Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies

Abstract

The human microbiome is composed of a collection of dynamic microbial communities that inhabit various anatomical locations in the body. Accordingly, the coevolution of the microbiome with the host has resulted in these communities playing a profound role in promoting human health. Consequently, perturbations in the human microbiome can cause or exacerbate several diseases. In this Review, we present our current understanding of the relationship between human health and disease development, focusing on the microbiomes found across the digestive, respiratory, urinary, and reproductive systems as well as the skin. We further discuss various strategies by which the composition and function of the human microbiome can be modulated to exert a therapeutic effect on the host. Finally, we examine technologies such as multiomics approaches and cellular reprogramming of microbes that can enable significant advancements in microbiome research and engineering.

References 481

1. 1.

   Hooper L. V.; Gordon J. I. Commensal Host-Bacterial Relationships in the Gut. Science 2001, 292, 1115–1118..

   Not in our library10.1126/science.1058709

2. 2.
   Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes · 2016

   No notice
3. 3.
   Host-microbiota interactions: from holobiont theory to analysis · 2019

   No notice
4. 4.
   Microbiome definition re-visited: old concepts and new challenges · 2020

   Corrected
5. 5.

   Kim S. A.; Kim B. R.; Chun M. Y.; Youn S. W. Relation between Ph in the Trunk and Face: Truncal Ph Can Be Easily Predicted from Facial Ph. Ann. Dermatol. 2016, 28, 216–221..

   Not in our library10.5021/ad.2016.28.2.216

6. 6.
   The Role of the Gastrointestinal Mucus System in Intestinal Homeostasis: Implications for Neurological Disorders · 2020

   No notice
7. 7.

   Yatsunenko T.; Rey F. E.; Manary M. J.; Trehan I.; Dominguez-Bello M. G.; Contreras M.; Magris M.; Hidalgo G.; Baldassano R. N.; Anokhin A. P.; et al. Human Gut Microbiome Viewed across Age and Geography. Nature 2012, 486, 222–227..

   Not in our library10.1038/nature11053

8. 8.

   Guigoz Y.; Dore J.; Schiffrin E. J. The Inflammatory Status of Old Age Can Be Nurtured from the Intestinal Environment. Curr. Opin. Clin. Nutr. Metab. Care 2008, 11, 13–20..

   Not in our library10.1097/mco.0b013e3282f2bfdf

9. 9.

   Aas J. A.; Paster B. J.; Stokes L. N.; Olsen I.; Dewhirst F. E. Defining the Normal Bacterial Flora of the Oral Cavity. J. Clin. Microbiol. 2005, 43, 5721–5732..

   Not in our library10.1128/jcm.43.11.5721-5732.2005

10. 10.

    Wade W. G. The Oral Microbiome in Health and Disease. Pharmacol. Res. 2013, 69, 137–143..

    Not in our library10.1016/j.phrs.2012.11.006

11. 11.

    Kumaraswamy K. L.; Vidhya M. Human Papilloma Virus and Oral Infections: An Update. J. Cancer. Res. Ther. 2011, 7, 120–127..

    Not in our library10.4103/0973-1482.82915

12. 12.

    Wantland W. W.; Wantland E. M.; Remo J. W.; Winquist D. L. Studies on Human Mouth Protozoa. J. Dent. Res. 1958, 37, 949–950..

    Not in our library10.1177/00220345580370052601

13. 13.

    Wescombe P. A.; Heng N. C.; Burton J. P.; Chilcott C. N.; Tagg J. R. Streptococcal Bacteriocins and the Case for Streptococcus Salivarius as Model Oral Probiotics. Future Microbiol. 2009, 4, 819–835..

    Not in our library10.2217/fmb.09.61

14. 14.

    Loesche W. Dental Caries and Periodontitis: Contrasting Two Infections That Have Medical Implications. Infect. Dis. Clin. North. Am. 2007, 21, 471–502..

    Not in our library10.1016/j.idc.2007.03.006

15. 15.

    Parahitiyawa N. B.; Scully C.; Leung W. K.; Yam W. C.; Jin L. J.; Samaranayake L. P. Exploring the Oral Bacterial Flora: Current Status and Future Directions. Oral Dis. 2010, 16, 136–145..

    Not in our library10.1111/j.1601-0825.2009.01607.x

16. 16.

    Fejerskov O. Changing Paradigms in Concepts on Dental Caries: Consequences for Oral Health Care. Caries Res. 2004, 38, 182–191..

    Not in our library10.1159/000077753

17. 17.

    Filoche S.; Wong L.; Sissons C. H. Oral Biofilms: Emerging Concepts in Microbial Ecology. J. Dent. Res. 2010, 89, 8–18..

    Not in our library10.1177/0022034509351812

18. 18.

    Zarco M. F.; Vess T. J.; Ginsburg G. S. The Oral Microbiome in Health and Disease and the Potential Impact on Personalized Dental Medicine. Oral Dis. 2012, 18, 109–120..

    Not in our library10.1111/j.1601-0825.2011.01851.x

19. 19.

    Horz H. P.; Conrads G. Diagnosis and Anti-Infective Therapy of Periodontitis. Expert Rev. Anti. Infect. Ther. 2007, 5, 703–715..

    Not in our library10.1586/14787210.5.4.703

20. 20.

    Williams R. C.; Barnett A. H.; Claffey N.; Davis M.; Gadsby R.; Kellett M.; Lip G. Y.; Thackray S. The Potential Impact of Periodontal Disease on General Health: A Consensus View. Curr. Med. Res. Opin. 2008, 24, 1635–1643..

    Not in our library10.1185/03007990802131215

21. 21.

    Li X.; Kolltveit K. M.; Tronstad L.; Olsen I. Systemic Diseases Caused by Oral Infection. Clin. Microbiol. Rev. 2000, 13, 547–558..

    Not in our library10.1128/cmr.13.4.547

22. 22.

    Vieira A. T.; Castelo P. M.; Ribeiro D. A.; Ferreira C. M. Influence of Oral and Gut Microbiota in the Health of Menopausal Women. Front. Microbiol. 2017, 8, 1884.

    Not in our library10.3389/fmicb.2017.01884

23. 23.

    Do L. G.; Ha D. H.; Bell L. K.; Devenish G.; Golley R. K.; Leary S. D.; Manton D. J.; Thomson W. M.; Scott J. A.; Spencer A. J. Study of Mothers’ and Infants’ Life Events Affecting Oral Health (Smile) Birth Cohort Study: Cohort Profile. BMJ. Open 2020, 10, e041185.

    Not in our library10.1136/bmjopen-2020-041185

24. 24.

    Craig S. J. C.; Blankenberg D.; Parodi A. C. L.; Paul I. M.; Birch L. L.; Savage J. S.; Marini M. E.; Stokes J. L.; Nekrutenko A.; Reimherr M.; et al. Child Weight Gain Trajectories Linked to Oral Microbiota Composition. Sci. Rep. 2018, 8, 14030.

    Not in our library10.1038/s41598-018-31866-9

25. 25.

    Jensen E. D.; Selway C. A.; Allen G.; Bednarz J.; Weyrich L. S.; Gue S.; Pena A. S.; Couper J. Early Markers of Periodontal Disease and Altered Oral Microbiota Are Associated with Glycemic Control in Children with Type 1 Diabetes. Pediatr. Diabetes 2021, 22, 474–481..

    Not in our library10.1111/pedi.13170

26. 26.
    The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems · 2020

    No notice
27. 27.

    Xue L.; Zou X.; Yang X. Q.; Peng F.; Yu D. K.; Du J. R. Chronic Periodontitis Induces Microbiota-Gut-Brain Axis Disorders and Cognitive Impairment in Mice. Exp. Neurol. 2020, 326, 113176.

    Not in our library10.1016/j.expneurol.2020.113176

28. 28.

    Lin D.; Hutchison K. E.; Portillo S.; Vegara V.; Ellingson J. M.; Liu J.; Krauter K. S.; Carroll-Portillo A.; Calhoun V. D. Association between the Oral Microbiome and Brain Resting State Connectivity in Smokers. Neuroimage 2019, 200, 121–131..

    Not in our library10.1016/j.neuroimage.2019.06.023

29. 29.

    Yang I.; Arthur R. A.; Zhao L.; Clark J.; Hu Y.; Corwin E. J.; Lah J. The Oral Microbiome and Inflammation in Mild Cognitive Impairment. Exp. Gerontol. 2021, 147, 111273.

    Not in our library10.1016/j.exger.2021.111273

30. 30.

    Cunha F. A.; Cota L. O. M.; Cortelli S. C.; Miranda T. B.; Neves F. S.; Cortelli J. R.; Costa F. O. Periodontal Condition and Levels of Bacteria Associated with Periodontitis in Individuals with Bipolar Affective Disorders: A Case-Control Study. J. Periodontal Res. 2019, 54, 63–72..

    Not in our library10.1111/jre.12605

31. 31.

    Shafquat A.; Joice R.; Simmons S. L.; Huttenhower C. Functional and Phylogenetic Assembly of Microbial Communities in the Human Microbiome. Trends Microbiol. 2014, 22, 261–266..

    Not in our library10.1016/j.tim.2014.01.011

32. 32.

    Baker J. L.; Bor B.; Agnello M.; Shi W.; He X. Ecology of the Oral Microbiome: Beyond Bacteria. Trends Microbiol. 2017, 25, 362–374..

    Not in our library10.1016/j.tim.2016.12.012

33. 33.

    Knight R.; Callewaert C.; Marotz C.; Hyde E. R.; Debelius J. W.; McDonald D.; Sogin M. L. The Microbiome and Human Biology. Annu. Rev. Genomics Hum. Genet. 2017, 18, 65–86..

    Not in our library10.1146/annurev-genom-083115-022438

34. 34.

    Yang I.; Nell S.; Suerbaum S. Survival in Hostile Territory: The Microbiota of the Stomach. FEMS Microbiol. Rev. 2013, 37, 736–761..

    Not in our library10.1111/1574-6976.12027

35. 35.

    Wu W. M.; Yang Y. S.; Peng L. H. Microbiota in the Stomach: New Insights. J. Dig. Dis. 2014, 15, 54–61..

    Not in our library10.1111/1751-2980.12116

36. 36.

    Oren A.; Garrity G. M. Valid Publication of the Names of Forty-Two Phyla of Prokaryotes. Int. J. Syst. Evol. Microbiol. 2021, 71, 005056.

    Not in our library10.1099/ijsem.0.005056

37. 37.

    Bik E. M.; Eckburg P. B.; Gill S. R.; Nelson K. E.; Purdom E. A.; Francois F.; Perez-Perez G.; Blaser M. J.; Relman D. A. Molecular Analysis of the Bacterial Microbiota in the Human Stomach. Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 732–737..

    Not in our library10.1073/pnas.0506655103

38. 38.

    Delgado S.; Cabrera-Rubio R.; Mira A.; Suarez A.; Mayo B. Microbiological Survey of the Human Gastric Ecosystem Using Culturing and Pyrosequencing Methods. Microb. Ecol. 2013, 65, 763–772..

    Not in our library10.1007/s00248-013-0192-5

39. 39.

    Liu X.; Shao L.; Liu X.; Ji F.; Mei Y.; Cheng Y.; Liu F.; Yan C.; Li L.; Ling Z. Alterations of Gastric Mucosal Microbiota across Different Stomach Microhabitats in a Cohort of 276 Patients with Gastric Cancer. EBioMedicine 2019, 40, 336–348..

    Not in our library10.1016/j.ebiom.2018.12.034

40. 40.

    Nardone G.; Compare D. The Human Gastric Microbiota: Is It Time to Rethink the Pathogenesis of Stomach Diseases?. United European Gastroenterol. J. 2015, 3, 255–260..

    Not in our library10.1177/2050640614566846

Cited by papers we hold 1

• A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation · 2024
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