at week 01, 20, 37 and 65 to act as a positive control for R-G.

Biome: root:Engineered:Bioreactor
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Biome: root:Engineered:Biogas plant
EMG produced TPA metagenomics assembly of the Pit mud of Chinese liqour fermentation reactorMetagenome (fermentation metagenome) data set.

The fermentation metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA260163.  This project includes samples from the following biomes: Engineered, Food production, Fermented beverages.

Biome: root:Engineered:Food production:Fermented beverages
Gut microbiomes from 359 European pig and poultry herds (EFFORT)

Antimicrobial resistance (AMR) in bacteria and associated morbidity and mortality is increasing. Use of antimicrobials for livestock selects for AMR that can subsequently be transferred to the human reservoir. This flow of AMR between reservoirs demands surveillance in livestock as well as in humans. As part of the EFFORT project (http://www.effort-against-amr.eu/), we have quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, generating more than 5,000 Gigabases of DNA sequence, using shotgun metagenomics. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than poultry. We found higher AMR loads in pigs, while poultry resistomes were more diverse. We detected several newly described, critical AMR genes, including mcr-1 and optrA, which differed both between host species and countries. We found that the total AMR level, was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns have similar resistomes.

Biome: root:Host-associated:Animal:Digestive system:Fecal
EMG produced TPA metagenomics assembly of the Campus Antibiotics Virome Study () data set.

The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA327423.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Oral, Host-associated, Human, Digestive system.

Biome: root:Host-associated:Human:Digestive system
LSA-COMPARE FOOD TRIAL

LSA-COMPARE FOOD TRIAL

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Choice of method for purification of bacterial DNA from faecal material influences community structure as detected by next generation sequencing (gut metagenome) data set.

The gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA243036.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Evaluating the Potential of using Next-Generation Sequencing for Direct Clinical Diagnostics of Faecal Samples from Patients with Diarrhoea () data set.

The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB14038.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Athlete Microbiome Project (AMP) (human gut metagenome) data set.

The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA305507.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Metagenomics of Japanese gut microbiomes (human gut metagenome) data set.

The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB3601.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine.

Biome: root:Host-associated:Human:Digestive system
Habitat Selection Effects on Brent Goose Gut Microbiomes

We quantified the microbial community structure and function of gut microbiomes of migratory light-bellied Brent geese in Iceland in May. We classified birds based on whether they were feeding on terrestrial grass, marine mudflats, or both.

Biome: root:Host-associated:Animal:Digestive system:Fecal
EMG produced TPA metagenomics assembly of the Raw DNA sequence of sludge samples from FO-AnMBR () data set.

The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA317285.  This project includes samples from the following biomes: Engineered, Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the An integrated catalog of reference genes in the human gut microbiome (IGC) data set.

The IGC Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB5224.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNTR2_MetaG metagenome (activated sludge metagenome) data set.

The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340756.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.

Biome: root:Engineered:Wastewater:Activated Sludge
EMG produced TPA metagenomics assembly of the compost enrichment single cell ciliate 20uM2 metagenome J21 metagenome (compost metagenome) data set.

The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366630.  This project includes samples from the following biomes: Engineered, Solid waste, Composting.

Biome: root:Engineered:Solid waste:Composting
EMG produced TPA metagenomics assembly of the Coastal seawater microbial communities from Marineland, Florida, United States - SWPA TP0 #3 metagenome (seawater metagenome) data set.

The seawater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441399.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Coastal.

Biome: root:Environmental:Aquatic:Marine:Brackish
EMG produced TPA metagenomics assembly of the Marine microbial communities from the Southern Atlantic ocean transect to study dissolved organic matter and carbon cycling - Knorr_S23_td_SurfaceB_ad_5m_LV_B metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375509.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.

Biome: root:Environmental:Aquatic:Marine
EMG produced TPA metagenomics assembly of the Ammonia-oxidizing marine microbial communities from Monterey Bay, California, USA - C0912_C43A7_35 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330317.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.

Biome: root:Environmental:Aquatic:Marine
Schistosoma mansoni infection is associated with quantitative and qualitative modifications of the mammalian intestinal microbiota

In spite of the extensive contribution of intestinal pathology to the pathophysiology of schistosomiasis, little is known of the impact of schistosome infection on the composition of the gut microbiota of its mammalian host. Here, we characterised the fluctuations in the composition of the gut microbial flora of the small and large intestine, as well as the changes in abundance of individual microbial species, of mice experimentally infected with Schistosoma mansoni with the goal of identifying microbial taxa with potential roles in the pathophysiology of infection and disease. Bioinformatic analyses of bacterial 16S rRNA gene data revealed an overall reduction in gut microbial alpha diversity, alongside a significant increase in microbial beta diversity characterised by expanded populations of Akkermansia muciniphila (phylum Verrucomicrobia) and lactobacilli, in the gut microbiota of S. mansoni-infected mice when compared to uninfected control animals. These data support a role of the mammalian gut microbiota in the pathogenesis of hepato-intestinal schistosomiasis and serves as a foundation for the design of mechanistic studies to unravel the complex relationships amongst parasitic helminths, gut microbiota, pathophysiology of infection and host immunity.

Biome: root:Host-associated:Mammals:Digestive system
Broiler caecal metagenomics

The caecum of broiler chickens were analysed using metagenomics

Biome: root:Host-associated:Animal:Digestive system
Alterations in the colon microbiota induced by the gastrointestinal nematode Trichuris suis

Helminth parasites have evolved to regulate host immunity to ensure their survival through mechanisms that dampen host inflammation. These properties have been recently exploited therapeutically to treat human diseases. The bio-complexity of the intestinal lumen would suggest that interactions between parasite and intestinal microbiota would also influence inflammation.  In this study, we characterized the porcine proximal colon microbiota in response to Trichuris suis (whipworm) infection using 16S rDNA-based and whole genome shotgun (WGS) approaches.  A 21-day T. suis infection in pigs induced a profound change in the composition of the proximal colon microbiota. The abundance of four of the 15 phyla identified, such as Proteobacteria, was changed in infected pigs. Approximately 10% of genera were significantly altered by infection. Notably, reduced Succinivibrio abundance in infected pigs implied that T. suis infection altered carbohydrate metabolism in the proximal colon microbial ecosystem. Conversely, Mucispirillum was significantly increased in infected pigs suggesting that mucosal disruption induced by parasitic infection and feeding perturbed this ecological niche. Infection led to a significant shift in the metabolic potential of the proximal colon microbiota. Approximately 26% of all metabolic pathways indentified were affected by infection. Two important functional categories repressed by infection were carbohydrate metabolism and lysine biosynthesis. Furthermore, changes in pathogen associated pathways suggested that T. suis infection could impact subsequent infection and modulate host-pathogen interactions. Our findings should facilitate development of strategies for parasitic control in pigs and humans and optimize successful helminth therapy to reduce inflammation.

Biome: root:Host-associated:Mammals:Digestive system
EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC096_MetaG metagenome (activated sludge metagenome) data set.

The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340754.  This project includes samples from the following biomes: Engineered, Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 13_49_3.3_201_A3 metaG metagenome (bioreactor metagenome) data set.

The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406034.  This project includes samples from the following biomes: Engineered, Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 10_41_5_180_A2 metaG metagenome (bioreactor metagenome) data set.

The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406031.  This project includes samples from the following biomes: Engineered, Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNNA6_MetaG metagenome (activated sludge metagenome) data set.

The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340770.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.

Biome: root:Engineered:Wastewater:Activated Sludge
EMG produced TPA metagenomics assembly of the Switchgrass associated microbial communities from Austin, Texas, USA, to study host-microbe interactions - LS_174 metaG metagenome (bioreactor metagenome) data set.

The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365230.  This project includes samples from the following biomes: Engineered, Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 15_59_3.3_214_A2 metaG metagenome (bioreactor metagenome) data set.

The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406036.  This project includes samples from the following biomes: Engineered, Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC077_MetaG metagenome (activated sludge metagenome) data set.

The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340503.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.

Biome: root:Engineered:Wastewater:Activated Sludge
EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1555C-3 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365246.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.

Biome: root:Environmental:Aquatic:Estuary
EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1555A-3 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365244.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.

Biome: root:Environmental:Aquatic:Estuary
EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1550A-3 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367299.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.

Biome: root:Environmental:Aquatic:Estuary
EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1546A-3 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367281.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.

Biome: root:Environmental:Aquatic:Estuary
EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1449C-3 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367277.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.

Biome: root:Environmental:Aquatic:Estuary
EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1371A-3 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367272.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.

Biome: root:Environmental:Aquatic:Estuary
EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1370B-3 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367269.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.

Biome: root:Environmental:Aquatic:Estuary
EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1371B-02 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367274.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.

Biome: root:Environmental:Aquatic:Estuary
EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1370A-3 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367268.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.

Biome: root:Environmental:Aquatic:Estuary
EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Freshwater metaG S.747 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365286.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.

Biome: root:Environmental:Aquatic:Estuary
EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Ebb tide ETM metaG S.573 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365271.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.

Biome: root:Environmental:Aquatic:Estuary