The WinCF Model - An Inexpensive and Tractable Microcosm of a Mucus Plugged Bronchiole to Study the Microbiology of Lung Infections

Comstock, William; Huh, Edwin; Weekes, Reiley; Watson, Connor; Xu, Tianyang; Dorrestein, Pieter C.; Quinn, Robert A.

doi:10.3791/55532-v

Cited by 2 publications

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“…Other proposed solutions include culture enrichment to increase microbial load prior to mNGS [12] though abundance estimates no longer re ect in vivo conditions after culture. Some arti cial sputum medium recipes also contain salmon sperm DNA [13], which will also be sequenced with mNGS and may overwhelm microbial-derived reads.…”

Section: Introductionmentioning

confidence: 99%

Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies

Kim,

II,

Shah

et al. 2024

Preprint

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Background Most respiratory microbiome studies have focused on amplicon rather than metagenomics sequencing due to high host DNA content. We evaluated efficacy of five host DNA depletion methods on previously frozen human bronchoalveolar lavage (BAL), nasal swabs, and sputum prior to metagenomic sequencing. Results Median sequencing depth was 76.4 million reads per sample. Untreated nasal, sputum and BAL samples had 94.1%, 99.2%, and 99.7% host-reads. The effect of host depletion differed by sample type. Most treatment methods increased microbial reads, species richness and predicted functional richness; the increase in species and predicted functional richness was mediated by higher effective sequencing depth. For BAL and nasal samples, most methods did not change Morisita-Horn dissimilarity suggesting limited bias introduced by host depletion. Conclusions Metagenomics sequencing without host depletion will underestimate microbial diversity of most respiratory samples due to shallow effective sequencing depth and is not recommended. Optimal host depletion methods vary by sample type.

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Section: Introductionmentioning

confidence: 99%

Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies

Kim,

II,

Shah

et al. 2024

Preprint

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The Microbiome in Cystic Fibrosis Pulmonary Disease

Françoise

Héry-Arnaud

2020

Genes

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Cystic fibrosis (CF) is a genetic disease with mutational changes leading to profound dysbiosis, both pulmonary and intestinal, from a very young age. This dysbiosis plays an important role in clinical manifestations, particularly in the lungs, affected by chronic infection. The range of microbiological tools has recently been enriched by metagenomics based on next-generation sequencing (NGS). Currently applied essentially in a gene-targeted manner, metagenomics has enabled very exhaustive description of bacterial communities in the CF lung niche and, to a lesser extent, the fungi. Aided by progress in bioinformatics, this now makes it possible to envisage shotgun sequencing and opens the door to other areas of the microbial world, the virome, and the archaeome, for which almost everything remains to be described in cystic fibrosis. Paradoxically, applying NGS in microbiology has seen a rebirth of bacterial culture, but in an extended manner (culturomics), which has proved to be a perfectly complementary approach to NGS. Animal models have also proved indispensable for validating microbiome pathophysiological hypotheses. Description of pathological microbiomes and correlation with clinical status and therapeutics (antibiotic therapy, cystic fibrosis transmembrane conductance regulator (CFTR) modulators) revealed the richness of microbiome data, enabling description of predictive and follow-up biomarkers. Although monogenic, CF is a multifactorial disease, and both genotype and microbiome profiles are crucial interconnected factors in disease progression. Microbiome-genome interactions are thus important to decipher.

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The WinCF Model - An Inexpensive and Tractable Microcosm of a Mucus Plugged Bronchiole to Study the Microbiology of Lung Infections

Cited by 2 publications

References 0 publications

Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies

Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies

The Microbiome in Cystic Fibrosis Pulmonary Disease

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