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 Small Molecule Modulation of Microbiome Ecosystem: A Systems Pharmacology Perspective

2020 ◽  
Author(s):  
Qiao Liu ◽  
Bohyun Lee ◽  
Lei Xie
Keyword(s):  
Drug Discovery ◽  
Human Health ◽  
Small Molecule ◽  
Drug Targets ◽  
Outer Membrane Proteins ◽  
Human Microbiome ◽  
Interaction Network ◽  
Fine Tune ◽  
Potential Drug Targets ◽  
Pathogenic Microbe

AbstractAn increasing body of evidence suggests that microbes are not only strongly associated with many human diseases but also responsible for the efficacy, resistance, and toxicity of drugs. Small-molecule drugs which can precisely fine-tune the microbial ecosystem on the basis of individual patients may revolutionize biomedicine. However, emerging endeavors in small-molecule microbiome drug discovery continue to follow a conventional “one-drug-one-target-one-disease” process. It is often insufficient and less successful in tackling complex systematic diseases. A systematic pharmacology approach that intervenes multiple interacting pathogenic species in the microbiome, could offer an attractive alternative solution. Advances in the Human Microbiome Project have provided numerous genomics data to study microbial interactions in the complex microbiome community. Integrating microbiome data with chemical genomics and other biological information enables us to delineate the landscape for the small molecule modulation of the human microbiome network. In this paper, we construct a disease-centric signed microbe-microbe interaction network using metabolite information of microbes and curated microbe effects on human health from published work. We develop a Signed Random Walk with Restart algorithm for the accurate prediction of pathogenic and commensal species. With a survey on the druggable and evolutionary space of microbe proteins, we find that 8-10% of them can be targeted by existing drugs or drug-like chemicals and that 25% of them have homologs to human proteins. We also demonstrate that drugs for diabetes are enriched in the potential inhibitors that target pathogenic microbe without affecting the commensal microbe, thus can be repurposed to modulate the microbiome ecosystem. We further show that periplasmic and cellular outer membrane proteins are overrepresented in the potential drug targets set in pathogenic microbe, but not in the commensal microbe. The systematic studies of polypharmacological landscape of the microbiome network may open a new avenue for the small-molecule drug discovery of microbiome.Author SummaryAs one of the most abundant components in human bodies, the microbiome has an extensive impact on human health. Pathogenic-microbes have become emerging potential therapeutic targets. Small-molecule drugs that only intervene in the growth of a specific pathogenic microbe without considering the interacting dynamics of the microbiome community may disrupt the ecosystem homeostasis, thus can cause drug side effect or prompt drug resistance. To discover novel drugs for safe and effective microbe-targeting therapeutics, a systematic approach is needed to fine-tune the microbiome ecosystem. To this end, we built a disease-centric signed microbe-microbe interaction network which accurately predicts the pathogenic or commensal effect of microbe on human health. Based on annotated and predicted pathogens and commensal species, we performed a systematic survey on therapeutic space and target landscape of existing drugs for modulating the microbiome ecosystem. Enrichment analysis on potential microbe-targeting drugs shows that drugs for diabetes could be repurposed to maintain the healthy state of microbiome. Furthermore, periplasmic and cellular outer membrane proteins are overrepresented in the potential drug targets of pathogenic-microbes, but not in proteins that perturb commensal-microbes. Our study may open a new avenue for the small molecule drug discovery of microbiome.

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 Probiotics: If It Does Not Help It Does Not Do Any Harm. Really?

2019 ◽  
Vol 7 (4) ◽  
pp. 104 ◽  
Author(s):  
Aaron Lerner ◽  
Yehuda Shoenfeld ◽  
Torsten Matthias
Keyword(s):  
Human Health ◽  
Research Design ◽  
Mode Of Action ◽  
Human Microbiome ◽  
Dark Side ◽  
Intestinal Lumen ◽  
Beneficial Effects ◽  
Expert Opinions ◽  
Scientific World ◽  
Meta Analyses

Probiotics per definition should have beneficial effects on human health, and their consumption has tremendously increased in the last decades. In parallel, the amount of published material and claims for their beneficial efficacy soared continuously. Recently, multiple systemic reviews, meta-analyses, and expert opinions expressed criticism on their claimed effects and safety. The present review describes the dark side of the probiotics, in terms of problematic research design, incomplete reporting, lack of transparency, and under-reported safety. Highlighted are the potential virulent factors and the mode of action in the intestinal lumen, risking the physiological microbiome equilibrium. Finally, regulatory topics are discussed to lighten the heterogeneous guidelines applied worldwide. The shift in the scientific world towards a better understanding of the human microbiome, before consumption of the probiotic cargo, is highly endorsed. It is hoped that better knowledge will extend the probiotic repertoire, re-confirm efficacy or safety, establish their efficacy and substantiate their beneficial effects.

Substituted 6,7-dimethoxy-5-oxo-2,3,5,9b-tetrahydrothiazolo[2,3-a]isoindole- 3-1,1-dioxide Derivatives with Antimicrobial Activity and Docking Assisted Prediction of the Mechanism of their Antibacterial and Antifungal Properties

2020 ◽  
Vol 20 (29) ◽  
pp. 2681-2691
Author(s):  
Athina Geronikaki ◽  
Victor Kartsev ◽  
Phaedra Eleftheriou ◽  
Anthi Petrou ◽  
Jasmina Glamočlija ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Antifungal Activity ◽  
Drug Targets ◽  
Bacterial Species ◽  
Pharmaceutical Research ◽  
Docking Studies ◽  
Fungal Species ◽  
Docking Analysis ◽  
E Coli ◽  
Antibacterial And Antifungal

Background: Although a great number of the targets of antimicrobial therapy have been achieved, it remains among the first fields of pharmaceutical research, mainly because of the development of resistant strains. Docking analysis may be an important tool in the research for the development of more effective agents against specific drug targets or multi-target agents 1-3. Methods: In the present study, based on docking analysis, ten tetrahydrothiazolo[2,3-a]isoindole derivatives were chosen for the evaluation of the antimicrobial activity. Results: All compounds showed antibacterial activity against eight Gram-positive and Gram-negative bacterial species being, in some cases, more potent than ampicillin and streptomycin against all species. The most sensitive bacteria appeared to be S. aureus and En. Cloacae, while M. flavus, E. coli and P. aeruginosa were the most resistant ones. The compounds were also tested for their antifungal activity against eight fungal species. All compounds exhibited good antifungal activity better than reference drugs bifonazole (1.4 – 41 folds) and ketoconazole (1.1 – 406 folds) against all fungal species. In order to elucidate the mechanism of action, docking studies on different antimicrobial targets were performed. Conclusion: According to docking analysis, the antifungal activity can be explained by the inhibition of the CYP51 enzyme for most compounds with a better correlation of the results obtained for the P.v.c. strain (linear regression between estimated binding Energy and log(1/MIC) with R 2 =0.867 and p=0.000091 or R 2 = 0.924, p= 0.000036, when compound 3 is excluded.

The Role of Purinergic Signaling in Trichomonas vaginalis Infection

2020 ◽  
Vol 20 ◽  
Author(s):  
Micheli Ferla ◽  
Tiana Tasca
Keyword(s):  
Drug Targets ◽  
Trichomonas Vaginalis ◽  
Hiv Transmission ◽  
Cell Damage ◽  
Purinergic Signaling ◽  
Host Cells ◽  
Purine Nucleotides ◽  
Cellular Effects ◽  
Adverse Pregnancy ◽  
Purine Salvage Pathways

: Trichomoniasis, one of the most common non-viral sexually transmitted infections worldwide, is caused by the parasite Trichomonas vaginalis. The pathogen colonizes the human urogenital tract and the infection is associated with complications such as adverse pregnancy outcomes, cervical cancer, and an increase in HIV transmission. The mecha-nisms of pathogenicity are multifactorial, and controlling immune responses is essential for infection maintenance. Extra-cellular purine nucleotides are released by cells in physiological and pathological conditions, and they are hydrolyzed by enzymes called ecto-nucleotidases. The cellular effects of nucleotides and nucleosides occur via binding to purinoceptors, or throughthe uptake by nucleoside transporters. Altogether, enzymes, receptors and transporters constitute the purinergic signaling, a cellular network that regulates several effects in practically all systems including mammals, helminths, proto-zoa, bacteria, and fungi. In this context, this review updates the data on purinergic signaling involved in T. vaginalis biol-ogy and interaction with host cells, focusing on the characterization of ecto-nucleotidases and on purine salvage pathways. The implications of the final products, the nucleosides adenosine and guanosine, for human neutrophil response and vagi-nal epithelial cell damage reveal the purinergic signaling as a potential new mechanism for alternative drug targets.

Effects of Minor Compounds of Edible Oils on Human Health

2020 ◽  
Vol 16 (8) ◽  
pp. 1196-1208
Author(s):  
Ramin Ghodsi ◽  
Rahmat Nosrati
Keyword(s):  
Human Health ◽  
Food Industry ◽  
Edible Oils ◽  
Food Groups ◽  
Bioactive Constituents ◽  
Beneficial Effects ◽  
Anti Cancer ◽  
Prevention And Treatment ◽  
Minor Compounds ◽  
Anti Inflammation

Background: Oils and fats are the densest sources of food energy among food groups. Vegetable oils are constituted predominantly of triglycerides. Due to the importance of edible oils in nutrition, food industry and human health, great attention has been paid to them in recent years. Some minor bioactive constituents in oils include phospholipids, tocols, sterols, carotenoid, chlorophyll, phenols, phylokynon and terpenes. Objective: The aim of the present study was to examine beneficial effects of minor compounds in edible oils on human health. Results: Minor compounds of edible oils that we use daily can produce remarkable results in the prevention and treatment of various diseases like diabetes, inflammation, hypertension, cancer, allergy and central nervous system disorders due to their antimicrobial, anti-cancer, anti-viral, anti-oxidative, anti-inflammation, anti-mutagenic, hypolipidemic, and hypoglycemic properties, among others. Conclusion: The results of this study showed that the presence of beneficial minor compounds in oils could have significant impact on the prevention and treatment of various diseases. Therefore, the type of consumed oil can play an important role in human health.

scholarly journals Burkholderia cenocepacia transcriptome during the early contacts with giant plasma membrane vesicles derived from live bronchial epithelial cells

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Andreia I. Pimenta ◽  
Nuno Bernardes ◽  
Marta M. Alves ◽  
Dalila Mil-Homens ◽  
Arsenio M. Fialho
Keyword(s):  
Membrane Vesicles ◽  
Bronchial Epithelial Cell ◽  
Host Cells ◽  
Burkholderia Cenocepacia ◽  
Transport Systems ◽  
Epithelial Cell Line ◽  
Plasma Membrane Vesicles ◽  
Bronchial Epithelial ◽  
Cellular Processes ◽  
Associated Functions

AbstractBurkholderia cenocepacia is known for its capacity of adherence and interaction with the host, causing severe opportunistic lung infections in cystic fibrosis patients. In this work we produced Giant Plasma Membrane Vesicles (GPMVs) from a bronchial epithelial cell line and validated their use as a cell-like alternative to investigate the steps involved in the adhesion process of B. cenocepacia. RNA-sequencing was performed and the analysis of the B. cenocepacia K56-2 transcriptome after the first contacts with the surface of host cells allowed the recognition of genes implicated in bacterial adaptation and virulence-associated functions. The sensing of host membranes led to a transcriptional shift that caused a cascade of metabolic and physiological adaptations to the host specific environment. Many of the differentially expressed genes encode proteins related with central metabolic pathways, transport systems, cellular processes, and virulence traits. The understanding of the changes in gene expression that occur in the early steps of infection can uncover new proteins implicated in B. cenocepacia-host cell adhesion, against which new blocking agents could be designed to control the progression of the infectious process.

scholarly journals Monoassociation with bacterial isolates reveals the role of colonization, community complexity and abundance on locomotor behavior in larval zebrafish

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Chelsea A. Weitekamp ◽  
Allison Kvasnicka ◽  
Scott P. Keely ◽  
Nichole E. Brinkman ◽  
Xia Meng Howey ◽  
...  
Keyword(s):  
Total Concentration ◽  
Bacterial Species ◽  
Locomotor Behavior ◽  
Host Cells ◽  
Individual Species ◽  
Zebrafish Model ◽  
Associated Bacteria ◽  
Larval Zebrafish ◽  
Toxicological Studies ◽  
Community Complexity

Abstract Background Across taxa, animals with depleted intestinal microbiomes show disrupted behavioral phenotypes. Axenic (i.e., microbe-free) mice, zebrafish, and fruit flies exhibit increased locomotor behavior, or hyperactivity. The mechanism through which bacteria interact with host cells to trigger normal neurobehavioral development in larval zebrafish is not well understood. Here, we monoassociated zebrafish with either one of six different zebrafish-associated bacteria, mixtures of these host-associates, or with an environmental bacterial isolate. Results As predicted, the axenic cohort was hyperactive. Monoassociation with three different host-associated bacterial species, as well as with the mixtures, resulted in control-like locomotor behavior. Monoassociation with one host-associate and the environmental isolate resulted in the hyperactive phenotype characteristic of axenic larvae, while monoassociation with two other host-associated bacteria partially blocked this phenotype. Furthermore, we found an inverse relationship between the total concentration of bacteria per larvae and locomotor behavior. Lastly, in the axenic and associated cohorts, but not in the larvae with complex communities, we detected unexpected bacteria, some of which may be present as facultative predators. Conclusions These data support a growing body of evidence that individual species of bacteria can have different effects on host behavior, potentially related to their success at intestinal colonization. Specific to the zebrafish model, our results suggest that differences in the composition of microbes in fish facilities could affect the results of behavioral assays within pharmacological and toxicological studies.

scholarly journals T6SS Mediated Stress Responses for Bacterial Environmental Survival and Host Adaptation

2021 ◽  
Vol 22 (2) ◽  
pp. 478
Author(s):  
Kai-Wei Yu ◽  
Peng Xue ◽  
Yang Fu ◽  
Liang Yang
Keyword(s):  
Protein Secretion ◽  
Stress Responses ◽  
Current Knowledge ◽  
Bacterial Species ◽  
Host Cells ◽  
Interspecies Interactions ◽  
Type Vi Secretion System ◽  
Membrane Complex ◽  
Type Vi Secretion ◽  
Bacterial Type

The bacterial type VI secretion system (T6SS) is a protein secretion apparatus widely distributed in Gram-negative bacterial species. Many bacterial pathogens employ T6SS to compete with the host and to coordinate the invasion process. The T6SS apparatus consists of a membrane complex and an inner tail tube-like structure that is surrounded by a contractile sheath and capped with a spike complex. A series of antibacterial or antieukaryotic effectors is delivered by the puncturing device consisting of a Hcp tube decorated by the VgrG/PAAR complex into the target following the contraction of the TssB/C sheath, which often leads to damage and death of the competitor and/or host cells. As a tool for protein secretion and interspecies interactions, T6SS can be triggered by many different mechanisms to respond to various physiological conditions. This review summarizes our current knowledge of T6SS in coordinating bacterial stress responses against the unfavorable environmental and host conditions.

scholarly journals Legionella pneumophila DotU and IcmF Are Required for Stability of the Dot/Icm Complex

2004 ◽  
Vol 72 (10) ◽  
pp. 5983-5992 ◽  
Author(s):  
Jessica A. Sexton ◽  
Jennifer L. Miller ◽  
Aki Yoneda ◽  
Thomas E. Kehl-Fie ◽  
Joseph P. Vogel
Keyword(s):  
Cell Surface ◽  
Legionella Pneumophila ◽  
Bacterial Species ◽  
Wide Distribution ◽  
Host Cells ◽  
Growth Defect ◽  
Intracellular Growth ◽  
Homologous Proteins ◽  
Type Iv ◽  
Cell Surface Structure

ABSTRACT Legionella pneumophila utilizes a type IV secretion system (T4SS) encoded by 26 dot/icm genes to replicate inside host cells and cause disease. In contrast to all other L. pneumophila dot/icm genes, dotU and icmF have homologs in a wide variety of gram-negative bacteria, none of which possess a T4SS. Instead, dotU and icmF orthologs are linked to a locus encoding a conserved cluster of proteins designated IcmF-associated homologous proteins, which has been proposed to constitute a novel cell surface structure. We show here that dotU is partially required for L. pneumophila intracellular growth, similar to the known requirement for icmF. In addition, we show that dotU and icmF are necessary for optimal plasmid transfer and sodium sensitivity, two additional phenotypes associated with a functional Dot/Icm complex. We found that these effects are due to the destabilization of the T4SS at the transition into the stationary phase, the point at which L. pneumophila becomes virulent. Specifically, three Dot proteins (DotH, DotG, and DotF) exhibit decreased stability in a ΔdotU ΔicmF strain. Furthermore, overexpression of just one of these proteins, DotH, is sufficient to suppress the intracellular growth defect of the ΔdotU ΔicmF mutant. This suggests a model where the DotU and IcmF proteins serve to prevent DotH degradation and therefore function to stabilize the L. pneumophila T4SS. Due to their wide distribution among bacterial species and their genetic linkage to known or predicted cell surface structures, we propose that this function in complex stabilization may be broadly conserved.

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