1887

Journal of Medical Microbiology logo

Volume 69, Issue 5

Diversity of navel microbiome in young adults Free

Abstract

Human skin microbial communities represent a tremendous source of genetic diversity that evolves as a function of human age. Microbiota differs between regions of oily and moist skin, and appears to stabilize with age.

We have a minimal understanding of the time frame required for the stabilization of skin microbiota, and the role played by gender. In the current study, we examined the microbiota present in the navel region of college-attending young adults in the age group of 18–25 years and investigated if diversity is associated with gender (male and female).

The study involved 16 female and six male subjects. Isolated DNA samples from navel swabs were processed using the Nextera XT library preparation kit and sequenced using the MiSeq platform. Data were analysed using QIIME and statistical analysis performed in R.

Microbiota of navel skin is dominated by and and includes opportunistic pathogens like and . Also present as the major component of the flora were the organisms normally associated with the gastrointestinal tract such as , , and organisms from the and families. Comparison of alpha and beta diversity of the microbiota in the male and female navel regions suggests that the flora is not statistically different (>0.05). However, pairwise comparison suggests that the abundance of 12 specific genera varied with gender, including higher abundance of and in females.

Our findings indicate that the navel skin microbiota of young adults has a core microbiota of and . We also noted the presence of a significant number of opportunistic pathogens. A minor gender difference in the abundance of individual organisms was also observed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Corynebacterium , MiSeq , Moist skin , skin microbiome and Staphylococcus
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/jmm/10.1099/jmm.0.001192
2020-05-05
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/jmm/69/5/721.html?itemId=/content/journal/jmm/10.1099/jmm.0.001192&mimeType=html&fmt=ahah

References

  1. Grice EA, Segre JA. The skin microbiome. Nat Rev Microbiol 2011; 9:244–253 [View Article][PubMed][PubMed]
     [Google Scholar]
  2. Grice EA, Kong HH, Renaud G, Young AC et al. NISC Comparative Sequencing Program A diversity profile of the human skin microbiota. Genome Res 2008; 18:1043–1050 [View Article][PubMed][PubMed]
     [Google Scholar]
  3. Kearney JN, Harnby D, Gowland G, Holland KT. The follicular distribution and abundance of resident bacteria on human skin. J Gen Microbiol 1984; 130:797–801 [View Article][PubMed][PubMed]
     [Google Scholar]
  4. Kong HH, Segre JA. Skin microbiome: looking back to move forward. J Invest Dermatol 2012; 132:933–939 [View Article][PubMed][PubMed]
     [Google Scholar]
  5. Dave M, Higgins PD, Middha S, Rioux KP. The human gut microbiome: current knowledge, challenges, and future directions. Transl Res 2012; 160:246–257 [View Article][PubMed][PubMed]
     [Google Scholar]
  6. Gao L, Xu T, Huang G, Jiang S, Gu Y et al. Oral microbiomes: more and more importance in oral cavity and whole body. Protein Cell 2018; 9:488–500 [View Article][PubMed][PubMed]
     [Google Scholar]
  7. Gao Z, Tseng C-h, Pei Z, Blaser MJ. Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci U S A 2007; 104:2927–2932 [View Article]
     [Google Scholar]
  8. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI et al. Bacterial community variation in human body habitats across space and time. Science 2009; 326:1694–1697 [View Article][PubMed][PubMed]
     [Google Scholar]
  9. Grice EA, Kong HH, Conlan S, Deming CB, Davis J et al. Topographical and temporal diversity of the human skin microbiome. Science 2009; 324:1190–1192 [View Article][PubMed][PubMed]
     [Google Scholar]
  10. Dréno B, Araviiskaia E, Berardesca E, Gontijo G, Sanchez Viera M et al. Microbiome in healthy skin, update for dermatologists. J Eur Acad Dermatol Venereol 2016; 30:2038–2047 [View Article][PubMed][PubMed]
     [Google Scholar]
  11. Byrd AL, Belkaid Y, Segre JA. The human skin microbiome. Nat Rev Microbiol 2018; 16:143–155 [View Article][PubMed][PubMed]
     [Google Scholar]
  12. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG et al. Human gut microbiome viewed across age and geography. Nature 2012; 486:222–227 [View Article][PubMed][PubMed]
     [Google Scholar]
  13. Turgeon EW. Adolescent skin: how to keep it healthy. Can Fam Physician 1986; 32:2427[PubMed][PubMed]
     [Google Scholar]
  14. Capone KA, Dowd SE, Stamatas GN, Nikolovski J. Diversity of the human skin microbiome early in life. J Invest Dermatol 2011; 131:2026–2032 [View Article][PubMed][PubMed]
     [Google Scholar]
  15. Oh J, Conlan S, Polley EC, Segre JA, Kong HH. Shifts in human skin and nares microbiota of healthy children and adults. Genome Med 2012; 4:77 [View Article][PubMed][PubMed]
     [Google Scholar]
  16. McMichael GL, Highet AR, Gibson CS, Goldwater PN, O'Callaghan ME et al. Comparison of DNA extraction methods from small samples of newborn screening cards suitable for retrospective perinatal viral research. J Biomol Tech 2011; 22:5[PubMed][PubMed]
     [Google Scholar]
  17. Jung JY, Yoon HK, An S, Lee JW, Ahn E-R et al. Rapid oral bacteria detection based on real-time PCR for the forensic identification of saliva. Sci Rep 2018; 8:1–10 [View Article]
     [Google Scholar]
  18. Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 2013; 79:5112–5120 [View Article][PubMed][PubMed]
     [Google Scholar]
  19. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biol 2014; 15:550 [View Article][PubMed][PubMed]
     [Google Scholar]
  20. Zhang W, Luo Q, Zhu Y, Ma J, Cao L et al. Microbial diversity in two traditional bacterial douchi from Gansu province in northwest China using Illumina sequencing. PLoS One 2018; 13:e0194876 [View Article][PubMed][PubMed]
     [Google Scholar]
  21. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L et al. Diversity of the human intestinal microbial flora. Science 2005; 308:1635–1638 [View Article][PubMed][PubMed]
     [Google Scholar]
  22. Gao Z, Tseng C-hong, Pei Z, Blaser MJ. Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci U S A 2007; 104:2927–2932 [View Article][PubMed][PubMed]
     [Google Scholar]
  23. Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner ACR et al. The human oral microbiome. J Bacteriol 2010; 192:5002–5017 [View Article][PubMed][PubMed]
     [Google Scholar]
  24. Zaura E, Keijser BJF, Huse SM, Crielaard W. Defining the healthy "core microbiome" of oral microbial communities. BMC Microbiol 2009; 9:259 [View Article][PubMed][PubMed]
     [Google Scholar]
  25. D'Argenio V, Salvatore F. The role of the gut microbiome in the healthy adult status. Clin Chim Acta 2015; 451:97–102 [View Article][PubMed][PubMed]
     [Google Scholar]
  26. Cundell AM. Microbial ecology of the human skin. Microb Ecol 2018; 76:113–120 [View Article][PubMed][PubMed]
     [Google Scholar]
  27. Schommer NN, Gallo RL. Structure and function of the human skin microbiome. Trends Microbiol 2013; 21:660–668 [View Article][PubMed][PubMed]
     [Google Scholar]
  28. Kwaszewska A, Sobiś-Glinkowska M, Szewczyk EM. Cohabitation--relationships of corynebacteria and staphylococci on human skin. Folia Microbiol 2014; 59:495–502 [View Article][PubMed][PubMed]
     [Google Scholar]
  29. Lai Y, Di Nardo A, Nakatsuji T, Leichtle A, Yang Y et al. Commensal bacteria regulate Toll-like receptor 3-dependent inflammation after skin injury. Nat Med 2009; 15:1377–1382 [View Article][PubMed][PubMed]
     [Google Scholar]
  30. Cogen AL, Yamasaki K, Muto J, Sanchez KM, Crotty Alexander L, Alexander LC et al. Staphylococcus epidermidis antimicrobial δ-toxin (phenol-soluble modulin-γ) cooperates with host antimicrobial peptides to kill group A Streptococcus. PLoS One 2010; 5:e8557 [View Article][PubMed][PubMed]
     [Google Scholar]
  31. Kong HH, Oh J, Deming C, Conlan S, Grice EA et al. Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome Res 2012; 22:850–859 [View Article][PubMed][PubMed]
     [Google Scholar]
  32. Iwase T, Uehara Y, Shinji H, Tajima A, Seo H et al. Staphylococcus epidermidis ESP inhibits Staphylococcus aureus biofilm formation and nasal colonization. Nature 2010; 465:346–349 [View Article][PubMed][PubMed]
     [Google Scholar]
  33. Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH et al. Structure, function and diversity of the healthy human microbiome. Nature 2012; 486:207–214 [View Article][PubMed][PubMed]
     [Google Scholar]
  34. US Bureau of Labor Statistics Web citation. https://www.bls.gov/cps/cpsaat18b.htm. Accessed on 1/13/2018.
  35. DeWaal CS. Playing Chicken: The Human Cost of Inadequate Government Regulation of the Poultry Industry. Center for Science in the Public Interest.; 1996
  36. Green LR, Selman C. Factors impacting food workers' and managers' safe food preparation practices: a qualitative study. Food Protection Trends 2005; 25:981–990
     [Google Scholar]
  37. Jones TF, Angulo FJ. Eating in restaurants: a risk factor for foodborne disease?. Clin Infect Dis 2006; 43:1324–1328 [View Article][PubMed][PubMed]
     [Google Scholar]
  38. Patil SR, Cates S, Morales R. Consumer food safety knowledge, practices, and demographic differences: findings from a meta-analysis. J Food Prot 2005; 68:1884–1894 [View Article][PubMed][PubMed]
     [Google Scholar]
  39. Aiolfi A, Asti E, Costa E, Ferrari D, Bonitta G et al. Umbilical microbiome and laparoscopic surgery: a descriptive clinical study. J Laparoendosc Adv Surg Tech A 2018; 28:1196–1201 [View Article][PubMed][PubMed]
     [Google Scholar]
  40. Hulcr J, Latimer AM, Henley JB, Rountree NR, Fierer N et al. A jungle in there: bacteria in belly buttons are highly diverse, but predictable. PLoS One 2012; 7:e47712 [View Article][PubMed][PubMed]
     [Google Scholar]
  41. Staudinger T, Pipal A, Redl B. Molecular analysis of the prevalent microbiota of human male and female forehead skin compared to forearm skin and the influence of make-up. J Appl Microbiol 2011; 110:1381–1389 [View Article][PubMed][PubMed]
     [Google Scholar]
  42. Ojha A, Sinha DK, Padmakumari AP, Bentur JS, Nair S. Bacterial community structure in the Asian rice gall midge reveals a varied microbiome rich in Proteobacteria. Sci Rep 2017; 7:1–13 [View Article]
     [Google Scholar]
  43. Ying S, Zeng D-N, Chi L, Tan Y, Galzote C et al. The influence of age and gender on skin-associated microbial communities in urban and rural human populations. PLoS One 2015; 10:e0141842 [View Article]
     [Google Scholar]
  44. Fransen F, van Beek AA, Borghuis T, Meijer B, Hugenholtz F et al. The impact of gut microbiota on gender-specific differences in immunity. Front Immunol 2017; 8:754 [View Article][PubMed][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jmm/10.1099/jmm.0.001192
Loading
Diversity of navel microbiome in young adults
J. Med. Microbiol. 69, 721 (2020); https://doi.org/10.1099/jmm.0.001192
/content/journal/jmm/10.1099/jmm.0.001192
/content/journal/jmm/10.1099/jmm.0.001192
Loading

Data & Media loading...

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error