SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Lung microbiome of non-small cell lung cancer

To investigate the relationship between lung microbiome and the phenotype of inflammatory stromal infiltrate, we studied 26 pairs of DNA samples from NSCLC (non-small cell lung cancer) and adjacent tissue. The lung microbiomes were analyzed by 16S rRNA amplicon-based sequencing. Phenotype of the tumor stroma for every sample was characterized using immunohistochemistry.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Whole lung tissue is the preferred sampling method for murine lung microbiota

The goal of this experiment was to determine the optimal specimen type for amplicon-based sequencing of the lung microbial communities in mice. Healthy adult C57BL/6 mice were sacrificed and either whole lung tissue or bronchoalveolar lavage fluid was collected, along with cecum and tongue tissue samples. Following DNA isolation from tissue samples and controls, bacterial communities were characterized using 16S rRNA gene sequencing.

Biome: root:Host-associated:Human
A high-risk airway mycobiome discerns COPD exacerbators with poor survival

Evaluation of airway mycobiome in COPD using targeted ITS sequencing

Biome: root:Host-associated:Human
Study of fungal clinical isolates from different anatomical sites and metagenomic of the lung microbiome of patients with cystic fibrosis

16S and ITS processed sequences.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
16S amplicon sequencing of sputa from tuberculosis patients

In this work we describe the results obtained from a multicenter study of the microbiota of sputum samples from patients with tuberculosis or unrelated lung diseases and healthy donors recruited in Switzerland, Italy and Bangladesh, with the ultimate goal of discovering a microbiota-based biomarker associated with tuberculosis. Bacterial 16S rDNA amplification, high-throughput sequencing and extensive bioinformatic analyses revealed patient-specific lung flora and high variability in taxon abundance. No common signature could be identified among the individuals enrolled and microbiota composition was found to be confounded by various factors, including the geographical setting. Moreover, anti-tuberculosis therapy did not cause any important variation in microbiota diversity, thus precluding its exploitation as a biomarker for the follow up of tuberculosis patients undergoing treatment.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Lung microbiota in healthy lung transplant recipients

The goal of this project was to determine the relationship between lung microbiota and clinical outcomes among asymptomatic lung transplant recipients with preserved lung function. Bacterial communities in acellular bronchoalveolar lavage fluid collected during routine one-year post-transplant surveillance bronchoscopy was characterized using 16S rRNA gene amplicon sequencing using the Illumina MiSeq platform.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Microbiome in Lung Explant: an IPF Study

To characterize the regional IPF lung tissue microbiome in the Microbiome In Lung Explants Study

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Acute Lung Injury Registry Microbiome

Microbiome in critical illness cohort study

Biome: root:Host-associated:Human
Start of ivacaftor/lumacaftor in adult cystic fibrosis patients with homozygous Phe508del results in temporal changes in lung microbiome and metabolome.

Rationale: Targeted cystic fibrosis therapy with ivacaftor/lumacaftor partly restores chloride channel function in the airways and increases of the epithelial fluid transport in the airways. Consequently, changes in the microbiome that is adapted to cystic fibrosis lungs can occur.Objectives: To investigate the effects of ivacaftor/lumacaftor on respiratory microbial composition and microbial metabolic activity in an observational cohort study, in which we repeatedly sampled the lower respiratory tract.Methods: This was a single-center longitudinal observational cohort study in adult cystic fibrosis patients with a homozygous Phe508del mutation. Lung function measurements and microbial cultures of sputum were performed as part of routine care. An oral and nasal wash, and an exhaled breath sample were collected before and every three months after starting therapy, up to one year.

Biome: root:Host-associated:Human
Nontuberculous mycobacteria disease in cystic fibrosis

Pulmonary infections with nontuberculous mycobacteria (NTM) are increasing in prevalence and can result in significant morbidity and mortality in people with cystic fibrosis (CF). The objective of this study is to identify features of the lower airway microbiota in patients with CF and NTM infection that differ between people with and without NTM disease.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Microbiota characterization in Lung Cancer

16s rRNA gene sequencing on pulmonar, oral, and faecal samples from Spanish lung cancer patients and controls.

Biome: root:Host-associated:Human
Lung microbiota of Mus musculus (C57BL/6J), Raw sequence reads

Under eubiotic conditions commensal microbes are known to provide a natural competitive shield against invading bacterial pathogens in the densely colonized intestinal tract, on the skin or on the vaginal mucosa. A comparable function of commensal bacteria in the respiratory tract was so far not described. Here, we evaluate the role of respiratory microbiota in Pneumococcus colonization of the lung in a mouse model.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Lung microbiome in adult cystic fibrosis patients

Influence of target and antibiotic therapy on microbiota composition in adult cystic fibrosis patients

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Mycobiome characterization in Lung Cancer

ITS1 amplicon sequencing for mycobiome characterization of pulmonar and saliva samples from Spanish lung cancer patients and controls.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Human respiratory tract mycobiome and alterations in HIV infection and lung disease Targeted Locus (Loci)

Whether there are resident fungal communities in the respiratory tract is unknown, and wide gaps exist in our understanding of occult fungal infections in chronic lung diseases or in individuals with systemic disease. In this study, we characterized fungal diversity at different levels of the respiratory tract including oral washes (OW), induced sputum (IS) and bronchoalveolar lavages (BAL) from 56 individuals. We also examined relationship of fungal communities to chronic obstructive pulmonary disease and to HIV infection.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
human lung microbial metagenome

detection of differences in microbial community composition harbored in lungs of patients with mild to moderate COPD compared to control individuals

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Stromal modulation through gastrointestinal microbial dysbiosis

The overall use of antibiotics has increased significantly in recent years. Besides fighting infections, antibiotics also alter the gut microbiota. Commensal bacteria in the gastrointestinal tract are crucial to maintain immune homeostasis, and microbial imbalance or dysbiosis affects disease susceptibility and progression. We hypothesized that antibiotic-induced dysbiosis of the gut microbiota would suppress cytokine profiles in the host, thereby leading to changes in the tumor microenvironment. Indeed, dysbiosis resulted in alterations in bacterial abundance, composition and diversity. On the host side, antibiotic-induced dysbiosis caused elongated small intestines and ceca, and B16-F10 melanoma and Lewis Lung carcinoma progressed more quickly than in orthobiotic control mice. Mechanistic studies revealed that this progression was mediated by suppressed TNF-a levels, both locally and systemically, resulting in reduced expression of tumor endothelial adhesion molecules, particularly intercellular adhesion molecule-1 (ICAM-1) and a subsequent decrease in the number of activated CD8+ T-cells in the tumor. However, suppression of ICAM-1 or its binding site, the alpha subunit of lymphocyte function-associated antigen-1, was not seen in the spleen or thymus during dysbiosis. TNF-a supplementation in dysbiotic mice was able to increase ICAM-1 expression and leukocyte trafficking into the tumor. Overall, these results demonstrate the importance of commensal bacteria in supporting anti-cancer immune surveillance, define an important role of tumor endothelial cells within this process, and suggest adverse consequences of antibiotics on distal cancer development. Significance: Antibiotic-induced dysbiosis enhances distal tumor progression by altering host cytokine levels resulting in suppression of leukocyte trafficking via modulation of tumor endothelial adhesion molecules.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Human cystic fibrosis lung

Characterization of the bacterial microbiome in cystic fibrosis subjects in various regions of the lung

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

Bacterial community in upper respiratory tract

Biome: root:Host-associated:Mammals:Respiratory system
Endotracheal tube bilfilm Targeted Locus (Loci)

To characterize bacteria in endochatracheal tube bilfilms related to VAP

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Trachea
Microbiome analysis in sputum of CF subjects

Characterization and quantification of the bacterial microbiome in cystic fibrosis subjects over the course of antibacterial therapy

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Comparison of Bacterial Communities in Bronchoalveolar Lavage between a U.S. and Malawi Population.

We have compared the lung microbiome in a U.S. and Malawi population. We identified several significant differences between the two populations which we hypothesize are related to different environmental exposures in the two countries.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Changes in the Lung Microbiome Following Lung Transplantation Include the Emergence of Two Distinct Pseudomonas Species with Distinct Clinical Associations

Comparison of lung microbiota in lung transplant recipients and non-transplant control subjects

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Human airway Targeted Locus (Loci)

Molecular ecology of the cystic fibrosis airway

Biome: root:Host-associated:Human:Digestive system:Oral:Throat
Bacteria Genome sequencing

Bacteria from sputum

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Human airway Targeted Locus (Loci)

Human sputum bacterial communities from cystic fibrosis patients collected during pulmonary exacerbation

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
The effects of freeze thaw cycles on the microbial community present in sputum samples from the CF lung


Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
The lung microbiome in young children with cystic fibrosis: a longitudinal cohort study

Cystic fibrosis (CF) is an autosomal recessive condition with impaired mucociliary clearance and innate airway defences 1. Chronic airway infection and inflammation culminating in bronchiectasis are the main drivers of the morbidity and mortality of CF 1. There is good evidence these processes start early in life, with asymptomatic infants and pre-school children demonstrating clear associations between the presence of lower airway infection and inflammation and impaired lung function and structural airway changes 1,2.The use of 16S ribosomal RNA sequencing provides compelling evidence that CF airways are inhabited by diverse microbial communities 3-7. Perturbations in the CF airway microbiome are well described, however it is unclear what affect these have on the “infection-inflammation-structural damage” model of CF lung disease 3-12. Limited studies in young children with CF suggest microbial diversity is initially low but increases with age 3,7,9,11,12. In contrast, in older children and adults, diversity decreases with age and declining lung function 3,7,13,14. In adults, with advancing lung disease and repeated exposure to antibiotics over an extended period of time, dominant CF pathogens emerge in a relatively fixed microbiome with limited diversity 4,6,15,16.We aimed to describe the lower airway microbiome in clinically stable pre-school aged children with CF, and, using longitudinal data, explore how age influences its composition. Further analysis focused on comparing the CF microbiome with that of the non-CF lung and on examining the effect of airway inflammation and antibiotic use.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Human airway Targeted Locus (Loci)

COPD related airway microbiota

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Longitudinal CF Study

A study of the longitudinal dynamics of microbiome and metabolomic data from 6 CF patients. Samples were collected daily or as frequently as possible through events of CF exacerbation and dual microbiome and metabolome data generated.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Airway microbiota and inflammation under Lumacaftor-ivacaftor

Rationale Lumacaftor-ivacaftor is a cystic fibrosis transmembrane conductance regulator (CFTR) modulator combination approved in patients with cystic fibrosis (CF) homozygous for the F508del allele. This treatment showed significant clinical improvement, however limited data have addressed the evolution of airway mycobiota-microbiota and airway inflammation under lumacaftor-ivacaftor.
Objectives To investigate the effects of lumacaftor-ivacaftor on airway mycobiota-microbiota and airway inflammation in a multicentric study.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Effects of postage on recovery of pathogens from cystic fibrosis respiratory samples

The study analysed the cultured pathogens, the abundance of pathogens using qPCR and the bacterial microbiota using targeted gene sequencing of fresh and posted samples.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Gut microbiome data of never-smoking subjects with lung adenocarcinoma

Gut microbiome data of never-smoking subjects with lung adenocarcinoma

Biome: root:Host-associated:Human:Digestive system:Intestine
lung microbiota and hypercapnic AECOPD

The aim of this study is to assess the link between lung microbiota composition and death in critically ill admitted for hypercapnic acute exacerbation of chronic obstructive pulmonary disease (AECOPD). Every patient receiving non-invasive or invasive ventilation for AECOPD admitted to intensive care unit from October 2018 to May 2019 were included (ADMIRE study, NCT03641235). Induced sputum or tracheal aspirate were sampled and DNA extraction was performed by QIAamp® PowerFecal® Pro DNA kit (QIAgen®). V3-V4 regions of 16SRNA coding gene was amplified to analyse the bacterial kingdom of lung microbiota (bacteriobiota) and ITS2 to analyse the fungal kingdom (mycobiota). Sequencing (2x250bp paired-end reads) was performed on MiSeq sequencer (Illumina®) and DADA2 pipeline on R software was used for bioinformatics analyses.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
16S rRNA lung microbiota study in mechanically ventilated patient: a pilot study

Characterization of the respiratory tract bacterial microbiota is in its infancy when compared to the gut microbiota knowledge. As key methodological steps can directly affect the accuracy of the results, it is crucial to determine a robust methodology in order to limit bias.We compared two methods of sample processing using these two different pairs of primers for bacterial microbiota analyses of respiratory samples from Intensive Care Unit (ICU) ventilated patients.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
nfection and rejection are the two most common complications after lung transplantation (LTx) and are associated with increased morbidity and mortality. We aimed to examine the association between airway microbiota and infection and rejection in lung transplant recipients (LTRs).

Distinct airway microbiota was observed between clinical stable recipients (or event free), infection and rejection after LTx. Alpha and beta diversity were significantly different between event free and rejection, and between infection and rejection recipients. Ten differential genera were identified by LEfSe analyses, with Corynebacterium, unclassified Enterococcaceae and unclassified Lactobacillales enriched in infection recipients, while Rothia, Granulicatella, Neisseria, Actinomyces, Leptotrichia, Lactobacillus and unclassified Aerococcaceae more abundant in rejection LTRs. Random forest analyses indicated that the combination of the 10 microbiota and procalcitonin (PCT) and T lymphocyte showed an AUC of 0.894, 0.955 and 0.913 to differentiate between event free and infection, event free and rejection, and infection and rejection recipients, respectively.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
EMG produced TPA metagenomics assembly of PRJNA757176 data set (Sus scrofa Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA757176, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system.

Biome: root:Host-associated:Mammals:Digestive system
Characterizing the Fungal Airway Microbiome in Cystic Fibrosis and Bronchiectasis by Next Generation Sequencing

The prevalence of fungal airways disease is increasing yet the lack of standardised diagnostic criteria make interpretation of culture results challenging. Development of effective management strategies requires a more accurate and comprehensive understanding of the fungal airway microbiome.Through the use of next generation sequencing of the ITS2 region we aimed to assess the load and diversity of fungi in patients with chronic bronchial infection. Sputum samples from 87 adults with cystic fibrosis and 24 with bronchiectasis were used to investigate patterns in fungal community composition between those with recognized fungal disease and disease controls. Only 49% of the samples were positive by fungal culture while all samples produced high quality fungal sequencing profiles. Patients with Cystic fibrosis were found to have a higher fungal biomass with lower fungal diversity than those with bronchiectasis. Candida was a common OTU is all individuals, however, Candida parapsilosis was found only in cystic fibrosis sputum while Candida albicans was most common in those with bronchiectasis. This study provides a more accurate framework to characterize the fungal airways disease-phenotypes in adult suppurative lung diseases.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
The lung microbiota in children with cystic fibrosis captured by induced sputum sampling

Background: Spatial topography of the cystic fibrosis (CF) lung microbiota is poorly understood in childhood. How best to sample the respiratory tract in children for microbiota analysis, and the utility of microbiota profiling in clinical management of early infection remains unclear. By comparison with bronchoalveolar lavage (BAL), we assessed the ability of induced sputum (IS) sampling to characterise the lower airway microbiota.

Methods: Sample sets from IS and two or three matched BAL compartments were obtained for microbiota analysis as part of the CF-Sputum Induction Trial (UKCRN_14615, ISRCTNR_12473810). Microbiota profiles and pathogen detection were compared between matched samples.

Results: Twenty-eight patients, aged 1.1–17.7 years, provided 30 sample sets. Within-patient BAL comparisons revealed spatial heterogeneity in 8/30 (27%) sample sets indicating that the lower airway microbiota from BAL is frequently compartmentalised in children with CF. IS samples closely resembled one or more matched BAL compartments in 15/30 (50%) sets, and were related in composition in a further 9/30 (30%). IS detected 86.2% of the Top 5 genera found across matched BAL samples. The sensitivity of IS to detect specific CF-pathogens identified in matched BAL samples at relative abundance ≥5% varied between 43 and 100%, with negative predictive values between 73 and 100%.

Conclusions: Spatial heterogeneity of the lower airway microbiota was observed in BAL samples and presents difficulties for consistent lung sampling. IS captured a microbiota signature representative of the lower airway in 80% of cases, and is a straightforward, non-invasive intervention that can be performed frequently to aid pathogen diagnosis and understand microbiota evolution in children with CF.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
EMG produced TPA metagenomics assembly of PRJNA597465 data set (Species Level Characterization of Dental Plaque Associated Microbiome of Native Indian Children using Metagenome Sequencing).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA597465, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque.

Biome: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
EMG produced TPA metatranscriptomics assembly of PRJNA560313 data set (Samail Ophiolite groundwater sequencing).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA560313, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Groundwater.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Mycobiome analysis in sputum of CF subjects

Characterization and quantification of the fungal microbiome in cystic fibrosis subjects over the course of antibacterial therapy

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
EMG produced TPA metagenomics assembly of PRJNA508385 data set (Comparative metagenomics reveals taxonomically idiosyncratic yet functionally congruent communities in periodontitis).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA508385, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque.

Biome: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
EMG produced TPA metagenomics assembly of PRJNA631294 data set (Putative amylases in the human vagina).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA631294, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Reproductive system:Vagina.

Biome: root:Host-associated:Human:Reproductive system:Vagina
EMG produced TPA metagenomics assembly of PRJNA612150 data set (Fred Hutch Vaginal Metagenomics (FHVM)).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA612150, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Reproductive system:Vagina.

Biome: root:Host-associated:Human:Reproductive system:Vagina