SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
EMG produced TPA metagenomics assembly of PRJEB15404 data set (Plastic Metagenome Study).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB15404, and was assembled with unknown v0.0. This project includes samples from the following biomes: root:Engineered.

Biome: root:Engineered
16s rDNA amplicon of rock samples Raw sequence reads

16s rDNA amplicon of rock samples

Biome: root:Environmental:Terrestrial:Geologic
16S rRNA amplicon sequencing of broiler caecal contents

16S rRNA amplicon sequencing of broiler caecal contents. Linked to this study: https://doi.org/10.1186/s42523-019-0015-1

Biome: root:Host-associated:Birds:Digestive system:Ceca
The environmental soil 16S rRNA amplicon

The environmental soil 16S rRNA amplicon data

Biome: root:Environmental:Terrestrial:Soil
Patterns of community assembly in the developing chicken microbiome reveal rapid primary succession

The fine-scale temporal dynamics of the chicken gut microbiome are unexplored, but thought to be critical for chicken health and productivity. Here, we monitored the fecal microbiome of healthy chickens on days 1-7, 10, 14, 21, 28, and 35 after hatching, and performed 16S rRNA amplicon sequencing in order to obtain a high-resolution census of the fecal microbiome over time. In the period studied, the fecal microbiomes of the developing chickens showed a linear-log increase in community richness and consistent shifts in community composition. Three successional stages were detected: the first stage was dominated by vertically-transmitted or rapidly-colonizing taxa including Streptococcus and Escherichia/Shigella; in the second stage beginning on day 4, these taxa were displaced by rapid-growing taxa including Lachnospiraceae and Ruminococcus-like SVs; and in the third stage, starting on day 10, slow-growing, specialist taxa including Candidatus Arthrobacter and Romboutsia were detected. The patterns of displacement and the previously reported ecological characteristics of many of the dominant taxa observed suggest that resource competition plays an important role in regulating successional dynamics in the developing chicken gut. We propose that the boundaries between successional stages (3-4 and 14-21 days after hatching) may be optimal times for microbiome interventions.

Biome: root:Host-associated:Birds:Digestive system:Fecal
EGB sediment data (raw sequence reads)

DNA and RNA from sediment samples collected in the Eastern Gotland Basin

Biome: root:Environmental:Aquatic:Marine:Sediment
The Core Equine Faecal Microbiome: A Broader Perspective

Background: Equine gut microbiology studies to date have primarily focused on horses and ponies which represent only one of the 8 extant equine species. This is despite asses and mules comprising almost half of the worlds domesticated equines, and donkeys being superior to horses/ponies in their ability to degrade dietary fibre. Limited attention has also been given to commensal anaerobic fungi and archaea even though anaerobic fungi are potent fibre degrading organisms, the activity of which is enhanced by methanogenic archaea. Therefore, the objective of this study was to broaden current bacterial, anaerobic fungal and archaeal knowledge of the equine hindgut to multiple species of equines. Taxa core to all the equine faecal samples (n=70) were determined and observations of the effect of equine type (horse, donkey, horse  donkey and zebras) on the hindgut microbiota conducted. Results: Equine type influenced both microbial concentrations and community composition. Donkeys generally were most distinct from the other equine types, with horses and zebra not differing. Despite this, a common bacterial core of 8 OTU and 16 genus level groupings of OTU was found in all the equines studied. This bacterial core represented a much larger proportion of the equine faecal microbiota than previously reported, primarily due to the detection of dominant core taxa belonging to the Kiritimatiellaeota (formerly Verrucomicrobia subdivision 5) and Spirochaete phyla. The majority of the core bacterial taxa lacked cultured representation. Archaea and anaerobic fungi were present in all animals, however, no core taxon was detected for either despite several taxa being prevalent and dominant.Conclusions: Whilst differences were observed between equine types, a core faecal microbiome existed across all the equines. This core was composed primarily of a few dominant bacterial taxa, the majority of which are novel and lack cultured representation. The lack of microbial cultures representing the dominant bacterial as well as anaerobic fungal taxa in the equine hindgut is of concern, and highlights an urgent need to isolate these taxa. Only then can fundamental knowledge of the microbial functions that underpin the equine hindgut ecosystem be elucidated.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
EMG produced TPA metagenomics assembly of PRJEB15448 data set (The influence of chitin addition on the lettuce rhizosphere microbiome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB15448, and was assembled with unknown v0.0. This project includes samples from the following biomes: root:Environmental:Terrestrial:Soil.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of PRJEB34410 data set (Secrets of the hospital underbelly: abundance of antimicrobial resistance genes in hospital wastewater reflects hospital antimicrobial use and inpatient length of stay).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB34410, and was assembled with metaSPAdes v3.13.1. This project includes samples from the following biomes: root:Engineered:Wastewater.

Biome: root:Engineered:Wastewater
International Space Station vacuum cleaner bag Targeted Locus (Loci)

International Space Station (ISS) environmental microbiome- Microbial inventories of ISS filter debris.  ISS vacuum cleaner bag contents (ISS-debris) and visible accumulations of fibers and other materials associated with the vacuum bag (ISS-debris).

Biome: root:Engineered:Built environment
Fecal Microbiota in Horses with Asthma

The goal was to analyze the bacterial fecal microbiota of horses with and without asthma under different diet and housing conditions, in remission and exacerbation.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
16S sequencing from full scale WWTP - UAE

16S sequencing from samples collected from the aeration tank of a full scale wastewater treatment plant in the UAE over a 10 month period

Biome: root:Engineered:Wastewater
Secrets of the hospital underbelly: abundance of antimicrobial resistance genes in hospital wastewater reflects hospital antimicrobial use and inpatient length of stay

Hospitals are nodal points for antimicrobial consumption and identification of resistant pathogens and therefore hospital wastewater is a potential major source of AMR. This study uses metagenomics to study how the abundances of resistance genes in hospital wastewater are related to clinical activity within different buildings of the hospital. Sewage was collected over a 24-hour period from multiple wastewater collection points representing different specialties within a tertiary hospital site and simultaneously from community sewage works. High throughput shotgun sequencing was performed using Illumina HiSeq4000. Sequence reads were assigned taxonomically and to the AMR genes in the ResFinder database. The measured AMR gene abundances were then correlated to hospital antimicrobial usage (AMU), other data on clinical activity such as patient/ward characteristics and resistance prevalence in clinical isolates.

Biome: root:Engineered:Wastewater
Metagenomic sequencing of microbial communities present in spontaneous fermentation of coffees in northern Peru

The quality of commercial coffee berry, the principal raw material for coffee production, depends on several factors including type of plantations, the agricultural practices and the post-harvest processing. Among these, fermentation are generally considered the most relevant step, since during these phases coffee flavors precursors are formed and fixed. Fermentation is characterized by a well-defined succession of yeasts, lactic acid bacteria and acetic acid bacteria, therefore the aim of this study is to explore total bacterial and fungal communities involved in coffee fermentation. To achieve these results, shotgun metagenomics was used on fermentations from good and bad quality coffees to assess the total bacterial and fungal community, indicating that this approach has the ability to provide a comprehensive view of the coffee fermentation microbiota at the species level.

Biome: root:Host-associated:Plants
Home chemical and microbial transitions across urbanization

Westernization has propelled changes in urbanization and architecture, altering our exposure to the outdoor environment from that experienced during most of human evolution. These changes might affect the developmental exposure of infants to bacteria, immune development, and human microbiome diversity. Contemporary urban humans spend most of their time indoors, and little is known about the microbes associated with different designs of the built environment and their interaction with the human immune system. This study addresses the associations between factors associated with westernization including architectural design and the microbial biogeography of households across a gradient of urbanization in South America.

Biome: root:Mixed
Galmide

Microbiota characterization of caecal, ileum, and jejunal contents of two lines of broiler chickens divergently selected on their digestive efficiency

Biome: root:Host-associated:Birds:Digestive system
Comprehensive longitudinal microbiome analysis of the chicken cecum reveals a shift from competitive to environmental drivers and a window of opportunity for Campylobacter

Chickens are a key food source for humans yet their microbiome contains bacteria that can be pathogenic to humans, and indeed potentially to chickens themselves. Campylobacter is present within the chicken gut and is the leading cause of bacterial foodborne gastroenteritis within humans worldwide. Infection can lead to secondary sequelae such as Guillain-Barre syndrome and stunted growth in children from low-resource areas. Despite the global health impact and economic burden of Campylobacter, how and when Campylobacter appears within chickens remains unclear. The lack of day to day microbiome data with replicates, relevant metadata, and a lack of natural infection studies have delayed our understanding of the chicken gut microbiome and Campylobacter. Here, we performed a comprehensive day to day microbiome analysis of the chicken cecum from day 3 to 35 (12 replicates each day; final n = 379). We combined metadata such as chicken weight and feed conversion rates to investigate what the driving forces are for the microbial changes within the chicken gut over time, and how this relates to Campylobacter appearance within a natural habitat setting. We found a rapidly increasing microbial diversity up to day 12 with variation observed both in terms of genera and abundance, before a stabilization of the microbial diversity after day 20. In particular, we identified a shift from competitive to environmental drivers of microbial community from days 12 to 20 creating a window of opportunity whereby Campylobacter can appear. Campylobacter was identified at day 16 which was 1 day after the most substantial changes in metabolic profiles observed. In addition, microbial variation over time is most likely influenced by the diet of the chickens whereby significant shifts in OTU abundances and beta dispersion of samples often corresponded with changes in feed. This study is unique in comparison to the most recent studies as neither sampling was sporadic nor Campylobacter was artificially introduced, thus the experiments were performed in a natural setting. We believe that our findings can be useful for future intervention strategies and help reduce the burden of Campylobacter within the food chain.

Biome: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
Commensal Enterobacteriaceae protect against Salmonella colonization by competing for oxygen

Neonatal chicks are highly susceptible to colonization with Salmonella enterica serovar (S.) Enteritidis, but the underlying mechanism is not fully resolved. We show that neonatal colonization with S. Enteritidis required a virulence factor-dependent increase in epithelial oxygenation, which drove expansion of the pathogen in the lumen of the chick intestine by aerobic respiration. Co-infection experiments with an Escherichia coli strain carrying an oxygen-sensitive reporter suggested that S. Enteritidis competes with commensal Enterobacteriaceae for oxygen. Association with either spore-forming bacteria or commensal Enterobacteriaceae from adult chicken microbiota did not protect germ-free mice from S. Enteritidis colonization. However, a combination of Enterobacteriaceae and spore-forming bacteria conferred colonization resistance against S. Enteritidis at levels similar to those observed in germ-free mice associated with adult chicken microbiota. Combining spore-forming bacteria with a single avian E. coli isolate protected germ-free mice from pathogen colonization, but protection was lost when the ability to respire oxygen under microaerophilic conditions was genetically ablated in E. coli. These results show that commensal Enterobacteriaceae contribute to colonization resistance by competing with S. Enteritidis for oxygen, a resource critical for pathogen expansion.

Biome: root:Host-associated:Birds:Digestive system
New strategies for the protection of PUFA from ruminal microbiome - Nannochloropsis oceanica as a source of rumen-protected EPA

Dietary n-3 PUFA fed to ruminants are extensively hydrogenated through ruminal biohydrogenation resulting in a very low efficiency of its transfer to tissues. The development or identification of novel strategies to protect PUFA from biohydrogenation, to increase the amount of PUFA bypassing the rumen could circumvent the problem. Using naturally PUFA-protected sources such as microalgae like Nannochloropsis sp. can be an alternative but there is a need to evaluate the impact on rumen an intestinal microbiome composition.

Biome: root:Host-associated:Mammals
Omega 3 sources impacts on lambs' microbiota

Different sources of Omega 3 were studied in vitro and in vivo on lambs' microbiota fed different diets

Biome: root:Host-associated:Mammals
Metagenomic analysis of lake sediment.

Shotgun sequencing of lake sediments.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Equine intestinal microbiota after feeding a prebiotic

The objective of this study was to investigate the impact of natural prebiotic active compounds on the microbial composition in different regions of the equine gastrointestinal tract. Twelve adult horses (body weight [bwt] 534  64.5 kg; age 14  7.5 years) were randomly divided into two feeding groups. Six horses received a basal diet consisting of 1.5 kg hay/100 kg bwt x d-1 and oat grains equal to 1.19 g starch/kg bwt x d-1, supplemented with Jerusalem artichoke meal providing prebiotic fructooligosaccharides + inulin in a quantity of 0.15 g/kg bwt x d-1. The remaining horses received a placebo added to the basal diet. The horses were fed for 21 d and euthanized at the end of the feeding period. Digesta samples from different parts of the gastrointestinal tract were taken, DNA extracted and the V1-V2 region of the 16S rRNA gene amplified. Supplementation with the prebiotic increased the relative abundance of Lactobacillus (P < 0.50), with a concurrent reduction of the relative abundance of Streptococcus mainly in the stomach (P < 0.05). In the hindgut, the supplemental prebiotic also increased the relative abundance of Lactobacillus but further reduced the relative abundance of fibrolytic bacteria, specifically the unclassified members of the families Lachnospiraceae (P < 0.05) and Ruminococcaceae. The relative abundance of the genus Ruminococcus increased solely in the caecum and colon transversum. Overall, the addition of the prebiotic significantly increased the diversity in nearly all parts of the gastrointestinal tract (P < 0.05). The feeding of this natural prebiotic compound to horses had an impact on the microbial community in the entire gastrointestinal tract. Furthermore, the effect on the bacterial community in the foregut (especially the stomach) was more pronounced in comparison to the effect in the hindgut. Therefore, the impact on stomach health should be carefully considered.

Biome: root:Host-associated:Mammals:Gastrointestinal tract
The microbiome of healthy fecal donor horses and recipients undergoing microbial transplantation for the treatment of diarrhea

Fecal microbial transplantation (FMT), a treatment for certain gastrointestinal conditions associated with dysbiosis in people, is also empirically employed in horses with colitis. We used high-throughput sequencing to compare the fecal microbial profile of healthy horses to that of microbial transplant recipients experiencing diarrhea, and to test whether FMT restores microbiome diversity. The fecal microbiome of horses with diarrhea was significantly more variable (higher -diversity) than that of healthy horses. An inverse correlation between diarrhea score and relative abundance of Verrucomicrobia was identified in FMT recipients. At study completion, the fecal microbiome of horses which responded to FMT was more diverse (higher -diversity) and phylogenetically more similar to that of the donor.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Kidney stone patient microbiome

Metagenomic sequencing of the gut from kidney stone patients and healthy controls

Biome: root:Host-associated:Human:Digestive system
Contribution of the broiler breeders' fecal microbiota to the establishment of the eggshell microbiota

In broiler chicken production, microbial populations on the eggshell surface following oviposition are still poorly characterized, though they may significantly impact both poultry and public health. The aim of this study was to describe the microbiota of both broiler breeder hens feces and the surface of their eggs to assess the contribution of the parental fecal microbiota to the eggshell microbiota. This work is innovative and will be important to all stakeholders, including producers, breeders, veterinarians, inspectors and researchers, in the broiler breeder production chain in order to better manage the risks of bacterial contamination for poultry and public health.

Biome: root:Host-associated:Birds:Digestive system:Fecal
Tibetan chicken feces Targeted Locus (Loci)

To reveal the bacteria related TCC

Biome: root:Host-associated:Birds:Digestive system:Fecal
Daheng broilers Chicken(DH) caecum feces Targeted Locus (Loci)

To reveal the bacterial cummunity of Daheng broilers Chicken(DH) caecum feces

Biome: root:Host-associated:Birds:Digestive system:Fecal
Lohmann laying hen(LM)caecum feces Targeted Locus (Loci)

To reveal the bacterial cummunity of Lohmann laying hen(LM)caecum

Biome: root:Host-associated:Birds:Digestive system:Fecal
Tibetan Chicken(DQ) caecum feces targeted loci targeted loci

To reveal the bacterial cummunity of Tibetan Chicken(DQ)caecum

Biome: root:Host-associated:Birds:Digestive system:Fecal
Tibetan Chicken(QH) caecum feces targeted loci

To reveal the bacteria community of TCC-QH caecum

Biome: root:Host-associated:Birds:Digestive system:Fecal
Metagenomic analysis of Lake Slone sediment.

Metagenomic analysis of Lake Slone sediment.

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
16S rRNA amplicon sequencing characterization of caecal microbiome composition of broilers and free-range slow-growing chickens throughout their productive lifespan

Gut microbiota affects health, metabolism and immunity of the host, and in the case of livestock,
also food-safety. Here, 16S rRNA gene high-throughput Illumina sequencing was used to describe the
microbiome of chicken caeca in two different breeds and management systems throughout their whole
productive lifespan. Broilers (Ross-308), as a fast-growing breed reared in an intensive system for 42-
days, and a slow-growing breed of chicken (Sasso-T451A) reared in an extensive farming system with
outdoor access for 86-days, were compared. The core microbiome and differentially abundant taxa,
as well as taxa associated with age were identified. Age was identified as the strongest influencing
factor in caecal microbiota composition, and, in general, each age-group showed an age-associated
community profile, with a transition period at the middle of their lifespan. However, substantial
differences were observed in the composition of caecal microbiota of both chicken breeds, microbiota
being richer and more complex in free-range chicken than in broilers. Several taxa positively/negatively
correlated with Campylobacter relative abundance were also identified. Especially noteworthy was
the identification by microbial community comparison of microbiota profiles suggestive of dysbiosis in
several free-range chickens, probably associated to the typhlitis observed in the lumen of their caeca.

Biome: root:Host-associated:Birds:Digestive system:Ceca
Trace element-contaminated soil Metagenome

We aimed to compare the community structure of fungi and bacteria in the rhizosphere of introduced willows to willow growth and metal uptake.

Biome: root:Environmental:Terrestrial:Soil:Contaminated
Microbial populations of Lascauxs Apse in relation to collembola and black stains on cave walls.

In the Apse of Lascaux Cave (France), the microorganisms of black stains and unstained parts of wall cave were identified with Illumina technology using three genes markers of microbial diversity were analyzed, the 16S rRNA genes specific for bacteria, the 18S rRNA genes specific for micro-eukaryotes and the second internal transcribed spacer (ITS2) specific for fungi.

Biome: root:Environmental:Terrestrial:Deep subsurface
Microbial contaminants of civil aviation jet fuel supply chains.

Contaminated water and fuel samples were obtained from ground tanks and aircraft wing tanks from airports in Europe and the Middle East. 16S rRNA and ITS genes were amplified and used to identify prokaryotic and eukaryotic taxa. Contaminated water samples were sequenced directly or placed in microcosms. Contaminated fuel samples were placed in microcosms then sequenced.

Biome: root:Engineered
Origin based predominance of Dothideomycetes and Saccharomycetes in the intestinal mycobiota of zebrafish

Fish intestinal mycobiota are hitherto poorly characterized. Using next generation sequencing, we have profiled the intestinal mycobiota of wild caught, laboratory-reared and wild-caught-laboratory-kept zebrafish, which contained more than 15 fungal classes. In wild zebrafish, mycobiota comprised mainly Dothideomycetes, whereas saprotrophic Saccharomycetes were predominant in their laboratory-reared counterparts. This pioneer study shed light into differences in intestinal fungal communities of wild-caught and laboratory-reared zebrafish, thus enriching our knowledge on fish mycobiota.

Biome: root:Host-associated:Fish:Digestive system:Intestine