Sequence-Based Characterization of Intratumoral Bacteria—A Guide to Best Practice

Walker, Sidney P.; Tangney, Mark; Claesson, Marcus J.

doi:10.3389/fonc.2020.00179

Cited by 43 publications

(52 citation statements)

References 57 publications

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“…Recent studies aimed at the determination of the urogenital tract (tumor) microbiome using culture-independent NGS-based techniques (Shrestha et al, 2018;Banerjee et al, 2019). Unfortunately, such low biomass studies often exclude C. acnes due to its notorious presence in control samples (Mollerup et al, 2016;Walker et al, 2020). Thus, NGS-based microbiome studies are unlikely to contribute significantly to the open questions regarding the presence and possible role of C. acnes in the prostate microenvironment.…”

Section: Prostate Pathologiesmentioning

confidence: 99%

A Janus-Faced Bacterium: Host-Beneficial and -Detrimental Roles of Cutibacterium acnes

et al. 2021

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The bacterial species Cutibacterium acnes (formerly known as Propionibacterium acnes) is tightly associated with humans. It is the dominant bacterium in sebaceous regions of the human skin, where it preferentially colonizes the pilosebaceous unit. Multiple strains of C. acnes that belong to phylogenetically distinct types can co-exist. In this review we summarize and discuss the current knowledge of C. acnes regarding bacterial properties and traits that allow host colonization and play major roles in host-bacterium interactions and also regarding the host responses that C. acnes can trigger. These responses can have beneficial or detrimental consequences for the host. In the first part of the review, we highlight and critically review disease associations of C. acnes, in particular acne vulgaris, implant-associated infections and native infections. Here, we also analyse the current evidence for a direct or indirect role of a C. acnes-related dysbiosis in disease development or progression, i.e., reduced C. acnes strain diversity and/or the predominance of a certain phylotype. In the second part of the review, we highlight historical and recent findings demonstrating beneficial aspects of colonization by C. acnes such as colonization resistance, immune system interactions, and oxidant protection, and discuss the molecular mechanisms behind these effects. This new insight led to efforts in skin microbiota manipulation, such as the use of C. acnes strains as probiotic options to treat skin disorders.

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Section: Prostate Pathologiesmentioning

confidence: 99%

A Janus-Faced Bacterium: Host-Beneficial and -Detrimental Roles of Cutibacterium acnes

et al. 2021

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“…In all samples a contamination control strategy was implemented in keeping with the RIDE checklist as proposed by Eisenhofer et al 18 , incorporating aseptic techniques and a variety of negative controls from different stages of the sample-to-sequence data process. Retrospective contamination assessment and removal based on sequencing data from negative controls was also performed following published guidelines 19 .…”

Section: Contamination Controlmentioning

confidence: 99%

Non-specific amplification of human DNA is a major challenge for 16S rRNA gene sequence analysis

Walker

Barrett

Hogan

et al. 2020

Sci Rep

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The targeted sequencing of the 16S rRNA gene is one of the most frequently employed techniques in the field of microbial ecology, with the bacterial communities of a wide variety of niches in the human body have been characterised in this way. This is performed by targeting one or more hypervariable (V) regions within the 16S rRNA gene in order to produce an amplicon suitable in size for next generation sequencing. To date, all technical research has focused on the ability of different V regions to accurately resolve the composition of bacterial communities. We present here an underreported artefact associated with 16S rRNA gene sequencing, namely the off-target amplification of human DNA. By analysing 16S rRNA gene sequencing data from a selection of human sites we highlighted samples susceptible to this off-target amplification when using the popular primer pair targeting the V3–V4 region of the gene. The most severely affected sample type identified (breast tumour samples) were then re-analysed using the V1–V2 primer set, showing considerable reduction in off target amplification. Our data indicate that human biopsy samples should preferably be amplified using primers targeting the V1–V2 region. It is shown here that these primers result in on average 80% less human genome aligning reads, allowing for more statistically significant analysis of the bacterial communities residing in these samples.

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“…SourceTracker (v1.0) 15 indicated low-to-moderate levels of contamination, which was subsequently removed with Decontam (v1.0.0) 16 (Fig. 1 ), per published guidelines 9 . For only four samples, more than half the sequencing data comprised contaminants (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…However, these findings are based on microbiome data drawn from tissues that were collected for The Cancer Genome Atlas (TCGA) project. These specimens are potentially unsuitable for analysis of microbial DNA, due to a high likelihood of contamination, a lack of negative controls, and DNA extraction techniques that are incompatible with bacterial cells 9 . While robust bioinformatic contamination control was applied to these microbiome data, no method exists that can decontaminate samples completely, in silico.…”

Section: Introductionmentioning

confidence: 99%

Biopsy bacterial signature can predict patient tissue malignancy

Hogan

Eckenberger

Narayanen

et al. 2021

Sci Rep

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Considerable recent research has indicated the presence of bacteria in a variety of human tumours and matched normal tissue. Rather than focusing on further identification of bacteria within tumour samples, we reversed the hypothesis to query if establishing the bacterial profile of a tissue biopsy could reveal its histology / malignancy status. The aim of the present study was therefore to differentiate between malignant and non-malignant fresh breast biopsy specimens, collected specifically for this purpose, based on bacterial sequence data alone. Fresh tissue biopsies were obtained from breast cancer patients and subjected to 16S rRNA gene sequencing. Progressive microbiological and bioinformatic contamination control practices were imparted at all points of specimen handling and bioinformatic manipulation. Differences in breast tumour and matched normal tissues were probed using a variety of statistical and machine-learning-based strategies. Breast tumour and matched normal tissue microbiome profiles proved sufficiently different to indicate that a classification strategy using bacterial biomarkers could be effective. Leave-one-out cross-validation of the predictive model confirmed the ability to identify malignant breast tissue from its bacterial signature with 84.78% accuracy, with a corresponding area under the receiver operating characteristic curve of 0.888. This study provides proof-of-concept data, from fit-for-purpose study material, on the potential to use the bacterial signature of tissue biopsies to identify their malignancy status.

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Sequence-Based Characterization of Intratumoral Bacteria—A Guide to Best Practice

Cited by 43 publications

References 57 publications

A Janus-Faced Bacterium: Host-Beneficial and -Detrimental Roles of Cutibacterium acnes

A Janus-Faced Bacterium: Host-Beneficial and -Detrimental Roles of Cutibacterium acnes

Non-specific amplification of human DNA is a major challenge for 16S rRNA gene sequence analysis

Biopsy bacterial signature can predict patient tissue malignancy

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