scholarly journals Towards Standards for Human Fecal Sample Preparation in Targeted and Untargeted LC-HRMS Studies

Metabolites ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 364
Author(s):  
Farideh Hosseinkhani ◽  
Anne-Charlotte Dubbelman ◽  
Naama Karu ◽  
Amy C. Harms ◽  
and Thomas Hankemeier
Keyword(s):  
Sample Preparation ◽  
Gut Microbiota ◽  
Human Health ◽  
Extraction Methods ◽  
Major Step ◽  
Bacterial Metabolites ◽  
Extraction Solvent ◽  
Solvent Type ◽  
Metabolic Products ◽  
Health And Disease

Gut microbiota and their metabolic products are increasingly being recognized as important modulators of human health. The fecal metabolome provides a functional readout of the interactions between human metabolism and the gut microbiota in health and disease. Due to the high complexity of the fecal matrix, sample preparation often introduces technical variation, which must be minimized to accurately detect and quantify gut bacterial metabolites. Here, we tested six different representative extraction methods (single-phase and liquid–liquid extractions) and compared differences due to fecal amount, extraction solvent type and solvent pH. Our results indicate that a minimum fecal (wet) amount of 0.50 gram is needed to accurately represent the complex texture of feces. The MTBE method (MTBE/methanol/water, 3.6/2.8/3.5, v/v/v) outperformed the other extraction methods, reflected by the highest extraction efficiency for 11 different classes of compounds, the highest number of extracted features (97% of the total identified features in different extracts), repeatability (CV < 35%) and extraction recovery (≥70%). Importantly, optimization of the solvent volume of each step to the initial dried fecal material (µL/mg feces) offers a major step towards standardization, which enables confident assessment of the contributions of gut bacterial metabolites to human health.

scholarly journals Modulation of Gut Microbiota for the Prevention and Treatment of COVID-19

2021 ◽  
Vol 10 (13) ◽  
pp. 2903
Author(s):  
Jiezhong Chen ◽  
Luis Vitetta
Keyword(s):  
Clinical Trials ◽  
Trace Elements ◽  
Gut Microbiota ◽  
Human Health ◽  
Intestinal Microbiota ◽  
Narrative Review ◽  
Bacterial Metabolites ◽  
Gut Dysbiosis ◽  
Prevention And Treatment

The gut microbiota is well known to exert multiple benefits on human health including protection from disease causing pathobiont microbes. It has been recognized that healthy intestinal microbiota is of great importance in the pathogenesis of COVID-19. Gut dysbiosis caused by various reasons is associated with severe COVID-19. Therefore, the modulation of gut microbiota and supplementation of commensal bacterial metabolites could reduce the severity of COVID-19. Many approaches have been studied to improve gut microbiota in COVID-19 including probiotics, bacterial metabolites, and prebiotics, as well as nutraceuticals and trace elements. So far, 19 clinical trials for testing the efficacy of probiotics and synbiotics in COVID-19 prevention and treatment are ongoing. In this narrative review, we summarize the effects of various approaches on the prevention and treatment of COVID-19 and discuss associated mechanisms.

scholarly journals Revisit gut microbiota and its impact on human health and disease

2019 ◽  
Vol 27 (3) ◽  
pp. 623-631 ◽  
Author(s):  
Rui-xue Ding ◽  
Wei-Rui Goh ◽  
Ri-na Wu ◽  
Xi-qing Yue ◽  
Xue Luo ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Health And Disease

scholarly journals Streamlined Genetic Manipulation of Diverse Bacteroides and Parabacteroides Isolates from the Human Gut Microbiota

mBio ◽  
2019 ◽  
Vol 10 (4) ◽  
Author(s):  
Leonor García-Bayona ◽  
Laurie E. Comstock
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Genetic Manipulation ◽  
Mechanistic Study ◽  
Type Vi Secretion System ◽  
Human Gut ◽  
Healthy Human ◽  
Content Type ◽  
Health And Disease ◽  
Multiresistant Strains

ABSTRACT Studies of the gut microbiota have dramatically increased in recent years as the importance of this microbial ecosystem to human health and disease is better appreciated. The Bacteroidales are the most abundant order of bacteria in the healthy human gut and induce both health-promoting and disease-promoting effects. There are more than 55 species of gut Bacteroidales with extensive intraspecies genetic diversity, especially in regions involved in the synthesis of molecules that interact with other bacteria, the host, and the diet. This property necessitates the study of diverse species and strains. In recent years, the genetic toolkit to study these bacteria has greatly expanded, but we still lack a facile system for creating deletion mutants and allelic replacements in diverse strains, especially with the rapid increase in resistance to the two antibiotics used for genetic manipulation. Here, we present a new versatile and highly efficient vector suite that allows the creation of allelic deletions and replacements in multiresistant strains of Bacteroides and Parabacteroides using a gain-of-function system based on polysaccharide utilization. These vectors also allow for easy counterselection independent of creating a mutant background strain, using a toxin from a type VI secretion system of Bacteroides fragilis. Toxin production during counterselection is induced with one of two different molecules, providing flexibility based on strain phenotypes. This family of vectors greatly facilitates functional genetic analyses and extends the range of gut Bacteroidales strains that can be genetically modified to include multiresistant strains that are currently genetically intractable with existing genetic tools. IMPORTANCE We have entered an era when studies of the gut microbiota are transitioning from basic questions of composition and host effects to understanding the microbial molecules that underlie compositional shifts and mediate health and disease processes. The importance of the gut Bacteroidales to human health and disease and their potential as a source of engineered live biotherapeutics make these bacteria of particular interest for in-depth mechanistic study. However, there are still barriers to the genetic analysis of diverse Bacteroidales strains, limiting our ability to study important host and community phenotypes identified in these strains. Here, we have overcome many of these obstacles by constructing a series of vectors that allow easy genetic manipulation in diverse gut Bacteroides and Parabacteroides strains. These constructs fill a critical need and allow streamlined allelic replacement in diverse gut Bacteroidales, including the growing number of multiantibiotic-resistant strains present in the modern-day human intestine.

scholarly journals Bacteriophages: Uncharacterized and Dynamic Regulators of the Immune System

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Anshul Sinha ◽  
Corinne F. Maurice
Keyword(s):  
Immune System ◽  
Gut Microbiota ◽  
Human Health ◽  
Human Body ◽  
Human Gut ◽  
Antibiotic Resistant ◽  
Active Involvement ◽  
Mediated Effects ◽  
Health And Disease ◽  
The Many

The human gut is an extremely active immunological site interfacing with the densest microbial community known to colonize the human body, the gut microbiota. Despite tremendous advances in our comprehension of how the gut microbiota is involved in human health and interacts with the mammalian immune system, most studies are incomplete as they typically do not consider bacteriophages. These bacterial viruses are estimated to be as numerous as their bacterial hosts, with tremendous and mostly uncharacterized genetic diversity. In addition, bacteriophages are not passive members of the gut microbiota, as highlighted by the recent evidence for their active involvement in human health. Yet, how bacteriophages interact with their bacterial hosts and the immune system in the human gut remains poorly described. Here, we aim to fill this gap by providing an overview of bacteriophage communities in the gut during human development, detailing recent findings for their bacterial-mediated effects on the immune response and summarizing the latest evidence for direct interactions between them and the immune system. The dramatic increase in antibiotic-resistant bacterial pathogens has spurred a renewed interest in using bacteriophages for therapy, despite the many unknowns about bacteriophages in the human body. Going forward, more studies encompassing the communities of bacteria, bacteriophages, and the immune system in diverse health and disease settings will provide invaluable insight into this dynamic trio essential for human health.

scholarly journals Impact of the gut microbiota, prebiotics, and probiotics on human health and disease

2014 ◽  
Vol 37 (5) ◽  
pp. 259 ◽  
Author(s):  
Hsin-Chih Lai ◽  
JohnD Young ◽  
Chuan-Sheng Lin ◽  
Chih-Jung Chang ◽  
Chia-Chen Lu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Health And Disease

scholarly journals Next Generation Microbiome Research: Identification of Keystone Species in the Metabolic Regulation of Host-Gut Microbiota Interplay

2021 ◽  
Vol 9 ◽  
Author(s):  
Héloïse Tudela ◽  
Sandrine P. Claus ◽  
Maya Saleh
Keyword(s):  
Gut Microbiota ◽  
Metabolic Regulation ◽  
Keystone Species ◽  
Epithelial Barrier ◽  
Intestinal Epithelial ◽  
Intestinal Epithelial Barrier ◽  
Nutrient Metabolism ◽  
Major Step ◽  
Microbiome Research ◽  
Health And Disease

The community of the diverse microorganisms residing in the gastrointestinal tract, known as the gut microbiota, is exceedingly being studied for its impact on health and disease. This community plays a major role in nutrient metabolism, maintenance of the intestinal epithelial barrier but also in local and systemic immunomodulation. A dysbiosis of the gut microbiota, characterized by an unbalanced microbial ecology, often leads to a loss of essential functions that may be associated with proinflammatory conditions. Specifically, some key microbes that are depleted in dysbiotic ecosystems, called keystone species, carry unique functions that are essential for the balance of the microbiota. In this review, we discuss current understanding of reported keystone species and their proposed functions in health. We also elaborate on current and future bioinformatics tools needed to identify missing functions in the gut carried by keystone species. We propose that the identification of such keystone species functions is a major step for the understanding of microbiome dynamics in disease and toward the development of microbiome-based therapeutics.

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