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Periodontology 2000 Feb 2021Periodontal microbiology has historically been based on an "us against them" paradigm, one that focuses mainly on identifying microbes and viruses that cause disease.... (Review)
Review
Periodontal microbiology has historically been based on an "us against them" paradigm, one that focuses mainly on identifying microbes and viruses that cause disease. However, such a bottom-up approach limits our appreciation of the incredible diversity of this ecosystem and the essential ways in which microbial interactions contribute to health and homeostasis of the subgingival niche. Microbiomics-the science of collectively characterizing and quantifying molecules responsible for the structure, function, and dynamics of a microbial community-has enabled us to study these communities in their natural habitat, thereby revolutionizing our knowledge of host-associated microbes and reconceptualizing our definition of "human." When this systems-biology approach is combined with ecologic principles, it explicates the complex relationship that exist between microbiota and between them and us, the human. In this volume of Periodontology 2000, a group of 12 female scientists take the lead in investigating how metagenomics, genomics, metatranscriptomics, proteomics, metaproteomics, and metabolomics have achieved the following: (a) widened our view of the periodontal microbiome; (b) expanded our understanding of the evolution of the human oral microbiome; (c) shone a light on not just bacteria, but also other prokaryotic and eukaryotic members of the community; (d) elucidated the effects of anthropogenic behavior and systemic diseases on shaping these communities; and (e) influenced traditional patterns of periodontal therapeutics.
Topics: Bacteria; Female; Humans; Metagenomics; Microbiota; Proteomics
PubMed: 33226670
DOI: 10.1111/prd.12373 -
International Journal of Biological... Mar 2023Schisandra chinensis (S. chinensis) is an herbal medicine used for the treatment of Alzheimer's disease (AD). The purified polysaccharide fraction, namely SCP2, was...
Schisandra chinensis (S. chinensis) is an herbal medicine used for the treatment of Alzheimer's disease (AD). The purified polysaccharide fraction, namely SCP2, was previously isolated from S. chinensis crude polysaccharide (SCP) and its structure and in vitro activity were investigated. However, the in vivo activity of SCP2 and its potential mechanism for the treatment of AD have yet to be determined. This study used a combination of microbiomics and metabolomics to comprehensively explore the microbiota and metabolic changes in AD rats under SCP2 intervention, with the aim of elucidating the potential mechanisms of SCP2 in the treatment of AD. SCP2 showed significant therapeutic effects in AD rats, as evidenced by improved learning and memory capacity, reduced neuroinflammation, and restoration of the integrity of the intestinal barrier. Fecal metabolomic and microbiomic analyses revealed that SCP2 significantly modulated 19 endogenous metabolites and reversed gut microbiota disorders in AD rats. Moreover, SCP2 significantly increased the content of short-chain fatty acid (SCFAs) in the AD rats. Correlation analysis showed a significant correlation between gut microbes, metabolites and the content of SCFAs. Collectively, these findings will provide the basis for further development of SCP2.
Topics: Rats; Animals; Alzheimer Disease; Gastrointestinal Microbiome; Schisandra; Metabolomics; Polysaccharides; Feces
PubMed: 36731694
DOI: 10.1016/j.ijbiomac.2023.123488 -
Trends in Molecular Medicine Oct 2023A growing number of human gut microbiome studies consistently describe differences between human populations. Here, we review how factors related to host genetics,... (Review)
Review
A growing number of human gut microbiome studies consistently describe differences between human populations. Here, we review how factors related to host genetics, ethnicity, lifestyle, and geographic location help explain this variation. Studies from contrasting environmental scenarios point to diet and lifestyle as the most influential. The effect of human migration and displacement demonstrates how the microbiome adapts to newly adopted lifestyles and contributes to the profound biological and health consequences attributed to migration. This information strongly suggests against a universal scale for healthy or dysbiotic gut microbiomes, and prompts for additional microbiome population surveys, particularly from less industrialized nations. Considering these important differences will be critical for designing strategies to diagnose and restore dysbiosis in various human populations.
Topics: Humans; Gastrointestinal Microbiome; Bacteria; Microbiota; Diet; Life Style
PubMed: 37516570
DOI: 10.1016/j.molmed.2023.07.002 -
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 -
Current Opinion in Microbiology Feb 2022Microbial communities are a key part to tackling global challenges in human health, environmental conservation, and sustainable agriculture in the coming decade. Recent... (Review)
Review
Microbial communities are a key part to tackling global challenges in human health, environmental conservation, and sustainable agriculture in the coming decade. Recent advances in synthetic biology to study and modify microbial communities have led to important insights into their physiology and ecology. Understanding how targeted changes to microbial communities result in reproducible alterations of the community's intrinsic fluctuations and function is important for mechanistic reconstruction of microbiomes. Studies of synthetic microbial consortia and comparative analysis of communities in normal and disrupted states have revealed ecological principles that can be leveraged to engineer communities towards desired functions. Tools enabling temporal modulation and sensing of the community dynamics offer precise spatiotemporal control of functions, help to dissect microbial interaction networks, and improve predictions of population temporal dynamics. Here we discuss recent advances to manipulate microbiome dynamics through control of specific strain engraftment and abundance, modulation of cell-cell signaling for tuning population dynamics, infiltration of new functions in the existing community with in situ engineering, and in silico modeling of microbial consortia to predict community function and ecology.
Topics: Humans; Microbial Consortia; Microbial Interactions; Microbiota; Synthetic Biology
PubMed: 34739926
DOI: 10.1016/j.mib.2021.10.009 -
Translational Research : the Journal of... Jan 2017The human microbiome plays an important and increasingly recognized role in human health. Studies of the microbiome typically use targeted sequencing of the 16S rRNA... (Review)
Review
The human microbiome plays an important and increasingly recognized role in human health. Studies of the microbiome typically use targeted sequencing of the 16S rRNA gene, whole metagenome shotgun sequencing, or other meta-omic technologies to characterize the microbiome's composition, activity, and dynamics. Processing, analyzing, and interpreting these data involve numerous computational tools that aim to filter, cluster, annotate, and quantify the obtained data and ultimately provide an accurate and interpretable profile of the microbiome's taxonomy, functional capacity, and behavior. These tools, however, are often limited in resolution and accuracy and may fail to capture many biologically and clinically relevant microbiome features, such as strain-level variation or nuanced functional response to perturbation. Over the past few years, extensive efforts have been invested toward addressing these challenges and developing novel computational methods for accurate and high-resolution characterization of microbiome data. These methods aim to quantify strain-level composition and variation, detect and characterize rare microbiome species, link specific genes to individual taxa, and more accurately characterize the functional capacity and dynamics of the microbiome. These methods and the ability to produce detailed and precise microbiome information are clearly essential for informing microbiome-based personalized therapies. In this review, we survey these methods, highlighting the challenges each method sets out to address and briefly describing methodological approaches.
Topics: Humans; Metagenome; Metagenomics; Microbiota; Molecular Sequence Annotation; RNA, Ribosomal, 16S
PubMed: 27513210
DOI: 10.1016/j.trsl.2016.07.012 -
The Journal of Pathology Jul 2021The human microbiome is essential for the correct functioning of many host physiological processes, including metabolic regulation and immune responses. Increasing... (Review)
Review
The human microbiome is essential for the correct functioning of many host physiological processes, including metabolic regulation and immune responses. Increasing evidence indicates that the microbiome may also influence cancer development, progression, and the response to therapy. Although most studies have focused on the effect of the gut microbiome, many other organs such as the skin, vagina, and lungs harbor their own microbiomes that are different from the gut. Tumor development has been associated with dysbiosis not only in the gut but also in the tissue from which the tumor originated. Furthermore, the intratumoral microbiota has a distinct signature in each tumor type. Here, we review the mechanisms by which the organ-specific microbiome can contribute to carcinogenesis: release of toxins that cause DNA damage and barrier failure; alteration of immune responses to create a local inflammatory or immunosuppressive environment; and regulation of nutrient levels in the tumor microenvironment through metabolite production and consumption. Solving the puzzle of how the microbiome influences the carcinogenesis process and treatment response requires an understanding of the two ways the microbiome can interact with cancer cells and the tumor microenvironment: through systemic effects exerted by the gut microbiota and local effects of the intratumoral microbiota. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Topics: Animals; Humans; Microbiota; Neoplasms
PubMed: 33723873
DOI: 10.1002/path.5661 -
Gut Microbes Dec 2023Avoiding immune destruction and polymorphic microbiomes are two key hallmarks of cancer. The tumor microenvironment (TME) is essential for the development of solid... (Review)
Review
Avoiding immune destruction and polymorphic microbiomes are two key hallmarks of cancer. The tumor microenvironment (TME) is essential for the development of solid tumors, and the function of tumor-associated macrophages (TAMs) in the TME is closely linked to tumor prognosis. Therefore, research on TAMs could improve the progression and control of certain tumor patients. Additionally, the intestinal flora plays a crucial role in metabolizing substances and maintaining a symbiotic relationship with the host through a complex network of interactions. Recent experimental and clinical studies have suggested a potential link between gut microbiome and TME, particularly in regulating TAMs. Understanding this association could improve the efficacy of tumor immunotherapy. This review highlights the regulatory role of intestinal flora on TAMs, with a focus on gut microbiota and their metabolites. The implications of this association for tumor diagnosis and treatment are also discussed, providing a promising avenue for future clinical treatment strategies.
Topics: Humans; Gastrointestinal Microbiome; Tumor-Associated Macrophages; Immunotherapy; Microbiota; Neoplasms; Tumor Microenvironment
PubMed: 37943609
DOI: 10.1080/19490976.2023.2276314 -
Molecular Medicine (Cambridge, Mass.) Oct 2023Diabetic kidney disease (DKD), has become the main cause of end-stage renal disease (ESRD) worldwide. Lately, it has been shown that the onset and advancement of DKD are... (Review)
Review
Diabetic kidney disease (DKD), has become the main cause of end-stage renal disease (ESRD) worldwide. Lately, it has been shown that the onset and advancement of DKD are linked to imbalances of gut microbiota and the abnormal generation of microbial metabolites. Similarly, a body of recent evidence revealed that biological alterations of mitochondria ranging from mitochondrial dysfunction and morphology can also exert significant effects on the occurrence of DKD. Based on the prevailing theory of endosymbiosis, it is believed that human mitochondria originated from microorganisms and share comparable biological characteristics with the microbiota found in the gut. Recent research has shown a strong correlation between the gut microbiome and mitochondrial function in the occurrence and development of metabolic disorders. The gut microbiome's metabolites may play a vital role in this communication. However, the relationship between the gut microbiome and mitochondrial function in the development of DKD is not yet fully understood, and the role of microbial metabolites is still unclear. Recent studies are highlighted in this review to examine the possible mechanism of the gut microbiota-microbial metabolites-mitochondrial axis in the progression of DKD and the new therapeutic approaches for preventing or reducing DKD based on this biological axis in the future.
Topics: Humans; Gastrointestinal Microbiome; Diabetic Nephropathies; Microbiota; Mitochondria; Diabetes Mellitus
PubMed: 37907885
DOI: 10.1186/s10020-023-00745-z -
Clinical Science (London, England :... Nov 2022The microbiome contributes to human development and maturation, and is essential for maintenance of health and prevention of disease. While the human genome encodes...
The microbiome contributes to human development and maturation, and is essential for maintenance of health and prevention of disease. While the human genome encodes one's identity, the microbiome - also individually unique - provides a window on one's lifestyle and exposure to environmental variables. The microbiome thus serves as a biomarker of host health and a driver of certain diseases. However, current understanding of the gut microbiome is largely based on studies of industrialised peoples of North America and Europe. Gaps in knowledge of the microbiomes of other groups, particularly those in developing or nonindustrialised societies, are important, particularly in view of contrasting epidemiological risks of acquiring chronic inflammatory and metabolic disorders. Here, we explore underlying mechanisms of microbiome differences and whether the potential benefits of nonindustrialised microbiome can be realised in a modern world.
Topics: Humans; Microbiota; Gastrointestinal Microbiome; Life Style
PubMed: 36416083
DOI: 10.1042/CS20220203