Integrity of the Human Faecal Microbiota following Long-Term Sample Storage

Kia, Elahe; Mackenzie, Brett Wagner; Middleton, Danielle; Lau, Anna F.; Waite, David W.; Lewis, Gillian; Chan, Yih-Kai; Silvestre, Marta P.; Cooper, Garth J. S.; Poppitt, Sally D.; Taylor, Michael W.

doi:10.1371/journal.pone.0163666

Cited by 40 publications

(40 citation statements)

References 14 publications

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“…For mammalian gut samples there is some evidence that storage in glycerol may result in more representative compositional results following long term frozen storage 132 . Similarly, freeze drying prior to long-term frozen storage may be a prudent approach 133 .…”

Section: Author Contributionsmentioning

confidence: 99%

Shotgun metagenomics, from sampling to analysis

et al. 2017

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Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes have crucial roles in the environment and in human health. However, microbes are frequently difficult to culture in the laboratory, which can confound cataloging of members and understanding of how communities function. High-throughput sequencing technologies and a suite of computational pipelines have been combined into shotgun metagenomics methods that have transformed microbiology. Still, computational approaches to overcome the challenges that affect both assembly-based and mapping-based metagenomic profiling, particularly of high-complexity samples or environments containing organisms with limited similarity to sequenced genomes, are needed. Understanding the functions and characterizing specific strains of these communities offers biotechnological promise in therapeutic discovery and innovative ways to synthesize products using microbial factories and can pinpoint the contributions of microorganisms to planetary, animal and human health.

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Section: Author Contributionsmentioning

confidence: 99%

Shotgun metagenomics, from sampling to analysis

et al. 2017

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“…Because these specimens remain sterile and are immediately frozen, they are ideal for microbiome analysis, as immediate freezing does not impact microbiome composition (16). Less is known regarding long-term (i.e., years) storage at À80 C, which may impact certain aspects of the microbiome (17,18); however, the length of storage time in our samples was not associated with overall microbiome diversity and composition (a-and b-diversity).…”

Section: Patients and Sample Collectionmentioning

confidence: 90%

The Microbiome in Lung Cancer Tissue and Recurrence-Free Survival

Peters

Hayes

Goparaju

et al. 2019

Cancer Epidemiology, Biomarkers &Amp; Prevention

117

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Background: Human microbiota have many functions that could contribute to cancer initiation and/or progression at local sites, yet the relation of the lung microbiota to lung cancer prognosis has not been studied. Methods: In a pilot study, 16S rRNA gene sequencing was performed on paired lung tumor and remote normal samples from the same lobe/segment in 19 patients with non-small cell lung cancer (NSCLC). We explored associations of tumor or normal tissue microbiome diversity and composition with recurrence-free (RFS) and disease-free survival (DFS), and compared microbiome diversity and composition between paired tumor and normal samples. Results: Higher richness and diversity in normal tissue were associated with reduced RFS (richness P ¼ 0.08, Shannon index P ¼ 0.03) and DFS (richness P ¼ 0.03, Shannon index P ¼ 0.02), as was normal tissue overall microbiome composition (Bray-Curtis P ¼ 0.09 for RFS and P ¼ 0.02 for DFS). In normal tissue, greater abundance of family Koribacteraceae was associated with increased RFS and DFS, whereas greater abundance of families Bacteroidaceae, Lachnospiraceae, and Ruminococcaceae were associated with reduced RFS or DFS (P < 0.05). Tumor tissue diversity and overall composition were not associated with RFS or DFS. Tumor tissue had lower richness and diversity (P 0.0001) than paired normal tissue, though overall microbiome composition did not differ between the paired samples. Conclusions: We demonstrate, for the first time, a potential relationship between the normal lung microbiota and lung cancer prognosis, which requires confirmation in a larger study. Impact: Definition of bacterial biomarkers of prognosis may lead to improved survival outcomes for patients with lung cancer.

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“…All stool samples used for microbiota analysis were collected at the same day or 1 day after collection of the blood sample, and immediately frozen and stored at −20°C before DNA isolation. Interim storage and long‐term sample storage (up to 14 years) at −20°C of faecal specimens guarantees high sample quality for 16S sequencing without altering results …”

Section: Methodsmentioning

confidence: 99%