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 A Putative Type V Pilus Contributes toBacteroides thetaiotaomicronBiofilm Formation Capacity

2019 ◽  
Vol 201 (18) ◽  
Author(s):  
Jovana Mihajlovic ◽  
Nathalie Bechon ◽  
Christa Ivanova ◽  
Florian Chain ◽  
Alexandre Almeida ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Selection Procedure ◽  
Bacteroides Thetaiotaomicron ◽  
Human Gut ◽  
Healthy Human ◽  
Content Type ◽  
Human Gut Microbiota ◽  
Type V

ABSTRACTBacteroides thetaiotaomicronis a prominent anaerobic member of the healthy human gut microbiota. While the majority of functional studies onB. thetaiotaomicronaddressed its impact on the immune system and the utilization of diet polysaccharides,B. thetaiotaomicronbiofilm capacity and its contribution to intestinal colonization are still poorly characterized. We tested the natural adhesion of 34B. thetaiotaomicronisolates and showed that although biofilm capacity is widespread amongB. thetaiotaomicronstrains, this phenotype is masked or repressed in the widely used reference strain VPI 5482. Using transposon mutagenesis followed by a biofilm positive-selection procedure, we identified VPI 5482 mutants with increased biofilm capacity corresponding to an alteration in the C-terminal region of BT3147, encoded by theBT3148-BT3147locus, which displays homology with Mfa-like type V pili found in manyBacteroidetes. We show that BT3147 is exposed on theB. thetaiotaomicronsurface and that BT3147-dependent adhesion also requires BT3148, suggesting that BT3148 and BT3147 correspond to the anchor and stalk subunits of a new type V pilus involved inB. thetaiotaomicronadhesion. This study therefore introducesB. thetaiotaomicronas a model to study proteinaceous adhesins and biofilm-related phenotypes in this important intestinal symbiont.IMPORTANCEAlthough the gut anaerobeBacteroides thetaiotaomicronis a prominent member of the healthy human gut microbiota, little is known about its capacity to adhere to surfaces and form biofilms. Here, we identify that alteration of a surface-exposed protein corresponding to a type of pili found in manyBacteroidetesincreasesB. thetaiotaomicronbiofilm formation. This study lays the ground for establishing this bacterium as a model organism forin vitroandin vivostudies of biofilm-related phenotypes in gut anaerobes.

scholarly journals Relationship between Nutrient Intake and Human Gut Microbiota in Monozygotic Twins

Medicina ◽  
2021 ◽  
Vol 57 (3) ◽  
pp. 275
Author(s):  
Natsuko Matsumoto ◽  
Jonguk Park ◽  
Rie Tomizawa ◽  
Hitoshi Kawashima ◽  
Koji Hosomi ◽  
...  
Keyword(s):  
Individual Differences ◽  
Environmental Factors ◽  
Gut Microbiota ◽  
Human Health ◽  
Negative Correlation ◽  
Nutrient Intake ◽  
Monozygotic Twins ◽  
Human Gut ◽  
Positive Correlation ◽  
Human Gut Microbiota

Background and Objectives: The gut microbiota is associated with human health and dietary nutrition. Various studies have been reported in this regard, but it is difficult to clearly analyze human gut microbiota as individual differences are significant. The causes of these individual differences in intestinal microflora are genetic and/or environmental. In this study, we focused on differences between identical twins in Japan to clarify the effects of nutrients consumed on the entire gut microbiome, while excluding genetic differences. Materials and Methods: We selected healthy Japanese monozygotic twins for the study and confirmed their zygosity by matching 15 short tandem repeat loci. Their fecal samples were subjected to 16S rRNA sequencing and bioinformatics analyses to identify and compare the fluctuations in intestinal bacteria. Results: We identified 12 genera sensitive to environmental factors, and found that Lactobacillus was relatively unaffected by environmental factors. Moreover, we identified protein, fat, and some nutrient intake that can affect 12 genera, which have been identified to be more sensitive to environmental factors. Among the 12 genera, Bacteroides had a positive correlation with retinol equivalent intake (rs = 0.38), Lachnospira had a significantly negative correlation with protein, sodium, iron, vitamin D, vitamin B6, and vitamin B12 intake (rs = −0.38, −0.41, −0.39, −0.63, −0.42, −0.49, respectively), Lachnospiraceae ND3007 group had a positive correlation with fat intake (rs = 0.39), and Lachnospiraceae UCG-008 group had a negative correlation with the saturated fatty acid intake (rs = −0.45). Conclusions: Our study is the first to focus on the relationship between human gut microbiota and nutrient intake using samples from Japanese twins to exclude the effects of genetic factors. These findings will broaden our understanding of the more intuitive relationship between nutrient intake and the gut microbiota and can be a useful basis for finding useful biomarkers that contribute to human health.

scholarly journals The Glycine Lipids ofBacteroides thetaiotaomicronAre Important for Fitness during GrowthIn VivoandIn Vitro

2018 ◽  
Vol 85 (10) ◽  
Author(s):  
Alli Lynch ◽  
Seshu R. Tammireddy ◽  
Mary K. Doherty ◽  
Phillip D. Whitfield ◽  
David J. Clarke
Keyword(s):  
Amino Acid ◽  
Gut Microbiome ◽  
Molecular Mechanisms ◽  
Cellular Membrane ◽  
Bacteroides Thetaiotaomicron ◽  
Human Gut ◽  
Acyltransferase Activity ◽  
Content Type ◽  
Health And Disease ◽  
And Function

ABSTRACTAcylated amino acids function as important components of the cellular membrane in some bacteria. Biosynthesis is initiated by theN-acylation of the amino acid, and this is followed by subsequentO-acylation of the acylated molecule, resulting in the production of the mature diacylated amino acid lipid. In this study, we use both genetics and liquid chromatography-mass spectrometry (LC-MS) to characterize the biosynthesis and function of a diacylated glycine lipid (GL) species produced inBacteroides thetaiotaomicron. We, and others, have previously reported the identification of a gene, namedglsBin this study, that encodes anN-acyltransferase activity responsible for the production of a monoacylated glycine calledN-acyl-3-hydroxy-palmitoyl glycine (or commendamide). In all of theBacteroidalesgenomes sequenced so far, theglsBgene is located immediately downstream from a gene, namedglsA, that is also predicted to encode a protein with acyltransferase activity. We use LC-MS to show that the coexpression ofglsBandglsAresults in the production of GL inEscherichia coli. We constructed a deletion mutant of theglsBgene inB. thetaiotaomicron, and we confirm thatglsBis required for the production of GL inB. thetaiotaomicron. Moreover, we show thatglsBis important for the ability ofB. thetaiotaomicronto adapt to stress and colonize the mammalian gut. Therefore, this report describes the genetic requirements for the biosynthesis of GL, a diacylated amino acid species that contributes to fitness in the human gut bacteriumB. thetaiotaomicron.IMPORTANCEThe gut microbiome has an important role in both health and disease of the host. The mammalian gut microbiome is often dominated by bacteria from theBacteroidales, an order that includesBacteroidesandPrevotella. In this study, we have identified an acylated amino acid, called glycine lipid, produced byBacteroides thetaiotaomicron, a beneficial bacterium originally isolated from the human gut. In addition to identifying the genes required for the production of glycine lipids, we show that glycine lipids have an important role during the adaptation ofB. thetaiotaomicronto a number of environmental stresses, including exposure to either bile or air. We also show that glycine lipids are important for the normal colonization of the murine gut byB. thetaiotaomicron. This work identifies glycine lipids as an important fitness determinant inB. thetaiotaomicronand therefore increases our understanding of the molecular mechanisms underpinning colonization of the mammalian gut by beneficial bacteria.

scholarly journals Does Consumption of Fermented Foods Modify the Human Gut Microbiota?

2020 ◽  
Vol 150 (7) ◽  
pp. 1680-1692 ◽  
Author(s):  
Leah T Stiemsma ◽  
Reine E Nakamura ◽  
Jennifer G Nguyen ◽  
Karin B Michels
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Food Consumption ◽  
Intervention Studies ◽  
Fermented Food ◽  
Fermented Foods ◽  
Human Intervention ◽  
Human Gut ◽  
Gut Dysbiosis ◽  
Human Gut Microbiota

ABSTRACT The human microbiota is a key contributor to many aspects of human health and its composition is largely influenced by diet. There is a growing body of scientific evidence to suggest that gut dysbiosis (microbial imbalance of the intestine) is associated with inflammatory and immune-mediated diseases (e.g., inflammatory bowel disease and asthma). Regular consumption of fermented foods (e.g., kimchi, kefir, etc.) may represent a potential avenue to counter the proinflammatory effects of gut dysbiosis. However, an assessment of the available literature in this research area is lacking. Here we provide a critical review of current human intervention studies that analyzed the effect of fermented foods on the composition and/or function of the human gut microbiota. A total of 19 human intervention studies were identified that met this search criteria. In this review, we discuss evidence that consumption of fermented foods may modify the gut microbiota in humans. Further, there is cursory evidence to suggest that gut microbiota compositional changes mediate associations between fermented food consumption and human health outcomes. Although promising, there remains considerable heterogeneity in the human populations targeted in the intervention studies we identified. Larger longitudinal feeding studies with longer follow-up are necessary to confirm and enhance the current data. Further, future studies should consider analyzing microbiota function as a means to elucidate the mechanism linking fermented food consumption with human health. This review highlights methodologic considerations for intervention trials, emphasizing an expanse of research opportunities related to fermented food consumption in humans.

scholarly journals Dietary Fatty Acids Sustain the Growth of the Human Gut Microbiota

2018 ◽  
Vol 84 (21) ◽  
Author(s):  
Richard Agans ◽  
Alex Gordon ◽  
Denise Lynette Kramer ◽  
Sergio Perez-Burillo ◽  
José A. Rufián-Henares ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Small Intestine ◽  
Fatty Acid ◽  
Gut Microbiota ◽  
Short Chain Fatty Acids ◽  
Dietary Fatty Acids ◽  
Dietary Fats ◽  
High Fat ◽  
Human Gut ◽  
Content Type

ABSTRACTWhile a substantial amount of dietary fats escape absorption in the human small intestine and reach the colon, the ability of resident microbiota to utilize these dietary fats for growth has not been investigated in detail. In this study, we used anin vitromultivessel simulator system of the human colon to reveal that the human gut microbiota is able to utilize typically consumed dietary fatty acids to sustain growth. Gut microbiota adapted quickly to a macronutrient switch from a balanced Western diet-type medium to its variant lacking carbohydrates and proteins. We defined specific genera that increased in their abundances on the fats-only medium, includingAlistipes,Bilophila, and several genera of the classGammaproteobacteria. In contrast, the abundances of well-known glycan and protein degraders, includingBacteroides,Clostridium, andRoseburiaspp., were reduced under such conditions. The predicted prevalences of microbial genes coding for fatty acid degradation enzymes and anaerobic respiratory reductases were significantly increased in the fats-only environment, whereas the abundance of glycan degradation genes was diminished. These changes also resulted in lower microbial production of short-chain fatty acids and antioxidants. Our findings provide justification for the previously observed alterations in gut microbiota observed in human and animal studies of high-fat diets.IMPORTANCEIncreased intake of fats in many developed countries has raised awareness of potentially harmful and beneficial effects of high fat consumption on human health. Some dietary fats escape digestion in the small intestine and reach the colon where they can be metabolized by gut microbiota. We show that human gut microbes are able to maintain a complex community when supplied with dietary fatty acids as the only nutrient and carbon sources. Such fatty acid-based growth leads to lower production of short-chain fatty acids and antioxidants by community members, which potentially have negative health consequences on the host.

scholarly journals Gut Microbiota Metabolism and Interaction with Food Components

2020 ◽  
Vol 21 (10) ◽  
pp. 3688 ◽  
Author(s):  
Pamela Vernocchi ◽  
Federica Del Chierico ◽  
Lorenza Putignani
Keyword(s):  
Gut Microbiota ◽  
Disease Onset ◽  
Human Gut ◽  
Food Components ◽  
Host Health ◽  
Wide Variability ◽  
Gut Microbe ◽  
A Cell ◽  
Health And Disease ◽  
Biochemical Mechanisms

The human gut contains trillions of microbes that play a central role in host biology, including the provision of key nutrients from the diet. Food is a major source of precursors for metabolite production; in fact, diet modulates the gut microbiota (GM) as the nutrients, derived from dietary intake, reach the GM, affecting both the ecosystem and microbial metabolic profile. GM metabolic ability has an impact on human nutritional status from childhood. However, there is a wide variability of dietary patterns that exist among individuals. The study of interactions with the host via GM metabolic pathways is an interesting field of research in medicine, as microbiota members produce myriads of molecules with many bioactive properties. Indeed, much evidence has demonstrated the importance of metabolites produced by the bacterial metabolism from foods at the gut level that dynamically participate in various biochemical mechanisms of a cell as a reaction to environmental stimuli. Hence, the GM modulate homeostasis at the gut level, and the alteration in their composition can concur in disease onset or progression, including immunological, inflammatory, and metabolic disorders, as well as cancer. Understanding the gut microbe–nutrient interactions will increase our knowledge of how diet affects host health and disease, thus enabling personalized therapeutics and nutrition.

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 Dietary Components, Microbial Metabolites and Human Health: Reading between the Lines

Foods ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1045
Author(s):  
Yao Guo ◽  
Xiaohan Bian ◽  
Jiali Liu ◽  
Ming Zhu ◽  
Lin Li ◽  
...  
Keyword(s):  
Linoleic Acid ◽  
Gut Microbiota ◽  
Human Health ◽  
Kynurenic Acid ◽  
Molecular Mechanisms ◽  
Eating Habits ◽  
Short Chain Fatty Acids ◽  
Human Gut ◽  
Dietary Components ◽  
Host Metabolism

Trillions of bacteria reside in the human gut and they metabolize dietary substances to obtain nutrients and energy while producing metabolites. Therefore, different dietary components could affect human health in various ways through microbial metabolism. Many such metabolites have been shown to affect human physiological activities, including short-chain fatty acids metabolized from carbohydrates; indole, kynurenic acid and para-cresol, metabolized from amino acids; conjugated linoleic acid and linoleic acid, metabolized from lipids. Here, we review the features of these metabolites and summarize the possible molecular mechanisms of their metabolisms by gut microbiota. We discuss the potential roles of these metabolites in health and diseases, and the interactions between host metabolism and the gut microbiota. We also show some of the major dietary patterns around the world and hope this review can provide insights into our eating habits and improve consumers’ health conditions.

Sign in / Sign up

Export Citation Format

Share Document