SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Functional and taxonomic profiling of microbial communities in caves of the Algarve, Southern Portugal.

This project is designed to deliver dense genetic data sets and sharply improve our understanding of microbial diversity, functioning and biogeography across cave ecosystems. The distinct Algarve karst region (southern Portugal) will be used as a model system in an unprecedented metagenomics quest for the hidden microbial taxa, genes and metabolic pathways present in pristine/undisturbed cave sediments. By overcoming the typical hurdles of traditional microbial cultivation approaches, and targeting cave microbial communities in a DNA-based, cultivation-independent fashion instead, this project will shed new light on the metabolic potential and life-style of hitherto “unculturable” microorganisms that inhabit these unique settings. Extensive data acquisition on key functional genes will ultimately permit future design of novel microbial cultivation platforms based on the predicted metabolism of cave sediment microorganisms. Furthermore, this analysis as a whole will considerably augment our current, limited knowledge of microbial diversity and function in these distinct ecosystems, which remain under-appreciated despite their relevance for global biogeochemistry.

Biome: root:Environmental:Terrestrial:Soil
Metagenomic study of composts produced onfarm

In order to characterize the microbial biodiversity of two composts produced “on-farm”, that have showed different suppressive activity against Rhizoctonia solani and Sclerotinia minor, a metagenomic approach by sequencing 16S r-DNA, for to study bacterial diversity and 18S r-DNA, for to study fungi diversity, both amplified from total DNA extracted from the two composts, will be perform.

Biome: root:Engineered:Solid waste:Composting
Cervical microbiota analysis

The human cervical microbiome may affect natural history of various sexually transmitted infections, including human papillomavirus (HPV). Persistent oncognic HPV infection is a necessary cause of cervical carcinoma. Subjects in this study consisted of 120 women, and they have visited three or more times to study hospital. Subjects enrolled with HPV infection were followed for about 18~24 months. Hybrid capture method was used for detection of oncogenic HPV. Metagenomic DNA was extracted from cervical swab samples of subjects, and bacterial 16S rRNA gene was amplified for microbial community analysis. The compositions of bacterial community were sequenced by pyrosequencing and analyzed.The composition of bacterial community was unique by disease status in each subject. The most predominant phyla were Firmicutes, Proteobacteria, and Actinobacteria. Relatively lower diversity values obtained from bacterial community in vaginal samples than other body sites were observed (41-117 OTUs and lower than 2.35 of Shannon diversity index). These results indicate that the composition of bacterial community in cervical sample of each subject is unique and the composition could be related to the disease status. Further studies of additional subjects will provide a significant difference of cervical bacterial communities among disease status, and this difference help to understand the correlation between microbiome and HPV infection.

Biome: root:Host-associated:Human:Reproductive system:Vagina
Forest harvesting reduces the soil metagenomic potential for biomass decomposition

Soil is the key resource that must be managed to ensure sustainable forest productivity. Soil microbial communities mediate numerous essential ecosystem functions, and recent studies show that forest harvesting alters soil community composition. From a long-term soil productivity study site in a temperate coniferous forest in British Columbia, 21 forest soil shotgun metagenomes were generated, totaling 187 Gb. A method to analyze unassembled metagenome reads from the complex community was optimized and validated. The subsequent metagenome analysis revealed that, 12 years after forest harvesting, there were 16% and 8% reductions in relative abundances of biomass decomposition genes in the organic and mineral soil layers, respectively. Organic and mineral soil layers differed markedly in genetic potential for biomass degradation, with the organic layer having greater potential and being more strongly impacted by harvesting. Gene families were disproportionately affected, and we identified 41 gene families consistently affected by harvesting, including families involved in lignin, cellulose, hemicellulose, and pectin degradation. The results strongly suggest that harvesting profoundly altered below-ground cycling of carbon and other nutrients at this site, with potentially important consequences for forest regeneration. Thus, it is important to determine whether these changes foreshadow long-term changes in forest productivity or resilience and whether these changes are broadly characteristic of harvested forests.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Diet determines bacterial diversity and community structure in Bornean pitcher plants

Carnivorous plants of the genus Nepenthes have been studied for over a century, but surprisingly little is known about associations with microorganisms. The two species Nepenthes rafflesiana and Nepenthes hemsleyana differ in their primary nutrient source, sequestering nitrogen from arthropod prey and bat faeces, respectively. We expected bacterial communities living in the pitchers to resemble this diet difference. Samples were taken from different parts of the pitchers (leaf, peristome, inside, outside, digestive fluid) of both species. Bacterial communities were determined using culture-independent high-throughput amplicon sequencing. Bacterial diversity and community structure was comparable across plant species and most tissues, except digestive fluids. These showed opposing trends with N. hemsleyana harbouring a more diverse bacterial community. In N. rafflesiana fluid, high levels of Acidocella spp. implied a close association with the plant. In N. hemsleyana fluid, vertebrate gut symbionts as well as saprophytic taxa could be detected, the latter of which might act as competitors for nutrients. Generally, digestive fluid communities were highly variable in structure, which might be applicable to a difference in digestion status. Nitrogen-fixing bacteria were present in both study species, which might provide essential nutrients to the plant at times of low prey capture and rare encounters with bats, respectively.

Biome: root:Host-associated:Plants
Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of cheese microbiota

Microbial communities of cheeses, in particular traditional ones are very diverse, questioning their origin, safety and functional role in cheese making. Metagenomic analysis of these communities by Very High Throughput Sequencing Technology (VHTST) with short read shotgun sequencing is a promising approach for their microbial profiling and functional study. However, VHTST requires an adequate genome sequence database to assign the short reads.  The objective of the present study was to constitute a reference genome catalogue suitable for short read metagenomic analysis. Bacteria isolated from dairy products, and belonging to 137 different species and 67 genera were selected, including isolates from the genera Alkalibacterium, Brochotrix, Kluyvera, Luteococcus, Marinilactibacillus and Vagococcus, for which no genome sequences were available. Draft genomes sequences were produced, and 117 among 142 were suitable for public databases and submitted, mainly at high quality level. As a proof of concept for the use of VHTST profiling, the microbial composition of the surfaces of two smear cheeses and one blue-veined cheese was analyzed with the use of these new genomes. A significant part of the cheese microbiota was composed of microorganisms that were not deliberately inoculated, including Gram-negative genera such as Pseudoalteromonas, Halomonas, Vibrio, Marinilactibacillus and Psychrobacter.  The depth of this metagenomic analysis revealed the presence of strains sharing almost complete gene set with over 99.9% identity with newly sequenced strains. They may correspond to 'terroir' strains that add typical values to traditional productions. The availability of the genomes sequenced in the present study and particularly those which are not deliberately inoculated, and the broaden use of VHTST will considerably extend our understanding of cheese microbiota, and of genetic determinants involved in the generation of desirable or undesirable properties.

Biome: root:Engineered:Food production:Dairy products
Kansas, Cultivated corn soil metagenome reference core Project

none provided

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Bacterial diversity in various environments such as cultivated soil, alpine soil,  semi-arid soil

For cultivated soil, alpine soil,  semi-arid soil, samples were taken in the field in 2012 and 2013. They were soil micro-samples as they all weighed between 70 and 150 mg.Samples labelled xb or a (69 samples) come from an alpine soil. They were taken along a 80-m long transect in La Vanoise Park (France). The transect was sampled twice in 2012 and 2013. Samples labelled GMV1 to GMV23 come from a 10-m long transect in Widou (Senegal) were the soil is semi-arid. Samples labelled LD1 to LD22 come from a 2-m long transect in a cultivated soil near Lyon.

Biome: root:Environmental:Terrestrial:Soil
Oral microbiome samples from the Philippines

Metagenomic sequencing of saliva samples from individuals with hunter-gatherer or agriculturalist lifestyles from locations in the Philippines.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Metagenome and metatranscriptome profiling of moderate and severe COPD sputum in Taiwanese Han males

Metagenome and metatranscriptome profiling of moderate and severe COPD sputum in Taiwanese Han males

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Local surveillance of infectious diseases and antimicrobial resistance from sewage

Adequately monitoring of large populations and their environments is essential if we want to monitor pathogens and antimicrobial resistance around the globe. Recent developments in high‐throughput sequencing allow to rapidly identify nucleic acids from various organisms in clinical and environmental samples. Sewage systems are recognized as an important source of human pathogens, especially in crowded settings with poor infrastructure. A temporal metagenomic analysis is applied to sewage samples collected from sewage system of Copenhagen (capital of Denmark) at three sewage plants prior to treatment plants inlet. The project is a proof‐of‐concept study for applying metagenomic approaches that could initiate a the local surveillance of human infectious diseases including antimicrobial resistance from sewage to detect, control, prevent and predict human infectious diseases.

Biome: root:Engineered:Wastewater:Water and sludge
Bacteria and yeast involved in red-browning defect in smear cheese

This study is focused on the characterisation of microbiota in red-spoiled (n=6) and not-spoiled cheeses (n=6), and onto the wooden shelves (12) used for ripenning.

Biome: root:Engineered:Food production:Dairy products
Cheese Processing Targeted Locus

Grana Trentino is a hard Parmesan-like cheese made from raw milk with a traditional technology. Microbiota development from raw milk to aged Grana Trentino cheese during production and maturation processes is the object of this study. This evaluation is important to understand the role of bacteria in determining cheese flavor and sensorial traits. The microbial composition and spatial distribution within Grana Trentino from raw milk to 18 month ripened cheese was characterised on two cheese-making days using partial 16S rRNA pyroseqeuncing 454 analysis of tagged amplicons.  <p> Milk, whey and cheese were collected at different times ripening and in different locations.

Biome: root:Engineered:Food production:Dairy products
Effects of different stages of lactation on the microbial evolution during cheese fermentation: from milk to DPO Fontina Cheese by 454 -pyrosequencing

The bacterial populations of raw milk and Fontina cheeses produced in two cheese factories were investigated by 454 - high-throughput sequencing. Total microbial DNA was isolated from milk and cheeses sampled at 24h and after 7, 28 and 84 day of ripening. In each cheese factory nine cheese-making days were followed in a four months long period: three in the first 40 days after partum (S1), three in the following 40 days when the cows had their estrus cycle (S2) and three in the last 40 days (P3) when cows were pregnant. DNA was used as template in Polymerase Chain Reaction (PCR) to study the hypervariable V1, V2 and V3 regions of the bacterial 16S rRNA gene and analysed by 454-pyrosequencing. A total of 2,518,829 sequence reads were generated by the pyrosequencing of 18 milk and 72 cheese samples

Biome: root:Engineered:Food production:Dairy products
Metagenomic characterization of three Swedish sewage treatment plants

Sewage treatment plants (STPs) have repeatedly been suggested as “hotspots” for the emergence and dissemination of antibiotic-resistant pathogens. A critical question still unanswered is if selection pressures within STPs, caused by residual antibiotics or other co-selective agents, are sufficient to specifically promote resistance. To address this, we employed shotgun metagenomic sequencing of samples from different steps of the treatment process in three Swedish STPs. In parallel, concentrations of selected antibiotics, biocides and metals were analyzed.

Biome: root:Engineered:Wastewater:Activated Sludge
Dietary silver nanoparticles can disturb the gut microbiota in mice

Humans are increasingly exposed via the diet to Ag nanoparticles (NP)used in the food industry. Because of their anti-bacterial activity, ingested Ag NP might disturb the gut microbiota that is essential for local and systemic homeostasis. We explored here the possible impact of dietary Ag NP on the gut microbiota in mice at doses relevant for currently estimated human intakeMice were orally exposed to food (pellets) supplemented with increasingdoses of Ag NP (0, 46, 460 or 4600 ppb) during 28 d. Body weight, systemicinflammation and gut integrity were investigated to determine overall toxicity, and feces DNA collected from the gut were analyzed by Next Generation Sequencing (NGS) to assess the effect of Ag NP on the bacterial population. Ag NP were characterized alone and in the supplemented pellets by scanning transmission electron microscopy (STEM) and energy dispersive X-ray analysis (EDX).

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Effect of phytostimulatory seed-inoculant Azospirillum lipoferum CRT1 on total bacterial comminity (rrs) in the maize rhizosphere

The field trials were run in 2015 in Chatonnay (site P), Cessieu (site BV) and Saint Savin (site FV), which are located in the vicinity of Bourgoin-Jallieu (Isère, France). Maize seeds were inoculated or not by a suspension of  Azospirillum lipoferum CRT1 cells. DNA was extracted from root-adhering soil and nifH gene diversity was sequenced  using 515/806 targeting V4 variable region by Illumina Miseq (2 × 125 bp). Samples 261 to 265 correspond to site BV non-inoculated (NI) formulation F1. Samples 286 to 290 correspond to BV inoculated (I) formulation F1. Samples 311 to 315 correspond to FV-NI-F1. Samples 331 to 335 correspond to FV-I-F1 Samples 351 to 355 correspond to P-NI-F1. Samples 371 to 375 correspond to P-I-F1. Samples 271 to 275 correspond to site BV non-inoculated (NI) formulation F2. Samples 296 to 300 correspond to BV inoculated (I) formulation F2. Samples 321 to 325 correspond to FV-NI-F2. Samples 341 to 345 correspond to FV-I-F2 Samples 361 to 365 correspond to P-NI-F2. Samples 381 to 385 correspond to P-I-F2.

Biome: root:Host-associated:Plants:Rhizosphere
Human gut bacteria that rescue growth and metabolic defects transmitted by microbiota from undernourished children

Human gut bacteria that rescue growth and metabolic defects transmitted by microbiota from undernourished children

Biome: root:Host-associated:Mammals:Digestive system:Fecal
To evaluate, using as model the major pest of commodities, Plodia interpunctella, and adopting a culture-independent approach, the impact of different food substrates on the host-associated bacterial communities.

The feeding behavior of insects may influence the associated bacterial community; this possibility and its magnitude are currently a matter of debate. Using as model the major pest of commodities, Plodia interpunctella, and adopting a culture-independent approach, the impact of different food substrates on the host-associated bacterial communities was evaluated. The analysis of similarity confirmed the differences among microbiotas of moths fed with five substrates and the diet is the only tested factor that explains the observed dissimilarity. The few bacteria shared between food and insect, provide evidences for a limited conveyance of bacteria to the host by diet; more likely, diets with different composition indirectly promote changes on the insect’s microbiota. Moth microbiotas were characterized by two enterotypes, associated with insect fed on diet rich in carbohydrates and proteins, respectively. These results were also confirmed by statistical analyses performed on the predicted functional potential. A core microbiota composed of six taxa was shared between eggs and adults, regardless of the population of origin. The finding of possible human and animal pathogens on chili and in the microbiotas of moths fed on it, open to the possibility that P. interpunctella may convey, through frass, potential pathogens to stored products.

Biome: root:Host-associated:Insecta:Digestive system
Daisy Lake Shotgun Test

Organic matter (OM) derived from terrestrial ecosystems influences both the food webs and biogeochemical cycles of lakes. The boreal ecozone holds an estimated 60% of the world’s fresh water, but lakes in this region tend to be nutrient-poor and less productive, making them especially reliant on carbon subsidies from riparian litterfall. The availability of these carbon subsidies for aquatic food webs depends on microbial communities, but little is known about how the taxonomic and functional diversity of heterotrophic bacteria might influence the rate at which this OM is decomposed in natural systems. Drawing upon biodiversity-ecosystem functioning theory, we predicted that decomposition rates, indicative of both food web production and whole-lake carbon cycling, increase with the taxonomic and functional diversity of bacterial communities. We characterized both bacterial community composition and microbial functional traits in nearshore sediments from 8 catchments along a gradient of terrestrial OM inputs using next-generation sequencing (16S rRNA amplicon sequencing and shotgun metagenomics). We found that both species richness and composition explained variation in rates of OM decomposition among sites. Differences in species composition were largely driven by 17 bacterial families, with abundances of Acidobacteria, Firmicutes and Actinobacteria changing along OM gradients. Ongoing shotgun sequencing will provide more detailed information on the functional traits present in lake sediments. This study highlights the role of microbial communities in the transfer of resources from terrestrial ecosystems, and improves our understanding of how catchment disturbances affect boreal aquatic ecosystems.

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
Effect of phytostimulatory seed-inoculant Azospirillum lipoferum CRT1 on functional community of diazotroph (nifH)in the maize rhizosphere

The field trials were run in 2015 in Chatonnay (site P), Cessieu (site BV) and Saint Savin (site FV), which are located in the vicinity of Bourgoin-Jallieu (Isère, France). Maize seeds were inoculated or not by a suspension of  Azospirillum lipoferum CRT1 cells. DNA was extracted from root-adhering soil and nifH gene diversity was sequenced  using polF/polR primers by Illumina Miseq (2 × 300 bp). Samples 261 to 265 correspond to site BV non-inoculated (NI) formulation F1. Samples 286 to 290 correspond to BV inoculated (I) formulation F1. Samples 311 to 315 correspond to FV-NI-F1. Samples 331 to 335 correspond to FV-I-F1 Samples 351 to 355 correspond to P-NI-F1. Samples 371 to 375 correspond to P-I-F1. Samples 271 to 275 correspond to site BV non-inoculated (NI) formulation F2. Samples 296 to 300 correspond to BV inoculated (I) formulation F2. Samples 321 to 325 correspond to FV-NI-F2. Samples 341 to 345 correspond to FV-I-F2 Samples 361 to 365 correspond to P-NI-F2. Samples 381 to 385 correspond to P-I-F2.

Biome: root:Host-associated:Plants:Rhizosphere
Effect of phytostimulatory seed-inoculant Azospirillum lipoferum CRT1 on functional community of ACC deaminase producers (acdS) in the maize rhizosphere

The field trials were run in 2015 in Chatonnay (site P), Cessieu (site BV) and Saint Savin (site FV), which are located in the vicinity of Bourgoin-Jallieu (Isère, France). Maize seeds were inoculated or not by a suspension of  Azospirillum lipoferum CRT1 cells. DNA was extracted from root-adhering soil and nifH gene diversity was sequenced  using acdSF5/acdSR8 primers by Illumina Miseq (2 × 125 bp). Samples 261 to 265 correspond to site BV non-inoculated (NI) formulation F1. Samples 286 to 290 correspond to BV inoculated (I) formulation F1. Samples 311 to 315 correspond to FV-NI-F1. Samples 331 to 335 correspond to FV-I-F1 Samples 351 to 355 correspond to P-NI-F1. Samples 371 to 375 correspond to P-I-F1. Samples 271 to 275 correspond to site BV non-inoculated (NI) formulation F2. Samples 296 to 300 correspond to BV inoculated (I) formulation F2. Samples 321 to 325 correspond to FV-NI-F2. Samples 341 to 345 correspond to FV-I-F2 Samples 361 to 365 correspond to P-NI-F2. Samples 381 to 385 correspond to P-I-F2.

Biome: root:Host-associated:Plants:Rhizosphere
The Effect of Probiotics with Antibiotics on Gut Microbiota during the Helicobacter Eradication: Randomized Controlled Trial

The effect of probiotics with antibiotics on gut microbiota during the Helicobacter eradication was analyzed using 16S rRNA gene pyrosequencing. The diversity of microbiota obtained from antibioitcs alone treatment group was more changed than that of probiotics cotreatment group. This study will provide information to treat Helicobacter infected patients.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Transient rapamycin treatment robustly increases lifespan and healthspan in middle-aged mice

The FDA approved drug rapamycin increases lifespan in rodents1 and improves measures of age-related function in rodents2 and humans3; thus, rapamycin has promising translational potential as an intervention to promote both longevity and healthspan. Nevertheless, significant questions remain regarding the optimal dose, treatment regimen, efficacy, and safety of rapamycin administration in the context of healthy ageing4. Here we show that 3 months of rapamycin treatment is sufficient to increase life expectancy by more than 50% and improve measures of healthspan in middle-aged mice. Transient treatment with rapamycin is also associated with a remodelling of the microbiome, including dramatically increased prevalence of segmented filamentous bacteria in the small intestine. We also define a dose in female mice that does not extend lifespan. This higher dose of rapamycin is associated with a striking shift in cancer prevalence toward aggressive haematopoietic cancers and away from non-haematopoietic malignancies in females. These data demonstrate that a single short-term rapamycin treatment late in life can be effective at delaying ageing and suggest that a similar regimen may be applicable to promote healthy ageing in people.

Biome: root:Host-associated:Mammals:Digestive system