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Genome Medicine Sep 2020The human gut microbiome is a dynamic collection of bacteria, archaea, fungi, and viruses that performs essential functions for immune development, pathogen colonization... (Review)
Review
The human gut microbiome is a dynamic collection of bacteria, archaea, fungi, and viruses that performs essential functions for immune development, pathogen colonization resistance, and food metabolism. Perturbation of the gut microbiome's ecological balance, commonly by antibiotics, can cause and exacerbate diseases. To predict and successfully rescue such perturbations, first, we must understand the underlying taxonomic and functional dynamics of the microbiome as it changes throughout infancy, childhood, and adulthood. We offer an overview of the healthy gut bacterial architecture over these life stages and comment on vulnerability to short and long courses of antibiotics. Second, the resilience of the microbiome after antibiotic perturbation depends on key characteristics, such as the nature, timing, duration, and spectrum of a course of antibiotics, as well as microbiome modulatory factors such as age, travel, underlying illness, antibiotic resistance pattern, and diet. In this review, we discuss acute and chronic antibiotic perturbations to the microbiome and resistome in the context of microbiome stability and dynamics. We specifically discuss key taxonomic and resistance gene changes that accompany antibiotic treatment of neonates, children, and adults. Restoration of a healthy gut microbial ecosystem after routine antibiotics will require rationally managed exposure to specific antibiotics and microbes. To that end, we review the use of fecal microbiota transplantation and probiotics to direct recolonization of the gut ecosystem. We conclude with our perspectives on how best to assess, predict, and aid recovery of the microbiome after antibiotic perturbation.
Topics: Age Factors; Anti-Bacterial Agents; Drug Resistance, Microbial; Gastrointestinal Microbiome; Humans; Microbiota
PubMed: 32988391
DOI: 10.1186/s13073-020-00782-x -
Signal Transduction and Targeted Therapy Jan 2024The lungs were long thought to be sterile until technical advances uncovered the presence of the lung microbial community. The microbiome of healthy lungs is mainly... (Review)
Review
The lungs were long thought to be sterile until technical advances uncovered the presence of the lung microbial community. The microbiome of healthy lungs is mainly derived from the upper respiratory tract (URT) microbiome but also has its own characteristic flora. The selection mechanisms in the lung, including clearance by coughing, pulmonary macrophages, the oscillation of respiratory cilia, and bacterial inhibition by alveolar surfactant, keep the microbiome transient and mobile, which is different from the microbiome in other organs. The pulmonary bacteriome has been intensively studied recently, but relatively little research has focused on the mycobiome and virome. This up-to-date review retrospectively summarizes the lung microbiome's history, composition, and function. We focus on the interaction of the lung microbiome with the oropharynx and gut microbiome and emphasize the role it plays in the innate and adaptive immune responses. More importantly, we focus on multiple respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD), fibrosis, bronchiectasis, and pneumonia. The impact of the lung microbiome on coronavirus disease 2019 (COVID-19) and lung cancer has also been comprehensively studied. Furthermore, by summarizing the therapeutic potential of the lung microbiome in lung diseases and examining the shortcomings of the field, we propose an outlook of the direction of lung microbiome research.
Topics: Humans; Retrospective Studies; Lung; Pulmonary Disease, Chronic Obstructive; Respiratory Tract Diseases; Microbiota
PubMed: 38228603
DOI: 10.1038/s41392-023-01722-y -
Current HIV/AIDS Reports Dec 2021Observations of differing bacterial, intestinal microbiomes in people living with HIV have propelled interest in contributions of the microbiome to HIV disease.... (Review)
Review
PURPOSE OF REVIEW
Observations of differing bacterial, intestinal microbiomes in people living with HIV have propelled interest in contributions of the microbiome to HIV disease. Non-human primate (NHP) models of HIV infection provide a controlled setting for assessing contributions of the microbiome by standardizing environmental confounders. We provide an overview of the findings of microbiome contributions to aspects of HIV disease derived from these animal models.
RECENT FINDINGS
Observations of differing bacterial, intestinal microbiomes are inconsistently observed in the NHP model following SIV infection. Differences in lentiviral susceptibility and vaccine efficacy have been attributed to variations in the intestinal microbiome; however, by-and-large, these differences have not been experimentally assessed. Although compelling associations exist, clearly defined contributions of the microbiome to HIV and SIV disease are lacking. The empirical use of comprehensive multi-omics assessments and longitudinal and interventional study designs in NHP models is necessary to define this contribution more clearly.
Topics: Animals; Gastrointestinal Microbiome; HIV Infections; Humans; Microbiota; Primates; Simian Acquired Immunodeficiency Syndrome; Simian Immunodeficiency Virus; Vaccine Efficacy
PubMed: 34735686
DOI: 10.1007/s11904-021-00584-9 -
International Journal of Molecular... Oct 2022Understanding of the gut microbiome's role in human physiology developed rapidly in recent years. Moreover, any alteration of this microenvironment could lead to a... (Review)
Review
Understanding of the gut microbiome's role in human physiology developed rapidly in recent years. Moreover, any alteration of this microenvironment could lead to a pathophysiological reaction of numerous organs. It results from the bidirectional communication of the gastrointestinal tract with the central nervous system, called the gut-brain axis. The signals in the gut-brain axis are mediated by immunological, hormonal, and neural pathways. However, it is also influenced by microorganisms in the gut. The disturbances in the gut-brain axis are associated with gastrointestinal syndromes, but recently their role in the development of different types of pain was reported. The gut microbiome could be the factor in the central sensitization of chronic pain by regulating microglia, astrocytes, and immune cells. Dysbiosis could lead to incorrect immune responses, resulting in the development of inflammatory pain such as endometriosis. Furthermore, chronic visceral pain, associated with functional gastrointestinal disorders, could result from a disruption in the gut microenvironment. Any alteration in the gut-brain axis could also trigger migraine attacks by affecting cytokine expression. Understanding the gut microbiome's role in pain pathophysiology leads to the development of analgetic therapies targeting microorganisms. Probiotics, FODMAP diet, and fecal microbiota transplantation are reported to be beneficial in treating visceral pain.
Topics: Female; Humans; Visceral Pain; Brain; Dysbiosis; Microbiota; Gastrointestinal Microbiome; Probiotics; Chronic Pain
PubMed: 36362056
DOI: 10.3390/ijms232113267 -
Clinics in Chest Medicine Mar 2022The microbiology in bronchiectasis has been historically defined by culture-based analysis of the airway microbiome and to date has largely focused on the detection and... (Review)
Review
The microbiology in bronchiectasis has been historically defined by culture-based analysis of the airway microbiome and to date has largely focused on the detection and eradication of specific bacterial pathogens. Although central to our current understanding of disease, microbial culture alone masks the holistic complexity of the microbiome and does not account for potential microbial interactions that define specific clinical phenotypes such as frequent exacerbators. Advances in next-generation sequencing including their analytical technologies can further complement and build upon our current understanding of the microbiology and microbiome in bronchiectasis providing improved patient stratification with prognostic significance.
Topics: Bronchiectasis; Humans; Microbiota; Phenotype
PubMed: 35236558
DOI: 10.1016/j.ccm.2021.11.002 -
Current Opinion in Rheumatology Mar 2024Rheumatic disease are characterized by their autoimmune nature, frequently affecting joints, bones, muscles, blood vessels, and connective tissues. The onset of these... (Review)
Review
PURPOSE OF REVIEW
Rheumatic disease are characterized by their autoimmune nature, frequently affecting joints, bones, muscles, blood vessels, and connective tissues. The onset of these conditions typically unfolds gradually and subtly. It is noteworthy that individuals with rheumatic diseases often experience shifts in their microbiome, specifically on mucosal surfaces. The purpose of this review is to delve into the intricate interplay between the microbiome, encompassing bacteria, viruses and fungi, and its role in the development and aggravation of various rheumatic diseases. Additionally, it aims to offer insights into microbiome-centered therapeutic approaches for patients in the field of rheumatology.
RECENT FINDINGS
The advent of next-generation sequencing has significantly improved our understanding of microbiome changes. Numerous studies have consistently revealed a strong link between rheumatism and the microbiome, especially in the oral and gut microbiota.
SUMMARY
A deeper comprehension of the microbiome's connection to rheumatism holds potential for enhancing disease diagnosis and treatment. Targeted therapeutic approaches, including probiotics, fecal microbiota transplantation, and combination therapies with medications, offer promising avenues for disease management.
Topics: Humans; Microbiota; Gastrointestinal Microbiome; Rheumatic Diseases; Probiotics
PubMed: 37976078
DOI: 10.1097/BOR.0000000000000993 -
Cancer Treatment Reviews Dec 2022Disturbance of the microbial balance of a habitat can have detrimental effects on the health of the individual and, in addition, polymorphic microbiomes were recently... (Review)
Review
Disturbance of the microbial balance of a habitat can have detrimental effects on the health of the individual and, in addition, polymorphic microbiomes were recently suggested as emerging cancer hallmarks. Modern sequencing and metagenomics techniques have allowed characterization of intratumoral microbiome composition even in tissues such as the breast. We conducted a comprehensive literature review on different aspects related to the microbial landscape of the breast tissue and breast tumors, as well as its relation to systemic therapy. Emerging data suggest varying microbiome composition intratumorally compared to the normal breast tissue and other tumor types. Differences in the microbes present in normal breast and cancerous lesions of the breast have also been described, as well as potential correlation between microbiome composition and breast cancer subtype and stage. The interplay between gut and breast microbiome is not well understood although bacterial allocation through mesenteric lymph nodes has been suggested as a possible pathway. Moreover, gut bacteria with estrogen metabolizing properties are of special interest in the context of breast cancer and available knowledge and reported studies are hereby described. The relationship of gut microbiome and cancer therapy is another aspect of interest and available data are presented. Notwithstanding, the field of microbiome in the context of breast cancer is starting to evolve and a number of questions arise, with the gut-breast-cancer therapy axis in the center.
Topics: Humans; Female; Breast Neoplasms; Microbiota; Bacteria; Gastrointestinal Microbiome
PubMed: 36283165
DOI: 10.1016/j.ctrv.2022.102470 -
International Journal of Molecular... Oct 2023While emerging evidence highlights the significance of gut microbiome in gastrointestinal infectious diseases, treatments like Fecal Microbiota Transplantation (FMT) and... (Review)
Review
While emerging evidence highlights the significance of gut microbiome in gastrointestinal infectious diseases, treatments like Fecal Microbiota Transplantation (FMT) and probiotics are gaining popularity, especially for diarrhea patients. However, the specific role of the gut microbiome in different gastrointestinal infectious diseases remains uncertain. There is no consensus on whether gut modulation therapy is universally effective for all such infections. In this comprehensive review, we examine recent developments of the gut microbiome's involvement in several gastrointestinal infectious diseases, including infection of , , , enteric viruses, serovar Typhimurium, , , and . We have also incorporated information about fungi and engineered bacteria in gastrointestinal infectious diseases, aiming for a more comprehensive overview of the role of the gut microbiome. This review will provide insights into the pathogenic mechanisms of the gut microbiome while exploring the microbiome's potential in the prevention, diagnosis, prediction, and treatment of gastrointestinal infections.
Topics: Humans; Gastrointestinal Microbiome; Fecal Microbiota Transplantation; Probiotics; Gastrointestinal Diseases; Diarrhea; Salmonella typhimurium
PubMed: 37958637
DOI: 10.3390/ijms242115654 -
Frontiers in Cellular and Infection... 2020Asthma is a group of inflammatory conditions that compromises the airways of a continuously increasing number of people around the globe. Its complex etiology comprises... (Review)
Review
Asthma is a group of inflammatory conditions that compromises the airways of a continuously increasing number of people around the globe. Its complex etiology comprises both genetic and environmental aspects, with the intestinal and lung microbiomes emerging as newly implicated factors that can drive and aggravate asthma. Longitudinal infant cohort studies combined with mechanistic studies in animal models have identified microbial signatures causally associated with subsequent asthma risk. The recent inclusion of fungi in human microbiome surveys has revealed that microbiome signatures associated with asthma risk are not limited to bacteria, and that fungi are also implicated in asthma development in susceptible individuals. In this review, we examine the unique properties of human-associated and environmental fungi, which confer them the ability to influence immune development and allergic responses. The important contribution of fungi to asthma development and exacerbations prompts for their inclusion in current and future asthma studies in humans and animal models.
Topics: Animals; Asthma; Fungi; Humans; Hypersensitivity; Infant; Microbiota; Mycobiome
PubMed: 33324573
DOI: 10.3389/fcimb.2020.583418 -
Current Opinion in Organ Transplantation Jun 2019Lung transplantation survival is still limited compared with other solid organ transplant modalities, due to a range of factors that are continuing to be elucidated.... (Review)
Review
PURPOSE OF REVIEW
Lung transplantation survival is still limited compared with other solid organ transplant modalities, due to a range of factors that are continuing to be elucidated. However, new research is emerging which indicates that the microbiome of the lungs, and of other organs, may have important implications for immune response and mediating transplant outcomes. Pathogenic bacterial and viral species are known to have deleterious effects on the allograft, but taking a more global view, and considering the overall composition of the community of microbial species may undercover a greater understanding of the complex interplay involved in allograft dysfunction.
RECENT FINDINGS
The microbiome appears to have an important modulatory role on immune response in both normal development, and after transplantation. A range of microbial species contributes to the resident microscopic community, with the gut and blood microbiomes having a significant impact on the function of the lungs and resistance to infection. Movement of species from within and outside the respiratory tract occurs in the early transplant period, leading to a modified donor microbiome in the recipient. There is evidence to suggest that chronic lung allograft dysfunction may be facilitated by the respiratory microbiome and interactions with immune cells within the allograft.
SUMMARY
Further investigation of the respiratory microbiome, interactions with the microbiome of other organs and impact on immune and allograft function posttransplantation is needed. Promising insights are being gained regarding certain microbial profiles which may be associated with negative outcomes, and the mechanisms through which this occurs. As our understanding expands, the ability to modify the microbiome offers novel treatment strategies for combating allograft dysfunction.
Topics: Humans; Lung Transplantation; Microbiota
PubMed: 31090640
DOI: 10.1097/MOT.0000000000000631