SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Contrasting the roles of mycorrhizal compatibility in community development between arbuscular- versus ecto-mycorhizal systems

Feedback between plant species and the soil mycorrhizal fungi (biotic agents) shapes interspecific plant interactions, but it remains uncertain whether its effects are an essential component of plant community development. Two most dominant mycorrhizal types in temperate forests, arbuscular mycorrhizal and ectomycorrhizal plant species, can drive distinct dynamics in which the composition of the fungal community changes due to associations with plant community composition, and these changes differentially feed back on plant growth through the effects of (i) plant-fungus compatibility and (ii) common fungal networks. Here we investigate how plant community development is linked with mycorrhizal types, contrasting the effects of arbuscular mycorrhizal (AM) versus ectomycorrhizal (EcM) associations on seedling establishment. By simulating the scenario where established tree community modifies the soil fungal component (i.e., AM versus EcM inocula) and alters the competitive environment for new seedlings, we found that competition for soil nutrients influenced seedling establishment. The results showed that compatible seedlings had significantly greater leaf and root biomasses than incompatible seedlings, a benefit from the presence of established competitors through enhancing positive nutrient feedbacks. While plant-soil feedback mediated tree-seedling interactions for both AM and EcM associations, the estimated compatibility effects were more positive for EcM relative to AM associations. Notably, this coincided with the more pronounced sharing of fungal species and more structured formation of common fungal network in EcM systems compared to AM systems. Together these results suggest the link between seedling establishment and mycorrhizal functional differentiation.

Biome: root:Host-associated:Plants:Root
CHILD gut microbiome and asthma

Asthma is a multifactorial disease with an alarming increase in prevalence. Like several other immune-mediated diseases, asthma pathogenesis is being studied in the context of the hygiene hypothesis. Antibiotic-driven gut microbial shifts exclusively in the neonatal period increase airway inflammation in mice. We hypothesized that similar microbial changes in infant humans have a causal role in disease. To test this, 319 children enrolled in the Canadian Healthy Infant Longitudinal Development (CHILD) study were grouped into four phenotypes: atopic + wheeze (AW), atopic only, wheeze only, and controls, based on clinical data at 1 year. The fecal microbiome of 3-month and 1-year samples was evaluated by 16S rRNA gene sequencing (Illumina). A subset of samples in the AW and control groups was selected for qPCR, short chain fatty acid (SCFA) and urine metabolomic analyses. Finally, germ-free mice were inoculated with feces from one AW patient or with the same inoculum plus 4 bacterial strains found more commonly in controls. These mice were bred and the F1 generation was evaluated for OVA-induced airway inflammation. Results: At 3 months of age, 4 OTUs were identified by sequencing and qPCR as decreased in AW children, who also had a significantly increased risk of asthma diagnosis, based on their asthma predictive index at 3 years of age. These children exhibited decreased fecal acetate and propionate, and alterations in bacterial and host-derived metabolites mostly at 3 months of age. Finally, oral inoculation of mice with these 4 bacterial strains ameliorated airway inflammation. These results reveal taxonomic and functional gut microbial changes in infants associated with an increased risk of asthma. Decreased production of SCFA at this young age may lead to changes in energy harvest, bile acid and urobilinogen metabolism. This study suggests an associative and possibly causal role of early infancy shifts in gut microbiota with risk of asthma in human infants.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
xenomicrobiota_transplanted_into_germfree_mice

Xenomicrobiota from a variety of different environments were transplanted into germfree mice. Assembly and composition of the gut-selected communities were analyzed by amplicon-sequencing. In a follow-up experiment, mice that harbored gut-selected communities were cohoused with each other.

Biome: root:Host-associated:Mammals:Digestive system
Bacterial variation in human body habitats across space and time

We applied multiplexed barcoded 16S ribosomal RNA gene pyrosequencing to survey the diversity and distribution of bacteria in and on healthy adults

Biome: root:Host-associated:Human
Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses

It is increasingly recognized that microbes that reside in and on human body sites play major roles in modifying the pathogenesis of several diseases, including cancer. However, specific microbes or microbial communities that can be mechanistically linked to cervical carcinogenesis remain largely unexplored. The purpose of the study was to examine the association between cervical microbiota and high-grade cervical intraepithelial neoplasia (CIN 2+) in women infected with high-risk (HR) human papillomaviruses (HPV) and to assess whether the cervical microbiota are associated with oxidative DNA damage as indicated by the presence of cervical cells positive for 8-hydroxy-2'-deoxyguanosine. The study included 340 women diagnosed with CIN 2+ (cases) and 90 diagnosed with CIN 1 (non-cases). Microbiota composition was determined by Illumina sequencing of the 16S rRNA gene amplified from DNA extracted from cervical mucus samples. Measures of alpha/beta-diversity were not associated with either CIN severity or oxidative DNA damage. However, a cervical mucosal community type (CT) dominated by L. iners and unclassified Lactobacillus spp. was associated with CIN 2+ (OR = 3.48; 95% CI, 1.279.55). Sequence reads mapping to Lactobacillaceae, Lactobacillus, L. reuteri, and several subgenus level Lactobacillus operational taxonomic units were also associated with CIN 2+ when examined independently (effect size >2.0; P < 0.05). Our 16S rRNA sequencing results need confirmation in independent studies using whole-genome shotgun sequencing and that would allow sharpening the suggested associations at finer taxonomic levels. Our results provide little evidence that DNA oxidative damage mediates the effect of the microbiome on the natural history of HPV infection and CIN severity. Cancer Prev Res; 9(5); 35766. 2016 AACR.

Biome: root:Host-associated:Human:Reproductive system:Vagina:posterior fornix
human vaginal metagenome Genome sequencing and assembly

The Multi-Omic Microbiome Study-Pregnancy Initiative (MOMS-PI) is a collaborative project with the Global Alliance to Prevent Prematurity and Stillbirth (GAPPS) based at Seattle Children's and is funded by the NIH Roadmap Human Microbiome Project. Together, we are committed to understanding the impact of the vaginal microbiome on pregnancy, pregnancy-related complications and the impact on the fetal microbiome. Preterm birth is the leading cause of death in neonates, thus our efforts are largely focused on assessing the role of the microbiome on preterm birth and maternal-infant health.MOMS-PI is a multifaceted initiative to generate large and comprehensive datasets using six "omics" technologies: 1) metagenomic rRNA gene sequencing, 2) whole metagenomic shotgun sequencing, 3) metatranscriptomics, 4) metabolomics/lipidomics, 5) immunoproteomics and 6) interactomics. Samples will be collected throughout the course of pregnancy from a cohort of ~2000 women. We believe this large-scale, innovative effort will lead to insights into how the microbiome impacts risk for preterm birth and the temporal dynamics of the pregnancy microbiome.

Biome: root:Host-associated:Human:Reproductive system:Vagina
Organic agricultural field soil Raw sequence reads

Study investigated effects of cover crops and organic fertilizers on bacterial community structure in organically managed agricultural field soils in Minnesota

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Metagenomic analysis of nematode beetle association

Insects and nematodes represent the most species-rich animal taxa and they occur together in a variety of associations. Necromenic nematodes of the genus Pristionchus are found on scarab beetles with more than 30 species known from worldwide samplings. However, little is known about the dynamics and succession of nematodes and bacteria during the decomposition of beetle carcasses. Here, we study nematode and bacterial succession of the decomposing rhinoceros beetle Oryctes borbonicus on La Reunion Island. We show that Pristionchus pacificus exits the arrested dauer stage seven days after the beetles  death. Surprisingly, new dauers are seen after 11 days suggesting that some worms return to the dauer stage already after one reproductive cycle. We used high-throughput sequencing of the 16S rRNA genes of decaying beetles, beetle guts and nematodes to study bacterial communities in comparison to soil. We find that soil environments have the most diverse bacterial communities. The bacterial community of living and decaying beetles are more stable but one single bacterial family dominates the microbiome of decaying beetles. In contrast, the microbiome of nematodes is relatively similar even across different families. This study represents the first characterization of the dynamics of nematode-bacterial interactions during the decomposition of insects.

Biome: root:Host-associated:Insecta
Infant airway microbiome Raw sequence reads

16s rRNA gene sequencing of aspirates from the hypopharynx of infants

Biome: root:Host-associated:Human:Respiratory system:Nasopharyngeal:Pharynx
uncultured prokaryote Targeted loci environmental

Survey of biofilm bacterial community diversity (16S rRNA) in New Zealand streams

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
Soil Microbial communities from weed germination bioassay targeted loci environmental

characterize soil bacterial and fungal communities that were associated with weed seed and seedling

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Capsule Patients

Illumina 16S rRNA gene sequence data from fecal samples of patients treated with capsules for recurrent Clostridium difficile infection.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Microbiome analysis complements fecal occult blood test for improved detection

Using microbiome-based models to differentiate healthy patients from those with colonic lesions.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
vaginal microbiota of pregnant women

vaginal microbiota of pregnant women

Biome: root:Host-associated:Human:Reproductive system:Vagina
Altering the intestinal microbiota during a critical developmental window

Disruption of the microbiota by low-dose antibiotic exposure can alter host metabolism and adiposity. We now show that low-dose penicillin (LDP) delivered from birth enhanced metabolic alterations, and that there were additive effects in combination with high fat diet. LDP that was limited to early life was sufficient for sustained effects on body composition. After the cessation of penicillin, the microbial communities recovered, yet metabolic phenotypes persisted, indicating that microbiota interactions in infancy may be critical determinants of long-term host effects. Early-life LDP was associated with alterations in ileal expression of genes involved in immunity. The growth promotion phenotype was transferrable to germ-free hosts by LDP-selected microbiota, not antibiotics per se. These studies characterize important variables in early-life microbe-host metabolic interaction, and identify several taxa consistently linked with metabolic alterations.

Biome: root:Host-associated:Mammals:Digestive system
Human skin microbiota Metagenome

The variability in skin microbial communities within a human population can be the cause of many factors, including occupation, diet, age, gender, surroundings and so on. In this study, we explored the differences in the bacterial community structure associated with seven skin sites in 71 healthy Chinese over six days and its correlations with age, gender, physical skin parameters, and whether participants lived in an urban versus suburban location of the same city.

Biome: root:Host-associated:Human:Skin
16S rRNA gene sequences of human gut microbiota

We characterized the gut microbiota of Korean twin and their families. The study population consisted of 155 monozygotic twin pairs (n=310), 37 dizygotic twin pairs (n=74), and their parents and siblings (n=288). Among them, fecal samples from 84 individuals were provided twice at two time points. Therefore, a total of 756 fecal samples were analyzed. The V4 region of the 16S rRNA gene was sequenced using an Illumina MiSeq platform.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Fecal microbiota of Japanese healthy adults

Fecal microbiota of Japanese healthy adults. 16s rRNA gene library of V1-V2 hyper variable regions derived from the fecal samples of 516 subjects.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Symbiodinium ITS2 Arabian Seas

Next-generation sequencing of the ITS2 marker gene was used to assess Symbiodinium community composition and diversity comprising 892 samples from 46 hard and soft coral genera.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
Root fungi in temperate forests Metagenome

In this study, we want to elucidate the influence of forest management on root associated fungal richness.

Biome: root:Host-associated:Plants:Root
Skin metagenomes

Skin shotgun metagenomes from psoriasis patients

Biome: root:Host-associated:Human:Skin
Understanding the microbial basis of body odor in teenagers and kids

Metagenomics samples of multiple skin sites (underarm, neck & head scalp) from teenagers and kids

Biome: root:Host-associated:Human:Skin
Rhizotypes of plant-root fungal biome

Here we show that diverse root-associated fungi form highly-compartmentalized networks of coexistence within host roots and that the structure of the fungal symbiont communities is partitioned into semi-discrete types even within a single host plant population. Intensive DNA-barcoding of root-associated fungi in a monodominant beech forest reveals that the network representing symbiont-symbiont co-occurrence pattern is compartmentalized into clear modules, which consist of diverse functional groups of mycorrhizal and endophytic fungi. As a result, each terminal root of the host plant is colonized by either of the two largest fugal species sets, forming rhizotypes. Thus, species-rich root microbiome can have alternative stable states as recently shown in relationship between gut microbiome type and human health.

Biome: root:Host-associated:Plants
EMG produced TPA metagenomics assembly of PRJEB34384 data set (Two metagenomes from outflow channels of Lost Hammer ultrasaline, perennial spring from Canadian High Arctic.).

TheThird Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set ERP117276, and was assembled with metSPAdes(v3.13.0).

Biome: root:Environmental:Aquatic:Sediment
Predicting antibiotic resistance in clinical infections caused by Enterobacterales from aggregated population-level taxonomy-adjusted AMR estimates derived from quantitative metagenomic analysis of pooled human faecal samples

Antimicrobial resistance (AMR) is a global health threat, especially in low-/middle-income countries (LMICs), where there is limited surveillance to inform empiric antibiotic treatment guidelines. Enterobacterales are a particular AMR problem, and a common cause of disease. We developed a novel approach for AMR surveillance in Enterobacterales by profiling metagenomes of pooled human faecal material from three sites (n=563 individuals; Cambodia, Kenya, UK) to derive a taxonomy-adjusted AMR metric which could be used to predict the aggregate burden of resistant Enterobacterales infections within each setting. Samples were sequenced (Illumina); taxonomic and resistance gene profiling was performed using ResPipe (https://gitlab.com/hsgweon/ResPipe). Data on organisms causing bacteraemia and meningitis and susceptibility results from 2010-2017 were collated for each site. Bayesian generalised linear models with a binomial likelihood were fitted to determine the capacity of the metric to predict AMR in Enterobacterales infections in each setting. The most informative model predicted the proportion of resistant infections in the target populations for 14/14 of antibiotics in the UK, 12/12 in Kenya, and 8/12 in Cambodia. Intermittent metagenomics of pooled human samples could be a powerful tool in determining and monitoring the burden of AMR in clinical infections, especially in resource-limited settings.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Soil metagenome from healthy and unhealthy agricultural soil

Soil samples were collected from healthy and unhealthy agricultural soil. Soil health was determined based on plant productivity and farmer's perception. DNA was extracted and subjected to metagenome sequencing.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
aquifer metagenome raw sequence reads

Microbial communities from subsurface basaltic aquifers in C sequestration operations

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
20150129pengxin.mouse

20150129pengxin.mouse

Biome: root:Host-associated:Mammals:Digestive system:Fecal
International Space Station Microbial Observatory - Microbial Diversity

The environmental microbiome study was designed to decipher microbial diversity of the International Space Station surfaces in terms of spatial and temporal distributions by the next-generation sequencing of 16S rRNA and ITS.

Biome: root:Engineered:Built environment
Temporal sampling of marine metagenomes from Station ALOHA and BATS


Biome: root:Environmental:Aquatic:Marine:Oceanic
International Space Station flight project EXTREMOPHILES.

16S rRNA sequences obtained of Wipe samples taken from ISS indoor surfaces

Biome: N/A
Inflated Lunar/Mars Analog Habitat Microbiome

The raw sequence data come from the microbial succession study of the Inflated Lunar/Mars Analog Habitat (ILMAH). Bacterial monitoring for several surfaces was conducted before and during a 30-day occupation by three student astronauts.

Biome: root:Engineered:Built environment
Microbial diversity on kitchen sinks and bathroom tiles

This study examined the microbial and chemical signatures of indoor surfaces that are periodically wet: kitchen sinks and bathroom shower tiles. Removable surfaces were installed in a home and subject to typical household conditions for one month. Both DNA and RNA from the surfaces were isolated, and 16S and ITS amplicons were generated to target the bacterial and fungal communities, respectively.

Biome: root:Engineered:Built environment
Networks depicting the fine-scale co-occurrences of fungi in soil horizons

Fungi in soil play pivotal roles in nutrient cycling, pest controls, and plant community succession in terrestrial ecosystems. Despite the ecosystem functions provided by soil fungi, our knowledge of the assembly processes of belowground fungi has been limited. Based on the high-throughput sequencing data of fungi in a cool temperate forest in northern Japan, we analyze how taxonomically and functionally diverse fungi show correlated fine-scale distributions in soil. By uncovering pairs of fungi that co-occurred in the same soil samples more/less frequently than expected by chance, networks depicting fine-scale distributions of fungi are inferred at the O and A horizons. The results then leads to the working hypothesis that mycorrhizal, endophytic, saprotrophic, and pathogenic fungi as well as fungi with unknown functions form compartmentalized networks of potential facilitative, antagonistic, and/or competitive interactions in belowground ecosystems. Overall, this study provides a research basis for further understanding how interspecific interactions, along with sharing of niches among fungi, drive the dynamics of poorly explored biospheres in soil.

Biome: root:Environmental:Terrestrial:Soil
mouse gut metagenome Raw sequence reads

This study presented the bacteria of feces sample from the C57BL/6 mice.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Lab-scale EBPR reactor Metagenome

Two lab-scale EBPR bioreactors were operated for approximately one year with samples taken at multiple time points to assess the dynamics of the microbial and viral communities.

Biome: root:Engineered:Bioreactor
Richness of human gut microbiome correlates with metabolic markers

We are facing a global metabolic health crisis provoked by an obesity epidemic. Here we report the human gut microbial composition in a population sample of 123 non-obese and 169 obese Danish individuals. We find two groups of individuals that differ by the number of gut microbial genes and thus gut bacterial richness. They harbour known and previously unknown bacterial species at different proportions; individuals with a low bacterial richness (23% of the population) are characterized by more marked overall adiposity, insulin resistance and dyslipidaemia and a more pronounced inflammatory phenotype when compared with high bacterial richness individuals. The obese individuals among the former also gain more weight over time. Only a few bacterial species are sufficient to distinguish between individuals with high and low bacterial richness, and even between lean and obese. Our classifications based on variation in the gut microbiome identify subsets of individuals in the general white adult population who may be at increased risk of progressing to adiposity-associated co-morbidities.

Biome: root:Host-associated:Human:Digestive system:Large intestine
Wastewater bioreactor microbial communities from Cape Town, South Africa - Thiocy_expt_500_biof metagenome


Biome: root:Engineered:Wastewater
Regulators of Gut Motility Revealed by a Gnotobiotic Model of Diet-Microbiome Interactions Related to Travel

To understand how different diets, the consumers gut microbiota, and the enteric nervous system (ENS) interact to regulate gut motility, we developed a gnotobiotic mouse model that mimics short-term dietary changes that happen when humans are traveling to places with different culinary traditions. Studying animals transplanted with the microbiota from humans representing each cuisine and fed a sequence of diets representing those of all donors, we find that correlations between bacterial species abundances and transit times are diet dependent. However, the levels of unconjugated bile acids  reflecting microbial bile salt hydrolase activity  correlate with faster transit across diets, including a Bangladeshi diet. Mice harboring a consortium of sequenced bacterial strains from the Bangladeshi donors microbiota and fed a Bangladeshi diet revealed that the commonly used spice, turmeric, slows transit times. Turmeric affects gut motility via bacterial bile acid deconjugation and modulation of Ret signaling in the ENS. These results demonstrate how a single food ingredient interacts with a functional microbiota trait to regulate host physiology.

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