SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Potential and active functions in the gut microbiota of a healthy human cohort

Gut microbiome research is rapidly moving towards the functional characterization of the microbiota by means of shotgun meta-omics. Here, we selected a cohort of healthy subjects from an indigenous and monitored Sardinian population to analyze their gut microbiota using both shotgun metagenomics and shotgun metaproteomics. We found a considerable divergence between genetic potential and functional activity of the human healthy gut microbiota, in spite of a quite comparable taxonomic structure revealed by the two approaches. Investigation of inter-individual variability of taxonomic features revealed Bacteroides and Akkermansia as remarkably conserved and variable in abundance within the population, respectively. Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the functional activity with the higher expression rate and the lower inter-individual variability in the study cohort, highlighting the key importance of the biosynthesis of this microbial by-product for the gut homeostasis. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several gut microbiota members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis and short-chain fatty acid production). In conclusion, our results provide useful indications regarding the main functions actively exerted by the gut microbiota members of a healthy human cohort, and support metaproteomics as a valuable approach to investigate the functional role of the gut microbiota in health and disease.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Fecal microbiota of fur animal

In this study, the fecal microbiota of the fox and raccoon dog were analyzed. Total DNA was extracted from fecal samples, and the v4 16S rRNA amplicons were characterized on an Illumina MiSeq platform.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Metagenomic, Metatranscriptomic and Metviriomic analysis of samples collected at four time points during a single day at the Gulf of Aqaba in the Red Sea.

To gain knowledge about the abundance of phage-harbored metabolic genes and the extent to which they are expressed in the marine environment, and to detect changes in viral and host populations as well as variations in gene expression, four samples were collected from the Gulf of Aqaba in the Rea Sea. gDNA, vDNA and RNA was collected in 2012 at four different time points over 24 hours. Using a unique approach, no amplification or enrichment methods were applied to any of the fractions prior to sequencing in order to limit sample-specific biases.

Biome: root:Environmental:Aquatic:Marine
Metagenomic investigation of the coastal region of south Gujarat using soil sample - Nargol, Umargam and Dandi

metagenomic investigation of the coastal region of south Gujarat. Soil and water samples were collected and pooled from three different location; dandi, umargam and nargol. From the pooled sample, environmental metagenomic DNA was isolated followed by WGS using  Illumina Miseq platform.

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
Citrate may stimulate the anaerobic hydrocarbon degraders

Citrate may stimulate the anaerobic hydrocarbon degraders

Biome: root:Environmental:Terrestrial:Soil:Clay:Oil-contaminated
Nitrogen  fertilization  directly  affects  soil  bacterial  diversity  and  indirectly  affects  bacterial community composition through soil acidification and plant community changes in grassland

Nitrogen  (N)  deposition  influences  both  above-  and  belowground  communities  and  influences  ecosystem  functioning.  However  the  mechanisms  underlying  alternations  in  bacterial  communities  following  N  enrichment  remain  elusive,  as  does  an  integrated  understanding  of  plant-soil-microbe interactions. In this study, the responses of soil bacterial community composition and diversity to N enrichment  were  investigated  at  surface  (0-10 cm)  and  sub-surface  (10-20 cm)  soils  in a  temperate  steppe  ecosystem.  N  addition  (>120  kg  N  ha -1   yr -1 )  resulted  in  a  significant  shift  in  bacterial community  composition  and  a  decrease  in  bacterial  diversity  in  surface  soil,  but  the  effect  on  the sub-surface  layer  was  far  less  pronounced,  even  at  the  highest  addition  rate  (240  kg  N  ha -1   yr -1 ). Bacterial  community  composition  was  significantly  correlated  with  soil  and  plant  characteristics. Hierarchical structural equation modeling showed that soil ammonium availability was responsible for the shift in bacterial richness, whereas alternation in soil pH and plant composition contributed to the change in bacterial communities. Our results suggest that N fertilization directly affects soil bacterial richness  and  indirectly  affects  bacterial  communities  via  soil  acidification  and  changes  in  plant composition. This indicates that N addition in a temperate steppe ecosystem influences soil bacterial diversity and community composition in an inconsistent manner.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Towards the core microbiome for a thermophilic biogas plant applying metagenome and metatranscriptome analyses complemented by cultivation and characterization if isolates for major functional groups.

Towards the core microbiome for a thermophilic biogas plant applying metagenome and metatranscriptome analyses complemented by cultivation and characterization if isolates for major functional groups.

Biome: root:Engineered:Biogas plant
Towards the core microbiome for a thermophilic biogas plant applying metagenome and metatranscriptome analyses complemented by cultivation and characterization of isolates for major functional groups.

Towards the core microbiome for a thermophilic biogas plant applying metagenome and metatranscriptome analyses complemented by cultivation and characterization of isolates for major functional groups.

Biome: root:Engineered:Biogas plant
Amplicon sequencing of four biogas plants

Amplicon sequencing of four biogas plants

Biome: root:Engineered:Biogas plant
Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health

BACKGROUND: To convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still not known. METHODOLOGY/PRINCIPAL FINDINGS: We studied the impact of long-term agriculture on desert soil in one of the most prominent examples for organic desert farming in Sekem (Egypt). Using a polyphasic methodological approach to analyse microbial communities in soil as well as associated with cultivated plants, drastic effects caused by 30 years of agriculture were detected. Analysing bacterial fingerprints, we found statistically significant differences between agricultural and native desert soil of about 60%. A pyrosequencing-based analysis of the 16S rRNA gene regions showed higher diversity in agricultural than in desert soil (Shannon diversity indices: 11.21/7.90), and displayed structural differences. The proportion of Firmicutes in field soil was significantly higher (37%) than in the desert (11%). Bacillus and Paenibacillus play the key role: they represented 96% of the antagonists towards phytopathogens, and identical 16S rRNA sequences in the amplicon library and for isolates were detected. The proportion of antagonistic strains was doubled in field in comparison to desert soil (21.6%/12.4%); disease-suppressive bacteria were especially enriched in plant roots. On the opposite, several extremophilic bacterial groups, e.g., Acidimicrobium, Rubellimicrobium and Deinococcus-Thermus, disappeared from soil after agricultural use. The N-fixing Herbaspirillum group only occurred in desert soil. Soil bacterial communities were strongly driven by the a-biotic factors water supply and pH. CONCLUSIONS/SIGNIFICANCE: After long-term farming, a drastic shift in the bacterial communities in desert soil was observed. Bacterial communities in agricultural soil showed a higher diversity and a better ecosystem function for plant health but a loss of extremophilic bacteria. Interestingly, we detected that indigenous desert microorganisms promoted plant health in desert agro-ecosystems.

Biome: root:Environmental:Terrestrial:Soil:Desert
Impact of faecal microbiota transplantation on the intestinal microbiome in metabolic syndrome patients

Ten individuals with metabolic syndrome underwent a single faecal microbiota transplantation (FMT): 5 of which were allogenic, the other 5 autologous. Stool samples were collected before FMT (day 0) and days 2, 14, 42 and 84 after FMT; and from the donor before FMT. Metagenomic shotgun sequencing was performed on all samples.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Comparisons of diazotrophic communities in native and agricultural desert ecosystems reveal plants as important drivers in diversity

Diazotrophs provide the only biological source of fixed atmospheric nitrogen in the biosphere. Although they are the key player for plant-available nitrogen, less is known about their diversity and potential importance in arid ecosystems. We investigated the nitrogenase gene diversity in native and agricultural desert soil as well as within root-associated microbiota of medicinal plants grown in Egypt through the combination of nifH-specific qPCR, fingerprints, amplicon pyrosequencing, and FISH-CLSM. Although the diazotrophic microbiota were characterized by generally high abundances and diversity, statistically significant differences were found between both soils, the different microhabitats, and between the investigated plants (Matricaria chamomilla L., Calendula officinalis L., and Solanum distichum Schumach. and Thonn.). We observed a considerable community shift from desert to agriculturally used soil that demonstrated a higher abundance and diversity in the agro-ecosystem. The endorhiza was characterized by lower abundances and only a subset of species when compared to the rhizosphere. While the microbiomes of the Asteraceae were similar and dominated by potential root-nodulating rhizobia acquired primarily from soil, the perennial S. distichum generally formed associations with free-living nitrogen fixers. These results underline the importance of diazotrophs in desert ecosystems and additionally identify plants as important drivers in functional gene pool diversity.

Biome: root:Host-associated:Plants:Rhizosphere
Retrieval of Commamox genomes using metagenomics

Retrieval of Commamox genomes using metagenomics.

Biome: root:Engineered:Wastewater:Industrial wastewater:Petrochemical
Extradiol dioxygenase pyrosequencing- Secondary successional trajectories of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid Poplar

It is envisaged that a detailed understanding of rhizospheric microbial populations will greatly contribute to a better design and implementation of rhizoremediation. In order to investigate the long-term succession of structural and catabolic bacterial communities in oil polluted soil planted with hybrid poplar, we carried out a 2-year field study. Hybrid aspen (Populus tremula x tremuloides) seedlings were planted in polluted soil excavated from an accidental oil-spill site. Vegetated and un-vegetated soil samples were collected for microbial community analyses at 7 different time-points during the course of 2 years and sampling time-points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing whereas catabolic communities were monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late phase communities.

Biome: root:Host-associated:Plants:Rhizosphere
16S rRNA gene pyrosequnecing- Secondary successional trajectories of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid Poplar

It is envisaged that a detailed understanding of rhizospheric microbial populations will greatly contribute to a better design and implementation of rhizoremediation. In order to investigate the long-term succession of structural and catabolic bacterial communities in oil polluted soil planted with hybrid poplar, we carried out a 2-year field study. Hybrid aspen (Populus tremula x tremuloides) seedlings were planted in polluted soil excavated from an accidental oil-spill site. Vegetated and un-vegetated soil samples were collected for microbial community analyses at 7 different time-points during the course of 2 years and sampling time-points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing whereas catabolic communities were monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late phase communities.

Biome: root:Host-associated:Plants:Rhizosphere
Alk B pyrosequencing -Secondary successional trajectories of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid Poplar

It is envisaged that a detailed understanding of rhizospheric microbial populations will greatly contribute to a better design and implementation of rhizoremediation. In order to investigate the long-term succession of structural and catabolic bacterial communities in oil polluted soil planted with hybrid poplar, we carried out a 2-year field study. Hybrid aspen (Populus tremula x tremuloides) seedlings were planted in polluted soil excavated from an accidental oil-spill site. Vegetated and un-vegetated soil samples were collected for microbial community analyses at 7 different time-points during the course of 2 years and sampling time-points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing whereas catabolic communities were monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late phase communities.

Biome: root:Host-associated:Plants:Rhizosphere
Diversity of Clostridium cluster I community in a biogas plant

A two stage biogas production plant was analyzed for the diversity of bacteria from Clostridium cluster I and presence of its pathogenic members. A group specific approach was used to amplify 16S rRNA genes of Clostridium cluster I. Amplicons were sequences by 454 technology. Samples include substrates used for anaerobe digestion, i.e. maize silage, whole plant silage and cattle manure, and material from main and secondary digester. The biogas plant consisted of two parallel digesters one operated with cattle manure, the other without.

Biome: root:Engineered:Biogas plant
The sapro-rhizosphere concept: Energy flow from plant roots via saprotrophic fungi to bacteria

Two common saprotrophic, rhizosphere-inhabiting fungi, Trichoderma harzianum and Mucor hiemalis, were confronted in a microcosm system with bacterial communities extracted from two plant rhizospheres (Carex arenaria and Festuca rubra).

Biome: root:Host-associated:Plants:Rhizosphere
Community structure and diversity of the root-associated microbiome of Ilex paraguariensis St. Hil (Yerba Mate) after bio-inoculation with Kosakonia radicincitans YD4

Using ITS amplicon sequencing, structure and diversity of the root-associated fungal community of Ilex paraguariensis St. Hil (Yerba Mate) was investigated in a pot experiment in Argentina.

Biome: root:Host-associated:Plants:Root
Community structure and diversity of the root-associated microbiome of Ilex paraguariensis St. Hil (Yerba Mate)

Using ITS amplicon sequencing, structure and diversity of the root-associated fungal communities of Ilex paraguariensis St. Hil (Yerba Mate) was investigated in different plantations from Argentina.

Biome: root:Host-associated:Plants:Root
Microbial diversity on Icelandic glaciers and ice caps

Algae are important primary colonizers of snow and glacial ice, but hitherto little is known about their ecology on Iceland?s glaciers and ice caps. Due do the close proximity of active volcanoes delivering large amounts of ash and dust, they are special ecosystems. This study provides the first investigation of the presence and diversity of microbial communities on all major Icelandic glaciers and ice caps over a three year period. Using high-throughput sequencing of the small subunit ribosomal RNA genes (16S and 18S), we assessed the snow community structure and complemented these analyses with a comprehensive suite of physical-, geo- and biochemical characterizations of the aqueous and solid components contained in snow and ice samples. Our data reveal that a limited number of snow algal taxa (Chloromonas polyptera, Raphidonema sempervirens and two uncultured Chlamydomonadaceae) support a rich community comprising of other micro-eukaryotes, bacteria and archaea. Proteobacteria and Bacteroidetes were the dominant bacterial phyla. Archaea were also detected in sites where snow algae dominated and they mainly belong to the Nitrososphaerales, which are known as important ammonia oxidizers. Multivariate analyses indicated no relationships between nutrient data and microbial community structure. However, the aqueous geochemical simulations suggest that the microbial communities were not nutrient limited because of the equilibrium of snow with the nutrient-rich and fast dissolving volcanic ash. Increasing algal secondary carotenoid contents in the last stages of the melt seasons have previously been associated with a decrease in surface albedo, which in turn could potentially have an impact on the melt rates of Icelandic glaciers.

Biome: root:Environmental:Aquatic:Freshwater:Ice:Glacier
The plant is crucial: specific composition and function of the phyllosphere microbiome of indoor ornamentals

The indigenous phyllosphere microbiome was identified as a key component for plant growth and health, and for positive effects on microbial diversity within a built environment. Nevertheless, there is still limited understanding of the phyllosphere microbiota and its driving factors. To study the variability of the microbiome in relation to plant genotype and climate, we investigated 14 phylogenetically diverse plant species grown under different controlled conditions in the greenhouses of the Botanical Garden in Graz (Austria). All investigated plants showed highly specific bacterial abundances of up to 106 CFU cm-2 on their leaves. Bacterial diversity (Shannon index H?: 4.1 ? 6.8) and number of putative OTUs (Chao 1: 501 ? 1,097) were strongly plant species-dependent, but comprised similar dominant phyla: Firmicutes, Proteobacteria and Actinobacteria. Non-metric multidimensional scaling and BIO-ENV analysis showed a higher correlation of community composition to plant genotype rather than the ambient climatic variables. The antagonistic potential of the phyllosphere microbiome towards the plant pathogen Botrytis cinerea measured by production of antifungal volatile organic compounds (VOCs) differed in a range of 2 up to 58% of the isolates. Frequently isolated VOCs produces were represented by Bacillus ssp., Stenotrophomonas rhizophila and Kocuria ssp. Surprisingly, the applied biopesticide B. thuringiensis Bt407 was found well-established in all phyllospheres. This study indicates that indoor ornamentals feature a distinct, stable microbiota with a high proportion of antifungal VOC-producers on leaves irrespective of the indoor climate. Hence, the microbiome of phyllospheres stabilize microbial diversity indoors, and can lead to beneficial effects on human health inside buildings.

Biome: root:Host-associated:Plants
Sedimentary DNA reveals cyanobacterial community diversity over 200 years in two perialpine lakes

We present a method for reconstructing past cyanobacterial communities using a temporally high resolved genetic approach on sedimentary DNA (sedDNA) from two stratified peri-alpine lakes in Switzerland (Lake Greifensee and Lake Zurich). We successfully sequenced a 400 nucleotides-long amplicon in the 16S rRNA gene using high-throughput sequencing. The amplicons were used to build a phylogeny summarizing the diversity over the past 200 years in the two lakes. Sequencing revealed a high diversity of cyanobacteria in both lakes. Operational taxonomic units (OTUs) spanned the whole phylum Cyanobacteria and included representatives of a newly described line of bacteria termed Malainabacteria which share common ancestry with cyanobacteria, and have not been previously reported in lakes. The sequencing data was validated using a dataset comprising of 40 years of pelagic phytoplankton microscopic identification from each lake. Common taxa identified in the pelagic samples were also recovered from the sediments. The linear model confirmed a strong and significant relationship (R2=0.86) between pelagic species richness estimated by microscopy and OTU richness from the sediments. The slope for each lake was close to the 1:1 line, but the diversity derived from the sedDNA had a higher baseline compared to microscopy. The water-sediments richness relationship differed among cyanobacterial orders, revealing that diversity of Chroococcales and Synechococcales was widely underestimated by microscopy. Our results demonstrate the feasibility of this approach for the reconstruction of past cyanobacterial pelagic communities using lake sedDNA, and its potential for exploring variation in phylogenetic diversity and community structure over long-term lake historical changes.

Biome: root:Environmental:Aquatic:Freshwater:Lake
Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge

Overgrowth of filamentous bacteria in activated sludge wastewater treatment plants (WWTPs) leads to impaired sludge settleability, a condition known as bulking, which is a common operational problem worldwide. Filaments with the Eikelboom 0092 morphotype are commonly associated with such bulking episodes. Members of the uncultured B45 phylotype, which is embraced within the phylum Chloroflexi, were recently shown to exhibit this morphology. Although these organisms are among the most abundant populations recorded in activated sludge processes, nothing is known about their metabolic characteristics. In this study, a genome sequence, representing the phylotype, was retrieved from a metagenome generated from an activated sludge WWTP plant. The genome consisted of two chromosomes and one plasmid, which were 4.0, 1.0, and 0.04 Mbps in size, respectively. A metabolic model was constructed for this organism, based on annotation of its genome, showing its ability to generate energy by aerobic respiration, utilizing oxygen, nitrite, or nitrous oxide as electron acceptors, or by fermentation of sugars. This model was validated partially in situ. The provisional name of Candidatus ?Promineofilum breve? is proposed for this species. This study represents the first detailed information on an uncultured genus of filamentous organisms from activated sludge.

Biome: root:Engineered:Wastewater:Activated Sludge