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Austin GI, Korem T. Planning and Analyzing a Low-Biomass Microbiome Study: A Data Analysis Perspective. J Infect Dis 2024:jiae378. [PMID: 39189314 DOI: 10.1093/infdis/jiae378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Indexed: 08/28/2024] Open
Abstract
As investigations of low-biomass microbial communities have become more common, so too has the recognition of major challenges affecting these analyses. These challenges have been shown to compromise biological conclusions and have contributed to several controversies. Here, we review some of the most common and influential challenges in low-biomass microbiome research. We highlight key approaches to alleviate these potential pitfalls, combining experimental planning strategies and data analysis methods.
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Affiliation(s)
- George I Austin
- Department of Biomedical Informatics
- Program for Mathematical Genomics, Department of Systems Biology
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York
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Nwokorogu VC, Pillai S, San JE, Pillay C, Nyaga MM, Sabiu S. A metagenomic investigation of the faecal RNA virome structure of asymptomatic chickens obtained from a commercial farm in Durban, KwaZulu-Natal province, South Africa. BMC Genomics 2024; 25:629. [PMID: 38914944 PMCID: PMC11194887 DOI: 10.1186/s12864-024-10517-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 06/12/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Virome studies on birds, including chickens are relatively scarce, particularly from the African continent. Despite the continuous evolution of RNA viruses and severe losses recorded in poultry from seasonal viral outbreaks, the information on RNA virome composition is even scantier as a result of their highly unstable nature, genetic diversity, and difficulties associated with characterization. Also, information on factors that may modulate the occurrence of some viruses in birds is limited, particularly for domesticated birds. Viral metagenomics through advancements in sequencing technologies, has enabled the characterization of the entire virome of diverse host species using various samples. METHODS The complex RNA viral constituents present in 27 faecal samples of asymptomatic chickens from a South African farm collected at 3-time points from two independent seasons were determined, and the impact of the chicken's age and collection season on viral abundance and diversity was further investigated. The study utilized the non-invasive faecal sampling method, mRNA viral targeted enrichment steps, a whole transcriptome amplification strategy, Illumina sequencing, and bioinformatics tools. RESULTS The results obtained revealed a total of 48 viral species spanning across 11 orders, 15 families and 21 genera. Viral RNA families such as Coronaviridae, Picornaviridae, Reoviridae, Astroviridae, Caliciviridae, Picorbirnaviridae and Retroviridae were abundant, among which picornaviruses, demonstrated a 100% prevalence across the three age groups (2, 4 and 7 weeks) and two seasons (summer and winter) of the 27 faecal samples investigated. A further probe into the extent of variation between the different chicken groups investigated indicated that viral diversity and abundance were significantly influenced by age (P = 0.01099) and season (P = 0.00099) between chicken groups, while there was no effect on viral shedding within samples in a group (alpha diversity) for age (P = 0.146) and season (P = 0.242). CONCLUSION The presence of an exceedingly varied chicken RNA virome, encompassing avian, mammalian, fungal, and dietary-associated viruses, underscores the complexities inherent in comprehending the causation, dynamics, and interspecies transmission of RNA viruses within the investigated chicken population. Hence, chickens, even in the absence of discernible symptoms, can harbour viruses that may exhibit opportunistic, commensal, or pathogenic characteristics.
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Affiliation(s)
- Vivian C Nwokorogu
- Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Santhosh Pillai
- Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - James E San
- Nelson Mandela School of Medicine, KwaZulu-Natal Research Innovation and Sequencing platform unit, University of KwaZulu- Natal, 719 Umbilo Road, Durban, 4001, South Africa
| | - Charlene Pillay
- Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Martin M Nyaga
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa.
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Healy HG, Ehde A, Bartholow A, Kantor RS, Nelson KL. Responses of drinking water bulk and biofilm microbiota to elevated water age in bench-scale simulated distribution systems. NPJ Biofilms Microbiomes 2024; 10:7. [PMID: 38253591 PMCID: PMC10803812 DOI: 10.1038/s41522-023-00473-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 12/04/2023] [Indexed: 01/24/2024] Open
Abstract
Reductions in nonresidential water demand during the COVID-19 pandemic highlighted the importance of understanding how water age impacts drinking water quality and microbiota in piped distribution systems. Using benchtop model distribution systems, we aimed to characterize the impacts of elevated water age on microbiota in bulk water and pipe wall biofilms. Five replicate constant-flow reactors were fed with municipal chloraminated tap water for 6 months prior to building closures and 7 months after. After building closures, chloramine levels entering the reactors dropped; in the reactor bulk water and biofilms the mean cell counts and ATP concentrations increased over an order of magnitude while the detection of opportunistic pathogens remained low. Water age, and the corresponding physicochemical changes, strongly influenced microbial abundance and community composition. Differential initial microbial colonization also had a lasting influence on microbial communities in each reactor (i.e., historical contingency).
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Affiliation(s)
- Hannah Greenwald Healy
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Aliya Ehde
- Division of Environmental and Ecological Engineering, Purdue University, West Lafayette, IN, USA
| | - Alma Bartholow
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Rose S Kantor
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, USA.
| | - Kara L Nelson
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, USA.
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Lou YC, Chen L, Borges AL, West-Roberts J, Firek BA, Morowitz MJ, Banfield JF. Infant gut DNA bacteriophage strain persistence during the first 3 years of life. Cell Host Microbe 2024; 32:35-47.e6. [PMID: 38096814 PMCID: PMC11156429 DOI: 10.1016/j.chom.2023.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/27/2023] [Accepted: 11/16/2023] [Indexed: 01/13/2024]
Abstract
Bacteriophages are key components of gut microbiomes, yet the phage colonization process in the infant gut remains uncertain. Here, we establish a large phage sequence database and use strain-resolved analyses to investigate DNA phage succession in infants throughout the first 3 years of life. Analysis of 819 fecal metagenomes collected from 28 full-term and 24 preterm infants and their mothers revealed that early-life phageome richness increases over time and reaches adult-like complexity by age 3. Approximately 9% of early phage colonizers, which are mostly maternally transmitted and infect Bacteroides, persist for 3 years and are more prevalent in full-term than in preterm infants. Although rare, phages with stop codon reassignment are more likely to persist than non-recoded phages and generally display an increase in in-frame reassigned stop codons over 3 years. Overall, maternal seeding, stop codon reassignment, host CRISPR-Cas locus prevalence, and diverse phage populations contribute to stable viral colonization.
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Affiliation(s)
- Yue Clare Lou
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - LinXing Chen
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94709, USA
| | - Adair L Borges
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jacob West-Roberts
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brian A Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Michael J Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA.
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Trivedi V, Noronha V, Sreekanthreddy P, Desai S, Poojary D, Varghese L, Gowda P, Butle A, Mishra R, Bal M, Mittal N, Rane S, Kane S, Basu S, Patil V, Menon N, Singh AK, Chaturvedi P, Chandrani P, Choughule A, Veldore V, Prabhash K, Dutt A. Association of Cutibacterium acnes with human thyroid cancer. Front Endocrinol (Lausanne) 2023; 14:1152514. [PMID: 38027096 PMCID: PMC10668118 DOI: 10.3389/fendo.2023.1152514] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The diverse subtypes of thyroid carcinoma have distinct clinical outcomes despite a comparable spectrum of underlying genetic alterations. Beyond genetic alterations, sparse efforts have been made to characterize the microbes associated with thyroid cancer. In this study, we examine the microbial profile of thyroid cancer. Methods We sequenced the whole transcriptome of 70 thyroid cancers (40 papillary and 30 anaplastic). Using Infectious Pathogen Detector IPD 2.0, we analysed the relative abundance of 1060 microbes across 70 tumours from patients with thyroid cancer against 118 tumour samples from patients with breast, cervical, colorectal, and tongue cancer. Results Our analysis reveals a significant prevalence of Cutibacterium acnes in 58.6% thyroid cancer samples compared to other cancer types (p=0.00038). Immune cell fraction analysis between thyroid cancer samples with high and low Cutibacterium loads identify enrichment of immunosuppressive cells, including Tregs (p=0.015), and other anti-inflammatory cytokines in the tumour microenvironment, suggesting an immune evasion/immunosuppression milieu is associated with the infection. A higher burden of Cutibacterium acnes was also found to be associated with poor survival defining a distinct sub-group of thyroid cancer. Conclusion Cutibacterium acnes is associated with immune suppression and poor prognosis in a subpopulation of thyroid cancer. This study may help design novel therapeutic measures involving appropriate antibiotics to manage the disease better.
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Affiliation(s)
- Vaishakhi Trivedi
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Vanita Noronha
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | | | - Sanket Desai
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Navi Mumbai, Maharashtra, India
| | - Disha Poojary
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Linu Varghese
- 4baseCare Oncosolutions Pvt ltd, Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India
| | - Pooja Gowda
- 4baseCare Oncosolutions Pvt ltd, Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India
| | - Ashwin Butle
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Navi Mumbai, Maharashtra, India
| | - Rohit Mishra
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Navi Mumbai, Maharashtra, India
| | - Munita Bal
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Department of Pathology, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Neha Mittal
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Department of Pathology, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Swapnil Rane
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Department of Pathology, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Shubhada Kane
- Consultant Onco-pathologist, Jaslok Hospital, Mumbai, Maharashtra, India
| | - Sandip Basu
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Vijay Patil
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Nandini Menon
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Ajay Kumar Singh
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Pankaj Chaturvedi
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Department of Head and Neck Oncology, Tata Memorial Centre, Mumbai, Maharashtra, India
| | - Pratik Chandrani
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Medical oncology molecular laboratory, Tata Memorial Hospital, Mumbai, Maharashtra, India
- Centre for Computational Biology, Bioinformatics and Crosstalk Lab, Advanced Centre for Treatment, Research, and Education in Cancer, Navi Mumbai, Maharashtra, India
| | - Anuradha Choughule
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Vidya Veldore
- 4baseCare Oncosolutions Pvt ltd, Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India
| | - Kumar Prabhash
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Amit Dutt
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Navi Mumbai, Maharashtra, India
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Xue KS, Walton SJ, Goldman DA, Morrison ML, Verster AJ, Parrott AB, Yu FB, Neff NF, Rosenberg NA, Ross BD, Petrov DA, Huang KC, Good BH, Relman DA. Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559480. [PMID: 37808827 PMCID: PMC10557656 DOI: 10.1101/2023.09.26.559480] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Humans constantly encounter new microbes, but few become long-term residents of the adult gut microbiome. Classical theories predict that colonization is determined by the availability of open niches, but it remains unclear whether other ecological barriers limit commensal colonization in natural settings. To disentangle these effects, we used a controlled perturbation with the antibiotic ciprofloxacin to investigate the dynamics of gut microbiome transmission in 22 households of healthy, cohabiting adults. Colonization was rare in three-quarters of antibiotic-taking subjects, whose resident strains rapidly recovered in the week after antibiotics ended. In contrast, the remaining antibiotic-taking subjects exhibited lasting responses, with extensive species losses and transient expansions of potential opportunistic pathogens. These subjects experienced elevated rates of commensal colonization, but only after long delays: many new colonizers underwent sudden, correlated expansions months after the antibiotic perturbation. Furthermore, strains that had previously transmitted between cohabiting partners rarely recolonized after antibiotic disruptions, showing that colonization displays substantial historical contingency. This work demonstrates that there remain substantial ecological barriers to colonization even after major microbiome disruptions, suggesting that dispersal interactions and priority effects limit the pace of community change.
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Affiliation(s)
- Katherine S Xue
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sophie Jean Walton
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Biophysics Training Program, Stanford, CA 94305, USA
| | - Doran A Goldman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Maike L Morrison
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Adrian J Verster
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | | | | | - Norma F Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Benjamin D Ross
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Benjamin H Good
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Applied Physics, Stanford, CA 94305, USA
| | - David A Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA
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Asao K, Hashida N, Maruyama K, Motooka D, Tsukamoto T, Usui Y, Nakamura S, Nishida K. Comparative evaluation of 16S rRNA metagenomic sequencing in the diagnosis and understanding of bacterial endophthalmitis. BMJ Open Ophthalmol 2023; 8:e001342. [PMID: 37709670 PMCID: PMC10503327 DOI: 10.1136/bmjophth-2023-001342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
OBJECTIVE To evaluate the usefulness of metagenomic analysis in the search for causative organisms of bacterial endophthalmitis. METHODS AND ANALYSIS Twenty-one consecutive treatment-naïve patients (13 men and 8 women; mean age, 60.8±19.8 years) with suspected endophthalmitis were recruited. Vitrectomy was performed to diagnose and treat endophthalmitis. Bacterial culture and metagenomic analysis of the vitreous body were performed. Extracted DNA was analysed using 16S rRNA sequences, and libraries were sequenced on an Illumina MiSeq sequencer. To compare the bacterial composition in each case, α and β diversities were determined. RESULTS Patients were categorised into three groups: endophthalmitis cases with matching predominant organisms according to metagenomic analysis and bacterial culture, those with negative results for bacterial culture and those with negative results in both cases. In 7 of 15 culture-negative cases, results from metagenomic analysis could detect pathogens. The diversity of bacterial populations was significantly lower in the group with positive results for predominant bacteria according to culture and metagenomic analysis. All patients with uveitis were included in the group for which the causative pathogen could not be determined by culture or metagenomic analysis. The structures of bacterial populations significantly differed between the positive and negative groups by culture and metagenomic analysis. CONCLUSIONS Metagenomic analysis could be useful for prompt detection of causative pathogens, for precise diagnosis of infection, and as a marker of inflammation processes such as uveitis.
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Affiliation(s)
- Kazunobu Asao
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Noriyasu Hashida
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Kazuichi Maruyama
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Department of Vision Informatics, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Daisuke Motooka
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Teruhisa Tsukamoto
- Biology and Translational Research Unit, Department of Medical Innovations, New Drug Research Division, Otsuka Pharmaceutical. Co. Ltd, Naruto, Tokushima, Japan
| | - Yoshihiko Usui
- Department of Ophthalmology, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - Shota Nakamura
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Kohji Nishida
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
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Santiago-Rodriguez TM, Le François B, Macklaim JM, Doukhanine E, Hollister EB. The Skin Microbiome: Current Techniques, Challenges, and Future Directions. Microorganisms 2023; 11:1222. [PMID: 37317196 DOI: 10.3390/microorganisms11051222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 06/16/2023] Open
Abstract
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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