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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 -
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 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 -
Drug Discovery Today Sep 2021A factor in our inability to meet the challenge of clinical antibiotic resistance has been the low productivity of research and development (R&D) efforts, with only... (Review)
Review
A factor in our inability to meet the challenge of clinical antibiotic resistance has been the low productivity of research and development (R&D) efforts, with only incremental improvements on existing broad-spectrum classes coming into clinical use recently. The disappointing returns from this approach have focussed attention on narrower-spectrum antibiotics; such new agents are directed against the pathogen of relevance with the additional benefit of preserving the human microbiome(s). Our knowledge of the gut microbiome and its contribution to health homeostasis increases yearly and suggests that broad-spectrum treatments incur health costs beyond the initial infection. Improved diagnostics, antibiotic stewardship, and the crucial role of the gut microbiome in health indicate targeted agents as a more viable approach for future antibiotic R&D.
Topics: Anti-Bacterial Agents; Bacterial Infections; Dysbiosis; Humans; Microbiota
PubMed: 34329771
DOI: 10.1016/j.drudis.2021.07.016 -
Methods (San Diego, Calif.) Oct 2018
Topics: Gastrointestinal Microbiome; High-Throughput Screening Assays; Humans; Metabolomics; Microbiota
PubMed: 30322643
DOI: 10.1016/j.ymeth.2018.09.007 -
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 -
Comprehensive Physiology Jun 2023Microbiomes include bacteria, viruses, fungi, and other microbes. The microbiome modulates numerous aspects of host physiology and is critical in the pathophysiology of... (Review)
Review
Microbiomes include bacteria, viruses, fungi, and other microbes. The microbiome modulates numerous aspects of host physiology and is critical in the pathophysiology of diseases, including colon cancer. Although gut bacterial pathogenesis has become an emerging area in colon cancer, the multi-kingdom aspect of microbiome has yet to be explored. Similar to the bacterial component of the microbiome, the virome contains certain makeup that varies between individuals. In the current review, we introduce the concepts of microbiome and microbiota, research history, methods for modern microbiome studies, and recent progress of mechanisms responsible for microbiome and virome in colon cancer. Furthermore, we discuss our understanding of microbial metabolites in the disease development and therapy of colon cancer. Finally, the gut microbiota can affect the efficacy and toxicity of cancer therapy. We discuss the challenges and future perspectives in microbiome and colon cancer. Exploring and understanding the mechanisms of microbiome will provide insights into effective approaches in potential prevention of treatment of colon cancer. © 2023 American Physiological Society. Compr Physiol 13:4685-4708, 2023.
Topics: Humans; Microbiota; Carcinogenesis; Gastrointestinal Microbiome; Viruses; Colonic Neoplasms
PubMed: 37358517
DOI: 10.1002/cphy.c210052 -
Nature Microbiology Aug 2018Why does a microorganism associate with a host? What function does it perform? Such questions are difficult to unequivocally address and remain hotly debated. This is... (Review)
Review
Why does a microorganism associate with a host? What function does it perform? Such questions are difficult to unequivocally address and remain hotly debated. This is partially because scientists often use different philosophical definitions of 'function' ambiguously and interchangeably, as exemplified by the controversy surrounding the Encyclopedia of DNA Elements (ENCODE) project. Here, I argue that research studying host-associated microbial communities and their genomes (that is, microbiomes) faces similar pitfalls and that unclear or misapplied conceptions of function underpin many controversies in this field. In particular, experiments that support phenomenological models of function can inappropriately be used to support functional models that instead require specific measurements of evolutionary selection. Microbiome research also requires uniquely clear definitions of 'who the function is for', in contrast to most single-organism systems where this is implicit. I illustrate how obscuring either of these issues can lead to substantial confusion and misinterpretation of microbiome function, using the varied conceptions of the holobiont as a current and cogent example. Using clear functional definitions and appropriate types of evidence are essential to effectively communicate microbiome research and foster host health.
Topics: Bacterial Physiological Phenomena; Evolution, Molecular; Gastrointestinal Microbiome; Genome, Bacterial; Host Microbial Interactions; Humans; Microbiota
PubMed: 30046174
DOI: 10.1038/s41564-018-0189-4 -
Cell Host & Microbe Jul 2023The human gut microbiome composition is generally in a stable dynamic equilibrium, but it can deteriorate into dysbiotic states detrimental to host health. To...
The human gut microbiome composition is generally in a stable dynamic equilibrium, but it can deteriorate into dysbiotic states detrimental to host health. To disentangle the inherent complexity and capture the ecological spectrum of microbiome variability, we used 5,230 gut metagenomes to characterize signatures of bacteria commonly co-occurring, termed enterosignatures (ESs). We find five generalizable ESs dominated by either Bacteroides, Firmicutes, Prevotella, Bifidobacterium, or Escherichia. This model confirms key ecological characteristics known from previous enterotype concepts, while enabling the detection of gradual shifts in community structures. Temporal analysis implies that the Bacteroides-associated ES is "core" in the resilience of westernized gut microbiomes, while combinations with other ESs often complement the functional spectrum. The model reliably detects atypical gut microbiomes correlated with adverse host health conditions and/or the presence of pathobionts. ESs provide an interpretable and generic model that enables an intuitive characterization of gut microbiome composition in health and disease.
Topics: Humans; Gastrointestinal Microbiome; Microbiota; Bacteria; Metagenome; Firmicutes; Bacteroides; Feces
PubMed: 37339626
DOI: 10.1016/j.chom.2023.05.024 -
Microbiology (Reading, England) May 2023In microbiome research, considerable effort has been invested in finding core microbiomes, which have been hypothesized to contain the species most important for host...
In microbiome research, considerable effort has been invested in finding core microbiomes, which have been hypothesized to contain the species most important for host function. Much less attention has been paid to microbiome members that are present in only a subset of hosts. Such accessory microbiomes must in large part consist of species that have no effect on fitness, but some will have deleterious effects on fitness (pathogens), and it is also possible that some accessory microbiome members benefit an ecologically distinct subset of hosts. This short paper discusses what we know about accessory microbiomes, specifically by comparing it with the concept of accessory genomes.
Topics: Microbiota
PubMed: 37167086
DOI: 10.1099/mic.0.001332