A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota

Ederveen, Thomas H. A.; Smits, Jos P.H.; Hajo, Karima; Schalkwijk, Saskia van; Kouwenhoven, T.; Lukovac, Sabina; Wels, Michiel; Bogaard, Ellen H. van den; Schalkwijk, Joost; Boekhorst, Jos; Zeeuwen, Patrick L.J.M.; Hijum, Sacha A. F. T. van

doi:10.1038/s41598-019-56065-y

Cited by 13 publications

(21 citation statements)

References 47 publications

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“…classified in this study could be neither S. aureus nor S. epidermidis . It is of interest to find out the exact species of staphylococci using the single locus sequence typing method (Ederveen et al, 2019) to elucidate the relationship between Staphylococcus spp. and RPI in greater detail.…”

Section: Discussionmentioning

confidence: 99%

Skin Physiology and its Microbiome as Factors Associated with the Recurrence of Pressure Injuries

Shibata

Ogai

Ogura

et al. 2020

Biological Research For Nursing

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Background: Preventing recurrent pressure injuries (RPIs) is one of the important challenges faced in healthcare, but the risk factors of RPIs have not been fully revealed. This study aims to explore factors associated with RPIs, by focusing on skin physiology and its microbiome as local factors crucial for the health of healed tissue after pressure injury healing. Methods: This prospective observational study was conducted in a long-term care facility in Japan with patients whose PIs had healed within 1 month. Skin physiology was evaluated by stratum corneum (SC) hydration, pH, and transepidermal water loss. Skin bacteria was collected by tape stripping, followed by 16S ribosomal RNA-based metagenomics analysis. These parameters were evaluated every two weeks over a period of six weeks. Results: A total of 30 patients were included in this study, and 8 patients (26.7%) had an RPI within 6 weeks. In this study, significantly lower SC hydration and a higher rate of Staphylococcus species on the healed site were found in the RPI group. Discussion: A high rate of RPIs (about one in four) points out the necessity of a further care strategy on the healed PIs. Lower skin hydration and/or the increase in Staphylococcus bacteria may have a potential to be used as a biomarker for the prediction of RPIs, or may be an intervention point for the prevention of RPIs by, for example, skin cleansing with moisturizing care.

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Section: Discussionmentioning

confidence: 99%

Skin Physiology and its Microbiome as Factors Associated with the Recurrence of Pressure Injuries

Shibata

Ogai

Ogura

et al. 2020

Biological Research For Nursing

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“…who use an alternative gene to specifically type Cutibacterium acnes species in high resolution. For more information on the use of alternative bacterial marker genes, we refer to our recently published generic workflow for discovery and analysis of single‐locus sequence typing (SLST) marker genes 4 . Please note that a marker gene in the context of bacterial MGS should not be confused with marker genes in the context of molecular cloning, where the term “marker gene” has been adopted for genes used to indicate successful genome editing.…”

Section: Mgsmentioning

confidence: 99%

“…Recently, it was reported that coal tar treatment of AD lesions induces AMP production via canonical aryl hydrocarbon receptor (AHR) signaling 56 . By application of a novel SLST MGS method, 4 a shift in microbiota composition toward that of healthy controls was observed, which suggests that restoring AMP levels in AD skin via AHR‐dependent transcription regulation can be beneficial by creating an (anti)microbial milieu that is less prone to infection and inflammation. However, more studies are required to address the causal relation between AMP profiles and their effect on the cutaneous microbiota composition of AD skin.…”

Section: Admentioning

confidence: 99%

Skin microbiota in health and disease: From sequencing to biology

Ederveen

Smits

Boekhorst

et al. 2020

The Journal of Dermatology

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Microbiota live in a closely regulated interaction with their environment, and vice versa. The presence and absence of microbial entities is greatly influenced by features of the niche in which they thrive. Characteristic of this phenomenon is that different human skin sites harbor niche-specific communities of microbes. Microbial diversity is considerable, and the current challenge lies in determining which microbes and (corresponding) functionality are of importance to a given ecological niche. Furthermore, as there is increasing evidence of microbial involvement in health and disease, the need arises to fundamentally understand microbiome processes for application in health care, nutrition and personal care products (e.g. diet, cosmetics, probiotics). This review provides a current overview of state-of-the-art sequencing-based techniques and corresponding data analysis methodology for profiling of complex microbial communities. Furthermore, we also summarize the existing knowledge regarding cutaneous microbiota and their human host for a wide range of skin diseases.

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“…The tuf gene, or rather fragments thereof, is also used as a target for analysing mixed staphylococcal communities with NGS methods, hereafter referred to as amplicon NGS [42][43][44][45]. Furthermore, the staphylococcal rpsK gene that encodes the 30S ribosomal protein S11 was recently proposed for amplicon NGS [46].…”

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confidence: 99%

“…Two tested amplicon NGS schemes target different tuf gene fragments; one was developed by Martineau et al [41] and the other one by Ahle et al [47], designated here tuf1 and tuf2 scheme, respectively. The third tested scheme, designated rpsK scheme, targets a fragment of the rpsK gene and was developed by Ederveen et al [46]. Lastly, the three amplicon NGS schemes were tested on skin swab samples obtained from healthy volunteers.…”

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confidence: 99%

Comparison of three amplicon sequencing approaches to determine staphylococcal populations on human skin

et al. 2021

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Background Staphylococci are important members of the human skin microbiome. Many staphylococcal species and strains are commensals of the healthy skin microbiota, while few play essential roles in skin diseases such as atopic dermatitis. To study the involvement of staphylococci in health and disease, it is essential to determine staphylococcal populations in skin samples beyond the genus and species level. Culture-independent approaches such as amplicon next-generation sequencing (NGS) are time- and cost-effective options. However, their suitability depends on the power of resolution. Results Here we compare three amplicon NGS schemes that rely on different targets within the genes tuf and rpsK, designated tuf1, tuf2 and rpsK schemes. The schemes were tested on mock communities and on human skin samples. To obtain skin samples and build mock communities, skin swab samples of healthy volunteers were taken. In total, 254 staphylococcal strains were isolated and identified to the species level by MALDI-TOF mass spectrometry. A subset of ten strains belonging to different staphylococcal species were genome-sequenced. Two mock communities with nine and eighteen strains, respectively, as well as eight randomly selected skin samples were analysed with the three amplicon NGS methods. Our results imply that all three methods are suitable for species-level determination of staphylococcal populations. However, the novel tuf2-NGS scheme was superior in resolution power. It unambiguously allowed identification of Staphylococcus saccharolyticus and distinguish phylogenetically distinct clusters of Staphylococcus epidermidis. Conclusions Powerful amplicon NGS approaches for the detection and relative quantification of staphylococci in human samples exist that can resolve populations to the species and, to some extent, to the subspecies level. Our study highlights strengths, weaknesses and pitfalls of three currently available amplicon NGS approaches to determine staphylococcal populations. Applied to the analysis of healthy and diseased skin, these approaches can be useful to attribute host-beneficial and -detrimental roles to skin-resident staphylococcal species and subspecies.

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A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota

Cited by 13 publications

References 47 publications

Skin Physiology and its Microbiome as Factors Associated with the Recurrence of Pressure Injuries

Skin Physiology and its Microbiome as Factors Associated with the Recurrence of Pressure Injuries

Skin microbiota in health and disease: From sequencing to biology

Comparison of three amplicon sequencing approaches to determine staphylococcal populations on human skin

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