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Current Opinion in Microbiology Jun 2022Microbiomes and their enzymes process many of the nutrients accessible in the gastrointestinal tract of bilaterians and play an essential role in host health and... (Review)
Review
Microbiomes and their enzymes process many of the nutrients accessible in the gastrointestinal tract of bilaterians and play an essential role in host health and nutrition. In this review, we describe recent insights into nutrient processing in microbiomes across three exemplary yet contrasting gastrointestinal ecosystems (humans, ruminants and insects), with focus on bacterial mechanisms for the utilization of common and atypical dietary glycans as well as host-derived mucus glycans. In parallel, we discuss findings from multi-omic studies that have provided new perspectives on understanding glycan-dependent interactions and the complex food-webs of microbial populations in their natural habitat. Using key examples, we emphasize how increasing understanding of glycan processing by gut microbiomes can provide critical insights to assist 'microbiome reprogramming', a growing field that seeks to leverage diet to improve animal growth and host health.
Topics: Animals; Bacteria; Gastrointestinal Microbiome; Gastrointestinal Tract; Microbiota; Polysaccharides
PubMed: 35338908
DOI: 10.1016/j.mib.2022.102143 -
Trends in Genetics : TIG Jan 2020While the human microbiome's structure and function have been extensively studied, its within-species genetic diversity is less well understood. However, genetic... (Review)
Review
While the human microbiome's structure and function have been extensively studied, its within-species genetic diversity is less well understood. However, genetic mutations in the microbiome can confer biomedically relevant traits, such as the ability to extract nutrients from food, metabolize drugs, evade antibiotics, and communicate with the host immune system. The population genetic processes by which these traits evolve are complex, in part due to interacting ecological and evolutionary forces in the microbiome. Advances in metagenomic sequencing, coupled with bioinformatics tools and population genetic models, facilitate quantification of microbiome genetic variation and inferences about how this diversity arises, evolves, and correlates with traits of both microbes and hosts. In this review, we explore the population genetic forces (mutation, recombination, drift, and selection) that shape microbiome genetic diversity within and between hosts, as well as efforts towards predictive models that leverage microbiome genetics.
Topics: Bacteria; Gastrointestinal Microbiome; Genetic Variation; Genetics, Population; Humans; Metagenome; Metagenomics; Microbiota
PubMed: 31780057
DOI: 10.1016/j.tig.2019.10.010 -
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 -
Philosophical Transactions of the Royal... Jun 2022Social corbiculate bees are major pollinators. They have characteristic bacterial microbiomes associated with their hives and their guts. In honeybees and bumblebees,... (Review)
Review
Social corbiculate bees are major pollinators. They have characteristic bacterial microbiomes associated with their hives and their guts. In honeybees and bumblebees, worker guts contain a microbiome composed of distinctive bacterial taxa shown to benefit hosts. These benefits include stimulating immune and metabolic pathways, digesting or detoxifying food, and defending against pathogens and parasites. Stressors including toxins and poor nutrition disrupt the microbiome and increase susceptibility to opportunistic pathogens. Administering probiotic bacterial strains may improve the health of individual bees and of hives, and several commercial probiotics are available for bees. However, evidence for probiotic benefits is lacking or mixed. Most bacterial species used in commercial probiotics are not native to bee guts. We present new experimental results showing that cultured strains of native bee gut bacteria colonize robustly while bacteria in a commercial probiotic do not establish in bee guts. A defined community of native bee gut bacteria resembles unperturbed native gut communities in its activation of genes for immunity and metabolism in worker bees. Although many questions remain unanswered, the development of natural probiotics for honeybees, or for commercially managed bumblebees, is a promising direction for protecting the health of managed bee colonies. This article is part of the theme issue 'Natural processes influencing pollinator health: from chemistry to landscapes'.
Topics: Animals; Bacteria; Bees; Gastrointestinal Microbiome; Microbiota; Probiotics; Urticaria
PubMed: 35491599
DOI: 10.1098/rstb.2021.0156 -
Cell Reports. Medicine Oct 2023The complex interplay between microbiota and immunity is important to human health. To explore how altered adaptive immunity influences the microbiome, we characterize...
The complex interplay between microbiota and immunity is important to human health. To explore how altered adaptive immunity influences the microbiome, we characterize skin, nares, and gut microbiota of patients with recombination-activating gene (RAG) deficiency-a rare genetically defined inborn error of immunity (IEI) that results in a broad spectrum of clinical phenotypes. Integrating de novo assembly of metagenomes from RAG-deficient patients with reference genome catalogs provides an expansive multi-kingdom view of microbial diversity. RAG-deficient patient microbiomes exhibit inter-individual variation, including expansion of opportunistic pathogens (e.g., Corynebacterium bovis, Haemophilus influenzae), and a relative loss of body site specificity. We identify 35 and 27 bacterial species derived from skin/nares and gut microbiomes, respectively, which are distinct to RAG-deficient patients compared to healthy individuals. Underscoring IEI patients as potential reservoirs for viral persistence and evolution, we further characterize the colonization of eukaryotic RNA viruses (e.g., Coronavirus 229E, Norovirus GII) in this patient population.
Topics: Humans; Microbiota; Gastrointestinal Microbiome; Skin; Metagenome
PubMed: 37757827
DOI: 10.1016/j.xcrm.2023.101205 -
Nature Aging Nov 2022The gut microbiome is a modifier of disease risk because it interacts with nutrition, metabolism, immunity and infection. Aging-related health loss has been correlated...
The gut microbiome is a modifier of disease risk because it interacts with nutrition, metabolism, immunity and infection. Aging-related health loss has been correlated with transition to different microbiome states. Microbiome summary indices including alpha diversity are apparently useful to describe these states but belie taxonomic differences that determine biological importance. We analyzed 21,000 fecal microbiomes from seven data repositories, across five continents spanning participant ages 18-107 years, revealing that microbiome diversity and uniqueness correlate with aging, but not healthy aging. Among summary statistics tested, only Kendall uniqueness accurately reflects loss of the core microbiome and the abundance and ranking of disease-associated and health-associated taxa. Increased abundance of these disease-associated taxa and depletion of a coabundant subset of health-associated taxa are a generic feature of aging. These alterations are stronger correlates of unhealthy aging than most microbiome summary statistics and thus help identify better targets for therapeutic modulation of the microbiome.
Topics: Humans; Adolescent; Young Adult; Adult; Middle Aged; Aged; Aged, 80 and over; Bacteria; Microbiota; Gastrointestinal Microbiome; Aging; Feces
PubMed: 37118093
DOI: 10.1038/s43587-022-00306-9 -
Clinical Science (London, England :... Sep 2022Smoking is associated with an increased risk of cancer, pulmonary and cardiovascular diseases, but the precise mechanisms by which such risk is mediated remain poorly... (Review)
Review
Smoking is associated with an increased risk of cancer, pulmonary and cardiovascular diseases, but the precise mechanisms by which such risk is mediated remain poorly understood. Additionally, smoking can impact the oral, nasal, oropharyngeal, lung and gut microbiome composition, function, and secreted molecule repertoire. Microbiome changes induced by smoking can bear direct consequences on smoking-related illnesses. Moreover, smoking-associated dysbiosis may modulate weight gain development following smoking cessation. Here, we review the implications of cigarette smoking on microbiome community structure and function. In addition, we highlight the potential impacts of microbial dysbiosis on smoking-related diseases. We discuss challenges in studying host-microbiome interactions in the context of smoking, such as the correlations with smoking-related disease severity versus causation and mechanism. In all, understanding the microbiome's role in the pathophysiology of smoking-related diseases may promote the development of rational therapies for smoking- and smoking cessation-related disorders, as well as assist in smoking abstinence.
Topics: Cardiovascular Diseases; Dysbiosis; Gastrointestinal Microbiome; Humans; Microbiota; Smoking
PubMed: 36156126
DOI: 10.1042/CS20220175 -
Annual Review of Microbiology Sep 2023For thousands of years, humans have enjoyed the novel flavors, increased shelf-life, and nutritional benefits that microbes provide in fermented foods and beverages.... (Review)
Review
For thousands of years, humans have enjoyed the novel flavors, increased shelf-life, and nutritional benefits that microbes provide in fermented foods and beverages. Recent sequencing surveys of ferments have mapped patterns of microbial diversity across space, time, and production practices. But a mechanistic understanding of how fermented food microbiomes assemble has only recently begun to emerge. Using three foods as case studies (surface-ripened cheese, sourdough starters, and fermented vegetables), we use an ecological and evolutionary framework to identify how microbial communities assemble in ferments. By combining in situ sequencing surveys with in vitro models, we are beginning to understand how dispersal, selection, diversification, and drift generate the diversity of fermented food communities. Most food producers are unaware of the ecological processes occurring in their production environments, but the theory and models of ecology and evolution can provide new approaches for managing fermented food microbiomes, from farm to ferment.
Topics: Humans; Fermented Foods; Microbiota
PubMed: 37713453
DOI: 10.1146/annurev-micro-032521-041956 -
Current Oncology Reports Mar 2023Head and neck tumors (HNC) rank sixth among cancers worldwide. Due to their late diagnosis and poor prognosis, they are a clinical challenge. However, recent years have... (Review)
Review
PURPOSE OF REVIEW
Head and neck tumors (HNC) rank sixth among cancers worldwide. Due to their late diagnosis and poor prognosis, they are a clinical challenge. However, recent years have seen a dynamic development of science on the microbiome. The aim of the study is to discuss the role of the microbiome in HNC, the impact of the microbiome on oncogenesis, the course of the disease, as well as on treatment, and its toxicity.
RECENT FINDINGS
The microbiome's influence on oncogenesis, the course of the disease, and the effectiveness of oncological treatment have been confirmed in cancers of the colon, pancreas, lungs, and prostate. There is no solid literature on HNC. Many studies indicate disruption of the oral microbiome and periodontal disease as potential cancer risk factors. Disruption of the microbiome increases radiotherapy's toxicity, intensifying radiation reactions. The microbiome plays an important role in cancer. It is a new target in research into new therapies. It may also be a prognostic marker of cancer development. Changes in the composition of the microbiome modulate the effectiveness of oncological treatment. More research is needed on the microbiome and its effects on HNC.
Topics: Male; Humans; Head and Neck Neoplasms; Microbiota; Carcinogenesis; Cell Transformation, Neoplastic; Medical Oncology
PubMed: 36696075
DOI: 10.1007/s11912-022-01352-7 -
Periodontology 2000 Jun 2021Oral bacteriophages (or phages), especially periodontal ones, constitute a growing area of interest, but research on oral phages is still in its infancy. Phages are... (Review)
Review
Oral bacteriophages (or phages), especially periodontal ones, constitute a growing area of interest, but research on oral phages is still in its infancy. Phages are bacterial viruses that may persist as intracellular parasitic deoxyribonucleic acid (DNA) or use bacterial metabolism to replicate and cause bacterial lysis. The microbiomes of saliva, oral mucosa, and dental plaque contain active phage virions, bacterial lysogens (ie, carrying dormant prophages), and bacterial strains containing short fragments of phage DNA. In excess of 2000 oral phages have been confirmed or predicted to infect species of the phyla Actinobacteria (>300 phages), Bacteroidetes (>300 phages), Firmicutes (>1000 phages), Fusobacteria (>200 phages), and Proteobacteria (>700 phages) and three additional phyla (few phages only). This article assesses the current knowledge of the diversity of the oral phage population and the mechanisms by which phages may impact the ecology of oral biofilms. The potential use of phage-based therapy to control major periodontal pathogens is also discussed.
Topics: Bacteria; Bacteriophages; Humans; Microbiota; Prophages; Virome
PubMed: 33690937
DOI: 10.1111/prd.12363