Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing

Mollerup, Sarah; Friis-Nielsen, Jens; Vinner, Lasse; Hansen, Thomas Arn; Richter, Stine Raith; Fridholm, Helena; Herrera, José Alejandro Romero; Lund, Ole; Brunak, Søren; Izarzugaza, Jose M. G.; Mourier, Tobias; Nielsen, Lars Peter; Hansen, Anders J.

doi:10.1128/jcm.02723-15

Cited by 89 publications

(72 citation statements)

References 50 publications

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“…Next, we investigated whether specific bacterial taxa that have previously been reported to be likely contaminants are present in our data set. Following read-based analyses, we found that our samples were dominated by Cutibacterium (Propionibacterium) acnes, which is abundant on human skin (Byrd et al, 2018) and a known contaminant of high-throughput sequencing data (Lusk, 2014;Mollerup et al, 2016). We therefore investigated the distribution of sequence identity between our C. acnes reads and the C. acnes reference genomes, with the expectation that human or laboratory contaminants would show high (close to 100) percentage identity, whereas killer whale-derived C. acnes would be more divergent.…”

Section: Known Bacterial Contaminantsmentioning

confidence: 97%

Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin

et al. 2018

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Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.

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Section: Known Bacterial Contaminantsmentioning

confidence: 97%

Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin

et al. 2018

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“…Besides the problem posed by the human DNA, also external bacterial contamination has to be considered before defining a microbial-disease causation. [52,53] The choice of the DNA extraction method is similarly important. Frequently, commercially available kits are used with popular choices being the Qiagen DNA Extraction Kit (Qiagen GmbH, Hilden, Germany), [12,47] the MO BIO PowerSoil DNA Isolation Kit (MoBio Laboratories, Inc., Carlsbad, CA) [5,17,54] or the MO BIO Ultraclean…”

Section: Sample Collection and Dna Extraction Proceduresmentioning

confidence: 99%

Experimental metagenomics and ribosomal profiling of the human skin microbiome

Ferretti

Farina

Cristofolini

et al. 2017

Experimental Dermatology

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The skin is the largest organ in the human body, and it is populated by a large diversity of microbes, most of which are co-evolved with the host and live in symbiotic harmony.There is increasing evidence that the skin microbiome plays a crucial role in the defense against pathogens, immune system training and homoeostasis, and microbiome perturbations have been associated with pathological skin conditions. Studying the skin resident microbial community is thus essential to better understand the microbiome-host crosstalk and to associate its specific configurations with cutaneous diseases. Several community profiling approaches have proved successful in unravelling the composition of the skin microbiome and overcome the limitations of cultivation-based assays, but these tools remain largely inaccessible to the clinical and medical dermatology communities. The study of the skin microbiome is also characterized by specific technical challenges, such as the low amount of microbial biomass and the extensive human DNA contamination. Here, we review the available community profiling approaches to study the skin microbiome, specifically focusing on the practical experimental and analytical tools necessary to generate and analyse skin microbiome data. We describe all the steps from the initial samples collection to the final data interpretation, with the goal of enabling clinicians and researchers who are not familiar with the microbiome field to perform skin profiling experiments. K E Y W O R D Smetagenomics, next generation sequencing, profiling, ribosomal, skin microbiome, skin microbiome, metagenomics, ribosomal profiling

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“…For confirmation of this hypothesis, healthy donors need to be recruited from the same population as the GC patients. P. acnes has been proposed as a possible contaminant of many experiments [Mollerup et al 2016]. That does not mean we need to discard the bacterium altogether, notably not if it shows significant increase in tumor sample locations as in data sets SRP172818 and SRP128749, but it could mean its baseline presence is overestimated and hence its status as a gastric mucosa commensal [Delgado et al 2011].…”

Section: Discussionmentioning

confidence: 99%

The Presence of Periodontal Pathogens in Gastric Cancer

Leeuw¹,

Duval²

2020

Preprint

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BackgroundThe microbiome is thought to play a role in the development of gastric cancer (GC). Several studies have put forward putatively carcinogenic species in addition to Helicobacter pylori, but are not in perfect alignment, possibly due to variable parameters in the experiments, including downstream processing. Meta-analyses have not been published so far, so there is lack in clinical guidance beyond H. pylori eradication therapy.MethodsHere, we analysed gastric mucosa samples from nine public data sets, including GC samples. Using both unsupervised and supervised learning, we defined fine grain bacterial networks of gastric mucosa and identified species associated with tumor status of samples.ResultsWe found anatomic locations and cohort regions among the possible factors leading to the observation of study specific gastric microbiomes. Despite this variability, the periodontal species Fusobacterium nucleatum, Parvimonas micra and Peptostreptococcus stomatis were found in association with tumor status in several datasets. The three species were predicted to be in interaction by ecological network analysis and also formed the intersection of tumor associated species between four GC data sets and five colorectal cancer (CRC) data sets we reanalyzed. We formulated a probiotic composition putatively competing with the GC pathogen spectrum, from correlation analysis in a large superset of gut samples (n=17,800) from clinical- and crowd-sourced studies.ImplicationsThe overlapping bacterial pathogen spectrum between two gastrointestinal tumor types, GC and CRC, has implications for etiology, treatment and prevention. In vitro testing results reported in literature suggest H. pylori eradication treatment should be efficient against the GC pathogen spectrum, yet the existence of an upstream periodontal reservoir is of concern. To address this, we propose longer term use of the formulated probiotics composition.

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Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing

Cited by 89 publications

References 50 publications

Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin

Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin

Experimental metagenomics and ribosomal profiling of the human skin microbiome

The Presence of Periodontal Pathogens in Gastric Cancer

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