The human scalp is an important prerequisite for healthy hair, comparable to the importance of an agricultural soil for healthy plant growth. Consequently, scalp care is gaining more and more importance for the field of “crown care”. This new beauty trend is about everything that makes head, scalp and hair more beautiful, healthier and more resistant , an area that includes scalp microbiome.
What is the scalp microbiome?
The scalp microbiota is a moderately diverse and dense (up 106 colony forming units per cm2) microbial community inhabiting the human scalp [2, 3]. It comprises mostly Gram-positive bacterial genera (such as staphylococci, cutibacteria, corynebacteria) and yeasts (Malassezia species). Per definition, multicellular organisms such as Demodex mites are not counted among the scalp microbiota. Similar to other skin sites, an imbalanced (dysbiotic) scalp microbial community composition is often associated with cosmetic problems and/or more severe disease states of the scalp, however, whether these deviations are cause or effect of the disorders is far from being understood .
Ask not what the scalp microbiome is, but what it does
My last TSLOS contribution dealing with the human scalp microbiota and its relation to scalp health was two years ago . I wished at the time that there were more studies that focused on the functionality of the scalp microbiota and its relation to scalp health, rather than just comparing the composition (species inventory) under different scalp health conditions. In plain words: Instead of simply asking “Who is there?”, a researcher should rather ask “What are they doing?”. To better understand what the scalp microbiota is actually doing, studies using technologies such as metagenomics, metatranscriptomics and/or metabonomics [for definitions see ) are needed, allowing insight into the genetic potential, gene expression and/or metabolite production of the microbial communities residing on the human scalp. What has happened since then?
How much research is there?
From 2021 until today (10.04.2023), the pubmed database lists 24 papers dealing with “human scalp AND microbiota” and 34 papers about “human scalp AND microbiome”. Compared to “human gut AND microbiome” with 14891 papers over the same period, this is not much. “Human scalp AND metagenome” yielded 5 hits, “human scalp AND metatranscriptome” no hits, and “human scalp AND metabonome” 3 hits. In comparison, “human gut AND metagenome” yielded 1703 hits. Clearly, functional human scalp microbiota/microbiome research is still rare, which is a bit disappointing.
What the research says
Nevertheless, let´s have a closer look on the 5 recent studies dealing with “Human scalp AND metagenome” published between 2021 and today. Metagenomic analyses are based on sequencing the total microbial DNA from a given habitat, without the need for PCR-amplification. This is a clear advantage, because PCR amplification is well known to introduce significant bias into the ratios of the analyzed genes compared to the ratio in the underlying sample . Metagenomic sequence data, mostly obtained by so-called shotgun sequencing, not only allow statements to be made about the identity and relative abundance of the microorganisms present, but also about their genetic potential, thereby delivering functional information .
Coconut oil and the benefits to scalp microbiome
One of the 5 papers is the landmark study by Saxena et al. on the influence of coconut oil on the scalp metagenome , that I already discussed previously . Unfortunately it represents the only recent metagenomic study that deals with the human scalp from a cosmetic point of view and also discusses functional aspects of the scalp microbiota. The authors could nicely show that coconut oil treatment increased the relative abundance of Cutibacterium acnes and Malassezia globosa in the samples from dandruff probands, accompanied by a relative decrease in fungal pathogenesis pathways and an increase in healthy-scalp-related bacterial pathways, such as biotin metabolism.
Skin microbiome as a new therapeutic target
Two other studies at least analyzed microbial DNA sampled from the human scalp without PCR-amplification. Tham et al.  investigated the microbial community structure from different skin areas (including scalp) of patients suffering from different forms of congenital ichtyosis, a rare genetic keratinizing disorder, and detected ichtyosis-subtype-specific patterns of microbial community composition. They assumed that the immunological characteristics observed with ichtyosis patients might represent a response to the altered microbial colonization, suggesting the skin microbiota as a new therapeutic target. Unfortunately, the authors limit themselves to report relative abundances of microbial taxa and do not provide data on potential microbial functionalities (I hope they just reserved it for follow-up publications!).
Lasers prove why different parts of hair follicles should be treated separately
In a pilot study, Lousada et al.  used laser capture microdissection to separate human hair follicles sampled from the scalps of three individuals into three anatomically distinct (lower, middle, upper) regions. Although the ratios of the relatively most abundant bacterial genera were largely similar, the authors describe region-specific differences in alpha-diversity, which they want to confirm using larger sample numbers. They also report that the amount of sampled DNA obtained from 5 sections per individual, respectively, was sufficient to sequence bacterial 16S rRNA genes without prior PCR-amplification. Notably, besides increasing the number of sampled individuals, the authors aim to couple their new technological approach to techniques such as rRNA-based fluorescence in-situ hybridization (FISH) or 16S rRNA (not 16S rRNA-gene!) sequencing to discriminate dead from live/active bacteria of interest. The authors stress that region-specific microbiota analyses are needed, as different diseases affect different regions of the hair follicle and therefore might require region-targeted therapies.
The scalp microbiome gut connection and hair loss
In a narrative review , Sánchez-Pellicer et al. aim to provide links between the human microbiome of skin and gut and the pathogenesis of Alopecia areata (spot baldness), i.e. a believed autoimmune disease causing hair loss, particularly at head and face. The many studies they present only comprise a single metagenomic study, in which stool samples from affected children were analyzed. Patients with Alopecia areata displayed lower relative abundances of a single species (Ruminococcus bicisculans), while overall, microbial community composition was strikingly similar between patients and control group. However, the relative abundances of 20 functional genes showed significant differences, suggesting that functional differences rather than structural differences might characterize the gut microbiota of the investigated patients. A strong argument for more metagenomics analyses.
Forensic scientists could use your scalp microbiome to identify you
Finally, Graham et al.  could show that the viral metagenome, sampled from the hands and the scalp of probands, might be used for human identification purposes in forensic sciences. They sampled 42 individuals over a period of 6 months and found 59 viral biomarker sequences that significantly different between individuals and were stable over time.
Why there isn’t more research into what the scalp microbiome does
It seems fair to ask why progress in functional scalp analyses is still quite slow. Some assumptions: While structural microbiota analyses (metataxonomic analyses), such as 16S rRNA gene sequencing, are well-established since decades, functional microbiome analyses are more complex and less standardized regarding workflow, data analysis and interpretation, and (therefore) also more expensive. In turn, compared to sequencing-based analyses, metabonomic analyses require totally different, expensive and sophisticated equipment and knowledge, particularly in the field of mass spectrometry. Finally, metataxonomic analyses are usually PCR-based, while functional analyses lack any significant amplification step, therefore requiring sufficient sample material (genomic DNA, mRNA, metabolites). Unfortunately, with respect to microbial biomass and in comparison to the intestinal tract, the scalp rather represents a low-biomass habitat. In addition, also based on my own experience, microbial samples from the human scalp usually contain significant amounts of human and/or other non-microbial eukaryotic DNA/RNA, which have to be removed during an analysis and lower the amount of microbial sequences, for instance in the case of metagenomics analyses.
Nevertheless, the few presented studies give hope that these obstacles can be met and that at least metagenomic scalp research is progressing, slowly but surely.
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Measuring and mitigating PCR bias in microbiota datasets. PLoS Comput Biol. 17(7):e1009113. doi: 10.1371/journal.pcbi.1009113 Zhang L, Chen F, Zeng Z, Xu M, Sun F, Yang L, Bi X, Lin Y, Gao Y, Hao H, Yi W, Li M, Xie Y (2021). Advances in Metagenomics and Its Application in Environmental Microorganisms. Front Microbiol. 12:766364. doi: 10.3389/fmicb.2021.766364 Saxena R, Mittal P, Clavaud C, Dhakan DB, Roy N, Breton L, Misra N, Sharma VK (2021).
Longitudinal study of the scalp microbiome suggests coconut oil to enrich healthy scalp commensals. Sci Rep. 11(1):7220. doi: 10.1038/s41598-021-86454-1 Tham KC, Lefferdink R, Duan K, Lim SS, Wong XFCC, Ibler E, Wu B, Abu-Zayed H, Rangel SM, Del Duca E, Chowdhury M, Chima M, Kim HJ, Lee B, Guttman-Yassky E, Paller AS, Common JEA. (2022). Distinct skin microbiome community structures in congenital ichthyosis. Br J Dermatol. 2022 Oct;187(4):557-570. doi: 10.1111/bjd.21687 Lousada MB, Edelkamp J, Lachnit T, Fehrholz M, Jimenez F, Paus R (2023).
Laser capture microdissection as a method for investigating the human hair follicle microbiome reveals region-specific differences in the bacteriome profile. BMC Res Notes 16(1):29. doi: 10.1186/s13104-023-06302-5. Sánchez-Pellicer P, Navarro-Moratalla L, Núñez-Delegido E, Agüera-Santos J, Navarro-López V (2022). How Our Microbiome Influences the Pathogenesis of Alopecia Areata. Genes (Basel) 13(10):1860. doi: 10.3390/genes13101860.  Graham EH, Clarke JL, Fernando SC, Herr JR, Adamowicz MS (2022). The application of the skin virome for human identification. Forensic Sci Int Genet 57:102662. doi: 10.1016/j.fsigen.2022.102662.