A review of next generation sequencing technologies used in the evaluation of the skin microbiome: what a time to be alive

Sandhu, Simran; Pourang, Aunna; Sivamani, Raja K

doi:10.5070/d3257044797

Cited by 13 publications

(15 citation statements)

References 28 publications

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“…Microbiome sequence processing was carried out in three steps: preprocessing, clustering similar sequences to obtain Operational Taxonomic Units (OTUs), and annotating the OTU sequences ( Sandhu, Pourang & Sivamani, 2019 ). The raw FASTQ files were filtered and trimmed at Q score 30 to remove low-quality reads and PCR-generated chimeric sequences.…”

Section: Methodsmentioning

confidence: 99%

Skin microbiota diversity among genetically unrelated individuals of Indian origin

Potbhare

RaviKumar

Munukka

et al. 2022

PeerJ

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Background Human skin harbors complex transient and resident microbial communities that show intra- & inter-individual variation due to various environmental and host-associated factors such as skin site, diet, age, gender, genetics, or the type and use of cosmetics. This variation remains largely uncharacterized in the Indian population; hence, the present study aims to characterize the variation in skin microbiota among individuals of Indian origin and quantify associations with age, diet, and geography. Methods Axillary sweat samples from genetically unrelated individuals (N = 58) residing in the three geographical locations of Maharashtra, India, were collected using a sterile cotton swab. Bacterial DNA was extracted using a standard protocol and checked for quality. Variable regions (V3–V4) of the 16S rRNA gene were sequenced using the Illumina platform. We used standard methods from microbiota bioinformatics, including alpha and beta diversity, community typing, and differential abundance, to quantify the association of skin microbiota with age, diet, and geographical location. Results Our study indicated the prevalence of phyla- Firmicutes, Proteobacteria, and Actinobacteria, consistent with previous reports on skin microbiota composition of the world population level. The alpha diversity (Shannon index) was significantly associated with the age group (Kruskal–Wallis test, p = 0.02), but not with geography (p = 0.62) or diet (p = 0.74). The overall skin microbiota community composition was significantly associated with geographical location based on Community State Types (CST) analysis and PERMANOVA (R2 = 0.07, p = 0.01). Differential abundance analysis at the genus level indicated a distinctively high abundance of Staphylococcus and Corynebacterium among individuals of the Pune district. Pseudomonas and Anaerococcus were abundant in individuals from Ahmednagar whereas, Paenibacillus, Geobacillus, Virgibacillus, Jeotgalicoccus, Pullulanibacillus, Delsulfosporomusa, Citinovibrio, and Calditerricola were abundant in individuals from Nashik district. Conclusion Our work provides one of the first characterizations of skin microbiota variation in different sub-populations in India. The analysis quantifies the level of individuality, as contrasted to the other factors of age, geography, and diet, thus helping to evaluate the applicability of skin microbiota profiles as a potential biomarker to stratify individuals.

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Section: Methodsmentioning

confidence: 99%

Skin microbiota diversity among genetically unrelated individuals of Indian origin

Potbhare

RaviKumar

Munukka

et al. 2022

PeerJ

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“…Bacterial rRNA depletion in complex samples can be challenging [ 72 ], and insufficient depletion leads to a high proportion of rRNA reads, which does not provide information on the functional activity of the microbiome. Other challenges include the adequate recovery of RNA from low-biomass skin samples and the potential for a high level of host RNA that effectively diminishes the recovery of microbial mRNA signals, requiring higher sequencing depths to overcome these obstacles [ 73 ]. Different sources of functional information can be used to assign annotation to reads, including, for example, Pfam [ 74 ], the Kyoto Encyclopedia of Genes and Genomes (KEGG) [ 75 ], Clusters of Orthologous Genes (COG) [ 76 ], and Swiss-Prot [ 77 ].…”

Section: Ongoing and Proposed Approaches To Study The Skin Microbiomementioning

confidence: 99%

The Skin Microbiome: Current Techniques, Challenges, and Future Directions

Santiago-Rodríguez

François²,

Macklaim

et al. 2023

Microorganisms

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Skin acts as a barrier that promotes the colonization of bacteria, fungi, archaea, and viruses whose membership and function may differ depending on the various specialized niches or micro-environments of the skin. The group of microorganisms inhabiting the skin, also known as the skin microbiome, offers protection against pathogens while actively interacting with the host’s immune system. Some members of the skin microbiome can also act as opportunistic pathogens. The skin microbiome is influenced by factors such as skin site, birth mode, genetics, environment, skin products, and skin conditions. The association(s) of the skin microbiome with health and disease has (have) been identified and characterized via culture-dependent and culture-independent methods. Culture-independent methods (such as high-throughput sequencing), in particular, have expanded our understanding of the skin microbiome’s role in maintaining health or promoting disease. However, the intrinsic challenges associated with the low microbial biomass and high host content of skin microbiome samples have hindered advancements in the field. In addition, the limitations of current collection and extraction methods and biases derived from sample preparation and analysis have significantly influenced the results and conclusions of many skin microbiome studies. Therefore, the present review discusses the technical challenges associated with the collection and processing of skin microbiome samples, the advantages and disadvantages of current sequencing approaches, and potential future areas of focus for the field.

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“…In contrast to above‐mentioned DNA‐based analyses, metatranscriptomics directly profiles actively transcribed genes within the community, which are a proxy for its active metabolism at the moment of sampling. The current limitations of this method are the low coverage of existing reference databases, increased effort in sample preparation, high risk of contamination and mRNA degradation, and high cost (Sandhu et al ., 2019 ). Despite these issues, metatranscriptomics has a high potential for elucidating the response of the skin microbiome to various conditions related to skin diseases.…”

Section: Current Analytical Approachesmentioning

confidence: 99%

“…This approach is highly adept at detecting small compounds produced by the microbiota and is often combined with amplicon or shotgun metagenomic sequencing. Similarly to metaproteomics, the high cost, laborious sample preparation and sparse reference databases have however limited its applications in microbiomes (Sandhu et al ., 2019 ). In skin microbial communities, metabolomics has been used to characterize biomarkers of healing wounds and their connections with specific bacteria in the associated microbial community (Ashrafi et al ., 2020 ).…”

Section: Current Analytical Approachesmentioning

confidence: 99%

Towards standardized and reproducible research in skin microbiomes

Ruuskanen

Vats

Potbhare

et al. 2022

Environmental Microbiology

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Summary Skin is a complex organ serving a critical role as a barrier and mediator of interactions between the human body and its environment. Recent studies have uncovered how resident microbial communities play a significant role in maintaining the normal healthy function of the skin and the immune system. In turn, numerous host‐associated and environmental factors influence these communities' composition and diversity across the cutaneous surface. In addition, specific compositional changes in skin microbiota have also been connected to the development of several chronic diseases. The current era of microbiome research is characterized by its reliance on large data sets of nucleotide sequences produced with high‐throughput sequencing of sample‐extracted DNA. These approaches have yielded new insights into many previously uncharacterized microbial communities. Application of standardized practices in the study of skin microbial communities could help us understand their complex structures, functional capacities, and health associations and increase the reproducibility of the research. Here, we overview the current research in human skin microbiomes and outline challenges specific to their study. Furthermore, we provide perspectives on recent advances in methods, analytical tools and applications of skin microbiomes in medicine and forensics.

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A review of next generation sequencing technologies used in the evaluation of the skin microbiome: what a time to be alive

Cited by 13 publications

References 28 publications

Skin microbiota diversity among genetically unrelated individuals of Indian origin

Skin microbiota diversity among genetically unrelated individuals of Indian origin

The Skin Microbiome: Current Techniques, Challenges, and Future Directions

Towards standardized and reproducible research in skin microbiomes

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