SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
16S rRNA gene sequencing data from throat swabs from participants in the Busselton Health Study

A population study of respiratory tract microbiome in a largely healthy cohort of participants in the Busselton Health Study, Perth, Western Australia.

Biome: root:Host-associated:Human:Respiratory system:Nasopharyngeal:Pharynx
Host Immune Response and Mortality Risk are  Related to Distinct Lung Microbiomes in  HIV-Pneumonia Patients

Clustering HIV-pneumonia patients based on airway bacterial community composition permits stratification of subjects into functionally and immunologically distinct groups that are differentially related to mortality risk.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Lower airway microbiota in patients with clinically suspected Mycobacterium avium complex lung disease

We tried to put some light on the relationship between Non-tuberculous mycobacterial lung disease and lower airway microbiota, based on clinical characterization of the patients and 16s rRNA sequencing.   The results reported Other than the genus Pseudomonas, there was no clear difference in the composition of and no significant difference in the diversity of the bacterial flora between the Mycobacterium Avium Complex-Lung Disease (MAC-LD) and non-MAC-LD groups. We found that the genus Pseudomonas and Mycobacterium Avium Complex tended to exist exclusively.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Trachea
Comparison of lung microbiota between antineutrophil cytoplasmic antibody-associated vasculitis and sarcoidosis

Bacterial involvements for the pathogenesis have been suggested in both antineutrophil cytoplasmic antibody-associated vasculitis (AAV) and sarcoidosis, which have lung involvements. However, exhaustive researches to assess the bacteria in the lung in AAV and in sarcoidosis have not been performed to elucidate the differences in bacterial characteristics. We sought to elucidate the distinct lung microbiota suggesting contributions of dysbiosis in the lung to the pathogenesis of AAV and sarcoidosis.

Biome: N/A
Early development of the airway microbiota in infants with cystic fibrosis

The pathogenesis of airway infection in cystic fibrosis (CF) is poorly understood.  We aimed to identify changes in the airway microbiota in infancy that could underpin deterioration and could potentially be targeted therapeutically. Thirty infants with CF diagnosed on newborn screening were followed up for up to two years.  Throat swabs were collected as a surrogate for lower airway microbiota (median 35 days between study visits). Quantitative PCR and sequencing of the 16S rRNA bacterial gene was performed using the Illumina MiSeq. Data analyses were performed in QIIME and Phyloseq in R.

Biome: root:Host-associated:Human:Digestive system:Oral:Throat
Pathogenesis of Obstruction/Emphysema and the Microbiome MiSeq

Examine the microbiome via 16S sequences of the human lung in subjects with and without COPD and HIV

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
The fungal intestinal microbiota predict the development of bronchopulmonary dysplasia

Prior investigations of the airway microbiome have inconsistently shown an association between bacterial community composition and bronchopulmonary dysplasia (BPD) development. However, these prior studies have focused exclusively on the bacterial microbiome. Here, we show features of the intestinal fungal microbiome predict the development of BPD in very low birthweight preterm newborns, and that this effect is transferable into mice with fecal microbiota transplant.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Pseudomonas aeruginosa population sequencing

To understand the allelic spectra in well documented genes in Pseudomonas aeruginosa and track their dynamics in longitudinal patient samples

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Examination of microbes in sarcoidosis BAL and tissue. Raw sequence reads

To determine if any microbes are enriched in sarcoidosis relative to healthy controls. 16S, ITS tagged sequencing; shotgun sequencing; viral purification and sequencing.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
LHMP - 16S V4 Sequencing of BAL/OW/IS samples on MiSeq Platform

A re-sequencing of Lung HIV Microbiome Project (LHMP) BAL/OW/IS gDNA samples on the Illumina MiSeq platform using the V4 Caporaso primer set.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Analysis of the Cystic Fibrosis Lung Microbiota via Serial Illumina Sequencing

The characterization of bacterial communities using DNA sequencing has revolutionized our ability to study microbes in nature and discover the ways in which microbial communities affect ecosystem functioning and human health. Here we describe Serial Illumina Sequencing (SI-Seq): a method for deep sequencing of the bacterial 16S rRNA gene using next-generation sequencing technology. SI-Seq serially sequences portions of the V5, V6 and V7 hypervariable regions from barcoded 16S rRNA amplicons using an Illumina short-read genome analyzer. SI-Seq obtains taxonomic resolution similar to 454 pyrosequencing for a fraction of the cost, and can produce hundreds of thousands of reads per sample even with very high multiplexing. We validated SI-Seq using single species and mock community controls, and via a comparison to cystic fibrosis lung microbiota sequenced using 454 FLX Titanium. Our control runs show that SI-Seq has a dynamic range of at least five orders of magnitude, can classify >96% of sequences to the genus level, and performs just as well as 454 and paired-end Illumina methods in estimation of standard microbial ecology diversity measurements. We illustrate the utility of SI-Seq in a pilot sample of central airway secretion samples from cystic fibrosis patients.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Augmentation of Standard Clinical Microbiological Culture with Next Generation Sequencing Improves Diagnosis in Bronchoalveolar Lavage Specimens

Immunocompromised patients are at increased risk for pneumonia. Standard microbiological culture may fail to identify unusual or unexpected organisms; culture-independent methods have improved our ability to deconvolute polymicrobial patient samples. We hypothesized that a more complete assessment of the microbial composition of bronchoalveolar lavage (BAL) samples would identify changes to routine clinical laboratory procedures that improve pathogen recovery. 20 consecutive BAL samples from oncology or transplant patients were plated to three standard and four additional media, and cultivable bacteria present were identified by next-generation 16S rRNA gene sequencing (NGS16S) analysis of DNA extracted from washed culture plates. NGS16S analysis was also performed on DNA extracted directly from patient samples. 96% of all organisms identified were cultivable, but only 21% were reported by standard culture, indicating that standard work-up can be further optimized. Direct NGS16S correlated well with standard culture results, identifying the same predominant organism in 50% of samples. When different predominant organisms were identified, NGS16S most often detected anaerobes, whose growth is unsupported by standard culture conditions. Brucella agar was the best single value-added media, supporting the growth of the largest number of organisms for the most specimens. Anaerobes are underappreciated BAL constituents. NGS16S identifies more organisms per sample and allows identification of fastidious organisms, while culture is better at capturing organisms when bacterial load is low, and allows incidental recovery of non-bacterial pathogens such as yeast or molds. Molecular and culture-based methods together detect more relevant organisms in clinical samples than either method alone.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Human respiratory disease lung microbiome

Microbiome sequencing of induced sputum samples from patients with COPD, Bronchiectasis or COPD and Bronchiectasis taking during periods of disease stability and during exacerbations.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Metagenomic Identification of Severe Pneumonia Pathogens in Mechanically-Ventilated Patients

Metagenomic sequencing of respiratory microbial communities for etiologic pathogen identification in pneumonia may help overcome the limitations of current culture-based methods. We examined the feasibility and clinical validity of rapid-turnaround metagenomics with Nanopore sequencing for severe pneumonia diagnosis. We conducted a case-control study of mechanically-ventilated patients with and without pneumonia. We collected endotracheal aspirate samples (ETAs) and applied a microbial DNA enrichment method prior to performing metagenomic sequencing with the Oxford Nanopore MinION device. We compared Nanopore results against clinical microbiologic cultures and bacterial 16S rRNA gene sequencing. We demonstrated technical feasibility and proof-of-concept clinical validity of Nanopore metagenomics for severe pneumonia diagnosis, with striking concordance with positive clinical cultures and insights into the composition of culture-negative samples. Prospective studies with real-time metagenomics are warranted to examine the impact on antimicrobial decision-making and clinical outcomes.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Lung Microbiota of Critically Ill Patients Receiving Mechanical Ventilation

The goal of this project was to determine the relationship between lung microbiota and clinical outcomes in critically ill patients. Miniature bronchoalveolar lavage was performed within 24 hours of admission on critically ill patients receiving mechanical ventilation. Bacterial communities were characterized using 16S rRNA gene amplicon sequencing using the Illumina MiSeq platform.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
The Investigation and Analysis of Microbiomic Data Relating to Diseases Surrounding the Deep Lung Tissue

Exhaled breath condensate is a promising way in identifying biomarkers of lung disease but the  current devices used have disadvantages. The EcoScreen has the disadvantage of not being portable and the R-Tube cannot efficiently keep the sample cool. A 'prototpye' was been created to alleviate these issues. With the 'prototype', EBC  samples were taken and files were concatenated together with md5 checksums allowing for data verification. Data was uploaded and results were compared to current type of collection devices.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Depletion of human DNA from complex clinical samples for metagenomic sequencing

Metagenomic sequencing is a promising approach for identifying and characterizing organisms and their functional characteristics in complex, polymicrobial infections, such as airway infections in people with cystic fibrosis. These analyses are often hampered, however, by overwhelming quantities of human DNA, yielding only a small proportion of microbial reads for analysis. Additionally, many abundant microbes in respiratory samples can produce large quantities of extracellular bacterial DNA originating either from biofilms or dead cells. This study describes a method for simultaneously depleting DNA from intact human cells and extracellular DNA (human and bacterial) in sputum, using selective lysis of eukaryotic cells and endonuclease digestion. This method increases microbial sequencing depth and, consequently, both the number of taxa detected and coverage of individual genes such as those involved in antibiotic resistance, underscoring the substantial impact of DNA from sources other than live bacteria in microbiological analyses of complex, chronic infection specimens.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
16S sequencing from human airway sites Raw sequence reads

The rationale for the present study is that evaluation of the pathogenic character of the COPD lung microbiota has been hindered by concerns that oral taxa found in the COPD lung microbiota are the result of sample contamination rather than aspiration. Therefore, we have designed the present study to sample the mild or moderate COPD lung tissue microbiota surgically—without passing the sample through the oropharynx—and avoiding potential upper airway contamination of lung samples. Demonstrating that oral microbes are true components of the COPD lung microbiota will implicate aspiration as a potential pathogenic mechanism in COPD. We hypothesized that oral bacteria are true members of the early-stage COPD lung microbiota and exhibit ecologic drift.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Lung microbiota in the acute respiratory distress syndrome

Here we assess for changes in the lung microbiome in the bronchoalveaolar lavage fluid of patients with the acute respiratory distress syndrome

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

Understanding the lung microbiome dynamics and its dysbiosis in COPDMAP cohort

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

We are the First study results clarify and characterize the variation of equilibrium of oral microbiome in non-smoking female lung cancer. Our ultimate goal is to put different experimental and methodological views into perspective for better understand flora changes upon disease onset or between different disease stages. The role of oral microbiota composition is important to evaluate how oral microbiomes biomarker at the community level could provide improved assessment in individuals and populations at risk, especially in the context of developing non-invasive diagnostic tests.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury, part III

The goal of this experiment was to determine the relationship between lung microbiota and lung inflammation in genetically-identical mice exposed to various durations of acute hyperoxia. 10-week old mice (C57Bl/6) were exposed to 95% FiO2 (hyperoxia) for 24 or 48 hours. Bacterial communities were characterized using 16S rRNA gene sequencing.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Analysis of the fetal lung microbiome

Fetal and placental tissue samples were assessed by targeted 16s rRNA gene amplicon sequencing to characterize associated microbiota.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury, part IV

The goal of this experiment was to determine the relationship between gut microbiota and lung inflammation in genetically-identical mice exposured to various durations of acute hyperoxia. 10-week old mice (C57Bl/6) were exposed to 95% FiO2 (hyperoxia) for 0, 24, 48, or 72 hours. Bacterial communities were characterized using 16S rRNA gene sequencing.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury, part I

The goal of this experiment was to determine the effects of hyperoxia on the microbiota of developing lungs. Newborn mouse pups were exposed either to 21% FiO2 (room air) or 75% FiO2 (hyperoxia) for two weeks. Bacterial communities were characterized using 16S rRNA gene sequencing.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury, part II

The goal of this experiment was to determine the effects of hyperoxia on the microbiota of lungs of adult mice. 10-week old mice (C57Bl/6) were exposed to 95% FiO2 (hyperoxia) for 0, 24, 48, or 72 hours. Bacterial communities were characterized using 16S rRNA gene sequencing.

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

Study of the lung microbiome of humans with COPD when clinically stable using sputum as samples.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Nasal sinuses and lung microbiome in cystic fibrosis patients.

Argumentation the provision that the nasal sinuses of the adult Cystic Fibrosis patients with chronic rhinosinusitis become additional reservoir of infection.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Allergic inflammation impacts synergistic viral-bacterial infections in C57BL/6 mice

To investigate viral-bacterial synergy in the allergic host, we developed a 'triple-threat model' by combining our fungal asthma model with a well-established model of IAV and Spn co-infection.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Mycobiome of mock communities and the human lung.

Invasive fungal infections are an increasingly important cause of human morbidity and mortality. Our goal was to use an amplicon next generation sequencing assay with demonstrated good recapitulation of mock communities to describe the fungal microbiome (mycobiome) of the lung during fungal infection.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Lung microbiota contribute to pulmonary inflammation and disease progression in pulmonary fibrosis, part 2

Rationale: Idiopathic pulmonary fibrosis (IPF) causes considerable global morbidity and mortality, with poorly understood mechanisms of disease progression. Recent observational studies have reported associations between lung dysbiosis, mortality and altered host defense gene expression, supporting a role for lung microbiota in IPF. However, the causal significance of altered lung microbiota in disease progression is undetermined.Objective: To examine the effect of microbiota on local alveolar inflammation and disease progression using both animal models and human IPF subjects.Methods: For human studies, we characterized lung microbiota in bronchoalveolar lavage fluid from 68 IPF patients. For animal modeling, we used a murine model of pulmonary fibrosis in conventional and germ free mice. Lung bacteria were characterized using 16S rRNA gene sequencing with novel techniques optimized for low biomass sample load. Microbiota were correlated with alveolar inflammation, measures of pulmonary fibrosis and disease progression.Main Measurements and Results: Disruption of the lung microbiome predicts disease progression, correlates with local host inflammation, and participates in disease progression. In IPF patients, lung bacterial burden predicts fibrosis progression, and microbiota diversity and composition correlate with increased alveolar pro-fibrotic cytokines. In murine models of fibrosis, lung dysbiosis precedes peak lung injury and is persistent. In germ-free animals, the absence of a microbiome protects against mortality.Conclusion: Our results demonstrate that lung microbiota contribute in the progression of IPF. We provide biologic plausibility for the hypothesis that lung dysbiosis promotes alveolar inflammation and aberrant repair. Manipulation of lung microbiota may represent a novel target for the treatment of IPF.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Lung microbiota contribute to pulmonary inflammation and disease progression in pulmonary fibrosis

Rationale: Idiopathic pulmonary fibrosis (IPF) causes considerable global morbidity and mortality, with poorly understood mechanisms of disease progression. Recent observational studies have reported associations between lung dysbiosis, mortality and altered host defense gene expression, supporting a role for lung microbiota in IPF. However, the causal significance of altered lung microbiota in disease progression is undetermined.Objective: To examine the effect of microbiota on local alveolar inflammation and disease progression using both animal models and human IPF subjects.Methods: For human studies, we characterized lung microbiota in bronchoalveolar lavage fluid from 68 IPF patients. For animal modeling, we used a murine model of pulmonary fibrosis in conventional and germ free mice. Lung bacteria were characterized using 16S rRNA gene sequencing with novel techniques optimized for low biomass sample load. Microbiota were correlated with alveolar inflammation, measures of pulmonary fibrosis and disease progression.Main Measurements and Results: Disruption of the lung microbiome predicts disease progression, correlates with local host inflammation, and participates in disease progression. In IPF patients, lung bacterial burden predicts fibrosis progression, and microbiota diversity and composition correlate with increased alveolar pro-fibrotic cytokines. In murine models of fibrosis, lung dysbiosis precedes peak lung injury and is persistent. In germ-free animals, the absence of a microbiome protects against mortality.Conclusion: Our results demonstrate that lung microbiota contribute in the progression of IPF. We provide biologic plausibility for the hypothesis that lung dysbiosis promotes alveolar inflammation and aberrant repair. Manipulation of lung microbiota may represent a novel target for the treatment of IPF.

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

Meta-genomic profiling of Human Lung microbiome

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
16S rRNA gene sequencing of the pulmonary microbiota in sarcoidosis

16S rRNA gene sequencing of the lung microbiota of patients with sarcoidosis and patients with other interstitial lung disease

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Bronchoalveolar lavage lung microbiota in children with cystic fibrosis

The goal of this study was to determine the lung microbiota in children with cystic fibrosis, differentiating true lung microbiota from contaminants that could come from the oropharynx, mouth, collection instruments, and/or reagents used to process and sequence samples. Bronchoalveolar lavage samples were collected, as well as throat, mouth, instrument, and reagent controls. DNA was isolated from each sample type and subjected to bacterial 16S rRNA gene sequencing.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Gut microbiota in lung cancer patients

Investigate phylogenetic compositions in gut microbiota between lung cancer patients and healthy volunteers

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Airway bacteria and P. aeruginosa pathogens under antibiotic therapy

We aimed to explore the effects of broad-spectrum combination antibiotic therapy on Pseudomonas aeruginosa populations in the lungs of cystic fibrosis patients. Sputum samples were collected daily to provide sufficient temporal resolution to capture rapid effects.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Respiratory microbiota in lung cancer, bronchiectasis and healthy populations

The respiratory microbiome is a role player in human health, therefore is significant to be addressed thoroughly. The respiratory tract is the main portal through which the microorganisms enter the human body. Lung cancer and bronchiectasis are chronic lung diseases that largely burdens the humans around the world.This study intended to identify bacteria in human respiratory tract (upper and lower) in the two diseases as well as in a healthy group.

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