SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
human lung metagenome targeted loci cystic fibrosis

We report an approach to detect diverse bacterial and fungal taxa incomplex samples by direct analysis of community RNA in one stepusing NanoString probe sets. We designed rRNA-targeting probe sets todetect forty two bacterial and fungal genera or species common incystic fibrosis (CF) sputum, and demonstrated taxon-specificity ofthese probes as well as a linear response over more than three logsof input RNA. Culture-based analyses correlated qualitatively withrelative abundance data on bacterial and fungal taxa obtained byNanoString and the analysis of serial samples demonstrated the useof this method simultaneously detect bacteria and fungi and todetect microbes at low abundance without an amplification step. Therelative abundances of bacterial taxa detected by analysis of RNAcorrelated strongly with the relative abundances of the same taxa asmeasured by sequencing of the 16S rRNA gene amplified from communityDNA from the same sample. This method may complement other methodsdesigned to understand dynamics microbial communities, may provideinformation on bacteria and fungi in the same sample with a singleassay, and, with further development, may provide quick andeasily-interpreted diagnostic information on diverse bacteria and fungiat the genus or species level. PI Deborah Hogan

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Lower respiratory microbiota from pediatric BAL samples

This study investigates the clinical utility of 16S rRNA gene-based sequencing of pediatric bronchoalveolar lavage (BAL) samples. Samples were taken from cystic fibrosis (CF), immunocompromised (IC) and non-immunocompromised (nIC) patients, and culture-independent results were compared to routine cultures of the same samples. Based on 16S rRNA gene sequencing results, we investigated the influence of diagnosis group and recent antibiotic exposure on sample diversity.While the vast majority of cultured organisms were also identified by culture-independent methods, many additional taxa, including a number of potential pathogens, were identified by 16S rRNA gene-based sequencing that were not detected by routine culture. We found that CF samples had lower alpha diversity than those from IC and nIC patients. We also saw reduced abundances of Escherichia and Corynebacterium in the CF group, and lower Streptococcus, Veillonella and Haemophilus abundance in samples from patients exposed to antibiotics. Lastly, we identified a core group of 15 taxa present in all diagnosis groups.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MEU Manchester lung microbiome

Association of sputum microbiome with exacerbations, patient subgroups and host response in chronic obstructive pulmonary disease

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
NTM Human Microbiome and Inflammation Study

These are airway samples from humans which contain metagenomic (microbiome) materials. They include sputum, oral wash, and BAL.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Respiratory mycobiome and microbiome in cystic fibrosis

Characterization of the respiratory mycobiome and microbiome in cystic fibrosis : first evidence for inter-kingdom cross-talk during acute pulmonary exacerbation

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Lung microbiota of C57BL/6J mice (Mus Musculus) Raw sequence reads

Commensal microbiota play an important role in many physiological processes. Importantly, they pose a natural threshold to colonization with pathogenic bacteria by direct competition. Here we show that acute infection of the lung with influenza A viruses causes elimination of a substantial proportion of bacteria from the small intestine. This weakens the natural shield against pathogenic bacteria and renders the intestinal epithelium vulnerable for invading bacteria. We further show that influenza A virus infection up-regulates the activity of Paneth cells a major source of antimicrobial peptides in the small intestine. This suggests that influenza A viruses affect a host mechanism of microbiota regulation to cause bacterial depletion in the small intestine. Surprisingly, the same mechanism does not apply in the respiratory tract, where influenza A virus infection causes subtle qualitative but not quantitative changes in the commensal microbiota. Overall, our date provide the first description of microbiota dynamics in an acute infection animal model.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
16S bacterial profiling in bronchoalveolar lavage fluid from patients with Cystic Fibrosis

Cross-sectional study to evaluate the composition of the lung microbiota through 16S profiling in bronchoalveolar lavage fluid from patients with Cystic fibrosis from the CF-AREST study cohort.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Human Lung Metagenome Raw sequence reads

Measuring stability of the lung-microibome in the COPD patients.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Homo sapiens Raw sequence reads

Human Lung Cancer Metagenome/Microbiome

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Clinical bronchoalveolar lavage (BAL) samples Targeted loci

lung microbiome in ventilated patients

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
direct sequencing of 16S rRNA V3-V4 region of lung tissue from lung cancer patients raw sequence reads

The main goal of the study is to characterize the lung tissue microbiome from non-malignant tissue of lung cancer patients, and related the microbiome features to epidemiologic and clinical data.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
The lung microbiota in COPD patients when clinically stable and during exacerbations.

Illumina MiSeq sequencing of the bacterial 16S rRNA amplicon in sputum samples taken longitudinally from COPD patients when clinically stable (free of antibiotic or corticosteroid therapy for 4 weeks), at start of exacerbation and at end of exacerbation (10 days post start of exacerbation after standardised treatment). Patients were followed up for up to 6 months with a second clinically stable sample obtained at end of study.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Human lung metagenome of 17 adult CF patients throughout the course of clinical exacerbation, treatment and recovery Targeted Locus (Loci)

Bacterial communities for sputum genomic DNA samples from 17 patients throughout the course of clinical exacerbation, treatment and recovery examined by 16S pyrotag sequencing.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
IPF lung tissue and swabs Targeted Locus (Loci)

Microbial community profiling of idiopathic pulmonary fibrosis patients.  Lung tissue and nasopharyngeal, oral, and rectal swabs from two patients with idiopathic pulmonary fibrosis.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
EMG produced TPA metagenomics assembly of PRJNA680735 data set (Metagenome of the lower urinary tract).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA680735, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Excretory system:Urethra:Urine.

Biome: root:Host-associated:Human:Excretory system:Urethra:Urine
Variation in the microbiome on the surfaces of a physical therapy gym

Various surfaces of a physical therapy gym were sampled using swabs, which were then subject to 16S rRNA analysis in order to describe how the microbiome changes according to porosity, contact frequency, cleaning frequency, and physical location within the environment.

Biome: root:Engineered:Built environment
Habitat models of wood-inhabiting fungi along a decay gradient of Norway spruce logs

Modern molecular techniques provide a comprehensive and high-resolution window into complex systems that are difficult to study with traditional macroscopic techniques. We applied culture-free DNA extraction and 454-pyrosequencing to study the fungal microflora of decaying Norway spruce (Picea abies [L.] Karst.) logs in five unmanaged boreal forests. Fungal diversity and wood density were inversely related, i.e., OTU richness generally increased as the log became increasingly decomposed. According to generalized additive mixed models white-rot fungi (e.g., Phellinus nigrolimitatus) and members of Hyphodontia did not show a clear response to the wood-density gradient, whereas Phellinus viticola and brown-rot fungi (e.g., Fomitopsis pinicola, Antrodia serialis, Coniophora olivaceae) peaked during intermediate decay and mycorrhizal fungi (e.g., Piloderma, Tylospora, Russula) increased in the later stages. This information on fungal habitat requirements facilitates development of management practices that preserve fungal diversity in managed forests.

Biome: root:Engineered:Solid waste:Composting:Wood
EMG produced TPA metagenomics assembly of PRJNA801448 data set (Metagenomic Analysis of the Urinary Microbiome of Postmenopausal Women).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA801448, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Excretory system:Urethra:Urine.

Biome: root:Host-associated:Human:Excretory system:Urethra:Urine
EMG produced TPA metagenomics assembly of PRJNA700071 data set (Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA700071, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Excretory system:Urethra:Urine.

Biome: root:Host-associated:Human:Excretory system:Urethra:Urine
EMG produced TPA metagenomics assembly of the Dechlorinating community (Dhgm_1) data set.

The Dhgm_1 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB8993.  This project includes samples from the following biomes: Host-associated, Microbial, Bacteria.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
EMG produced TPA metagenomics assembly of PRJNA679884 data set (Interstitial Cystitis Urinary Metagenomics).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA679884, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Excretory system:Urethra:Urine.

Biome: root:Host-associated:Human:Excretory system:Urethra:Urine
Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis

We sequenced the V3-V5 hypervariable region of the bacterial 16S rRNA gene in DNA derived from 631 CF sputum specimens collected from 111 subjects over 10 years. We observed fluctuations in the abundances of typical CF pathogens, as well as anaerobic species, relative to changes in patients' clinical state and lung disease stage.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
EMG produced TPA metagenomics assembly of PRJNA385350 data set (Microbial metagenome of urinary tract infection).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA385350, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Excretory system:Urethra:Urine.

Biome: root:Host-associated:Human:Excretory system:Urethra:Urine
Respiratory Microbiota Metagenome

Alcohol-associated respiratory microbiota

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Sputum microbiome in COPD patients

Microbiome data studying which microorganisms are responsible for exacerbations are limited in sputa of COPD patients. The lung microbiome is a new approach to add additional insights about the causal pathogens and the shift in bacterial community of COPD patients.The goal of this study was to identify which microorganism(s) may have triggered the exacerbations of COPD patients. We compared the sputa microbiome of COPD patients when clinically stable and during an exacerbation.This study shows a clear shift in the microbiome of patients during exacerbation, mostly toward Proteobacteria and Firmicutes.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
GlaxoSmithKline - UofSouthampton - AERIS COPD Lung Microbiome

Healthy human lungs are not sterile and contain a variety of commensal microbiota. Alterations in the composition of the lung microbiome, known as dysbiosis, have been associated with lung disease and in particular may play a functional role in disease severity and exacerbations in chronic obstructive pulmonary disease (COPD). The AERIS study (Acute Exacerbation and Respiratory Infections in COPD; GSK Study 114378; NCT01360398) provides a unique opportunity to observe dynamic changes in the lung microbiome and associated biomarkers in a cohort of 127 COPD patients, who were followed monthly and within 72 h of exacerbation onset over two years. We surveyed 584 sputum samples from 104 patients to analyze the lung microbiome at both stable and exacerbation time points in the first year of the study via 16S rRNA sequencing. We obtained a mean of 5.7 samples per subject, 2.1 of which were collected during an exacerbation event. Ranking subjects by GOLD status showed a significant decrease in entropy of the microbiome (Shannon diversity index) and an increase in the relative abundance of Proteobacteria, such as Haemophilus, with an increase in disease severity. The genus with the most significant increase between stable and exacerbation events was Moraxella. Exacerbations with different phenotypes (containing bacterial pathogens detected by culture compared to eosinophils in sputum) had significantly distinct ratios of Proteobacteria to Firmicutes. Moreover, using a Markov chain analysis of exacerbation phenotypes, we found that bacterial and eosinophilic but not viral exacerbations were more likely to be repeated in subsequent exacerbations within a subject. Markov chain analysis also revealed that bacterial exacerbations containing Haemophilus influenzae (Hi, mostly nontypeable) had an increased probability of repeating relative to bacterial (e.g. Moraxella) exacerbations without Hi. Finally, we analyzed the temporal stability of the lung microbiome within each subject and found that microbiome composition in both stable and exacerbation states became more variable in patients experiencing exacerbations during the year. Patients with bronchiectasis showed notably more stability in microbiome composition, which was characterized by a high proportion of Haemophilus relative to that in patients without bronchiectasis. These findings improve our understanding of lung microbiome behavior over time in COPD, providing insight into our ability to use dysbiosis as a biomarker in COPD classification and establishing for the first time infective and inflammatory longitudinal phenotypes that may be used to guide future therapeutic strategies.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
microbial diversity in human respiratory tract

microbial diversity in human respiratory tract of pneumonia children

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Mouse Lung Microbiome Heterogeneity Across Vendors

We studied the heterogeneity of lung microbiota in C57/BL-6 mice acquired from two vendors via four shipments. We compared variation in lung microbiota with variation in lung immune tone, as assessed by concentrations of inflammatory cytokines measured via Luminex Multiplex assay.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
pulmonary capillary bronchitis Targeted loci environmental

To discovery involvement of pulmonary capillary bronchitis microbiome,and distinct microbial correlation under RSA infected and healthy.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Effects of silver nanoparticles on mouse lung microbiome

Here we describe dose-dependent effects of different coated silver nanoparticles on the mouse lung microbiome using 16S rRNA gene sequencing on Illumina Miseq.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Longitudinal Sampling of the Lung Microbiota in Individuals with Cystic Fibrosis

1 year long study of the cystic fibrosis lung microbiome via DNA isolation from sputum. 16S rRNA gene sequencing of the variable 3 region using 250bp, paired-end Illumina sequencing.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
human respiratory metagenome Targeted loci environmental

Twelve adult cystic fibrosis patients were enrolled in a cross-sectional study to investigate the biodiversity in paired lung sputum and sinus mucus samples by 16S sequencing of the V4 hypervariable region. The goal of the investigation was to compare and contrast the bacterial communities in these specimens, in order to better understand the ecological landscape of the cystic fibrosis respiratory system. Sputum samples were collected by expectoration immediately prior to functional endoscopic sinus surgery to treat chronic upper respiratory infections. Genomic DNA was isolated from these samples, and the V4 hypervariable region was amplified from this DNA and sequenced at the University of Minnesota Genomics Center.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Anaerobic bacteria fermentation products increase tuberculosis risk in antiretroviral treated HIV-infection Sequence

Sequence data from bronchoscopy study

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Human sputum 16S rDNA profiles - children with cystic fibrosis

The lung microbiome in cystic fibrosis (CF) is home to numerous pathogens shortening the life of patients. In contrast to adults whose lung infections are mostly resilient, children are more responsive to therapy. Our aim was to assess changes in the lung microbiome in children with CF that were induced by antibiotic therapy against the most important of the pathogens, Pseudomonas aeruginosa.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Lung Microbiome in Idiopathic Pulmonary Fibrosis and Interferon-?

Bronchoalveolar lavage samples Genome sequencing and assembly

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Diversity and Dynamics of tracheal microbiota in patients with tracheostomy

We describe the longitudinal diversity of the tracheal microbiome in patients with tracheostomy using 16S V4 rRNA gene sequencing of tracheal aspirates.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Trachea
human lung metagenome Targeted Locus (Loci)

microbiota clinical bronchoalveolar lavage (BAL) samples

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
sequencing for human-associated microbes by 16S rRNA gene Raw sequence reads

The study goal is to examine lung tissue microbiome in lung cancer patients.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
The Bacterial Topography of the Healthy Human Respiratory Tract

Here we study there bacterial topography of the human respiratory tract in health and demonstrate that micro-aspiration is the method of microbial dispersion in the lungs

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
human lung metagenome Raw sequence reads

PBB (protracted bacterial bronchitis) is a widespread pediatric disease, and relative lung microbiota dysbiosis remains unclear.In this study,12 tracheomalacia infants samples were selected for analyzed.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Human pulmonary secretions and tissue Targeted Locus (Loci)

Human pulmonary microbiome - pulmonary secretions and tissue from cystic fibrosis patients and pulmonary secretions from healthy volunteers.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Dynamics of airway microbiota in CF children

Here we describe the diversity of the airway microbiome in CF children using 16S V4 rRNA gene sequencing of sputum samples.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
16S rRNA amplicons isolated from microbial communities from the cystic fibrosis lung

Microbial communities from cystic fibrosis lung tissue.  This project sought to spatially profile microbial and viral communities in the cystic fibrosis lung using high throughput sequencing.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Gut microbial community diversity of mice with allergic lung inflammation

The gut microbiome remodeling by polygonatum odoratum polysaccharide in mice with allergic lung inflammation

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
short read sequencing of distinct cheese rinds

Cheese rinds are a semi-complex microbial community with bacteria, fungi, and viruses. Here, we harvested cheese rinds from 11 different cheeses, and extracted DNA from the 11 microbial communities as well as the associated virome of one cheese rind.

Biome: root:Engineered:Food production:Dairy products
ITS2 and whole metagenomics from stool of human lung cancer patients from hungary

Investigating Bacteriome and Mycobiome interactions, and their contribution to lung cancer treatment. For treatment, anti-cancer combination therapy was used.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Intestinal flora sequence in a mouse model of lung cancer

The effect of intestinal flora in mouse models of lung cancer and the regulation of intestinal flora after adjuvant administration

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
16S-based bacterial profiling of the microbiota associated with the bronchoalveolar lavage fluid of patients with COPD, healthy smokers and healthy controls. Targeted loci

16S-based amplicon sequencing profiling of the microbiota associated with the bronchial wash of COPD patients, healthy smokers and healthy controls.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Comparison of the lung microbiota in patients with respiratory infection, tuberculosis, and lung cancer: a preliminary study

Recent evidence suggested that lung microbiota can be recognized as one of the ecological determinants for many respiratory diseases. However, the different of the lung microbiota and its associated lung immunity were still unclear.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Bacterial microbiome of sputum samples from patients with bronchiectasis recruited in stable state

The aim of the study was to evaluate the bacterial microbiome composition and to determine associations between the observed microbial diversity and biological and clinical characteristics in sputum samples collected from patients with bronchiectasis, recruited in stable state.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
The respiratory tract microbiome in children with Cystic Fibrosis

Metagenomic sequencing of respiratory tract microbiome in children with Cystic Fibrosis.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung