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Microorganisms colonize various regions of the human body, including the mouth, nasal passages, throat, stomach, intestines, urogenital tract, and skin. The total number of microbial cells is estimated to range from 10¹³ to 10¹⁴—comparable to, or exceeding, the number of human somatic cells. This host–microbiome relationship has led to the conceptualization of humans as supraorganisms, wherein microbial communities perform vital roles in development, immunity,...
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Parasitism is a form of microbial interaction in which parasitic microbes exploit a host organism for nutrients and shelter, often at the host's expense. Unlike mutualistic relationships, where both organisms benefit, parasitism benefits only the parasite and harms the host.Classification of ParasitesMicrobial parasites are broadly classified based on their location relative to the host.Ectoparasites remain on the host’s surface, such as the skin or outer tissues, drawing nutrients...
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The human gastrointestinal (GI) tract is characterized by distinct physicochemical conditions that shape its microbial communities. Among these, the stomach presents a particularly challenging environment for microbial colonization due to its highly acidic pH, ranging from 1 to 3. This extreme acidity effectively limits microbial density. However, certain acid-tolerant microorganisms are capable of surviving in this niche. Notably, Helicobacter pylori can colonize the gastric mucosa,...
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The human microbiota begins developing at birth and undergoes continual change as we age. Infancy marks a critical period of microbial sensitivity, offering a “window of opportunity” during which beneficial microbes help mature the immune system. By age three, children typically develop a more stable and diverse microbial community. Newborns acquire microbes from their immediate environment; vaginal delivery favors maternal vaginal microbes, while cesarean births favor microbes from...
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The gut microbiota includes trillions of microorganisms that colonize the human gastrointestinal tract, including bacteria, archaea, viruses, and fungi. This complex ecosystem plays a critical role in maintaining intestinal and systemic health. Most of these microbes inhabit the large intestine, establishing a relatively stable and diverse community that contributes to gut homeostasis through various metabolic, immunological, and protective mechanisms.Dominant bacterial phyla, such as...
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The large intestine hosts the most densely populated microbial ecosystem in the human body. This complex community primarily consists of anaerobic bacteria, with Bacillota (formerly Firmicutes) and Bacteroidota (formerly Bacteroidetes) as the predominant groups. The distribution of these microbes varies along different sections of the large intestine, influenced by local environmental factors such as oxygen availability and nutrient composition.The cecum, located at the beginning of the large...
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The hallmarks of host-microbiome decoupling.

Jhommara Bautista1, Andrés López-Cortés1

  • 1Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador.

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Summary

Host-microbiome decoupling describes the loss of functional coordination between host systems and microbial behavior, impacting health. This framework identifies hallmarks of this breakdown across diseases, offering new insights into host-microbiome compatibility.

Keywords:
circadian-host microbiome desynchronizationhost-microbiome decouplingimmune miscalibrationmicrobial metabolite signalingmicrobiome functional resilience

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Area of Science:

  • Microbiome research
  • Host-microbiome interactions
  • Systems biology

Background:

  • The human microbiome and host continuously interact, influencing immunity, metabolism, and circadian rhythms.
  • Current models often focus on composition, missing dynamic aspects like temporal instability in disease.
  • Host-microbiome decoupling is introduced as a loss of functional coordination between host and microbial systems.

Purpose of the Study:

  • To define and propose a framework for understanding host-microbiome decoupling.
  • To identify key biological hallmarks indicating the deterioration of host-microbial coordination.
  • To explore the implications of this decoupling across various disease states.

Main Methods:

  • Conceptual framework development based on hallmarks.
  • Analysis of host-microbiome interactions across different biological domains.
  • Integration of multi-omics data to understand mechanistic insights.

Main Results:

  • Host-microbiome decoupling is characterized by hallmarks like breakdown of signaling fidelity, immune miscalibration, and temporal desynchronization.
  • This decoupling is observed across inflammatory, metabolic, neurodegenerative, and neoplastic conditions.
  • Microbial activity can operate outside ecological constraints, affecting host processes.

Conclusions:

  • Host-microbiome compatibility relies on resilience, signaling proportionality, and temporal coordination.
  • The proposed framework provides a new lens for studying microbiome-associated diseases.
  • Understanding decoupling is crucial for developing targeted therapeutic strategies.