Towards standardized and reproducible research in skin microbiomes

Ruuskanen, Matti O.; Vats, Deepti; Potbhare, Renuka; RaviKumar, Ameeta; Munukka, Eveliina; Ashma, Richa; Lahti, Leo

doi:10.1111/1462-2920.15945

Cited by 8 publications

(13 citation statements)

References 220 publications

(301 reference statements)

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“…Thousands of microorganisms live on the skin including bacteria, fungi, and viruses. 117 , 118 Like microbiomes in the gut, skin microbiomes also play important roles in resisting the invasion of harmful substances. As the largest organ in the body, the skin hosts many beneficial microorganisms, forming a physical barrier against pathogens.…”

Section: Human Carcinogenic or Cancer‐promoting Microbiomesmentioning

confidence: 99%

Human microbiomes in cancer development and therapy

Xia

Liu

et al. 2023

MedComm

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Colonies formed by bacteria, archaea, fungi, and viral groups and their genomes, metabolites, and expressed proteins constitute complex human microbiomes. An increasing evidences showed that carcinogenesis and disease progression were link to microbiomes. Different organ sources, their microbial species, and their metabolites are different; the mechanisms of carcinogenic or procancerous are also different. Here, we summarize how microbiomes contribute to carcinogenesis and disease progression in cancers of the skin, mouth, esophagus, lung, gastrointestinal, genital, blood, and lymph malignancy. We also insight into the molecular mechanisms of triggering, promoting, or inhibiting carcinogenesis and disease progress induced by microbiomes or/and their secretions of bioactive metabolites. And then, the strategies of application of microorganisms in cancer treatment were discussed in detail. However, the mechanisms by which human microbiomes function are still poorly understood. The bidirectional interactions between microbiotas and endocrine systems need to be clarified. Probiotics and prebiotics are believed to benefit human health via a variety of mechanisms, in particular, in tumor inhibition. It is largely unknown how microbial agents cause cancer or how cancer progresses. We expect this review may open new perspectives on possible therapeutic approaches of patients with cancer.

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Section: Human Carcinogenic or Cancer‐promoting Microbiomesmentioning

confidence: 99%

Human microbiomes in cancer development and therapy

Xia

Liu

et al. 2023

MedComm

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“…Sampling mostly consists of swabbing (dry or moist), tape stripping, scraping and the taking of punch biopsies. Sample processing and storage needs to be standardized as much as possible to assure study reproducibility (Ruuskanen et al, 2022). Sample quality may differ depending on prior skin treatments (showering, swimming, bathing, sauna, exposure to direct sunlight etc.)…”

Section: In Vivo Testingmentioning

confidence: 99%

“…The need for validated NGS protocols, bioinformatics pipelines and microbial catalogues is huge to work with such sample kinds. Studies need to be sufficiently powered to allow statistically significant data interpretation and one needs to realize that markers such as skin lesion surface, bodily location, ethnicity, age of volunteer, (close) contacts with others and gender may be strongly confounding factors (Ruuskanen et al, 2022). Statistical analyses are essential and combined application of multiple validated tools is recommended.…”

Section: In Vivo Testingmentioning

confidence: 99%

“…These are early stage suggestions that require further international acceptation and standardization. We here have limited ourselves to bacterial microbiota not including important viruses, parasites and molds (Ruuskanen et al, 2022). We propose that in vitro and ex vivo analyses only provide basic knowledge and that such findings need to be substantiated by in vivo data.…”

Section: Quantifying Microbiome Friendlinessmentioning

confidence: 99%

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Being friendly to the skin microbiome: Experimental assessment

Belkum

Lisotto²,

Pirovano³

et al. 2023

Front. Microbiomes

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Both academia and dermatological and cosmetic industries have acknowledged that healthy skin microbiota contribute to overall skin integrity and well-being. This implies that formulations developed for personal care (skin, scalp, hair etc) or (medical and cosmetic) treatment need to be compatible with microbiota conservation or possibly even improvement. The various chemical and biological components and mixtures thereof intended for direct application to the skin should not extensively affect the qualitative and quantitative composition of the skin microbiota. A compound should promote beneficial microbes and inhibit pathogens. Compounds but also final products could be considered at least theoretically “microbiome friendly” while in some cases changes to the microbiota may even be considered beneficial. An important hurdle lies in the practical and methodological approaches to be used for defining microbiota inertia of compounds and formulations. Clear guidelines for assessing microbiome friendliness are lacking. We propose three testing concepts that may help to define microbiome friendliness based on the assessment of minimal microbiota perturbation and possibly elimination of potential pathogens. Methods to prove microbiome friendliness should ultimately be based upon (metagenomic rather than amplicon-based) next generation sequencing of naive versus compound- or final product-exposed skin microbiota in vivo, but preferably also including in vitro and ex vivo pre-screening methodologies to build an understanding of their consequences. As in many domains of microbiome research, the development of experimental process controls and internal standards, which are essentially lacking to date, should be taken as a future prerequisite. There is also a requirement from regulatory agencies to define and harmonize acceptance criteria.

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“…In one such study, the authors developed a CRISPR/Cas9 editing protocol for Bodo saltans , a free‐living kinetoplastid with tolerance to both marine and freshwater conditions and a close non‐parasitic relative of trypanosomatids (Gomaa et al ., 2022). Another review published in this issue of environmental microbiology tends to summarize the current state of research in human skin microbiome and outlines challenges specific to it (Ruuskanen et al ., 2022).…”

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confidence: 99%