scholarly journals Current Knowledge About the Implication of Bacterial Microbiota in Human Health and Disease

2021 ◽  
Vol 48 (4) ◽  
pp. 43-49
Author(s):  
D. Nikolova
Keyword(s):  
Human Health ◽  
New Technologies ◽  
Current Knowledge ◽  
Bacterial Species ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Human Diseases ◽  
Human Microbiota ◽  
Bacterial Microbiota ◽  
Key Issues

Abstract Recent advances in molecular genetics and the invention of new technologies led to a development in our knowledge about human microbiota, specifically bacterial one. The microbiota plays a fundamental role in the immunologic, hormonal and metabolic homeostasis of the host. After the initiation of the Human Microbiome Project, it became clear that the human microbiota consists of the 10-100 trillion symbiotic microbial cells harbored by each person, primarily bacteria in the gut, but also in other spots as the skin, mouth, nose, and vagina. Despite of the differences in studying bacterial species, decreased bacterial diversity and persistence has been connected with several diverse human diseases primarily diabetes, IBD (inflammatory bowel disease) and others; attempts were made even to explain psychiatric pathology. Several species emerged as dominant and were clearly linked to certain disorders or accepted as biomarkers of others. The current review aims to discuss key issues of our current knowledge about bacteria in human, the difficulties and methods of its analysis, its contribution to human health and responsibility for human diseases.

scholarly journals Computational Modeling of the Human Microbiome

2020 ◽  
Vol 8 (2) ◽  
pp. 197
Author(s):  
Shomeek Chowdhury ◽  
Stephen S. Fong
Keyword(s):  
Computational Modeling ◽  
Human Health ◽  
Large Scale ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Microbial Composition ◽  
Site Specific ◽  
Microbiome Research ◽  
High Level ◽  
The Impact

The impact of microorganisms on human health has long been acknowledged and studied, but recent advances in research methodologies have enabled a new systems-level perspective on the collections of microorganisms associated with humans, the human microbiome. Large-scale collaborative efforts such as the NIH Human Microbiome Project have sought to kick-start research on the human microbiome by providing foundational information on microbial composition based upon specific sites across the human body. Here, we focus on the four main anatomical sites of the human microbiome: gut, oral, skin, and vaginal, and provide information on site-specific background, experimental data, and computational modeling. Each of the site-specific microbiomes has unique organisms and phenomena associated with them; there are also high-level commonalities. By providing an overview of different human microbiome sites, we hope to provide a perspective where detailed, site-specific research is needed to understand causal phenomena that impact human health, but there is equally a need for more generalized methodology improvements that would benefit all human microbiome research.

scholarly journals Gut Microbiota as a Source of Uremic Toxins

2022 ◽  
Vol 23 (1) ◽  
pp. 483
Author(s):  
Vasily A. Popkov ◽  
Anastasia A. Zharikova ◽  
Evgenia A. Demchenko ◽  
Nadezda V. Andrianova ◽  
Dmitry B. Zorov ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Bacterial Species ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Uremic Toxins ◽  
Enzymatic Reactions ◽  
Bacterial Strains ◽  
Excretory Function ◽  
High Concentrations ◽  
Stage Renal Disease

Uremic retention solutes are the compounds that accumulate in the blood when kidney excretory function is impaired. Some of these compounds are toxic at high concentrations and are usually known as “uremic toxins”. The cumulative detrimental effect of uremic toxins results in numerous health problems and eventually mortality during acute or chronic uremia, especially in end-stage renal disease. More than 100 different solutes increase during uremia; however, the exact origin for most of them is still debatable. There are three main sources for such compounds: exogenous ones are consumed with food, whereas endogenous ones are produced by the host metabolism or by symbiotic microbiota metabolism. In this article, we identify uremic retention solutes presumably of gut microbiota origin. We used database analysis to obtain data on the enzymatic reactions in bacteria and human organisms that potentially yield uremic retention solutes and hence to determine what toxins could be synthesized in bacteria residing in the human gut. We selected biochemical pathways resulting in uremic retention solutes synthesis related to specific bacterial strains and revealed links between toxin concentration in uremia and the proportion of different bacteria species which can synthesize the toxin. The detected bacterial species essential for the synthesis of uremic retention solutes were then verified using the Human Microbiome Project database. Moreover, we defined the relative abundance of human toxin-generating enzymes as well as the possibility of the synthesis of a particular toxin by the human metabolism. Our study presents a novel bioinformatics approach for the elucidation of the origin of both uremic retention solutes and uremic toxins and for searching for the most likely human microbiome producers of toxins that can be targeted and used for the therapy of adverse consequences of uremia.

scholarly journals Exploring the Parallel Development of Microbial Systems in Neonates with Cystic Fibrosis

mBio ◽  
2012 ◽  
Vol 3 (6) ◽  
Author(s):  
Geraint B. Rogers ◽  
Kenneth D. Bruce
Keyword(s):  
Cystic Fibrosis ◽  
Human Health ◽  
Human Body ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Healthy Individuals ◽  
Parallel Development ◽  
Microbial Systems ◽  
Analytical Power ◽  
Over Time

ABSTRACT Recent studies have greatly extended our understanding of the microbiota present in and on the human body. Here, advanced sequencing strategies have provided unprecedented analytical power. The important implications that the emerging data have for human health emphasize the need to intensify research in this area (D. A. Relman, Nature 486:194-195, 2012). It is already clear from these studies that the microbiotas characterized in different body locations of healthy individuals are both complex and diverse (The Human Microbiome Project Consortium, Nature 486:215-221). These studies also provide a point of contrast for investigations that aim to characterize the microbiota present in disease conditions. In this regard, Madan et al. (mBio 3(4):e00251-12, 2012) monitored the development over time of microbiota in the oropharynges and feces of neonates with cystic fibrosis and explored the potential for interactions between these complex microbial systems.

scholarly journals The Impact of Diet on Microbiota Evolution and Human Health. Is Diet an Adequate Tool for Microbiota Modulation?

Nutrients ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1654
Author(s):  
Laura Moles ◽  
David Otaegui
Keyword(s):  
Human Health ◽  
Human Evolution ◽  
Human Microbiome ◽  
Microbiota Composition ◽  
Dietary Changes ◽  
Human Microbiota ◽  
Factors Influencing ◽  
Complex Ecosystem ◽  
Dietary Strategies ◽  
The Impact

The human microbiome is emerging as an interesting field in research into the prevention of health problems and recovery from illness in humans. The complex ecosystem formed by the microbiota is continuously interacting with its host and the environment. Diet could be assumed to be one of the most prominent factors influencing the microbiota composition. Nevertheless, and in spite of numerous strategies proposed to modulate the human microbiota through dietary means, guidelines to achieve this goal have yet to be established. This review assesses the correlation between social and dietary changes over the course of human evolution and the adaptation of the human microbiota to those changes. In addition, it discusses the main dietary strategies for modulating the microbiota and the difficulties of putting them properly into practice.

scholarly journals Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species

2021 ◽  
pp. 1-15
Author(s):  
Hassan Zafar ◽  
Milton H. Saier Jr.
Keyword(s):  
Human Health ◽  
Drug Targets ◽  
Bacterial Species ◽  
Human Microbiome ◽  
Transport Proteins ◽  
Host Cells ◽  
Transport Systems ◽  
Ecological Niches ◽  
Beneficial Effects ◽  
Secondary Carriers

The human microbiome influences human health in both negative and positive ways. Studies on the transportomes of these organisms yield information that may be utilized for various purposes, including the identification of novel drug targets and the manufacture of improved probiotic strains. Moreover, these genomic analyses help to improve our understanding of the physiology and metabolic capabilities of these organisms. The present study is a continuation of our studies on the transport proteins of the major gut microbes. <i>Bifidobacterium</i> species are essential members of the human gut microbiome, and they initiate colonization of the gut at birth, providing health benefits that last a lifetime. In this study we analyze the transportomes of nine bifidobacterial species: <i>B. adolescentis, B. animalis, B. bifidum, B. breve, B. catenulatum, B. dentium, B. longum</i> subsp. <i>infantis, B. longum</i> subsp. <i>longum, and B. pseudocatenulatum</i>. All of these species have proven probiotic characteristics and exert beneficial effects on human health. Surprisingly, we found that all nine of these species have similar pore-forming toxins and drug exporters that may play roles in pathogenesis. These species have transporters for amino acids, carbohydrates, and proteins, essential for their organismal lifestyles and adaption to their respective ecological niches. The strictly probiotic species, <i>B. bifidum</i>, however, contains fewer such transporters, thus indicative of limited interactions with host cells and other gut microbial counterparts. The results of this study were compared with those of our previous studies on the transportomes of multiple species of <i>Bacteroides, Escherichia coli/Salmonella</i>, and <i>Lactobacillus</i>. Overall, bifidobacteria have larger transportomes (based on percentages of total proteins) than the previously examined groups of bacterial species, with a preference for primary active transport systems over secondary carriers. Taken together, these results provide useful information about the physiologies and pathogenic potentials of these probiotic organisms as reflected by their transportomes.

scholarly journals ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 103 ◽  
Author(s):  
Subina Mehta ◽  
Marie Crane ◽  
Emma Leith ◽  
Bérénice Batut ◽  
Saskia Hiltemann ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Human Health ◽  
Genetic Material ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Taxonomic Composition ◽  
Sequencing Technologies ◽  
The Galaxy ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data

The Human Microbiome Project (HMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the ‘microbiome’) in human health and disease. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). Conversely, metatranscriptomics, the study of a microbial community’s RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome.  In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking.  In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.

scholarly journals The Human Microbiome: History and Future

2020 ◽  
Vol 23 ◽  
pp. 406-411
Author(s):  
Wallace Hayes ◽  
Saura Sahu
Keyword(s):  
Human Health ◽  
New Technologies ◽  
Human Microbiome ◽  
Current Understanding ◽  
Review Of The Literature ◽  
Health And Disease ◽  
Host Metabolism ◽  
Made In

The microbiome plays an important role in human health and disease. Our current understanding of the human microbiome is limited. A significant amount of progress has been made in this area of research in the last two decades. The human microbiome plays an important role in host metabolism and physiology. Recent studies suggest a critical relationship between the human microbiome and host metabolism. The interactions between the microbiome and host metabolism affect human health and disease. However, this review of the literature indicates that more studies are required using new technologies to have a greater understanding of the role the human microbiome plays in human health and disease.

scholarly journals Habitat Fluctuations Drive Species Covariation in the Human Microbiota

2015 ◽  
Author(s):  
Charles K. Fisher ◽  
Thierry Mora ◽  
Aleksandra M. Walczak
Keyword(s):  
Resource Sharing ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Mathematical Framework ◽  
Bacterial Populations ◽  
Human Microbiota ◽  
Resource Requirements ◽  
Species Abundances ◽  
Common Resource ◽  
Small Set

Two species with similar resource requirements respond in a characteristic way to variations in their habitat -- their abundances rise and fall in concert. We use this idea to learn how bacterial populations in the microbiota respond to habitat conditions that vary from person-to-person across the human population. Our mathematical framework shows that habitat fluctuations are sufficient for explaining intra-bodysite correlations in relative species abundances from the Human Microbiome Project. We explicitly show that the relative abundances of phylogenetically related species are positively correlated and can be predicted from taxonomic relationships. We identify a small set of functional pathways related to metabolism and maintenance of the cell wall that form the basis of a common resource sharing niche space of the human microbiota.

scholarly journals The Human Microbiota and Prostate Cancer: Friend or Foe?

Cancers ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 459 ◽  
Author(s):  
Francesco Massari ◽  
Veronica Mollica ◽  
Vincenzo Di Nunno ◽  
Lidia Gatto ◽  
Matteo Santoni ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Gut Microbiota ◽  
Current Knowledge ◽  
Human Microbiome ◽  
Medical Community ◽  
Male Population ◽  
Human Microbiota ◽  
Common Cancer ◽  
Urinary Microbiota ◽  
The Relationship

The human microbiome is gaining increasing attention in the medical community, as knowledge on its role not only in health but also in disease development and response to therapies is expanding. Furthermore, the connection between the microbiota and cancer, especially the link between the gut microbiota and gastrointestinal tumors, is becoming clearer. The interaction between the microbiota and the response to chemotherapies and, more recently, to immunotherapy has been widely studied, and a connection between a peculiar type of microbiota and a better response to these therapies and a different incidence in toxicities has been hypothesized. As knowledge on the gut microbiota increases, interest in the residing microbial population in other systems of our body is also increasing. Consequently, the urinary microbiota is under evaluation for its possible implications in genitourinary diseases, including cancer. Prostate cancer is the most common cancer in the male population; thus, research regarding its etiology and possible factors correlated to disease progression or the response to specific therapies is thriving. This review has the purpose to recollect the current knowledge on the relationship between the human microbiota and prostate cancer.

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