Spatial and Environmental Variation of the Human Hair Microbiota

Sample collecting methods for bacterial community structure analysis of scalp hair: non-invasive swabbing versus intrusive hair shaft cutting

Human skin samples for microbiome analysis are traditionally collected using a non-invasive swabbing method. Here, we compared the differences in bacterial community structures on scalp hair and scalps with samples collected using non-invasive swabbing and cutting/removal of scalp hair in 12 individuals. Hair-related samples, such as hair shafts and hair swabs, had significantly higher alpha diversity than scalp swab samples, whereas there were no significant differences between hair shafts and hair swabs. The relative abundances of the three major phyla and five major operational taxonomic units were not significantly different between the hair shaft and hair swab samples. The principal coordinate analysis plots based on weighted UniFrac distances were grouped into two clusters: samples from hair-related areas and scalp swabs, and there were significant differences only between samples from hair-related areas and scalp swabs. In addition, a weighted UniFrac analysis revealed that the sampling site-based category was a statistical category but not a hair sampling method-based category. These results suggest that scalp hair bacteria collected using non-invasive swab sampling were comparable to those collected cutting/removal of scalp hair.

Exploring the role of the human microbiome in forensic identification: opportunities and challenges

Forensic microbiology is rapidly emerging as a novel tool for human identification. The human microbiome, comprising diverse microbial communities including fungi, bacteria, protozoa, and viruses, is unique to each individual, offering a new dimension to forensic investigations. While traditional identification methods primarily rely on DNA profiling and fingerprint analysis, they face limitations when complete DNA or fingerprints profiles are unattainable or degraded. In this context, the microbial signatures of the human skin microbiome present a promising alternative due to their resilience to environmental stresses and individual-specific composition. This review explores the potential of microbiome analysis in forensic human identification, evaluating its applications, advantages, limitations, and future prospects. The uniqueness of an individual's microbial community, particularly the skin microbiota, can provide distinctive biological markers for identification purposes, while technological advancements like 16 S rRNA sequencing and metagenomic shotgun sequencing are enhancing the specificity of microbial identification, enabling detailed analysis of these complex ecological communities. Despite these promising findings, current research has not yet achieved a level of identification probability that could establish microbial analysis as a stand-alone evidence tool. Therefore, it is presently considered ancillary to traditional methods, contributing to a more comprehensive biological profile of individuals.

Alterations in microbiome of COVID-19 patients and its impact on forensic investigations

The human microbiome is vital for maintaining human health and has garnered substantial attention in recent years, particularly in the context of the coronavirus disease 2019 (COVID-19) outbreak. Studies have underscored significant alterations in the microbiome of COVID-19 patients across various body niches, including the gut, respiratory tract, oral cavity, skin, and vagina. These changes manifest as shifts in microbiota composition, characterized by an increase in opportunistic pathogens and a decrease in beneficial commensal bacteria. Such microbiome transformations may play a pivotal role in influencing the course and severity of COVID-19, potentially contributing to the inflammatory response. This ongoing relationship between COVID-19 and the human microbiome serves as a compelling subject of research, underscoring the necessity for further investigations into the underlying mechanisms and their implications for patient health. Additionally, these alterations in the microbiome may have significant ramifications for forensic investigations, given the microbiome's potential in establishing individual characteristics. Consequently, changes in the microbiome could introduce a level of complexity into forensic determinations. As research progresses, a more profound understanding of the human microbiome within the context of COVID-19 may offer valuable insights into disease prevention, treatment strategies, and its potential applications in forensic science. Consequently, this paper aims to provide an overarching review of microbiome alterations due to COVID-19 and the associated impact on forensic applications, bridging the gap between the altered microbiome of COVID-19 patients and the challenges forensic investigations may encounter when analyzing this microbiome as a forensic biomarker.

Distribution of bacterial community structures on human scalp hair shaft in relation to scalp sites

Bacterial community structure on the human skin is specific to each individual and varies among different body sites. In this study, we investigated differences in bacterial community structure among 5 hair sampling sites and among 12 individuals. Significant differences were found between individuals in terms of alpha diversity and relative abundance of major bacterial phyla and genera, whereas no differences were found between hair sampling sites. The principal coordinate analysis plots of within-individual group tended to converge individually, whereas those of within-hair sampling site group did not cluster. In addition, weighted UniFrac analysis showed that the individual-based category was a statistically significant category but not the scalp hair sampling site-based category. These results suggest that the distribution of bacterial community structures on scalp hair shafts within individuals was relatively steady, even when the scalp hair sampling site was different.

The Future Is Now: Unraveling the Expanding Potential of Human (Necro)Microbiome in Forensic Investigations

The relevance of postmortem microbiological examinations has been controversial for decades, but the boom in advanced sequencing techniques over the last decade is increasingly demonstrating their usefulness, namely for the estimation of the postmortem interval. This comprehensive review aims to present the current knowledge about the human postmortem microbiome (the necrobiome), highlighting the main factors influencing this complex process and discussing the principal applications in the field of forensic sciences. Several limitations still hindering the implementation of forensic microbiology, such as small-scale studies, the lack of a universal/harmonized workflow for DNA extraction and sequencing technology, variability in the human microbiome, and limited access to human cadavers, are discussed. Future research in the field should focus on identifying stable biomarkers within the dominant Bacillota and Pseudomonadota phyla, which are prevalent during postmortem periods and for which standardization, method consolidation, and establishment of a forensic microbial bank are crucial for consistency and comparability. Given the complexity of identifying unique postmortem microbial signatures for robust databases, a promising future approach may involve deepening our understanding of specific bacterial species/strains that can serve as reliable postmortem interval indicators during the process of body decomposition. Microorganisms might have the potential to complement routine forensic tests in judicial processes, requiring robust investigations and machine-learning models to bridge knowledge gaps and adhere to Locard's principle of trace evidence.

MPrESS: An R-Package for Accurately Predicting Power for Comparisons of 16S rRNA Microbiome Taxa Distributions including Simulation by Dirichlet Mixture Modeling

Deep sequencing has revealed that the 16S rRNA gene composition of the human microbiome can vary between populations. However, when existing data are insufficient to address the desired study questions due to limited sample sizes, Dirichlet mixture modeling (DMM) can simulate 16S rRNA gene predictions from experimental microbiome data. We examined the extent to which simulated 16S rRNA gene microbiome data can accurately reflect the diversity within that identified from experimental data and calculate the power. Even when experimental and simulated datasets differed by less than 10%, simulation by DMM consistently overestimates power, except when using only highly discriminating taxa. Admixtures of DMM with experimental data performed poorly compared to pure simulation and did not show the same correlation with experimental data p-value and power values. While multiple replications of random sampling remain the favored method of determining the power, when the estimated sample size required to achieve a certain power exceeds the sample number, then simulated samples based on DMM can be used. We introduce an R-Package, MPrESS, to assist in power calculation and sample size estimation for a 16S rRNA gene microbiome dataset to detect a difference between populations. MPrESS can be downloaded from GitHub.

Laser capture microdissection as a method for investigating the human hair follicle microbiome reveals region-specific differences in the bacteriome profile

OBJECTIVE

Human hair follicles (HFs) are populated by a rich and diverse microbiome, traditionally evaluated by methods that inadvertently sample the skin microbiome and/or miss microbiota located in deeper HF regions. Thereby, these methods capture the human HF microbiome in a skewed and incomplete manner. This pilot study aimed to use laser-capture microdissection of human scalp HFs, coupled with 16S rRNA gene sequencing to sample the HF microbiome and overcome these methodological limitations.

RESULTS

HFs were laser-capture microdissected (LCM) into three anatomically distinct regions. All main known core HF bacterial colonisers, including Cutibacterium, Corynebacterium and Staphylococcus, were identified, in all three HF regions. Interestingly, region-specific variations in α-diversity and microbial abundance of the core microbiome genera and Reyranella were identified, suggestive of variations in microbiologically relevant microenvironment characteristics. This pilot study therefore shows that LCM-coupled with metagenomics is a powerful tool for analysing the microbiome of defined biological niches. Refining and complementing this method with broader metagenomic techniques will facilitate the mapping of dysbiotic events associated with HF diseases and targeted therapeutic interventions.

Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes

Studies of human microbiomes using new sequencing techniques have increasingly demonstrated that their ecologies are partly determined by the lifestyle and habits of individuals. As such, significant forensic information could be obtained from high throughput sequencing of the human microbiome. This approach, combined with multiple analytical techniques demonstrates that bacterial DNA can be used to uniquely identify an individual and to provide information about their life and behavioral patterns. However, the transformation of these findings into actionable forensic information, including the geolocation of the samples, remains limited by incomplete understanding of the effects of confounding factors and the paucity of diverse sequences. We obtained 16S rRNA sequences of stool and oral microbiomes collected from 206 young and healthy females from four globally diverse populations, in addition to supporting metadata, including dietary and medical information. Analysis of these microbiomes revealed detectable geolocation signals between the populations, even for populations living within the same city. Accounting for other lifestyle variables, such as diet and smoking, lessened but does not remove the geolocation signal.

Hair Microbiome Diversity within and across Primate Species

Primate hair and skin are substrates upon which social interactions occur and are host-pathogen interfaces. While human hair and skin microbiomes display body site specificity and immunological significance, little is known about the nonhuman primate (NHP) hair microbiome. Here, we collected hair samples (n = 158) from 8 body sites across 12 NHP species housed at three zoological institutions in the United States to examine the following: (1) the diversity and composition of the primate hair microbiome and (2) the factors predicting primate hair microbiome diversity and composition. If both environmental and evolutionary factors shape the microbiome, then we expect significant differences in microbiome diversity across host body sites, sexes, institutions, and species. We found our samples contained high abundances of gut-, respiratory-, and environment-associated microbiota. In addition, multiple factors predicted microbiome diversity and composition, although host species identity outweighed sex, body site, and institution as the strongest predictor. Our results suggest that hair microbial communities are affected by both evolutionary and environmental factors and are relatively similar across nonhuman primate body sites, which differs from the human condition. These findings have important implications for understanding the biology and conservation of wild and captive primates and the uniqueness of the human microbiome. IMPORTANCE We created the most comprehensive primate hair and skin data set to date, including data from 12 nonhuman primate species sampled from 8 body regions each. We find that the nonhuman primate hair microbiome is distinct from the human hair and skin microbiomes in that it is relatively uniform-as opposed to distinct-across body regions and is most abundant in gut-, environment-, and respiratory-associated microbiota rather than human skin-associated microbiota. Furthermore, we found that the nonhuman primate hair microbiome varies with host species identity, host sex, host environment, and host body site, with host species identity being the strongest predictor. This result demonstrates that nonhuman primate hair microbiome diversity varies with both evolutionary and environmental factors and within and across primate species. These findings have important implications for understanding the biology and conservation of wild and captive primates and the uniqueness of the human microbiome.

Antibiotic-producing Micrococcales govern the microbiome that inhabits the fur of two- and three-toed sloths

Sloths have a dense coat on which insects, algae, and fungi coexist in a symbiotic relationship. This complex ecosystem requires different levels of control, however, most of these mechanisms remain unknown. We investigated the bacterial communities inhabiting the hair of two- (Choloepus Hoffmani) and three-toed (Bradypus variegatus) sloths and evaluated their potential for producing antibiotic molecules capable of exerting control over the hair microbiota. The analysis of 16S rRNA amplicon sequence variants (ASVs) revealed that the communities in both host species are dominated by Actinobacteriota and Firmicutes. The most abundant genera were Brevibacterium, Kocuria/Rothia, Staphylococcus, Rubrobacter, Nesterenkonia, and Janibacter. Furthermore, we isolated nine strains of Brevibacterium and Rothia capable of producing substances that inhibited the growth of common mammalian pathogens. The analysis of the biosynthetic gene clusters (BCGs) of these nine isolates suggests that the pathogen-inhibitory activity could be mediated by the presence of siderophores, terpenes, beta-lactones, Type III polyketide synthases (T3PKS), ribosomally synthesized, and post-translationally modified peptides (RiPPs), non-alpha poly-amino acids (NAPAA) like e-Polylysin, ectoine or nonribosomal peptides (NRPs). Our data suggest that Micrococcales that inhabit sloth hair could have a role in controlling microbial populations in that habitat, improving our understanding of this highly complex ecosystem. This article is protected by copyright. All rights reserved.

Analysis of Microbial Communities: An Emerging Tool in Forensic Sciences

The objective of forensic sciences is to find clues in a crime scene in order to reconstruct the scenario. Classical samples include DNA or fingerprints, but both have inherent limitations and can be uninformative. Another type of sample has emerged recently in the form of the microbiome. Supported by the Human Microbiome Project, the characteristics of the microbial communities provide real potential in forensics. They are highly specific and can be used to differentiate and classify the originating body site of a human biological trace. Skin microbiota is also highly specific and different between individuals, leading to its possibility as an identification tool. By extension, the possibilities of the microbial communities to be deposited on everyday objects has also been explored. Other uses include the determination of the post-mortem interval or the analysis of soil communities. One challenge is that the microbiome changes over time and can be influenced by many environmental and lifestyle factors. This review offers an overview of the main methods and applications to demonstrate the benefit of the microbiome to provide forensically relevant information.

Aging Associated Changes in the Adult Human Skin Microbiome and the Host Factors That Affect Skin Microbiome Composition

Understanding changes in the skin microbiome and their relationship to host skin factors during aging remains largely unknown. To better understand this phenomenon, we collected samples for metagenomic and host skin factor analyses from forearm, buttock, and facial skin from 158 Caucasian females at 20-24, 30-34, 40-44, 50-54, 60-64, and 70-74 years of age. Metagenomics analysis was performed using 16S rRNA gene sequencing, while host sebocyte gland area, skin lipids, natural moisturizing factors (NMFs) and anti-microbial peptides (AMPs) measurements were also performed. These analyses demonstrated that skin bacterial diversity increased at all the skin sites with increasing age. Of the bacterial genera with average relative abundance of >1%, only Lactobacillus and Cutibacterium demonstrated a significant change (decrease) in abundance at all sampled skin sites with increasing age. Additional bacterial genera demonstrated significant age and site-specific changes in abundance. Analysis of sebocyte area, NMFs, lipids and AMPs demonstrated an age-related decrease in sebocyte area and increases in NMFs/AMPs/skin lipids, all which correlated with changes in specific bacterial genera. In conclusion, the human skin microbiome undergoes age-associated alterations that may reflect underlying age-related changes in cutaneous biology.

Usefulness of Microbiome for Forensic Geolocation: A Review

Forensic microbiomics is a promising tool for crime investigation. Geolocation, which connects an individual to a certain place or location by microbiota, has been fairly well studied in the literature, and several applications have been found. The aim of this review is to highlight the main findings in this field, including the current sample storage, DNA extraction, sequencing and data analysis techniques that are being used, and its potential applications in human trafficking and ancient DNA studies. Second, the challenges and limitations of forensic microbiomics and geolocation are emphasised, providing recommendations for the establishment of this tool in the forensic science community.

A Journey on the Skin Microbiome: Pitfalls and Opportunities

The human skin microbiota is essential for maintaining homeostasis and ensuring barrier functions. Over the years, the characterization of its composition and taxonomic diversity has reached outstanding goals, with more than 10 million bacterial genes collected and cataloged. Nevertheless, the study of the skin microbiota presents specific challenges that need to be addressed in study design. Benchmarking procedures and reproducible and robust analysis workflows for increasing comparability among studies are required. For various reasons and because of specific technical problems, these issues have been investigated in gut microbiota studies, but they have been largely overlooked for skin microbiota. After a short description of the skin microbiota, the review tackles methodological aspects and their pitfalls, covering NGS approaches and high throughput culture-based techniques. Recent insights into the "core" and "transient" types of skin microbiota and how the manipulation of these communities can prevent or combat skin diseases are also covered. Finally, this review includes an overview of the main dermatological diseases, the changes in the microbiota composition associated with them, and the recommended skin sampling procedures. The last section focuses on topical and oral probiotics to improve and maintain skin health, considering their possible applications for skin diseases.

Host factors that shape the bacterial community structure on scalp hair shaft

In this study, we performed 16S rRNA amplicon sequencing analysis of scalp hair shaft from 109 volunteers, who were surveyed using a questionnaire about daily scalp hair care, and employed multiple statistical analyses to elucidate the factors that contribute to the formation of bacterial community structures on scalp hair shaft. Scalp hair microbiota were found to be specific for each individual. Their microbiota were clearly divided into two clusters. Genus level richness of Pseudomonas (Ps) and Cutibacterium (Cu) contributed to the clusters. The clusters around Pseudomonas and Cutibacterium were named Ps-type and Cu-type, respectively. The host gender influenced the bacterial cell numbers of the major genera that included Cutibacterium, Lawsonella, Moraxella, and Staphylococcus on scalp hair shaft. In addition to host intrinsic factors, extrinsic factors such as hair styling and colouring affected the bacterial cell numbers of the major genera. These factors and chemical treatments, such as bleaching and perming, also affected the Ps-type to Cu-type ratios. These results suggest that bacterial community structures on scalp hair shaft are influenced by both intrinsic and extrinsic factors.

Characterizing Microbial Signatures on Sculptures and Paintings of Similar Provenance

The preservation of artwork challenges museums, collectors, and art enthusiasts. Currently, reducing moisture, adjusting the type of lighting, and preventing the formation of mold are primary methods to preserving and preventing deterioration. Other methods such as ones based in detailed knowledge of molecular biology such as microbial community characterization using polymerase chain reaction (PCR) and sequencing have yet to be explored. Such molecular biology approaches are essential to explore as some environmental bacteria are capable of oxidizing nonpolar chemical substances rich in hydrocarbons such as oil-based paints. Using 16S rDNA Illumina Sequencing, we demonstrate a novel finding that there are differing bacterial communities for artwork from roughly the same era when comparing paintings on wood, paintings on canvases, and sculptures made of stone and marble. We also demonstrate that there are specific genera such as Aeromonas known for having oxidase positive strains, present on paintings on wood and paintings on canvas that could potentially be responsible for deterioration and fading as such organisms produce water or hydrogen peroxide as a byproduct of cytochrome c oxidase activity. The advantages of these genomics-based approaches to characterizing the microbial population on deteriorating artwork provides immense potential by identifying potentially damaging species that may not be detected using conventional methods in addition to addressing challenges to identification, restoration, and preservation efforts.

Forensic Microbiome Database: A Tool for Forensic Geolocation Meta-Analysis Using Publicly Available 16S rRNA Microbiome Sequencing

The human microbiome has been proposed as a tool to investigate different forensic questions, including for the identification of multiple personal information. However, the fragmented state of the publicly available data has retarded the development of analysis techniques and, therefore, the implementation of microbiomes as a forensic tool. To address this, we introduce the forensic microbiome database (FMD), which is a collection of 16S rRNA data and associated metadata generated from publicly available data. The raw data was further normalized and processed using a pipeline to create a standardized data set for downstream analysis. We present a website allowing for the exploration of geolocation signals in the FMD. The website allows users to investigate the taxonomic differences between microbiomes harvested from different locations and to predict the geolocation of their data based on the FMD sequences. All the results are presented in dynamic graphics to allow for a rapid and intuitive investigation of the taxonomic distributions underpinning the geolocation signals and prediction between locations. Apart from the forensic aspect, the database also allows exploration and comparison of microbiome samples from different geolocation and between different body sites. The goal of the FMD is to provide the scientific and non-scientific communities with data and tools to explore the possibilities of microbiomes to answer forensic questions and serve as a model for any future such databases.

Randomized clinical trial of preoperative skin preparation with 2% chlorhexidine versus conventional hair shaving in percutaneous coronary intervention

BACKGROUND

Preoperative skin preparation is associated with surgical site infection (SSI). Traditional preoperative shaving fails to reduce the risk of SSI. The efficacy of 2% chlorhexidine for preoperative skin preparation in percutaneous coronary intervention (PCI) is sketchy. The aim of this trial was to evaluate whether preoperative skin preparation performed with chlorhexidine was not inferior to a conventional hair removal method.

METHODS

Seventy-eight patients undergoing PCI were randomized into 2 groups of 39 patients, receiving either single sterilization with 2% chlorhexidine or hair shaving respectively between July 2016 and October 2016. The primary endpoints were wound infection rate and bacterial counts. Secondary endpoints were rate of SSI and adverse effects of 2% chlorhexidine.

RESULTS

The results showed that 2% chlorhexidine significantly reduced the colonization of Staphylococcus aureus (P = .032), S epidermidis (P = .000), and miscellaneous bacteria (P = .244) in comparison with hair shaving, respectively. Redness in 24 hours after surgery was observed in 6 patients in the control group (15.4%) and 5 patients (12.8%) in 2% chlorhexidine group. There was no statistically significant difference in SSI rate between 2 skin preparations.

CONCLUSION

In PCI, preoperative skin preparation with 2% chlorhexidine was not inferior to conventional hair shaving in terms of the wound infection rate and SSI rate.

Impact of the Human Microbiome in Forensic Sciences: a Systematic Review

Numerous studies relate differences in microbial communities to human health and disease; however, little is known about microbial changes that occur postmortem or the possible applications of microbiome analysis in the field of forensic science. The aim of this review was to study the microbiome and its applications in forensic sciences and to determine the main lines of investigation that are emerging, as well as its possible contributions to the forensic field. A systematic review of the human microbiome in relation to forensic science was carried out by following PRISMA guidelines. This study sheds light on the role of microbiome research in the postmortem interval during the process of decomposition, identifying death caused by drowning or sudden death, locating the geographical location of death, establishing a connection between the human microbiome and personal items, sexual contact, and the identification of individuals. Actinomycetaceae, Bacteroidaceae, Alcaligenaceae, and Bacilli play an important role in determining the postmortem interval. Aeromonas can be used to determine the cause of death, and Corynebacterium or Helicobacter pylori can be used to ascertain personal identity or geographical location. Several studies point to a promising future for microbiome analysis in the different fields of forensic science, opening up an important new area of research.

Relationship between the bacterial community structures on human hair and scalp

In this study, we investigated and compared characteristics of the bacterial community structures on hair (scalp hair) and scalp in 18 individuals. Significant differences were found between the sites, in terms of cell density, alpha and beta diversity, and relative abundance of the phyla, Firmicutes and Proteobacteria, whereas no difference was found in relative abundance of the phylum Actinobacteria. Bacteria of the genus Cutibacterium showed similar relative abundance at both sites, whereas those of genus Pseudomonas were highly abundant on hair, and those of genus Staphylococcus were significantly lesser in abundance on hair than on scalp. Statistical correlations between the sites were high for the individual relative abundance of five major operational taxonomic units (OTUs). This suggests that the bacterial community structure on hair is composed of hair-specific genus, Pseudomonas, and skin-derived genera, Cutibacterium and Staphylococcus, and is distinguishable from other human skin microbiomes.

Malassezia and Staphylococcus dominate scalp microbiome for seborrheic dermatitis

Seborrheic dermatitis (SD) is a common disease of the human scalp that causes physical damage and psychological problems for patients. Studies have indicated that dysbiosis of the scalp microbiome results in SD. However, the specific fungal and bacterial microbiome changes related to SD remain elusive. To further investigate the fungal and bacterial microbiome changes associated with SD, we recruited 57 SD patients and 53 healthy individuals and explored their scalp microbiomes using next generation sequencing and the QIIME and LEfSe bioinformatics tools. Skin pH, sebum secretion, hydration, and trans-epidermal water loss (TWEL) were also measured at the scalp. We found no statistically significant differences between the normal and lesion sites in SD patients with different subtypes of dandruff and erythema. However, the fungal and bacterial microbiome could differentiate SD patients from healthy controls. The presence of Malassezia and Aspergillus was both found to be potential fungal biomarkers for SD, while Staphylococcus and Pseudomonas were found to be potential bacterial biomarkers. The fungal and bacterial microbiome were divided into three clusters through co-abundance analysis and their correlations with host factors indicated the interactions and potential cooperation and resistance between microbe communities and host. Our research showed the skin microbe dysbiosis of SD and highlighted specific microorganisms that may serve as potential biomarkers of SD. The etiology of SD is multi-pathogenetic-dependent on the linkage of several microbes with host. Scalp microbiome homeostasis could be a promising new target in the risk assessment, prevention, and treatment of SD disease.