Understanding dysbiosis and resilience in the human gut microbiome: biomarkers, interventions, and challenges
The healthy gut microbiome is important in maintaining health and preventing various chronic and metabolic diseases through interactions with the host via different gut–organ axes, such as the gut-brain, gut-liver, gut-immune, and gut-lung axes. The human gut microbiome is relatively stable, yet can...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2025-03-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1559521/full |
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| author | Azadeh Safarchi Azadeh Safarchi Ghanyah Al-Qadami Ghanyah Al-Qadami Cuong D. Tran Michael Conlon |
| author_facet | Azadeh Safarchi Azadeh Safarchi Ghanyah Al-Qadami Ghanyah Al-Qadami Cuong D. Tran Michael Conlon |
| author_sort | Azadeh Safarchi |
| collection | DOAJ |
| description | The healthy gut microbiome is important in maintaining health and preventing various chronic and metabolic diseases through interactions with the host via different gut–organ axes, such as the gut-brain, gut-liver, gut-immune, and gut-lung axes. The human gut microbiome is relatively stable, yet can be influenced by numerous factors, such as diet, infections, chronic diseases, and medications which may disrupt its composition and function. Therefore, microbial resilience is suggested as one of the key characteristics of a healthy gut microbiome in humans. However, our understanding of its definition and indicators remains unclear due to insufficient experimental data. Here, we review the impact of key drivers including intrinsic and extrinsic factors such as diet and antibiotics on the human gut microbiome. Additionally, we discuss the concept of a resilient gut microbiome and highlight potential biomarkers including diversity indices and some bacterial taxa as recovery-associated bacteria, resistance genes, antimicrobial peptides, and functional flexibility. These biomarkers can facilitate the identification and prediction of healthy and resilient microbiomes, particularly in precision medicine, through diagnostic tools or machine learning approaches especially after antimicrobial medications that may cause stable dysbiosis. Furthermore, we review current nutrition intervention strategies to maximize microbial resilience, the challenges in investigating microbiome resilience, and future directions in this field of research. |
| format | Article |
| id | doaj-art-b9213a1ac45d40e1833aae8bbcc11e49 |
| institution | DOAJ |
| issn | 1664-302X |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj-art-b9213a1ac45d40e1833aae8bbcc11e492025-08-20T02:46:28ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-03-011610.3389/fmicb.2025.15595211559521Understanding dysbiosis and resilience in the human gut microbiome: biomarkers, interventions, and challengesAzadeh Safarchi0Azadeh Safarchi1Ghanyah Al-Qadami2Ghanyah Al-Qadami3Cuong D. Tran4Michael Conlon5Microbiome for One Systems Health FSP, CSIRO, Westmead, NSW, AustraliaHealth and Biosecurity Research Unit, CSIRO, Adelaide, SA, AustraliaMicrobiome for One Systems Health FSP, CSIRO, Westmead, NSW, AustraliaHealth and Biosecurity Research Unit, CSIRO, Adelaide, SA, AustraliaHealth and Biosecurity Research Unit, CSIRO, Adelaide, SA, AustraliaHealth and Biosecurity Research Unit, CSIRO, Adelaide, SA, AustraliaThe healthy gut microbiome is important in maintaining health and preventing various chronic and metabolic diseases through interactions with the host via different gut–organ axes, such as the gut-brain, gut-liver, gut-immune, and gut-lung axes. The human gut microbiome is relatively stable, yet can be influenced by numerous factors, such as diet, infections, chronic diseases, and medications which may disrupt its composition and function. Therefore, microbial resilience is suggested as one of the key characteristics of a healthy gut microbiome in humans. However, our understanding of its definition and indicators remains unclear due to insufficient experimental data. Here, we review the impact of key drivers including intrinsic and extrinsic factors such as diet and antibiotics on the human gut microbiome. Additionally, we discuss the concept of a resilient gut microbiome and highlight potential biomarkers including diversity indices and some bacterial taxa as recovery-associated bacteria, resistance genes, antimicrobial peptides, and functional flexibility. These biomarkers can facilitate the identification and prediction of healthy and resilient microbiomes, particularly in precision medicine, through diagnostic tools or machine learning approaches especially after antimicrobial medications that may cause stable dysbiosis. Furthermore, we review current nutrition intervention strategies to maximize microbial resilience, the challenges in investigating microbiome resilience, and future directions in this field of research.https://www.frontiersin.org/articles/10.3389/fmicb.2025.1559521/fullhuman gut microbiomedysbiosisperturbationantibioticsresilient gut microbiomemicrobiome recovery |
| spellingShingle | Azadeh Safarchi Azadeh Safarchi Ghanyah Al-Qadami Ghanyah Al-Qadami Cuong D. Tran Michael Conlon Understanding dysbiosis and resilience in the human gut microbiome: biomarkers, interventions, and challenges Frontiers in Microbiology human gut microbiome dysbiosis perturbation antibiotics resilient gut microbiome microbiome recovery |
| title | Understanding dysbiosis and resilience in the human gut microbiome: biomarkers, interventions, and challenges |
| title_full | Understanding dysbiosis and resilience in the human gut microbiome: biomarkers, interventions, and challenges |
| title_fullStr | Understanding dysbiosis and resilience in the human gut microbiome: biomarkers, interventions, and challenges |
| title_full_unstemmed | Understanding dysbiosis and resilience in the human gut microbiome: biomarkers, interventions, and challenges |
| title_short | Understanding dysbiosis and resilience in the human gut microbiome: biomarkers, interventions, and challenges |
| title_sort | understanding dysbiosis and resilience in the human gut microbiome biomarkers interventions and challenges |
| topic | human gut microbiome dysbiosis perturbation antibiotics resilient gut microbiome microbiome recovery |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1559521/full |
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