SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
EMG produced TPA metagenomics assembly of the Impact of the Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition (DNA Isolation Methodology for Microbiome Genomics) data set.

The DNA Isolation Methodology for Microbiome Genomics Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB14814.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Fecal, Engineered, Modeled, Simulated communities (microbial mixture), Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC059_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: PRJNA340498.  This project includes samples from the following biomes: Engineered, Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the Biogas fermentation microbial communities from Germany - Plant 1 DNA2 metagenome (biogas fermenter metagenome) data set.

The biogas fermenter metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA311381.  This project includes samples from the following biomes: Engineered, Biogas plant.

Biome: root:Engineered:Biogas plant
EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 16_60_3.3_214_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: PRJNA406037.  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 - 6_20_20_110_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: PRJNA405537.  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_JPNNA5_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: PRJNA340767.  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 1555B-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: PRJNA365245.  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 1554B-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: PRJNA367310.  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 1553A-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: PRJNA367307.  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.541 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365287.  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 - Flood tide ETM metaG S.705 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365279.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.

Biome: root:Environmental:Aquatic:Estuary
EMG produced TPA metagenomics assembly of the Anaerobic biogas reactor microbial communites from Washington, USA - Biogas_R1_B C12 SIP DNA metagenome (bioreactor metagenome) data set.

The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340513.  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_JPNTR4_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: PRJNA340758.  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 Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC078_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: PRJNA340504.  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 Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Seattle, Washington, United States - P3_0mM metagenome (mixed culture metagenome) data set.

The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441894.  This project includes samples from the following biomes: Environmental, Aquatic, Lentic, Brackish.

Biome: root:Environmental:Aquatic:Lentic:Brackish
EMG produced TPA metagenomics assembly of the Evaluation of Enriched Background Microflora of Wheat flour Spiked with E. coli O157 and E. coli O121 through metagenomics (E.coli O157 and E.coli O121 spiked in wheat flour) data set.

The E.coli O157 and E.coli O121 spiked in wheat flour Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA430401.  This project includes samples from the following biomes: Engineered, Food production.

Biome: root:Engineered:Food production
EMG produced TPA metagenomics assembly of the Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Seattle, Washington, USA - P5_16mM MetaG metagenome (mixed culture metagenome) data set.

The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406752.  This project includes samples from the following biomes: Environmental, Aquatic, Lentic, Brackish.

Biome: root:Environmental:Aquatic:Lentic:Brackish
EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage D2F08 metagenome (bioreactor metagenome) data set.

The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367151.  This project includes samples from the following biomes: Engineered, Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the anaerobic reactor metagenome for  ARGs (bioreactor metagenome) data set.

The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA399632.  This project includes samples from the following biomes: Engineered, Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the CSTR anaerobic reactor Raw sequence reads (bioreactor metagenome) data set.

The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA303948.  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 Hong Kong - AD_UKC113_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: PRJNA340749.  This project includes samples from the following biomes: Engineered, Wastewater, Industrial wastewater.

Biome: root:Engineered:Wastewater:Industrial wastewater
Description of the bacterial microbiota of EntomoPathogenic Nematodes (EPNs)of Steinernema genus

Entomopathogenic nematodes from the genus Steinernema are used in biological control of insect pests. The free form of the nematode (infective juvenile) is in closed symbiotic association with the intestinal bacteria Xenorhabdus (Enterobacteriaceae). In the well-studied Steinernema carpocapsae - Xenorhabdus nematophila couple, it was largely shown that the bacterial symbiont played an important role in the death of the insect and in the elimination of the microbial competitors inside the insect cadaver. However, in addition to symbiotic bacteria, other cultivable bacteria have been regularly isolated from infective juveniles nematodes.In this study,we used both culture-dependent and multigenic metabarcoding methods to obtain a comprehensive survey of S. carpocapsae bacterial microbiota. We used two markers, the V3-V4 region of the 16S rRNA gene and a region of the rpoB gene, for which a database was built. We identified a core-microbiota of about 10 OTUs that were present in more than 70% of the samples. Representative bacterial strains of the core-microbiota were tested for their insecticidal performances and their ability to produce antimicrobial molecules.

Biome: root:Engineered:Modeled:Simulated communities (microbial mixture)
The process-related dynamics of microbial community during the fermentation of Chinese strong-flavored liquor

Chinese strong-flavored liquor (CSFL) is one of the most typical representatives of Chinese liquor. It is brewed by multiple-microorganism consortia in a special fermention pit (FT). However, the fermentation process was not fully understood owing to its complicated metabolisms involved many microorganisms. In this study, we investigated the process-related dynamics of microbial communities and main flavor compounds during the 70-day fermentation process using MiSeq-sequencing method. Results showed that during the early fermentation period (1-23 days), the prokaryotic diversity decreased significantly, Lactobacillaceae (Lactobacillus) gradually dominated in prokaryotic community. By contrast, the eukaryotic diversity raise remarkably. Thermoascus, Aspergillus, Rhizopus and unidentified Saccharomycetales were dominant eukaryotic members. Glucose was produced from macromolecular carbohydrates (e.g., starch) in the fermentation. During the middle fermentation period (23-days), microbial diversity did not change significantly. Prokaryotic community was almost dominated by Lactobacillaceae (Lactobacillus), while eukaryotic community was mainly comprised of Thermoascus, Emericella and Aspergillus. Glucose concentration decreased significantly, while the concentrations of lactate acid, propanoic acid and ethanol increase constantly. During the later fermentation period (48-70 days). Microbial community kept relative constant. The ester acetate, ethyl lactate and ethyl hexanoate began to be produced. Canonical correspondence analysis (CCA) showed that Lactobacillaceae, Bacilli, Botryotinia, Aspergillus, unidentified Pleosporales, and Capnodiales  were positively correlative to the producion of organic acids and ethyl ester ( P<0.05 ). Additionally, Saccharomycetales, Monascus, and Rhizopus were positive corelative  to glucose production ( P<0.05 ), highlighting their roles in the degradation of carbohydrates. This study contributes to our understanding of microbial community composition, successsion and their function in the fermentation process of CSFL fermentation.

Biome: root:Engineered:Food production:Fermented beverages
Prior dietary practices and connections to a human gut microbial metacommunity alter responses to diet interventions

It is unclear how to ensure that the gut microbiota of individuals with disparate dietary practices (DPs) respond consistently to prescribed dietary interventions. To address this, we identified DP-associated gut bacterial taxa in individuals either practicing chronic calorie restriction with adequate nutrition (CRON) or without dietary restrictions (AMER). Transplanted into gnotobiotic mice, AMER and CRON microbiota responded predictably to CRON and AMER diets but with variable response strength. Individual microbiota exist within a population of host communities (metacommunity) connected by microbial exchange. Sequentially cohousing AMER-colonized mice with two different groups of CRON-colonized mice emulated metacommunity effects, resulting in enhanced responses to a CRON diet intervention and changes in several metabolic features in AMER animals. This response was driven by an influx of CRON DP-associated taxa. Certain DPs may impair responses to dietary interventions, necessitating introduction of absent diet-responsive bacterial lineages present in other individuals and identified using the strategies described.

Biome: root:Host-associated:Animal:Digestive system:Fecal
Carrot juice fermentations as man-made microbial ecosystems dominated by lactic acid bacteria

During the present study, the microbial characteristics of carrot juice fermentations were evaluated via combined culture-dependent, culture-independent, and metabolite target analysis approaches. In total, the dynamics of more than 200 fermentation samples from a Michelin star chef, laboratory fermentations, and a citizen science fermentation project, were analyzed.

Biome: root:Engineered:Food production:Fermented vegetables
Biodiversity-function relationships in methanogenic communities

Methanogenic communities play a crucial role in carbon cycling and biotechnology (anaerobic digestion), but our understanding of how their diversity, or composition in general, determines the rate of methane production is very limited. Studies to date have been correlational because of the difficulty in cultivating their constituent species in pure culture. Here we investigate the causal link between methanogenesis and diversity in laboratory anaerobic digesters by experimentally manipulating the diversity of cultures by dilution and subsequent equilibration of biomass. This process necessarily leads to the loss of the rarer species from communities. We find a positive relationship between methane production and the number of taxa, with little evidence of functional saturation, suggesting that rare species play an important role in methane producing communities. No correlations were found between the initial composition and methane production across natural communities, but a positive relationship between species richness and methane production emerged following ecological selection imposed by the laboratory conditions. Our data suggest methanogenic communities show little functional redundancy, hence any loss of diversity– both natural and resulting from changes in propagation conditions during anaerobic digestion – is likely to reduce methane production.

Biome: root:Engineered:Bioreactor
Characterization of archaeal and bacterial communities in UASB reactors fed pig manure supernatant, operated at high ammonia concentrations

Four UASB reactors fed pig manure supernatant were operated at two ammonium concentrations (1.9 and 3.7 g L-1 for LA and HA reactors, respectively) and at variable temperatures over 358 days. The granules used as inoculum originated from a UASB reactor treating pulp and paper process wastewater. The reactors were all operated at HRT 1.0 day. The organic loading rate (OLR) was 16±2 g COD L-1 d-1 for the entire experiment. Archaeal and bacterial communities were characterized by Illumina sequencing of 16S rRNA amplicons covering the v3 and v4 regions.

Biome: root:Engineered:Bioreactor
Acetate- and glucose-fed microbial fuel cells. Samples of bioanodes as well as biomass not associated with electrodes.

We operated microbial fuel cells (MFCs) on acetate or glucose and investigated the responses to starvation, exposure to alternative electron donors, and conversion of the bioanodes into biocathodes. Samples for DNA extraction, PCR of the V4 region of the 16S rRNA gene, and Illumina MiSeq sequencing was carried out on samples collected from three acetate-fed and three glucose-fed MFCs. Samples were collected from the bioanodes, liquid, and biofilm growing on non-conductive areas of the MFCs.

Biome: root:Engineered:Bioreactor
The microbial communities in anaerobic digesters

Anaerobic digestion is regarded as a key environmental technology in the present and future bio-based economy. The microbial community completing the anaerobic digestion process is considered complex, and several attempts already have been carried out to determine the key microbial populations. However, the key differences in the anaerobic digestion microbiomes, and the environmental/process parameters that drive these differences, remain poorly understood. In this research, we hypothesized that differences in operational parameters lead to a particular composition and organization of microbial communities in full-scale installations. A total of 38 samples were collected from 29 different full-scale anaerobic digestion installations, showing constant biogas production in function of time. Microbial community analysis was carried out by means of amplicon sequencing and real-time PCR. The bacterial community in all samples was dominated by representatives of the Firmicutes, Bacteroidetes and Proteobacteria, covering 86.1 ± 10.7% of the total bacterial community. Acetoclastic methanogenesis was dominated by Methanosaetaceae, yet, only the hydrogenotrophic Methanobacteriales correlated with biogas production, confirming their importance in high-rate anaerobic digestion systems. In-depth analysis of operational and environmental parameters and bacterial community structure indicated the presence of three potential clusters in anaerobic digestion. These clusters were determined by total ammonia concentration, free ammonia concentration and temperature, and characterized by an increased relative abundance of Bacteroidales, Clostridiales and Lactobacillales, respectively. None of the methanogenic populations, however, could be significantly attributed to any of the three clusters. Nonetheless, further experimental research will be required to validate the existence of these different clusters, and to which extent the presence of these clusters relates to stable or sub-optimal anaerobic digestion.

Biome: root:Engineered:Wastewater:Water and sludge
nirs nirK nosZ batch tests transcripts

nirs nirK nosZ batch tests transcripts

Biome: root:Engineered:Wastewater:Water and sludge
Microbiology of portuguese WWTP

Microbiology of portuguese WWTP

Biome: root:Engineered:Wastewater:Activated Sludge
Influence of electron acceptors in transcript diversity of active members of the denitrifying community

The aim of this work was to study the effect of various combinations of electron acceptors, nitrate (NO3-), nitrite (NO2-) and N2O, on the denitrification pathway of a d-EBPR system. Batch tests were performed with different electron acceptor combinations, to explore the denitrification pathway. The changes in community structure were evaluated by MiSeq Illumina high throughput sequencing.

Biome: root:Engineered:Wastewater:Activated Sludge
Metagenomic analysis of microbial psychrotolerant consortia leaching of metal sulfides at low temperatures.

The bioleaching processes are limited by the availability of O2 and low temperatures (3°C to 15°C) in Andean mining zones. These parameters limit bacterial leaching operations because decrease the rate of iron oxidation by mesophilic microorganisms. This study aimed to isolate and characterize microbial psychrotolerant consortia leaching (MPCL) that can be used in industrial processes for metal recovery units at high altitude mining operation. We collected and cultured 11 samples of acidic water from the Volcan mining company (4261 m.a.s.l) located in the city of Cerro de Pasco, the Huarón mine (4534 m.a.s.l) located in the district of Huayllay, and Yanamate Lake (4358 m.a.s.l) located at the southeast of Cerro de Pasco city. We obtained 6 MPCL that oxidized copper sulfide 0.5%(w/v) and zinc sulfide 0.5%(w/v) at 5ºC. Growth kinetics of the 6 MPCL were evaluated and doubling times of 49.5 hours for CuS and 60.8 hours for ZnS were obtained. The release of copper kinetics on a sulphide ore and synthetic sulphide (CuS) were evaluated, obtaining better results in CuS, where copper (II) was released to 1.51 mg/L for every 10^5 cells/ml. Metagenomic DNA of the 6 consortia were extracted. The amplicons libraries were built and sequenced using 27F and 518R primers. The consortia were mostly composed for the genus Acidithiobacillus sp. and only in one of them Leptospirillum ferroxidans was present.

Biome: root:Engineered:Bioreactor