Introduction
The vast and diverse microbial community that colonizes our gastrointestinal tract is collectively referred to as the gut microbiome. All these bacteria, archaea, viruses and fungi [1] comprise an entire ecosystem increasingly recognized as a principal regulator of host physiology, playing essential roles in nutrient metabolism, maintaining epithelial integrity and modulating immune responses [2]. A balanced and functionally diverse microbiome is considered fundamental to human health. However, defining a “normal” gut microbiome poses a challenge, given the considerable variability among individuals that is influenced by diet, age, genetics, geography and environmental exposures.
A healthy human gut microbiome contains approximately 100 trillion microbes. The types and numbers of these microorganisms vary throughout the gastrointestinal tract, as a result of different pH levels and host secretions [3].
In addition to internal genetic and physiological traits, external factors, such as antibiotic use, lifestyle, diet, stress, aging, and diseases, can significantly alter the composition and diversity of the gut microbiota. These external forces shape the balance of bacteria in the gut, influencing both gut health and overall well-being [4].
All the above intrinsic and extrinsic factors highlight the challenge of defining a normal gut microbiome, especially when the concept of the “healthy individual” is taken into consideration. The term “healthy” is, in fact, very personalized, even if it does not seem so, because apart from the absence of any diagnosed disease, each person’s healthy state refers to different standards in terms of physical status and behavioral habits, such as sleep or mood.
Furthermore, microbiome research raises several points open to interpretation. To begin with, as research methods, data collection and analysis are not standardized among researchers, inconsistencies in findings are always present. Additionally, the functional aspects of the microbiome, beyond simple composition, are complex, as the presence of a gene does not guarantee its function, and the relationship between dysbiosis (an altered microbiome) and disease is not always clear [5].
The current review presents literature findings on the composition of a supposedly healthy gut microbiome, based on data from diverse geographical areas. In addition, it presents factors that influence the shape of a normal microbiome throughout human life. Lastly, it demonstrates the role of several microbes normally found in the intestinal flora in various normal functions of different organ systems, such as the immune system, the nervous system and the gastrointestinal system.
Prior reviews, such as those by Van Hul et al [1] and McBurney et al [5], have emphasized the conceptual frameworks and the regulatory perspectives of the normal microbiome. In contrast, the present review integrates global taxonomic data, host- and lifestyle-dependent modifiers, and multi-system functional roles of the microbiome. The goal of the writers was, via a combined perspective, to better delineate the range of microbial states compatible with health.
The normal gut microbiome - composition in healthy individuals
A structured search was performed in PubMed, Embase, and Google Scholar using the terms ‘healthy’, ‘gut microbiome’, ‘microbiota composition’, and ‘adults’. Studies published between January 2000 and December 2024 were considered. Inclusion criteria were: (1) adults ≥18 years; (2) clearly defined healthy population; (3) taxonomic data based on 16S rRNA or metagenomics; (4) English language. Exclusion criteria included recent antibiotic use, chronic disease, pregnancy, or incomplete methodological description. After a thorough literature review and using the snowball technique, 13 original research articles containing information on the gut microbiota of healthy individuals worldwide were identified [6-18].
As considerable methodological heterogeneity and variable risk of bias were detected after a critical appraisal of the included studies, most were classified as moderate risk using the ROBINS-2 tool, with several rated as having serious risk due to small sample sizes, limited dietary or medication controls, and cross-sectional designs. Another obstacle to direct comparison across studies was the inconsistent sequencing platforms and DNA extraction methods. Only larger, well-characterized studies [11,18] approached higher methodological rigor, though they too remained observational. These limitations underscore the need for standardized study protocols, copious covariate adjustment, and longitudinal study designs to more reliably define the characteristics of a “normal” gut microbiome. Extended data on the risk of bias are presented in Supplementary Table 1.
In total, 2238 healthy individuals from Asia, America and Northern Europe were included in the qualitative synthesis. Eleven articles provided information on the participants’ sex, with 52.7% (1110/2105) being men and 47.3% (995/2105) women. Their ages and body mass indexes varied and are presented in Table 1.
Table 1 Patients’ demographics
These articles give a perception of what “healthy” looks like, and make it very apparent how tricky this phrase can be. Most researchers consider as “healthy”, the microbiome of individuals not demonstrating any other illness. This is also depicted in the exclusion criteria of 6 of the studies included in the synthesis (Table 2).
Table 2 Exclusion criteria of research on the normal (healthy) gut microbiome
A “healthy” or “normal” gut microbiome does not correspond to a single universal microbial composition; rather, it reflects a state of balance and functionality that supports host physiology. Core features of a healthy microbiome include high microbial diversity, functional redundancy, and relative stability over time, even in the face of external perturbations, such as dietary changes or minor infections [19].
Some large cross-continent studies demonstrate that a healthy gut microbiome varies significantly with age and geographical location, with diet and lifestyle being key influencing factors [11,14,20]. Research shows that microbiome composition changes throughout life, with distinct microbial communities linked to industrialized vs. non-Western diets and further influenced by factors like long-term diet quality or living in a long-term care facility [20,21].
The findings summarized in Table 3 describe the gut microbiome characteristics of individuals living in different geographic areas. It is evident that some commonalities exist, but at the same time one can spot significant regional variations. The predominance of the phyla Firmicutes and Bacteroidetes highlights them as the core constituents of the healthy gut across populations [6,8-12,14-15,18]. Other taxa, such as Actinobacteria and Proteobacteria, also emerge consistently across populations, although usually in lower relative abundance [6,10-12,14,18]. These shared features suggest that, despite dietary, environmental and genetic differences, a “baseline” microbial signature of health can be defined at higher taxonomic levels.
Table 3 Normal gut microbiome of healthy adults from different geographical areas
Additionally, one can detect marked geographical and population-specific differences, as the relatively high abundances of Prevotella [6,8,10-11,13,15] in Estonian and Asian studies, consistent with dietary patterns rich in plant-based carbohydrates and fibers. In contrast, Western populations (e.g. the USA and France) that follow diets rich in animal protein and fat demonstrate higher Bacteroides abundance [7,14,16]. French individuals also showed higher levels of Verrucomicrobia and Bifidobacterium than Saudi participants, underscoring how regional lifestyle, diet, and possibly host genetics, shape gut microbial composition [16]. Such differences provide evidence for the adaptive plasticity of the gut microbiome in response to external factors, while still maintaining core microbial taxa associated with health.
Differences in alpha-diversity further enrich these findings: for example, healthy Chinese participants had lower alpha-diversity than constipated individuals, challenging the assumption that greater diversity is always beneficial [6]. Additionally, throughout the gastrointestinal tract, a significant spatial variation in alpha-diversity is observed, with greater diversity in the small intestine than in distal regions [7]. These observations suggest that alpha diversity must be interpreted contextually, considering anatomical site, health status and ecological balance, rather than being treated as a uniform marker of gut health.
Finally, large-scale, multi-ethnic studies reinforce the notion that, while core taxa remain relatively stable, there is significant heterogeneity in the gut microbiome across populations [14]. The need to move beyond a universal definition of the “normal” microbiome is evident when considering this variability. Instead, a range of healthy microbial profiles shaped by geography, culture and lifestyle should define “healthy”. The evidence suggests that gut health is best understood not as a fixed microbial composition. To better understand it, we should look at it as a flexible equilibrium that balances shared functional capacities with population-specific adaptations.
Thus, taxonomically healthy gut microbial communities are often dominated by members of the phyla Firmicutes and Bacteroidetes, with contributions from Actinobacteria and Proteobacteria at lower levels. However, the emphasis of the global research community has shifted from strictly compositional profiles toward the metabolic and functional capacity of these microbes. Key functions provided by a balanced microbiome include the fermentation of dietary fibers into short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate; modulation of the immune system; maintenance of gut epithelial integrity; and competitive exclusion of pathogenic microorganisms [22,23].
Gut health is not only the absence of gastrointestinal disease, but also the optimal functioning of digestive and absorptive processes. Towards this goal, the intact intestinal barrier, effective immune regulation and minimal gastrointestinal discomfort are all of profound significance [24]. A healthy intestine is increasingly recognized as a fundamental factor in systemic health, influencing metabolic, neurological and immunological processes. Disruptions in microbiome composition and function—commonly referred to as dysbiosis—have been associated with conditions ranging from inflammatory bowel disease and obesity to mental health disorders, highlighting the importance of microbial homeostasis [25].
In summary, the concept of a “normal” and “healthy” gut is not defined by a fixed microbial signature. It is rather the dynamic balance, diversity, and resilience of the gut microbiome, along with its ability to sustain host health through key metabolic, immune, and protective functions.
Host, environmental and lifestyle influences on the gut microbiome in healthy adults
The studies summarized in Table 4 reveal both common patterns and notable differences in the gut microbiome of healthy adults. Despite differences across geographic regions, one consistent finding is the predominance of the Firmicutes and Bacteroidetes phyla, which form the backbone of microbial communities in the human gastrointestinal tract [6,9,18]. These groups are closely linked to key metabolic functions that support host health, such as the production of SCFAs and the maintenance of the gut lining. However, the varying levels of these microbes across different studies suggest that the gut microbiome is not static—it is a flexible ecosystem shaped by factors related to both the host and their environment.
Table 4 The gut microbiome of healthy adults and related conditions
Multiple researchers emphasize the influence of host physiology and health on microbiome composition. For example, individuals with constipation had lower levels of Bacteroidaceae and higher levels of Ruminococcaceae, whereas individuals with hyperlipidemia showed elevated levels of Campilobacterota and Proteobacteria [6,10]. Similarly, obesity seems to coexist with a higher proportion of Gram-negative bacteria, suggesting a potential link between metabolic disorders, inflammation, and shifts in the microbial population [9]. These results highlight how sensitive the microbiome is to changes in health, even among people considered generally healthy, and suggest its value as both a marker and a possible contributor to disease risk.
Diet also stands out as a significant factor in shaping the gut microbiome. Data are still limited, but research so far indicates that, while overall microbial diversity was not significantly affected by fiber supplementation, specific groups such as Bacteroides and Prevotella did change in response to diet, often in ways unique to each individual [8]. Additionally, macronutrient intake in athletes has been linked to the abundance of certain bacteria: Prevotella was less common with higher sucrose intake, while Agathobacter was more prevalent in those consuming more fiber [17]. These findings demonstrate that the microbiome responds, not just to overall diet quality, but also to particular nutrients, highlighting the importance of personalized nutrition in this field.
The gut microbiome is also influenced by geography and lifestyle. For instance, a study in urban and rural areas of China by Zhao et al [11] found significant differences between adolescents living in those areas, with Bifidobacterium more common in rural populations and Bacteroides more prevalent in urban populations. Across geographical compartments, French participants exhibited greater gut microbial diversity than Saudi participants. This finding was independent of weight, suggesting that cultural and dietary differences shape microbiome diversity [16]. Likewise, clear distinctions between East Asian and White populations, independent of obesity status, were detected, while a subtle yet significant variation across ethnicities was observed in a large multi-ethnic cohort [14,16]. These findings emphasize the role of geography, culture and lifestyle as fundamental determinants of microbial composition.
In addition to diet and geography, sex and gender contribute to microbiome variability. For example, male participants had a higher relative abundance of Firmicutes than females, suggesting that sex-specific hormonal and physiological factors may shape microbial communities [12]. Taxonomic differences between population groups that may intersect with both sex and ethnicity were also noted [15]. Taken together, these results suggest that host biological sex interacts with other determinants, such as diet, culture, and environment, producing subtle but measurable differences in microbiota composition.
Sleep and circadian rhythms also seem to influence gut microbial ecology. In a study of 302 individuals, a significant correlation was observed between poor sleep quality and an increased abundance of Erysipelotrichaceae, accompanied by a reduction in Tenericutes [13]. Microbial beta-diversity was also positively associated with sleep duration among adolescents, with those who slept more than 6 h demonstrating a microbiome of “higher” diversity and quality [11]. These findings support emerging evidence that circadian misalignment and sleep disruption alter host metabolism and immune function, thereby reshaping microbial communities. Such observations extend the scope of microbiome research beyond diet and disease, highlighting the importance of behavioral and lifestyle factors.
Another determinant not consistently addressed in the reviewed studies is host genetics. Although the studies summarized here primarily focus on environmental and lifestyle influences, previous research has shown that specific host genotypes can shape microbial composition, particularly for taxa such as Bifidobacterium and Christensenellaceae. The interaction between host genetic background and external exposures may partially explain the inter-individual variability observed across geographically or culturally similar groups [14]. Similarly, age and developmental stage play a crucial role: while the included studies focused on adults, Zhao et al [11] highlighted adolescence as a period of transition, during which factors such as urbanization and lifestyle strongly modulate microbial composition.
Finally, medication use and external exposures represent critical yet underreported factors in many of the included studies. As highlighted by current evidence, antibiotics and dietary fiber can have detrimental effects on gut microbial composition, with sometimes radical effects even among healthy individuals [7]. Apart from antibiotics, other commonly used drugs, such as proton pump inhibitors, metformin and non-steroidal anti-inflammatory drugs, are known to have varying effects on microbial communities. Environmental exposures, including pollutants, sanitation and early-life microbial colonization, also leave lasting imprints on gut ecology. Their absence from many datasets indicates a gap in current research that must be addressed in future cross-population studies.
The various factors that synthesize a normal gut microbiome are depicted in Fig. 1. In addition, data presented in Table 4 further reinforce the concept of the gut microbiome as both stable and adaptable. While certain phyla, such as Firmicutes and Bacteroidetes, serve as universal hallmarks of gut health, significant variability arises from physiological states, diet, geography, sex, lifestyle behaviors and external exposures. Factors not explicitly covered in the reviewed studies, such as host genetics, age, medication use and circadian rhythm, further enrich this picture, underscoring the complexity of defining a universal “normal” microbiome. The evidence supports viewing gut health as a dynamic equilibrium, rather than a fixed system, in which microbial composition and function reflect a balance between shared core features and individualized, context-dependent adaptations.
Figure 1 Key host, environmental and lifestyle determinants of the healthy gut microbiome
Normal functions of the gut microbiome
The gut microbiome plays diverse and systemic roles in maintaining human health. In a normal microbiome, each microbial element contributes to homeostasis of the gastrointestinal lumen, and across immune, neuroendocrine, hepatic, cardiovascular and metabolic axes. By producing metabolites and activating host signaling pathways, these microorganisms function as an integrated metabolic organ. As summarized in Table 5, many of these effects converge on conserved mechanisms, particularly the production of SCFAs, tryptophan-derived metabolites and neurotransmitter-like compounds—core features of a well-functioning microbial ecosystem.
Table 5 Normal functions of the gut microbiota in several systems
A normal gut microbiome contributes substantially to immune homeostasis. Laboratory research has found that certain bacteria, like Peptostreptococcus russellii and Lactobacillus, can transform tryptophan (an amino acid found in many foods) into molecules that activate the aryl hydrocarbon receptor. This process helps guide the development of immune cells, the release of signaling molecules called cytokines, and the strength of the gut’s protective lining [26,27]. Studies in people also suggest that some byproducts made by these bacteria, such as indole-3-propionic acid (IPA) and 4-hydroxyphenylpropionic acid (4-OH-PPA), support a healthy immune response [28,29]. Together, these findings show that when the microbiome is working well, it helps regulate our immune defenses, while disruptions in these pathways are often seen in people with gut imbalances and inflammatory diseases.
The normal microbiome participates directly in gut-brain communication via neural, immune and endocrine pathways. Multiple studies, combining animal models and human clinical research, demonstrate that taxa such as Bacteroides, Lactobacillus, Bifidobacterium and Ruminococcus produce neurotransmitter precursors (e.g., serotonin from tryptophan), induce ghrelin secretion, or modulate GABA receptor activity [30-38]. Butyrate-producing bacteria, characteristic of a healthy adult microbiome, have been associated with improved cognitive performance and reduced depressive symptoms in both preclinical and human studies.
The gut-liver axis is yet another paradigm of the systemic functions of a normal microbiome. Human data show that Lactobacillus spp. increase intestinal-derived HDL3, reduce hepatic endotoxin exposure, and limit macrophage activation [39,40]. SCFAs produced by Clostridium and Bifidobacterium species similarly modulate hepatic immune responses, an observation primarily based on animal data [41]. All the above imply a protective role of specific bacteria against liver inflammation, fibrosis, and metabolic disturbances.
Cardiovascular regulation constitutes another system that is influenced in various ways. Other researchers report, using both animal and human evidence, that members of Firmicutes and Lachnospiraceae produce SCFAs that contribute to blood pressure regulation and the control of inflammation [42-44]. Lactobacillus and Bifidobacterium are proposed to potentially lower serum cholesterol and improve vascular function. Eubacterium coprostanoligenes converts cholesterol into coprostanol in humans, an efficiently excreted form, indicating that a normal microbiome helps maintain cardiometabolic health [44].
Changes in the gut microbiota help to maintain the body’s protective barriers and ensure a healthy metabolism. For example, Bacteroidetes are involved in the breakdown of carbohydrates and bile acids. Firmicutes, especially Clostridium and Lactobacillus, are known for producing butyrate, an important source of energy for the colon lining and vital for gut health [45-48]. In early childhood, Bifidobacterium (a member of the Actinobacteria group) stands out for its ability to digest the sugars in human milk. Another important organism, Akkermansia muciniphila, contributes to healthy mucus layers and overall metabolic balance [49,50]. Each of these microbes seems to help the digestive system and support the body’s natural defenses in its own unique way.
Taken together, current research suggests that the microbiome acts as a bridge between metabolism, the immune system and other body systems. Microbial byproducts like SCFAs, IPA, and caseinolytic protease B do not just affect the gut: they also shape our immune responses, brain function, liver metabolism and even heart health. Still, much of what we know comes from studies in animals. While research in humans is increasing, the evidence is still limited—often based on small groups of people and short-term studies. Although scientists have mapped some key processes, such as the breakdown of SCFAs and tryptophan, many questions remain about the gut microbiome and its interactions with our bodies. For example, the influence of genetics, medications, sleep patterns and early-life experiences has not been fully explored in most studies.
Collectively, these findings demonstrate that the gut microbiome operates as a dynamic, multisystemic metabolic organ. Its effects extend across immune, neural, hepatic, cardiovascular and intestinal networks. Despite rapid advances, current knowledge remains limited, as a result of heterogeneity in study protocols, small sample sizes, and selective research focused on a narrow subset of microbial metabolites. To better interpret the interactions between microbial pathways and host physiology, larger-scale human studies are needed. Metagenomics, metatranscriptomics, metabolomics, proteomics and immune profiling are all essential components of our deep understanding of the microbiome and its complexity. Such approaches will be essential for distinguishing causal relationships from correlation, identifying temporal signatures of microbial activity, and uncovering currently uncharacterized biochemical pathways. Advancing toward this systems-level understanding will provide the mechanistic resolution needed to translate microbiome research into predictive, personalized, and clinically actionable insights.