Table of Contents
Overview
Definition of Microbiome
The microbiome refers to the full array of microorganisms, collectively known as the microbiota, that inhabit the human body. More specifically, it encompasses the collection of microbial genomes that contribute to the broader genetic landscape, or metagenome, of an individual. The understanding of the human microbiome has significantly advanced since the initiation of the Human Microbiome Project (HMP) in 2007, which aimed to characterize the microbial communities present in the human body and elucidate the role of each microorganism in relation to health and disease. Among the various microorganisms that constitute the microbiome, lactic-acid bacteria, particularly strains of Lactobacillus and Streptococcus, are notable. These bacteria are not only integral components of the human microbiome but have also been utilized for centuries in the production of fermented foods such as yogurt, cheese, and pickled products.[4.1]Importance in Human Health
The human microbiome plays a crucial role in maintaining health and influencing disease processes. It is composed of trillions of microorganisms that inhabit various parts of the human body, forming complex ecosystems that have coevolved with human physiology. These microbial communities significantly impact metabolic and immune functions, contributing to both health and disease outcomes.[3.1] Understanding the composition and activities of the microbiome is essential, as systematic differences have been observed between the microbiomes of healthy individuals and those with conditions such as colorectal cancer and inflammatory bowel disease.[5.1] Factors influencing microbiome composition include diet, genetics, environment, and lifestyle choices. For instance, dietary patterns rich in fiber and diverse food sources are associated with increased microbial diversity, which is often linked to better health outcomes.[14.1] Conversely, diets high in processed foods and sugars can reduce microbial diversity and promote pro-inflammatory bacteria.[8.1] Additionally, the use of antibiotics has been shown to significantly lower microbiome diversity and alter its composition.[6.1] Other factors, such as having siblings, have also been identified as influencing microbiome diversity in early life, with older siblings associated with greater diversity.[9.1] The relationship between the microbiome and chronic diseases is an evolving area of public health research. Strategies to leverage this understanding for disease prevention include developing personalized dietary recommendations and therapeutic approaches that target the microbiome.[13.1] The Harvard Chan Microbiome in Public Health Center aims to enhance population health through research and education focused on the microbiome's role in health.[11.1] Overall, the microbiome's influence on human health underscores the importance of continued research to explore its potential for disease prediction and treatment.History
Early Discoveries in Microbiology
The early discoveries in microbiology were pivotal in transforming scientific understanding of microorganisms and their roles in biological processes. Antonie van Leeuwenhoek, a Dutch tradesman and scientist, is widely recognized as the father of microbiology due to his pioneering work in the 17th century. He invented the microscope and was the first to observe and describe microorganisms, including bacteria and protozoa, by examining water samples and dental plaque, providing the first detailed descriptions of the microscopic world.[84.1] By the end of his life, Van Leeuwenhoek had written approximately 560 letters to the Royal Society and other scientific institutions concerning his observations, significantly contributing to the scientific community's understanding of microorganisms.[63.1] His groundbreaking efforts established the foundation for microbiology and positioned him as a key figure in the study of microscopic organisms, influencing future research in the field.[63.1] Prior to these advancements, misconceptions about the nature of life and disease were prevalent, including the belief in spontaneous generation—the idea that living organisms could arise from non-living matter. This belief was challenged during the 19th century, particularly through the work of Louis Pasteur and Robert Koch. Pasteur's experiments debunked spontaneous generation and led to the formulation of the germ theory of disease, which posits that microorganisms are responsible for many diseases.[85.1] Koch further advanced this understanding by establishing Koch's postulates, a series of criteria used to link specific microorganisms to specific diseases, thus laying the groundwork for modern microbiology and infectious disease research.[86.1] The field of scientific microbiology further developed in the 19th century through the work of pioneers such as Louis Pasteur and Robert Koch. This period, often referred to as the Transitional Period in microbiology, marked a significant shift from the belief in spontaneous generation to a more scientific understanding of microorganisms and their roles in disease transmission.[46.1] Historical evidence indicates that humans have had some notion of microbial life since prehistoric times, utilizing this knowledge to develop foods and to prevent and treat diseases.[47.1] Among the early thinkers, Marcus Terentius Varro was one of the first to propose that unseen entities, which we now recognize as microorganisms, could cause disease.[47.1] Pasteur's work was pivotal in the development of the germ theory of disease, fundamentally transforming the perception of these organisms from mere contaminants to essential components of biological processes.[46.1]Evolution of Microbiome Research
Research into the human microbiome has undergone significant evolution since its inception, marked by key milestones that have shaped our understanding of its role in health and disease. The journey began in the 17th century when Antonie van Leeuwenhoek first studied microorganisms, laying the groundwork for future microbiome research.[49.1] By the late 1800s, critical contributions from European scientists further advanced the field, leading to initial observations of intestinal microorganisms.[47.1] This period marked a paradigm shift from viewing microbes solely as agents of disease to recognizing their integral role in human health, encapsulated in the holistic One Health Concept.[48.1] The advent of modern genomics and sequencing technologies has catalyzed a new era in microbiome research. These advancements have enabled scientists to explore the complex interactions between the microbiome and various aspects of human health, including drug efficacy and safety.[51.1] The concept of pharmacomicrobiomics has emerged, highlighting how gut microbiota can influence drug absorption, metabolism, and overall pharmacological effects.[53.1] This understanding is crucial for developing microbiota-targeted approaches that enhance drug efficacy and minimize adverse drug reactions.[53.1] As research in microbiome science progresses, the mission of the Harvard Chan Microbiome in Public Health Center (HCMPH) is to enhance our understanding of the microbiome to improve population health through various means, including basic research, translation, policy, education, and outreach.[69.1] The establishment of the Microbiome Collection Core at the Harvard T.H. Chan School of Public Health (HCMCC) reflects a strong demand within the research community for validated microbiome sample collection kit configurations that facilitate easy usability for in-home sampling.[69.1] Additionally, the Harvard T.H. Chan Microbiome Analysis Core (HCMAC) was created to support the rapidly evolving field of microbiome science by aiding in the design and interpretation of human microbiome studies, thereby helping researchers develop and apply quantitative methods to investigate the role of microbial community function in health.[69.1]In this section:
Recent Advancements
Technological Innovations
Recent advancements in sequencing technologies have significantly transformed the field of microbiome research, particularly in the context of personalized medicine. The integration of 16S rRNA and shotgun metagenomics sequencing has enhanced the accuracy of microbiome data, facilitating precision diagnostics and personalized treatments for microbiome-related diseases.[100.1] Genome-resolved metagenomics has emerged as a pivotal method, allowing researchers to reconstruct microbial genomes directly from whole-metagenome sequencing data, thereby providing deeper insights into the prokaryotic microbiota of the human gut.[101.1] This approach has proven effective in distinguishing taxonomic differences between diseased and healthy microbiomes, which is crucial for developing targeted therapies.[101.1] Recent advancements in long-read sequencing technologies have significantly transformed metagenomics, enhancing strain-level pathogen characterization and enabling the generation of accurate and complete metagenome-assembled genomes.[106.1] These improvements have also advanced microbiome taxonomic classification and profiling, which is crucial for understanding the diversity of microbial communities.[106.1] Furthermore, next-generation sequencing (NGS) technology has facilitated the discovery and characterization of previously unculturable microbes, allowing for predictions regarding their functions.[103.1] The integration of advanced sequencing methods with bioinformatics pipelines has improved the accuracy of microbiome data, which is essential for disease diagnosis and personalized treatment approaches.[107.1] Additionally, the concept of "precision microbiome" has gained prominence, focusing on the precise analysis of microbiota interactions within specific hosts, supported by high-throughput sequencing and artificial intelligence tools.[105.1] This approach underscores the potential of leveraging the human microbiome for early disease detection and prevention, highlighting its role in health outcomes.[107.1] The field of microbiome research has significantly expanded in recent years, driven by the generation of massive datasets and the development of numerous bioinformatics analysis tools.[108.1] The resulting complex, often multi-omics datasets demand powerful yet user-friendly bioinformatics tools to reveal key patterns, important biomarkers, and potential activities within the microbiome.[109.1] Recently, unsupervised learning methods have been developed to integrate multi-omics data from the same samples, although these methods were not initially designed for microbiome data analysis.[110.1] As human microbiome studies gain increasing attention for their potential clinical applications, advancements in omics technologies and artificial intelligence have led to promising outcomes in the discovery of potential biomarkers using machine learning tools.[122.1]Key Findings in Microbiome Studies
Recent research has highlighted the intricate interactions between the bacterial microbiome and various physiological processes, underscoring its potential as a therapeutic target for enhancing human health outcomes. This body of work aims to consolidate the latest advancements in bacterial microbiome research, providing a comprehensive understanding of its implications for human health, including its role in disease and the identification of biomarkers and metabolites associated with health conditions.[98.1] Over the past two decades, scientific exploration into the microbiome has experienced remarkable growth, with over $1.7 billion spent on human microbiome research since 2009.[91.1] This expansion has led to unprecedented discoveries regarding the molecular mechanisms that dictate host-microbiota interactions and their crucial roles in human health.[92.1] Advancements in sequencing technology have empowered researchers to elucidate the microbiome's critical role in health and disease, chart the development of the infant microbiome, and begin to define how behavior can shape microbial composition.[91.1] The human microbiome has been recognized as a key factor in health, providing unique signatures that may facilitate early disease detection and prevention. Recent advancements in sequencing techniques, such as 16S rRNA and metagenomics, along with improved bioinformatics pipelines, have enhanced the accuracy of microbiome data for disease diagnosis and personalized treatment approaches. These developments emphasize the importance of standardized methods and comprehensive data integration for microbiome-based disease prevention.[114.1] Despite the rapid growth in microbiome research, translating these findings into clinical applications remains a challenge. Issues such as the reliance on correlational studies and the need for standardized data acquisition and analysis protocols have been identified as significant barriers. To address these challenges, researchers propose an iterative approach that incorporates in silico, in vitro, ex vivo, and in vivo studies to facilitate successful preclinical and clinical trials.[115.1]In this section:
Personalized MedicineMetagenomicsPersonalized TreatmentsLong-read SequencingPathogen Characterization
Microbiome Composition
Types of Microorganisms
The human microbiome is composed of a diverse array of microorganisms, including bacteria, fungi, viruses, and archaea, each playing a crucial role in maintaining health. Among these, gut microbiota is considered the most significant, comprising six major phyla: Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia, with Firmicutes and Bacteroidetes being the predominant types.[171.1] The gut bacteria perform essential functions such as food fermentation, pathogen protection, immune response stimulation, and vitamin production.[171.1] In addition to bacteria, the gut microbiota also includes fungi, with the most studied genera being Candida, Saccharomyces, Malassezia, and Cladosporium.[171.1] Furthermore, the presence of viruses, particularly bacteriophages, is notable; these phages can integrate their DNA into bacterial genomes and replicate alongside their hosts, highlighting the complexity of microbial interactions within the microbiome.[169.1] Research has identified specific bacterial genera that are prevalent in various human body sites, including Staphylococcus, Pseudomonas, Corynebacterium, Bacillus, Acinetobacter, and Propionibacterium, particularly in the context of vascular health.[170.1] The interplay between these microorganisms and their host is vital, as they can significantly influence metabolic and immune functions, contributing to both health and disease states.[173.1] Studies such as the Integrative Human Microbiome Project (iHMP) have further elucidated the relationship between microbial community composition and specific health conditions, including preterm birth, inflammatory bowel disease (IBD), and prediabetes, indicating that changes in microbial populations can be closely associated with these states.[172.1] Understanding the composition and activities of these microorganisms is essential for comprehending their roles in human health and the potential implications for mental health and dysbiosis.[173.1]Diversity and Variability
The human microbiome exhibits significant diversity and variability, which is crucial for understanding its role in health and disease. The composition of the microbiome is dynamic and influenced by various factors, including early development, environmental conditions such as diet and antibiotic use, and the presence of diseases. Notably, the most dramatic changes in microbiome composition occur during infancy and early childhood, highlighting the importance of these developmental stages in shaping microbial communities.[131.1] Research has shown that the human body hosts a diverse assemblage of symbiotic microbes that varies predictably across different spatial scales and body sites. This spatially distinct microbial consortia can be affected by stochastic events and deterministic factors, further complicating the understanding of microbiome composition.[129.1] Advances in DNA sequencing technologies have facilitated the identification of these microbial communities, revealing patterns in microbiome composition that correlate with specific health conditions, such as inflammatory bowel disease and colorectal cancer.[137.1] Moreover, systematic differences in microbiome composition have been observed between healthy individuals and those with microbiota-linked conditions, underscoring the significance of understanding the determinants of variation in the microbiome.[137.1] Recent studies have profiled the stool microbiome composition across large, well-characterized population-based cohorts, providing insights into the variations in gut microbiota among children and adults.[138.1] These findings emphasize the need to consider individual characteristics, clinical variables, and dietary factors when examining inter-individual variations in the gut microbiome and its implications for health.[139.1]In this section:
Microbiome And Health
Role in Digestion and Nutrition
The gut microbiota plays a critical role in digestion and nutrition by regulating various physiological processes, including metabolism and immune function. A nutritionally balanced diet is essential for maintaining a healthy gut microbiome, which in turn supports the integrity of the intestinal barrier and immune tolerance. Conversely, an unbalanced diet, such as the typical Western diet, can lead to reduced diversity and dysbiosis of the gut microbiome, resulting in conditions like leaky gut and chronic inflammation, as observed in inflammatory bowel disease (IBD).[203.1] Dietary fiber (DF) is particularly significant as it serves as a fermentable substrate for beneficial gut bacteria, promoting the production of short-chain fatty acids (SCFAs) and other bioactive molecules that positively influence gut health.[191.1] The diversity of carbohydrates and associated molecules in fiber-rich foods can significantly impact microbiota composition and function, further enhancing metabolic health.[190.1] Emerging research emphasizes the importance of dietary interventions, particularly those rich in fiber and polyphenols, in modulating gut microbiota composition and function, thereby promoting overall health.[191.1] The human microbiome is a complex ecosystem composed of trillions of microorganisms that significantly influences various aspects of human health, including digestion, immune function, metabolism, and neurological health.[199.1] The composition and activities of the microbiome are crucial, as they can enhance or impair metabolic and immune functions, thereby contributing to overall health and disease.[197.1] Diet plays a critical role in shaping the gut microbiome, influencing its taxonomic and functional diversity.[201.1] A nutritionally balanced diet is essential for maintaining a healthy gut microbiome, which supports the integrity of the intestinal barrier and immune tolerance.[203.1] Conversely, an unbalanced diet, such as the typical Western diet, can lead to reduced diversity and dysbiosis of the gut microbiome, resulting in conditions like leaky gut and chronic inflammation.[203.1] Despite the importance of these interactions, current dietary guidelines have not adequately integrated the knowledge of diet-microbiome-host interactions, which is vital for health promotion.[202.1] Therefore, there is a pressing need for the systematic incorporation of microbiome science into nutrition research to refine and innovate dietary recommendations.[202.1]Impact on Immune System
The human microbiome plays a crucial role in the development and function of the immune system, influencing both innate and adaptive immune responses. Evidence suggests that the infant gut microbiome is fundamental in immune development during the perinatal and neonatal periods, directing intestinal development and training the immune system.[204.1] The intrauterine environment provides initial stimulation for the fetal innate immune system, establishing a foundation for immune function.[204.1] Microbiota contribute to various immune functions, including the production of cytokines, maintenance of immune homeostasis, and regulation of T cell responses.[205.1] Short-chain fatty acids, such as butyrate, produced by gut microbiota, enhance the antipathogenic function of CD8+ T cells by up-regulating interferon-gamma (IFN-γ).[205.1] Additionally, the microbiome interacts with immune system components, influencing the differentiation and efficacy of immune responses.[205.1] The intestinal microbiome acts as a signaling hub that integrates environmental inputs, such as diet, with genetic and immune signals, thereby affecting the host's metabolism and response to infections.[206.1] This interplay highlights the microbiome's significant role in shaping immune responses and its potential implications for disease susceptibility and resistance.[206.1] Understanding these interactions is essential for developing targeted therapies that leverage the microbiome to enhance immune function and combat diseases.In this section:
Microbiome And Disease
Association with Inflammatory Diseases
The human microbiome has been increasingly recognized for its significant role in the development and modulation of inflammatory diseases. Characterization of the microbiome in healthy individuals is essential for understanding its contributions to health and disease, as healthy adult humans typically harbor over 1000 species of bacteria, predominantly from the phyla Bacteroidetes and Firmicutes.[208.1] The commensal, symbiotic, and pathogenic microbial communities residing in the human body can influence host energy metabolism and immunity, thereby affecting the development of various inflammatory diseases.[209.1] Research indicates that the composition and diversity of the microbiome are linked to several inflammatory conditions, including autoimmune diseases and metabolic disorders.[218.1] For instance, chronic inflammatory responses induced by dysbiosis in gut microbiota have been implicated in the pathogenesis of autoimmune diseases such as systemic lupus erythematosus (SLE). Patients with active SLE exhibit altered gut microbiota profiles, characterized by changes in specific genera, which may contribute to disease severity.[225.1] Furthermore, the gut microbiota plays a crucial role in maintaining health by performing functions such as food fermentation, pathogen protection, and immune system stimulation.[212.1] Disruptions in these microbial communities can lead to dysbiosis, which has been associated with the exacerbation of inflammatory diseases. For example, interventions such as oral antibiotic administration during active SLE can reshape the gut microbiota, potentially ameliorating systemic autoimmunity.[225.1] The exploration of microbiome profiles has also led to the identification of potential biomarkers for disease prediction and diagnosis, highlighting the microbiome's role as a valuable tool in understanding inflammatory diseases.[218.1] Advances in sequencing technologies and bioinformatics have improved the accuracy of microbiome data, paving the way for personalized treatments that target specific microbial signatures associated with inflammatory conditions.[221.1]In this section:
Dietary Influences On Microbiome
Effects of Macronutrients
The effects of macronutrients on the gut microbiome are significant and vary notably between high-fat and high-fiber diets. High-fat diets (HFD) have been shown to induce obesity and alter gut microbiota composition, leading to inconsistent results regarding their impact on microbiome diversity. Specifically, HFDs have been associated with a decrease in the abundance of Ruminococcaceae and an increase in Rikenellaceae, indicating a shift in the dominant gut bacteria.[264.1] Furthermore, studies have established a correlation between HFDs and changes in gut microbiota diversity, with a notable reduction in Bacteroidetes and an increase in Firmicutes.[265.1] The prevalence of metabolic diseases, such as obesity and diabetes, has surged in recent decades, largely attributed to the consumption of high-fat diets. These diets are linked to specific alterations in the composition and function of the gut microbiome, which may contribute to the pathogenesis of these diseases.[266.1] Research indicates that the gut microbiota responds to dietary changes in a linear dose-dependent manner, with significant shifts occurring within an average of 3.5 days following dietary perturbations.[267.1] In contrast, high-fiber diets have been shown to positively influence the gut microbiome by promoting the growth of beneficial bacteria. For instance, a high-fiber diet derived from pulse sources, such as pea fiber, has been hypothesized to improve microbial composition and diversity compared to low-fiber diets.[268.1] Short-term interventions have demonstrated that increased fiber intake can lead to compositional changes in the gut microbiome, including an increase in fiber-degrading bacteria like Bifidobacterium and Lactobacillus.[269.1] The decline in dietary fiber consumption over the past century is thought to correlate with the rising prevalence of health issues such as type II diabetes and colon cancer, underscoring the importance of dietary fiber in maintaining a healthy gut microbiome.[269.1]Role of Prebiotics and Probiotics
Prebiotics and probiotics play a significant role in fostering a healthy gut microbiome, which is essential for overall health. High-fiber diets that include prebiotics and probiotics are known to promote a healthy gut microbiome.[260.1] Research indicates that a diverse gut microbiome, supported by the consumption of high-fiber foods such as vegetables, nuts, and healthy animal products, is associated with lower risks of chronic diseases, including heart disease, type 2 diabetes, and obesity.[258.1] Furthermore, incorporating prebiotic and probiotic supplements into one's diet may enhance gut health, while reducing the intake of processed, sugary, and high-fat foods can also contribute positively to gut microbiome health.[262.1] Overall, emphasizing minimally processed plant foods allows the gut microbiome to thrive and provides protection against various chronic diseases.[258.1] Probiotics, found in fermented foods, also contribute to gut health by introducing beneficial microorganisms into the digestive system. Research indicates that consuming fermented foods can enhance gut microbiome diversity and reduce inflammation markers.[271.1] The microbiome of fermented food products can have varied effects on the host gut microbiome, with many resident bacteria associated with beneficial responses.[270.1] However, the effects of commercial fermented products may differ from those studied in clinical settings, highlighting the need for further research to establish optimal consumption practices.[271.1] The health of the gut microbiome is critically influenced by dietary choices, particularly the consumption of added sugars and highly processed foods. Research indicates that added sugars are known to decrease beneficial gut bacteria and increase inflammation, which can lead to dysbiosis and a compromised intestinal barrier.[261.1] A nutritionally balanced diet is essential for maintaining a healthy gut microbiome, the integrity of the intestinal barrier, and normal gut physiology. In contrast, an unbalanced diet, such as the typical Western diet, results in reduced diversity within the gut microbiome, potentially leading to chronic inflammation and conditions like inflammatory bowel disease (IBD).[259.1] Given the overwhelming nature of dietary changes, individuals can improve their chances of success by viewing the transition to a healthier eating plan as a long-term project and proceeding gradually.[261.1] Therefore, incorporating prebiotics and probiotics into the diet while reducing the intake of processed and sugary foods can be beneficial for enhancing gut health and promoting a more diverse and resilient gut microbiome.[259.1]Future Directions In Microbiome Research
Emerging Therapeutic Approaches
Recent advancements in microbiome research have catalyzed the development of innovative therapeutic strategies that harness the microbiome's potential for health improvement. The "precision microbiome" approach, which involves detailed analysis and characterization of microbiota in specific hosts using high-throughput sequencing and artificial intelligence (AI), has become a focal point in this field.[298.1] This precision enables the exploration of intricate microbiota-host interactions, essential for crafting targeted therapies. A key area of interest is the modulation of the human microbiome to positively influence health outcomes. This strategy holds promise for addressing both acute and chronic diseases by engineering the microbiome for therapeutic purposes.[300.1] By utilizing the unique signatures provided by human microbiomes, researchers can enhance disease prediction and treatment, facilitating early detection and personalized therapeutic strategies.[299.1] The integration of advanced sequencing technologies and bioinformatics is crucial for accurate microbiome data, which underpins effective disease diagnosis and management. Incorporating microbiome data into personalized medicine is increasingly vital, as microbial communities significantly affect individual treatment responses, including medication efficacy and potential side effects.[301.1] By integrating microbiome analysis into clinical decision-making, healthcare providers can better understand treatment responses, thereby improving patient outcomes.[303.1] However, challenges such as the need for standardized methods and ethical guidelines regarding informed consent and privacy must be addressed.[306.1] Recent advancements in single-cell isolation and sequencing technologies offer promising solutions for analyzing host-microbiome interactions, particularly in clinical settings where patient outcomes are closely linked to individual physiologies and immune responses.[315.1] Dual single-cell RNA sequencing (scRNA-seq) techniques have emerged as powerful tools, capturing and sequencing the mRNA of both host and microbial cells in bacterially exposed environments.[316.1] These methodologies have shown significant potential in elucidating the complexities of host-microbe interactions, enhancing our understanding of these critical relationships.[316.1]Integration with Public Health Policies
The integration of microbiome science into public health policies is increasingly recognized as essential for addressing health outcomes at both individual and community levels. Recent global summits, such as ‘Microbiomes, Biodiversity & Their Impact on Global and One Health’, have highlighted the need for a comprehensive roadmap that incorporates microbiome considerations into the One Health framework. These summits brought together microbiome scientists, industry leaders, and public health experts to discuss strategies for monitoring microbiome shifts, which can serve as early warning systems for disease risks, and to explore how legal frameworks can embed microbiome insights into public health and agricultural policies.[312.1] Despite the promising potential of microbiome research, there are significant challenges that must be addressed to standardize methodologies across studies. Issues such as sample storage, microbial sharing among animals, and longitudinal microbial instability complicate the research landscape.[314.1] Furthermore, while much of the current research has focused on individual health, there is a critical need to expand this focus to public health implications, given the shared nature of the human microbiome across communities.[313.1] To enhance collaboration between microbiome researchers and public health officials, cross-sectoral conversations are vital. Such dialogues can facilitate the integration of emerging evidence into health systems and identify areas requiring further research.[331.1] Initiatives like the Nature Awards Microbiome Accelerator and the Microbiome Times Partnering Forum are beginning to foster collaboration between basic researchers and industry, which is crucial for translating microbiome research into actionable public health strategies.[332.1] Additionally, fostering partnerships that include social and population scientists alongside biologists will be essential to fully realize the potential of microbiome research in modifying health outcomes.[333.1]In this section:
References
[3] The Healthy Human Microbiome - National Institutes of Health (NIH) — The accomplishment sets the stage for better understanding how bacterial communities affect human health and disease. The human body is host to trillions of microbes. These microbes outnumber the body's cells by 10 to 1. Most of the time they are beneficial to human health, but sometimes they can cause illness.
[4] Human microbiome | Definition, Examples, & Facts | Britannica — Human microbiome | Definition, Examples, & Facts | Britannica human microbiome, the full array of microorganisms (the microbiota) that live on and in humans and, more specifically, the collection of microbial genomes that contribute to the broader genetic portrait, or metagenome, of a human. Knowledge of the human microbiome expanded appreciably after 2007, the year the Human Microbiome Project (HMP)—a five-year-long international effort to characterize the microbial communities found in the human body and to identify each microorganism’s role in health and disease—was launched. Some of the most commonly used probiotics are lactic-acid bacteria, namely strains of Lactobacillus and Streptococcus, which are normal components of the human microbiome and have been used for centuries in the production of yogurt, cheese, and some pickled foods. https://www.britannica.com/science/human-microbiome
[5] Integration of 168,000 samples reveals global patterns of the human gut ... — The human microbiome is an important factor in understanding health and disease. Systematic differences have been observed between the composition of the microbiome in healthy individuals and those with microbiota-linked conditions such as colorectal cancer 1,2,3 and inflammatory bowel disease, 4 informing the importance of understanding the determinants of variation in the microbiome. Studies
[6] Diversity, compositional and functional differences between gut ... — In GenR, individuals who used antibiotics in the last year had a significantly lower microbiome diversity and altered microbiome composition (Supp. Table 1). For probiotic use and recent travelling activity outside the Netherlands we could not detect significant effects on diversity or composition in the two cohorts (Supp. Table 1).
[8] Factors Affecting Microbiome Health and Stability — Such diets are associated with increased microbial diversity, which is often linked to better health outcomes. Conversely, diets high in processed foods, refined sugars, and unhealthy fats can negatively influence the microbiome. These dietary patterns often lead to a reduction in microbial diversity and an increase in pro-inflammatory bacteria.
[9] Human microbiome acquisition and transmission - Nature — Having siblings was identified as one of the main factors influencing microbiome composition in early life 56, with the presence of older siblings associated with higher gut microbiome diversity
[11] Harvard Chan Microbiome in Public Health Center — The mission of the Harvard Chan Microbiome in Public Health Center (HCMPH) is to expand our understanding of the microbiome to improve population health, through basic research, translation, policy, education, and outreach. The Microbiome Collection Core at the Harvard T.H. Chan School of Public Health (HCMCC) was established in response to a strong demand among the research community for validated microbiome sample collection kit configurations and easy usability for in-home sampling. The Harvard T.H. Chan Microbiome Analysis Core (HCMAC), established to advance the rapidly emerging field of microbiome science, aids in human microbiome study design and interpretation, helping researchers develop and apply quantitative methods to investigate the role of microbial community function in health.
[13] Leveraging human microbiomes for disease prediction and treatment — Leveraging human microbiomes for disease prediction and treatment - ScienceDirect Leveraging human microbiomes for disease prediction and treatment The human microbiome is key to health, providing unique signatures that may enable early disease detection and prevention. Advances in 16S rRNA and metagenomics sequencing, along with bioinformatics pipelines, improve microbiome data accuracy for disease diagnosis and personalized treatments. Standardized methods, comprehensive data, and integration of advanced sequencing with epidemiological methods provide scope for individualized, microbiome-based disease prevention. Microbiome predictors of human disease Exploration of the role of the human microbiome in health and disease has highlighted both its potential and challenges in clinical applications. An integrated catalog of reference genes in the human gut microbiome
[14] The Impact of Dietary Fiber on Gut Microbiota in Host Health and ... — The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease - ScienceDirect Search ScienceDirect The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease Type, quality, and origin of our food shape our gut microbes and affect their composition and function, impacting host-microbe interactions. In this review, we will focus on dietary fibers, which interact directly with gut microbes and lead to the production of key metabolites such as short-chain fatty acids, and discuss how dietary fiber impacts gut microbial ecology, host physiology, and health. Previous article in issue Next article in issue Recommended articles © 2018 Elsevier Inc. Recommended articles No articles found. Article Metrics View article metrics For all open access content, the Creative Commons licensing terms apply.
[46] Harnessing the Human Microbiome: 30 Years of Discovery and Innovation ... — The human microbiome has evolved into a key area of biopharma innovation, thanks to advances in genomics and sequencing. Research has revealed its major role in health, disease, and treatments. Breakthroughs include fecal microbiota transplants and FDA-approved live biotherapeutics, reshaping personalized medicine. This journey highlights key milestones, therapies, and challenges, showcasing
[47] The origins of gut microbiome research in Europe: From Escherich to ... — Microbiome research is rapidly changing the way we understand medicine. However, unbeknownst to many, several critical milestones of microbiome research took place in the late 1800s in Europe. In this article, we review the most important contributions in the area of microbiome research by leading scientists in Europe. Following the initial observations of intestinal microorganisms, German
[48] Microbiome definition re-visited: old concepts and new challenges — The history of microbiome research from seventieth century until our days, highlighting the shift of the paradigm from microbes as unsocial organisms causing diseases to the holistic view of microorganisms being the center of the One Health Concept: positively interconnecting all areas of our lives.
[49] The origins of human microbiota research - Nature — Research into human-associated microbiota has come a long way since Antonie van Leeuwenhoek first began to study microorganisms back in the 17th century. ... If we accept that the microbiome is
[51] The Influence of the Microbiome on Drug Action - AZoLifeSciences — The advancements in genome sequence technologies and metagenomic analysis have paved the way for scientists to explore the human microbiome. The human microbiome can be described as the genomic sequence of all microbes residing inside the human body.
[53] Drug-microbiota interactions: an emerging priority for precision ... — The term pharmacomicrobiomics has been coined to describe the interactions between gut microbiota and drug response that can alter PK (i.e., changes in drug absorption, distribution, metabolism, excretion, and its plasma drug concentration dynamics) or PD (i.e., changes in drug targets or biological pathways resulting in differential susceptibility of the organism to pharmacological effects).59,60,61,62,63,64,65 Understanding this interaction can help develop microbiota-targeted approaches to enhance drug efficacy and reduce ADRs.66,67,68 Clearly, pharmacomicrobiomics is becoming an integral part of the advances in precision medicine, and modifying gut microbiota could be a highly appealing option for managing the efficiency and safety of drugs at an individualistic level.58,61 This review outlines pharmacomicrobiomics advances in human diseases to better understand the impact of IVDR in future precision medicine.
[63] Antonie van Leeuwenhoek - Wikipedia — By the end of his life, Van Leeuwenhoek had written approximately 560 letters to the Royal Society and other scientific institutions concerning his observations and discoveries. ^ Van Leeuwenhoek is universally acknowledged as the father of microbiology because he was the first to undisputedly discover/observe, describe, study, conduct scientific experiments with microscopic organisms (microbes), and relatively determine their size, using single-lensed microscopes of his own design. Leeuwenhoek is also considered to be the father of bacteriology and protozoology (recently known as protistology). Schierbeek, Measuring the Invisible World: The Life and Works of Antoni van Leeuwenhoek F R S, Abelard-Schuman (London and New York, 1959), QH 31 L55 S3, LCCN 59-13233. ^ Life and work of Antoni van Leeuwenhoek of Delft in Holland; 1632–1723 (1980) Published by the Municipal Archives Delft, p.
[69] Harvard Chan Microbiome in Public Health Center — The mission of the Harvard Chan Microbiome in Public Health Center (HCMPH) is to expand our understanding of the microbiome to improve population health, through basic research, translation, policy, education, and outreach. The Microbiome Collection Core at the Harvard T.H. Chan School of Public Health (HCMCC) was established in response to a strong demand among the research community for validated microbiome sample collection kit configurations and easy usability for in-home sampling. The Harvard T.H. Chan Microbiome Analysis Core (HCMAC), established to advance the rapidly emerging field of microbiome science, aids in human microbiome study design and interpretation, helping researchers develop and apply quantitative methods to investigate the role of microbial community function in health.
[84] Microbiologists and Their Discoveries: Pioneering Contributions to ... — 1. Antonie van Leeuwenhoek (1632-1723): Father of Microbiology. Discovery of Microorganisms: Antonie van Leeuwenhoek, a Dutch tradesman and scientist, is credited with inventing the microscope and being the first to observe microorganisms. In the 17th century, he examined water samples and dental plaque, describing the microscopic world for the first time.
[85] History of Microbiology - Biology Notes Online — The field of scientific microbiology further developed in the 19th century through the work of pioneers such as Louis Pasteur and Robert Koch. Microbiology, the study of microscopic living organisms, is a relatively recent scientific field that has significantly advanced our understanding of biology and disease. The Transitional Period in microbiology was marked by a shift from the belief in spontaneous generation to a more scientific understanding of microorganisms and disease transmission. This period was characterized by significant advances in the understanding of microorganisms and their roles in disease, fermentation, and other biological processes. Theory: Pasteur’s work led to the development of the germ theory of disease, which posits that microorganisms are the cause of many diseases.
[86] History of Microbiology and Contributors in Microbiology - Microbe Notes — The Golden age of microbiology began with the work of Louis Pasteur and Robert Koch who had their own research institute. Around the same time that Pasteur was doing his experiments, a doctor named Robert Koch was working on finding the causes of some very nasty animal diseases (first anthrax, and then tuberculosis). He proposed Koch postulate which were published in 1884 and are the corner stone of the germ theory of diseases and are still in use today to prove the etiology (specific cause) of an infectious disease. Thus contribution of Robert Koch, Fanny Angelina Hesse and Richard Petri made possible the isolation of pure cultures of microorganisms and directly stimulated progress in all areas of microbiology.
[91] 7 Microbiome Discoveries That Will Change How You "Do Health" In ... - Seed — In the last two decades, scientific exploration into the microbiome has skyrocketed, with over $1.7 billion spent on human microbiome research since 2009.1 Advancements in sequencing technology empowered discoveries that elucidate the microbiome's critical role in health and disease, charted the development of the infant microbiome, and have even begun to define how our behavior can shape
[92] New opportunities in mechanistic and functional microbiome studies — The field of microbiome research has experienced remarkable growth, leading to unprecedented discoveries of the molecular mechanisms that dictate host-microbiota interactions and their crucial roles in human health. In this "chemical biology of the microbiome" focus issue from Cell Chemical Biology, this Voices piece asks researchers from a range of backgrounds to share their insights on
[98] Recent Advances of Bacterial Microbiome in Human Health — Find a journal Publish with us Track your research Recent Advances of Bacterial Microbiome in Human Health Recent research has unveiled the intricate interactions between the bacterial microbiome and various physiological processes, highlighting its potential as a therapeutic target for improving human health outcomes. This Collection seeks to consolidate the latest advancements in bacterial microbiome research to provide a comprehensive understanding of its impact on human health. The primary goal of this Collection is to showcase the most recent discoveries and breakthroughs in bacterial microbiome research and their implications for human health. Keywords: bacterial microbiome, human health, physiology, disease, metabolites, biomarkers Journal Discover Bacteria is an open access journal publishing research from all fields relevant to bacteriology. Find a journal
[100] Leveraging human microbiomes for disease prediction and treatment — Leveraging human microbiomes for disease prediction and treatment - ScienceDirect Leveraging human microbiomes for disease prediction and treatment The human microbiome is key to health, providing unique signatures that may enable early disease detection and prevention. Advances in 16S rRNA and metagenomics sequencing, along with bioinformatics pipelines, improve microbiome data accuracy for disease diagnosis and personalized treatments. Standardized methods, comprehensive data, and integration of advanced sequencing with epidemiological methods provide scope for individualized, microbiome-based disease prevention. Microbiome predictors of human disease Exploration of the role of the human microbiome in health and disease has highlighted both its potential and challenges in clinical applications. An integrated catalog of reference genes in the human gut microbiome
[101] Genome-resolved metagenomics: a game changer for microbiome medicine — In the last decade, genome-resolved metagenomics, which aims to reconstruct microbial genomes directly from whole-metagenome sequencing data, has made significant strides and continues to unveil the mysteries of various human-associated microbial communities. This review provides an overview of the capabilities and methods of genome-resolved metagenomics for studying the human microbiome, with a focus on investigating the prokaryotic microbiota of the human gut. For many years, human microbiome research has adopted methodologies based on bacterial phylogeny and taxonomy, particularly 16S rRNA gene sequence analysis1, which is adequate for revealing differences in taxonomic composition between diseased microbiomes and their healthy counterparts. The study focuses on the gut microbiome, using advanced computer methods to build metagenome-assembled genomes from DNA sequencing data. Researchers conclude that genome-resolved metagenomics is a significant advancement in microbiome research, offering understanding of microbial communities and their functions.
[103] Next-generation sequencing: insights to advance clinical investigations ... — Next-generation sequencing (NGS) technology has advanced our understanding of the human microbiome by allowing for the discovery and characterization of unculturable microbes with prediction of their function. ... Finally, we share insights as to how NGS might further be integrated into and advance microbiome research and clinical care in the
[105] Precision Microbiome: A New Era of Targeted Therapy with Core ... — In recent years, the concept of "precision microbiome" has received a lot of attention from researchers. It involves the precise analysis and typing of microbiota in specific hosts (e.g., humans or animals) using advanced tools like high-throughput sequencing, genomics, and artificial intelligence (AI). These tools help explore the complex interactions between microbiota and hosts to
[106] Unveiling microbial diversity: harnessing long-read sequencing ... — Long-read sequencing has recently transformed metagenomics, enhancing strain-level pathogen characterization, enabling accurate and complete metagenome-assembled genomes, and improving microbiome taxonomic classification and profiling. These advancements are not only due to improvements in sequencing accuracy, but also happening across rapidly changing analysis methods. In this Review, we
[107] Leveraging human microbiomes for disease prediction and treatment — Leveraging human microbiomes for disease prediction and treatment - ScienceDirect Leveraging human microbiomes for disease prediction and treatment The human microbiome is key to health, providing unique signatures that may enable early disease detection and prevention. Advances in 16S rRNA and metagenomics sequencing, along with bioinformatics pipelines, improve microbiome data accuracy for disease diagnosis and personalized treatments. Standardized methods, comprehensive data, and integration of advanced sequencing with epidemiological methods provide scope for individualized, microbiome-based disease prevention. Microbiome predictors of human disease Exploration of the role of the human microbiome in health and disease has highlighted both its potential and challenges in clinical applications. An integrated catalog of reference genes in the human gut microbiome
[108] Bioinformatics for Human Microbiome | SpringerLink — Advances in Bioinformatics. Chapter. Bioinformatics for Human Microbiome. Chapter; First Online: 01 August 2021; pp 333-350; Cite this chapter; Download book PDF. ... Presently, microbiome research field has bloomed with generation of massive datasets and development of huge number of analysis tools. However, the complexity of the workflows
[109] MicrobiomeAnalyst 2.0: comprehensive statistical, functional and ... — The resulting complex, often multi-omics datasets demand powerful, yet user-friendly bioinformatics tools to reveal key patterns, important biomarkers, and potential activities. Here we introduce MicrobiomeAnalyst 2.0 to support comprehensive statistics, visualization, functional interpretation, and integrative analysis of data outputs commonly
[110] HONMF: integration analysis of multi-omics microbiome data via matrix ... — Recently, unsupervised learning methods have been developed to integrate multi-omics data from the same samples, including the SNF framework and its variants (Wang et al. 2014, Zhang et al. 2017, Liu and Shang 2018), but these methods are not initially designed for microbiome data analysis. The integration methods for multi-omics microbiome
[114] Leveraging human microbiomes for disease prediction and treatment — Leveraging human microbiomes for disease prediction and treatment - ScienceDirect Leveraging human microbiomes for disease prediction and treatment The human microbiome is key to health, providing unique signatures that may enable early disease detection and prevention. Advances in 16S rRNA and metagenomics sequencing, along with bioinformatics pipelines, improve microbiome data accuracy for disease diagnosis and personalized treatments. Standardized methods, comprehensive data, and integration of advanced sequencing with epidemiological methods provide scope for individualized, microbiome-based disease prevention. Microbiome predictors of human disease Exploration of the role of the human microbiome in health and disease has highlighted both its potential and challenges in clinical applications. An integrated catalog of reference genes in the human gut microbiome
[115] From big data and experimental models to clinical trials: Iterative ... — Microbiome research has expanded significantly in the last two decades, yet translating findings into clinical applications remains challenging. This perspective discusses the persistent issue of correlational studies in microbiome research and proposes an iterative method leveraging in silico, in vitro, ex vivo, and in vivo studies toward successful preclinical and clinical trials. The
[122] Methodology for biomarker discovery with reproducibility in microbiome ... — Background: In recent years, human microbiome studies have received increasing attention as this field is considered a potential source for clinical applications. With the advancements in omics technologies and AI, research focused on the discovery for potential biomarkers in the human microbiome using machine learning tools has produced positive outcomes.
[129] The microbiome: Composition and locations - PubMed — The composition of these spatially distinct microbial consortia can be impacted by a variety of stochastic and det … The human body is home to a diverse and functionally important assemblage of symbiotic microbes that varies predictably over different spatial scales, both within and across body sites.
[131] What is the microbiome? | ADC Education & Practice Edition — Microbiome composition. Unlike the host genome, which is relatively constant, the microbiome is dynamic and changes with early development, environmental factors such as diet and use of antibiotics and especially in response to disease.4 The most dramatic changes in composition occur in infancy and early childhood.5 The intestinal microbiome of an infant is affected by gestational age (full
[137] Integration of 168,000 samples reveals global patterns of the human gut ... — The human microbiome is an important factor in understanding health and disease. Systematic differences have been observed between the composition of the microbiome in healthy individuals and those with microbiota-linked conditions such as colorectal cancer 1, 2, 3 and inflammatory bowel disease, 4 informing the importance of understanding the determinants of variation in the microbiome.
[138] Diversity, compositional and functional differences between gut ... — The above-mentioned considerations prompted us to profile the stool microbiome composition of children and adults within two large, independent and extensively characterized population-based cohorts: the Generation R Study (GenR, visit at 9 years) and the Rotterdam Study (RS, sub-cohort RSIII-2). In this publication we report on the 16S stool microbiota profiles of 3,538 subjects from two large, deeply phenotyped and well-characterized population-based cohorts: the Generation R (GenR) Study and the Rotterdam Study (RS). Thus, as both our RS and GenR datasets contain many characteristics that are similar to previously published large cohort studies, we conclude that our datasets allow valid investigations into the composition and variation of the gut microbiota across child and adult subjects.
[139] Gut physiology and environment explain variations in human gut ... — To quantify how participant characteristics, clinical variables, diet and gut environmental and physiological factors explain inter-individual variations in the gut microbiome and metabolomes, we performed a db-RDA using data derived from faecal and 24 h urine collections on day 2 from all participants (n = 61; Supplementary Table 4). N.P., T.R.L., L.O.D. and H.M.R. conceived and designed the human study as part of the PRIMA collaboration headed by T.R.L. N.P. conducted the study under the supervision of L.O.D. and H.M.R. Urine metabolomics was performed by N.P. Metabolite annotations were done by N.P., G.L.B. and L.O.D. Metabolite synthesis and fine identification were done by G.L.B. Faecal SCFAs were analysed by E.T. and N.P. The faecal metabolome was analysed by M.S.J. and N.P. M.F.L. generated the microbiome data.
[169] Microbiota's role in health and diseases - PMC - PubMed Central (PMC) — Recent studies have indicated the tremendous influence of the microbiome on health and disease. ... type is known as lysogenic phages that integrate their DNA in the bacterial genome and replicate passively with the bacteria. As bacteriophages are host-specific, they ... (2010) Cardiovascular disease and the role of oral bacteria. Journal of
[170] A systematic framework for understanding the microbiome in human health ... — analyzed microbiomes in femoral arteries from brain-dead donors, mainly those with hemorrhagic or ischemic strokes.65 They identified Proteobacteria, Firmicutes, and Actinobacteria as the predominant phyla, with Staphylococcus, Pseudomonas, Corynebacterium, Bacillus, Acinetobacter, and Propionibacterium being prevalent genera.65 Additionally, they observed a notable correlation between blood type and microbiota diversity.65 Although limitations such as the small sample size (14 participants) and the older age range of donors (40–60 years) reduce the power of this study and the lack of characterization of microbial function,65 it however provides valuable insights into the possible presence of the microbiome in the normal human vasculature and potential research directions for unraveling vasculature-based diseases.
[171] Microbiota in health and diseases — Gut microbiota is considered the most significant one in maintaining our health.4 The gut bacteria serve several functions, such as fermentation of food, protection against pathogens, stimulating immune response, and vitamin production.5 Generally, the gut microbiota is composed of 6 phyla including Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia, among which Firmicutes and Bacteroidetes are the major types.6 The most studied fungi (gut mycobiota) are Candida, Saccharomyces, Malassezia, and Cladosporium.7 In addition to bacteria and fungi, the human gut microbiota also contain viruses, phages, and archaea, mainly M. How informative is the mouse for human gut microbiota research?
[172] Role of microbes in human health and disease - National Human Genome ... — The researchers applied these methods to study three model microbiome-associated conditions: preterm birth, inflammatory bowel disease (IBD) and prediabetes. The iHMP has produced the largest collection of biological information on microbial community composition and gene expression, proteins, metabolites and immune system properties from both the human body and its microbiome followed over time through three microbiome-related conditions. By tracking biological features within the human body and its microbiome, the iHMP projects revealed that loss or gain of certain microbes and their properties is closely associated with the state of preterm birth, IBD and prediabetes in individuals.
[173] The Human Microbiome and Its Impacts on Health - PMC — These organisms impact human physiology, both in health and in disease, contributing to the enhancement or impairment of metabolic and immune functions. It is therefore important to understand the microbial composition and activities of the human microbiome as they contribute to health and disease. The human microbiome is referred to as the genomic content of organisms (microbiota) inhabiting a particular site in the human body. In addition, further studies should emphasize on the effects of the human microbiome on mental health and also the impacts of mycobiome and the virome community on indigenous microbiota as they may contribute to dysbiosis. K. The gut microbiota shapes intestinal immune responses during health and disease. K. The human gut microbiome-a potential controller of wellness and disease.
[190] Interactions between dietary fibre and the gut microbiota — However, fibres differ in their physicochemical properties, their effects on the gut and their fermentation characteristics. The diversity of carbohydrates and associated molecules in fibre-rich foods can have a major influence on microbiota composition and production of bioactive molecules, for example SCFAs and phenolic acids.
[191] The mutual effect of dietary fiber and polyphenol on gut microbiota ... — Gut microbiota plays a critical role in maintaining human health by regulating digestion, metabolism, and immune function. Emerging research highlights the potential of dietary interventions, particularly dietary fiber (DF) and polyphenols, in modulating gut microbiota composition and function. DF serves as a fermentable substrate for beneficial gut bacteria, promoting the production of short
[197] The Human Microbiome and Its Impacts on Health - PMC — These organisms impact human physiology, both in health and in disease, contributing to the enhancement or impairment of metabolic and immune functions. It is therefore important to understand the microbial composition and activities of the human microbiome as they contribute to health and disease. The human microbiome is referred to as the genomic content of organisms (microbiota) inhabiting a particular site in the human body. In addition, further studies should emphasize on the effects of the human microbiome on mental health and also the impacts of mycobiome and the virome community on indigenous microbiota as they may contribute to dysbiosis. K. The gut microbiota shapes intestinal immune responses during health and disease. K. The human gut microbiome-a potential controller of wellness and disease.
[199] The Human Microbiome: Its Impact on Health and Disease — The Human Microbiome: Its Impact on Health and Disease - BiologyInsights Explore how the human microbiome influences health, immunity, metabolism, and neurological functions. The human microbiome, a community of trillions of microorganisms residing in and on our bodies, plays a role in maintaining health. Its influence extends beyond digestion to areas such as immune function, metabolism, and neurological health. The human microbiome is a diverse ecosystem, with each individual hosting a unique microbial signature influenced by genetics, diet, environment, and lifestyle. The connection between the microbiota and the brain, often referred to as the “gut-brain axis,” is a burgeoning area of research that highlights the influence of gut bacteria on neurological health. Microbial-induced changes in immune function can impact brain health by influencing neuroinflammation, a factor implicated in conditions like depression and Alzheimer’s disease.
[201] Gut microbiome and its potential link to personalized nutrition — Diet is increasingly appreciated to have a tremendous impact on many aspects of the host's biology in health and disease. Dietary content and timing are also central in shaping the gut microbiome, and contribute to its taxonomic and functional diversity. Regardless, current dietary recommendations remain largely non-personalized, and feature disappointing long-term efficacy in treating
[202] Rethinking healthy eating in light of the gut microbiome — Evidence-based dietary guidelines are crucial for health promotion but so far have not considered the gut microbiome. Armet et al. review how the knowledge of diet-microbiome-host interactions can validate, refine, and innovate dietary guidelines. They advocate for the systematic integration of microbiome science into nutrition research to further improve healthy eating.
[203] Influence of Foods and Nutrition on the Gut Microbiome and Implications ... — Keywords: gut microbiome, gut microbiota, nutrition, foods, dietary fiber, dietary fats, dietary protein, intestinal health, colitis, IBD A nutritionally balanced diet is critical for maintaining a healthy gut microbiome, the integrity of the intestinal barrier, immune tolerance, and normal gut physiology, whereas an unbalanced diet, like the typical western diet, results in reduced diversity and dysbiosis of the gut microbiome, which can lead to a leaky gut and chronic inflammation, as seen in IBD. 97.Ren Y., Geng Y., Du Y., Li W., Lu Z.M., Xu H.Y., Xu G.H., Shi J.S., Xu Z.H. Polysaccharide of Hericium erinaceus attenuates colitis in C57BL/6 mice via regulation of oxidative stress, inflammation-related signaling pathways and modulating the composition of the gut microbiota. 105.Lanklema J.M., Cranendonk D.R., Belzer C., de vos A.F., de vos W.M., van der Poll T., Wiersinga W.J. Antibiotic-induced gut microbiota disruption during human endotoxemia: A randomized controlled study.
[204] The microbiome and immune system development - ScienceDirect — There is overwhelming evidence that the infant gut microbiome plays a fundamental role in immune development in the perinatal and neonatal period, assisting in directing the development of the intestines and in both innate and adaptive immune training , .The intrauterine environment provides initial stimulation and signaling for the fetal innate immune system, and passive immunity is
[205] Impact of the Microbiome on the Immune System - PMC - PubMed Central (PMC) — Short-chain fatty acids, like butyrate, are a common product of gut microbiota which potentially enhance the antipathogenic function of CD8+ T cells via up-regulation of IFN-γ.53 CD4+ T cells are helper cells that regulate immune responses through the release of cytokines and activation of other immune components. Microbiota have been linked to multiple immune functions, including the production of cytokines, maintenance of homeostasis, T cell production, and regulation of the immune system.75–77 The microbiome is involved in heavy interplay with the immune system and is affected to a great degree by environmental factors through birth and infancy.78 It has also been identified as a potential player in the development of certain immune system components such as myeloid cell derivatives,79 suggesting that the microbiota have various roles in the differentiation and efficacy of immune responses.
[206] The microbiome and innate immunity | Nature — The intestinal microbiome is a signalling hub that integrates environmental inputs, such as diet, with genetic and immune signals to affect the host's metabolism, immunity and response to infection.
[208] The gut microbiome in health and in disease - PMC - PubMed Central (PMC) — Characterization of the microbiome in healthy individuals is an important initial step in understanding the role of the microbiome in contributing to health and disease. Healthy adult humans each typically harbor more than 1000 species of bacteria belonging to a relatively few known bacterial phyla with Bacteroidetes and Firmicutes being the
[209] Involvement of gut microbiome in human health and disease: brief ... — The commensal, symbiotic, and pathogenic microbial community which resides inside our body and on our skin (the human microbiome) can perturb host energy metabolism and immunity, and thus significantly influence development of a variety of human diseases. Therefore, the field has attracted unprecedented attention in the last decade. Although a large amount of data has been generated, there are
[212] Microbiota in health and diseases — Gut microbiota is considered the most significant one in maintaining our health.4 The gut bacteria serve several functions, such as fermentation of food, protection against pathogens, stimulating immune response, and vitamin production.5 Generally, the gut microbiota is composed of 6 phyla including Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia, among which Firmicutes and Bacteroidetes are the major types.6 The most studied fungi (gut mycobiota) are Candida, Saccharomyces, Malassezia, and Cladosporium.7 In addition to bacteria and fungi, the human gut microbiota also contain viruses, phages, and archaea, mainly M. How informative is the mouse for human gut microbiota research?
[218] Targeting the microbiome to improve human health with the approach of ... — The composition and diversity of the microbiome have been linked to several diseases and conditions, such as metabolic disorders, autoimmune diseases, and even certain types of cancer. Thus, the microbiome serves as a potential source of valuable biomarkers for disease prediction, diagnosis, and prognosis [ , , ].
[221] Leveraging human microbiomes for disease prediction and treatment — Leveraging human microbiomes for disease prediction and treatment - ScienceDirect Leveraging human microbiomes for disease prediction and treatment The human microbiome is key to health, providing unique signatures that may enable early disease detection and prevention. Advances in 16S rRNA and metagenomics sequencing, along with bioinformatics pipelines, improve microbiome data accuracy for disease diagnosis and personalized treatments. Standardized methods, comprehensive data, and integration of advanced sequencing with epidemiological methods provide scope for individualized, microbiome-based disease prevention. Microbiome predictors of human disease Exploration of the role of the human microbiome in health and disease has highlighted both its potential and challenges in clinical applications. An integrated catalog of reference genes in the human gut microbiome
[225] The Dynamic Interplay between the Gut Microbiota and Autoimmune Diseases — Growing experimental and clinical evidence has suggested that the chronic inflammatory response induced by gut microbiota dysbiosis can strongly contribute to the development of autoimmune diseases. SLE patients with active lupus disease possess an altered gut microbiota that differed in the genera Odoribacter and Blautia as well as an unnamed genus in the family Rikenellaceae and exhibit increased representation of gram-negative bacteria. Oral antibiotic administration during active SLE disease might reshape the gut microbiota, remove harmful Lachnospiraceae, increase the relative abundance of Lactobacillus spp., attenuate SLE-like disease in lupus-prone mice termed MRL/lpr mice, and ameliorate systemic autoimmunity and kidney histopathology when given after disease onset .
[258] Diet, disease, and the microbiome - Harvard Health — Diet, disease, and the microbiome - Harvard Health Health conditions such as heart disease, type 2 diabetes, obesity, and general inflammation appeared to be most impacted by diet-influenced changes to the microbiome. In contrast, a more diverse gut microbiome was tied to healthy dietary patterns (high-fiber vegetables like spinach and broccoli, nuts, and, heathy animal foods such as fish and eggs) and was linked to measurements tied to lower risk of certain chronic diseases. Emphasizing minimally processed plant foods allows the gut microbiome to thrive, providing protection against, or decreasing the risk of, chronic diseases such as heart disease, diabetes, metabolic disease, and obesity. The Best Diets for Cognitive Fitness, is yours absolutely FREE when you sign up to receive Health Alerts from Harvard Medical School
[259] Influence of Foods and Nutrition on the Gut Microbiome and Implications ... — Keywords: gut microbiome, gut microbiota, nutrition, foods, dietary fiber, dietary fats, dietary protein, intestinal health, colitis, IBD A nutritionally balanced diet is critical for maintaining a healthy gut microbiome, the integrity of the intestinal barrier, immune tolerance, and normal gut physiology, whereas an unbalanced diet, like the typical western diet, results in reduced diversity and dysbiosis of the gut microbiome, which can lead to a leaky gut and chronic inflammation, as seen in IBD. 97.Ren Y., Geng Y., Du Y., Li W., Lu Z.M., Xu H.Y., Xu G.H., Shi J.S., Xu Z.H. Polysaccharide of Hericium erinaceus attenuates colitis in C57BL/6 mice via regulation of oxidative stress, inflammation-related signaling pathways and modulating the composition of the gut microbiota. 105.Lanklema J.M., Cranendonk D.R., Belzer C., de vos A.F., de vos W.M., van der Poll T., Wiersinga W.J. Antibiotic-induced gut microbiota disruption during human endotoxemia: A randomized controlled study.
[260] Building a Healthy Gut Microbiome - Mayo Clinic Connect — Building a Healthy Gut Microbiome | Mayo Clinic Connect Foods that help create a healthy gut microbiome are prebiotics/fiber and probiotics/fermented foods. High fiber diets containing prebiotics and probiotics promote a healthy gut microbiome. If you would like to meet others who are dealing with this as well, here is a link to a discussion that you might find helpful and interesting, https://connect.mayoclinic.org/discussion/lymphocitic-cholitis/ I would encourage you to read the posts in this discussion. Chicory root fiber, especially when added to processed foods like bars or cereal, can cause gas, bloating, or other GI symptoms. A FODMAP diet can be helpful to help people identify their food triggers, though it can be overly restrictive if used long-term. Related Mayo Clinic Blogs
[261] Resetting gut microbiome is a long-term project - UCLA Health — Added sugars in the diet are known to decrease beneficial gut bacteria, and to increase inflammation, as well. We're talking about a lot of changes here, which can be overwhelming. You can improve your chance of success if you picture this new eating plan as a long-term project and proceed gradually.
[262] How to Improve and Reset Gut Health — Foods for gut health How does the gut microbiome affect your health? There is also some research indicating that food allergies may be related to gut health. While research is ongoing, adding a prebiotic or probiotic supplement to your diet may help improve your gut health. Reducing the amount of processed, sugary, and high fat foods that you eat may lead to better gut health. 4 types of food for gut health Research indicates that high fiber foods have a positive impact on gut health. Still, other research suggests that probiotics may significantly affect the makeup of the gut microbiome and positively impact other areas of health, like immunity. Impacts of gut bacteria on human health and diseases.
[264] High-fat diet alters gut microbiota physiology in mice — High-fat diet caused shifts in the diversity of dominant gut bacteria and altered the proportion of Ruminococcaceae (decrease) and Rikenellaceae (increase). FT-IR spectroscopy revealed that the
[265] Effect of Diet and Dietary Components on the Composition of the Gut ... — Studies have proven that diet is a main contributor to the alteration in gut microbiome diversity, both in the short term and the long term. ... evidence from these studies show a correlation between a high-fat diet and gut microbiota changes; Bacteroidetes were reduced and Firmicutes were increased ... Effect of Plant-Based Diet on Gut Microbiome.
[266] Impact of a High-Fat Diet on the Gut Microbiome: A Comprehensive Study ... — Over the last few decades, the prevalence of metabolic diseases such as obesity, diabetes, non-alcoholic fatty liver disease, hypertension, and hyperuricemia has surged, primarily due to high-fat diet (HFD). The pathologies of these metabolic diseases show disease-specific alterations in the composition and function of their gut microbiome. How HFD alters the microbiome and its metabolite to
[267] Influence of high-fat diet on gut microbiota: a driving forc ... — Their findings indicate that a high-fat and high-sugar diet reproducibly altered the gut microbiota despite differences in host genotype . More specifically, the gut microbiota exhibited a linear dose response to dietary perturbations, taking an average of 3.5 days for each diet-responsive bacterial group to reach a new steady state [5 ] .
[268] Gut Microbiome Responses to a 4-Week High-Fiber Feeding: Preliminary ... — Objectives. Dietary components high in fiber have been shown to uniquely influence the gut microbiome through growth of beneficial bacteria. To determine if fiber from a pulse source (pea fiber) improves microbiome profiles, we tested the hypothesis that a high-fiber (HiFi) diet will result in improvements in microbial composition and diversity compared to a low-fiber (LowFi) diet.
[269] High-Fiber, Whole-Food Dietary Intervention Alters the Human Gut ... — High-Fiber, Whole-Food Dietary Intervention Alters the Human Gut Microbiome but Not Fecal Short-Chain Fatty Acids - PubMed Collectively, our results demonstrate that on a short-term timescale of 2 weeks, increased fiber intake can induce compositional changes of the gut microbiome, including an increase in MAC-degrading bacteria.IMPORTANCE A profound decrease in the consumption of dietary fiber in many parts of the world in the last century may be associated with the increasing prevalence of type II diabetes, colon cancer, and other health problems. The high-fiber diet intervention altered the gut microbiome of the study participants, including increases in known fiber-degrading microbes, such as Bifidobacterium and Lactobacillus. Change in macronutrients across the 3-week diet intervention for fiber (B), carbohydrates (C), protein (D), fat (E), and calories (F).
[270] Fermented Foods, Health and the Gut Microbiome - PMC — The above studies suggest that it is possible for the microbiome of fermented food products to have varied effects on the host gut microbiome, with many of the resident bacteria present in the food microbiome associated with beneficial responses in the gut and able to harbour potentially probiotic microorganisms. 100.Unno T., Choi J.H., Hur H.G., Sadowsky M.J., Ahn Y.T., Huh C.S., Kim G.B., Cha C.J. Changes in human gut microbiota influenced by probiotic fermented milk ingestion. 157.Haller D., Colbus H., Gänzle M.G., Scherenbacher P., Bode C., Hammes W.P. Metabolic and functional properties of lactic acid bacteria in the gastro-intestinal ecosystem: A comparative in vitro study between bacteria of intestinal and fermented food origin.
[271] Why Eat Fermented Foods? | Nutrition - Stanford Medicine — Why Eat Fermented Foods? Why Eat Fermented Foods? Fermented foods provide several health benefits, making them a focus of ongoing scientific research and interest. Studies have shown that consuming fermented foods can positively impact gut microbiome diversity and reduce markers of inflammation. While some fermented foods have been shown to support gut health in clinical studies, commercial products often differ from those studied, making their effects uncertain. Future research is needed to determine the optimal dosage, frequency, and timing of fermented food consumption, as well as their effects on diverse populations. Studies comparing homemade and commercial fermented foods, along with variations in gut microbiome diversity, will be essential for developing evidence-based dietary recommendations. Stanford Health Care Stanford Children's Health
[298] Precision Microbiome: A New Era of Targeted Therapy with Core ... — In recent years, the concept of "precision microbiome" has received a lot of attention from researchers. It involves the precise analysis and typing of microbiota in specific hosts (e.g., humans or animals) using advanced tools like high-throughput sequencing, genomics, and artificial intelligence (AI). These tools help explore the complex interactions between microbiota and hosts to
[299] Leveraging human microbiomes for disease prediction and treatment — Leveraging human microbiomes for disease prediction and treatment - ScienceDirect Leveraging human microbiomes for disease prediction and treatment The human microbiome is key to health, providing unique signatures that may enable early disease detection and prevention. Advances in 16S rRNA and metagenomics sequencing, along with bioinformatics pipelines, improve microbiome data accuracy for disease diagnosis and personalized treatments. Standardized methods, comprehensive data, and integration of advanced sequencing with epidemiological methods provide scope for individualized, microbiome-based disease prevention. Microbiome predictors of human disease Exploration of the role of the human microbiome in health and disease has highlighted both its potential and challenges in clinical applications. An integrated catalog of reference genes in the human gut microbiome
[300] Microbiome and Human Health: Current Understanding, Engineering, and ... — 3. Strategies To Engineer the Microbiome for Therapeutic Applications. As described in section 2, the human microbiome plays a crucial role in health maintenance as it can influence the development of various diseases.This knowledge has led to the emergence of new therapeutic approaches that target both acute and chronic diseases by modulating the host microbiome.
[301] Targeting the microbiome to improve human health with the approach of ... — The microbiome adds another layer of complexity to this equation. Microbial communities can impact how individuals respond to treatments, including medications and therapies. Therefore, integrating microbiome data into personalized medicine approaches enables a more comprehensive understanding of treatment response and potential side effects
[303] Taking it Personally: Personalized Utilization of the Human Microbiome ... — Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease - ScienceDirect Search ScienceDirect Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease The gut microbiome, our “second genome,” dynamically integrates signals from the host and its environment, impacting health and risk of disease. Herein, we summarize how individualized characterization of the microbiome composition and function may assist in personalized diagnostic assessment, risk stratification, disease prevention, treatment decision-making, and patients’ follow up. Previous article in issue Next article in issue Co-first author Copyright © 2016 Elsevier Inc. All rights reserved. No articles found. All content on this site: Copyright © 2025 or its licensors and contributors. For all open access content, the relevant licensing terms apply.
[306] Ethical challenges in conducting and the clinical application of human ... — We highlight the urgent need to develop ethical guidelines concerning informed consent, privacy, microbiome biobanks, disclosure of the results of microbiome research, and translation of human microbiome research into practical applications such as FMT. Acknowledgements. The study was not funded. Notes: Citation to this article:
[312] Microbiomes should be incorporated into The One Health Joint Plan of Action — Two global summits, ‘Microbiomes, Biodiversity & Their Impact on Global and One Health’, held in October 2023 in Annecy, France, and in February 2025 at the University of South Florida (Tampa, FL), brought together a diverse group of microbiome scientists, industry leaders, educators, and food systems experts to develop a roadmap that explicitly integrates microbiomes into the One Health framework. Surveillance systems monitoring microbiome shifts can provide early warnings of disease risks, while legal frameworks could incorporate microbiome considerations into public health and agricultural policies. Open Access Government produces compelling and informative news, publications, eBooks, and academic research articles for the public and private sector looking at health, diseases & conditions, workplace, research & innovation, digital transformation, government policy, environment, agriculture, energy, transport and more.
[313] The Human Microbiome and Public Health: Social and Ethical ... — Rapid advances in human microbiome research point to an increasing range of health outcomes related to the composition of an individual's microbiome. To date, much research has focused on individual health, with a paucity of attention to public health implications. This is a critical oversight owing to the potentially shared nature of the human microbiome across communities and vertical and
[314] Optimizing methods and dodging pitfalls in microbiome research — Other challenges mentioned below include changes associated with sample storage, microbial sharing among animals during cohousing, and authentic longitudinal microbial instability in the body site of a host animal. The goal of this article is to catalog major challenges in microbiome research and to outline approaches to address them.
[315] Host-Microbiome Interactions in the Era of Single-Cell Biology — Recent advancements in single cell isolation and sequencing technologies offer a potential solution to the technically limited analysis of ... The application of our understanding of host-microbiome interactions is especially relevant in a clinical context, where patient outcomes are often tied to their unique physiologies and immune
[316] Single-cell approaches in human microbiome research — Dual scRNA-seq techniques, which leverage existing eukaryote approaches to capture and sequence the mRNA of host and microbes in bacterially exposed host cells, have demonstrated great potential in illuminating host-microbe interactions. In single-cell Dual sequencing (scDual-seq), the first method to simultaneously sequence both host and
[331] The Future of the Microbiome in Public Health - CIFAR — Cross-sectoral conversations between microbiome researchers and public health leaders will help ensure that this emerging evidence can be integrated into our health system, while at the same time identify areas where more research is needed. ... genomes (i.e., the microbiome) is amenable to change, presenting a possible way to modify diseases
[332] A global partnership to advance the microbiome in human ... - The Lancet — Nevertheless, collaboration between basic researchers and industry in the microbiome field is beginning to improve, driven by recent initiatives such as the Nature Awards Microbiome Accelerator and the Microbiome Times Partnering Forum. Such collaborations, along with cross-training fellowships and other innovative partnerships, should be
[333] Social and population health science approaches to understand the human ... — 5 CUNY Graduate School of Public Health and Health Policy, New York, NY, USA. Find articles by Jennifer B Dowd. 4, 5. ... Fulfilling the promise of microbiome research — particularly the microbiome's potential for modification — will require collaboration between biologists and social and population scientists. For life scientists, the