scholarly journals Dissecting the collateral damage of antibiotics on gut microbes

2020 ◽  
Author(s):  
Lisa Maier ◽  
Camille V. Goemans ◽  
Mihaela Pruteanu ◽  
Jakob Wirbel ◽  
Michael Kuhn ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Bacteria ◽  
Commensal Bacteria ◽  
Strong Impact ◽  
Collateral Damage ◽  
Microbiota Composition ◽  
Human Gut ◽  
Gut Microbes ◽  
Species Specific ◽  
Gut Microbiota Composition

AbstractAntibiotics are used for fighting pathogens, but also target our commensal bacteria as a side effect, disturbing the gut microbiota composition and causing dysbiosis and disease1-3. Despite this well-known collateral damage, the activity spectrum of the different antibiotic classes on gut bacteria remains poorly characterized. Having monitored the activities of >1,000 marketed drugs on 38 representative species of the healthy human gut microbiome4, we here characterize further the 144 antibiotics therein, representing all major classes. We determined >800 Minimal Inhibitory Concentrations (MICs) and extended the antibiotic profiling to 10 additional species to validate these results and link to available data on antibiotic breakpoints for gut microbes. Antibiotic classes exhibited distinct inhibition spectra, including generation-dependent effects by quinolones and phylogeny-independence by β-lactams. Macrolides and tetracyclines, two prototypic classes of bacteriostatic protein synthesis inhibitors, inhibited almost all commensals tested. We established that both kill different subsets of prevalent commensal bacteria, and cause cell lysis in specific cases. This species-specific activity challenges the long-standing divide of antibiotics into bactericidal and bacteriostatic, and provides a possible explanation for the strong impact of macrolides on the gut microbiota composition in animals5-8 and humans9-11. To mitigate the collateral damage of macrolides and tetracyclines on gut commensals, we exploited the fact that drug combinations have species-specific outcomes in bacteria12 and sought marketed drugs, which could antagonize the activity of these antibiotics in abundant gut commensal species. By screening >1,000 drugs, we identified several such antidotes capable of protecting gut species from these antibiotics without compromising their activity against relevant pathogens. Altogether, this study broadens our understanding of antibiotic action on gut commensals, uncovers a previously unappreciated and broad bactericidal effect of prototypical bacteriostatic antibiotics on gut bacteria, and opens avenues for preventing the collateral damage caused by antibiotics on human gut commensals.

Changes in Human Gut Microbiota Composition Are Linked to the Energy Metabolic Switch During Ten Days of Fasting

2019 ◽  
Author(s):  
Robin Mesnage ◽  
Franziska Grundler ◽  
Andreas Schwiertz ◽  
Yvon Le Maho ◽  
Françoise Wilhelmi de Toledo
Keyword(s):  
Gut Microbiota ◽  
Microbiota Composition ◽  
Human Gut ◽  
Metabolic Switch ◽  
Human Gut Microbiota ◽  
Gut Microbiota Composition

scholarly journals Sex differences in the phylum‐level human gut microbiota composition

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Alexander Koliada ◽  
Vladislav Moseiko ◽  
Mariana Romanenko ◽  
Oleh Lushchak ◽  
Nadiia Kryzhanovska ◽  
...  
Keyword(s):  
Sex Differences ◽  
Gut Microbiota ◽  
Age Groups ◽  
Microbiota Composition ◽  
Human Gut ◽  
Cross Sectional ◽  
Total N ◽  
Human Gut Microbiota ◽  
Gut Microbiota Composition

Abstract Background Evidence was previously provided for sex-related differences in the human gut microbiota composition, and sex-specific discrepancy in hormonal profiles was proposed as a main determinant of these differences. On the basis of these findings, the assumption was made on the role of microbiota in the sexual dimorphism of human diseases. To date, sex differences in fecal microbiota were demonstrated primarily at lower taxonomic levels, whereas phylum-level differences between sexes were reported in few studies only. In the present population-based cross-sectional research, sex differences in the phylum-level human gut microbiota composition were identified in a large (total n = 2301) sample of relatively healthy individuals from Ukraine. Results Relative abundances of Firmicutes and Actinobacteria, as determined by qRT-PCR, were found to be significantly increased, while that of Bacteroidetes was significantly decreased in females compared to males. The Firmicutes to Bacteroidetes (F/B) ratio was significantly increased in females compared to males. Females had 31 % higher odds of having F/B ratio more than 1 than males. This trend was evident in all age groups. The difference between sexes was even more pronounced in the elder individuals (50+): in this age group, female participants had 56 % higher odds of having F/B ratio > 1 than the male ones. Conclusions In conclusion, sex-specific differences in the phylum-level intestinal microbiota composition were observed in the Ukraine population. The F/B ratio was significantly increased in females compared to males. Further investigation is needed to draw strong conclusions regarding the mechanistic basis for sex-specific differences in the gut microbiota composition and regarding the role of these differences in the initiation and progression of human chronic diseases.

scholarly journals Effects of phlorotannin and polysaccharide fractions of brown seaweed Silvetia compressa on human gut microbiota composition using an in vitro colonic model

2021 ◽  
Vol 84 ◽  
pp. 104596
Author(s):  
Benjamín Vázquez-Rodríguez ◽  
Liliana Santos-Zea ◽  
Erick Heredia-Olea ◽  
Laura Acevedo-Pacheco ◽  
Arlette Santacruz ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Brown Seaweed ◽  
Microbiota Composition ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Gut Microbiota Composition

scholarly journals Analysis of Human Gut Microbiota Composition Associated to the Presence of Commensal and Pathogen Microorganisms in Côte d’Ivoire

2021 ◽  
Vol 9 (8) ◽  
pp. 1763
Author(s):  
Veronica Di Cristanziano ◽  
Fedja Farowski ◽  
Federica Berrilli ◽  
Maristella Santoro ◽  
David Di Cave ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Cote D'ivoire ◽  
Côte D’Ivoire ◽  
Enteric Pathogens ◽  
Microbiota Composition ◽  
Human Gut ◽  
Cote D’Ivoire ◽  
Human Gut Microbiota ◽  
Côte D'ivoire ◽  
Gut Microbiota Composition

Background: The human gut microbiota is a microbial ecosystem contributing to the maintenance of host health with functions related to immune and metabolic aspects. Relations between microbiota and enteric pathogens in sub-Saharan Africa are scarcely investigated. The present study explored gut microbiota composition associated to the presence of common enteric pathogens and commensal microorganisms, e.g., Blastocystis and Entamoeba species, in children and adults from semi-urban and non-urban localities in Côte d’Ivoire. Methods: Seventy-six stool samples were analyzed for microbiota composition by 16S rRDNA sequencing. The presence of adeno-, entero-, parechoviruses, bacterial and protozoal pathogens, Blastocystis, and commensal Entamoeba species, was analyzed by different molecular assays. Results: Twelve individuals resulted negative for any tested microorganisms, 64 subjects were positive for one or more microorganisms. Adenovirus, enterovirus, enterotoxigenic Escherichia coli (ETEC), and Blastocystis were frequently detected. Conclusions: The bacterial composition driven by Prevotellaceae and Ruminococcaceae confirmed the biotype related to the traditional dietary and cooking practices in low-income countries. Clear separation in UniFrac distance in subjects co-harboring Entamoeba hartmanni and Blastocystis was evidenced. Alpha diversity variation in negative control group versus only Blastocystis positive suggested its possible regulatory contribution on intestinal microbiota. Pathogenic bacteria and virus did not affect the positive outcome of co-harbored Blastocystis.

The effect of various diets on the human gut microbiota composition

2021 ◽  
Vol 70 (7) ◽  
pp. 5-10
Author(s):  
K.A. Aitbaev ◽  
I.T. Murkamilov ◽  
V.V. Fomin ◽  
Zh.A. Murkamilova ◽  
I.O. Kudaibergenova ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbiota Composition ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Gut Microbiota Composition

scholarly journals Shifts in the gut microbiota structure caused by Helicobacter pylori eradication therapy

2018 ◽  
Author(s):  
Evgenii I. Olekhnovich ◽  
Alexander I. Manolov ◽  
Nikita A. Prianichniikov ◽  
Andrei E. Samoilov ◽  
Maja V. Malakhova ◽  
...  
Keyword(s):  
Duodenal Ulcer ◽  
Antibiotic Resistance ◽  
Gut Microbiota ◽  
Eradication Therapy ◽  
Microbiota Composition ◽  
Human Gut ◽  
Metabolic Potential ◽  
Health And Disease ◽  
Gut Microbiota Composition ◽  
Microbiota Structure

AbstractThe human gut microbiome plays an important role both in health and disease. The use of antibiotics can alter gut microbiota composition, which can cause complications of various kinds. Here we report a whole genome sequencing metagenomic study of the intestinal microbiota changes caused by Helicobacter pylori eradication therapy. We have found the decrease in taxonomic alpha-diversity due to the therapy. The changes observed were more extensive for patients with duodenal ulcer and female ones. As well across the patients under the therapy we have detected the shifts in the metabolic potential and resistome. Seven KEGG pathways associated with quorum sensing, genetic Information processing and environmental Information processing were increased, while metabolic pathways related with metabolism of cofactors and vitamins and glycan biosynthesis and metabolism decreased. Changes in the resistome profile have also been identified. We observed perturbations in intraspecies structures, which were higher in group of patients under the therapy than in control group of people without treatment. The Eubacterium rectale pangenome extracted from metagenomic data were changed. We also isolated and sequenced Enterococcus faecium strains from two patients before and after eradication therapy. After the therapy this bacterium increased as the antibiotic resistance in vitro, as well the number of ARGs to macrolides and tetracyclines and metagenomic relative abundance in comparison with strains before therapy. In summary, microbial community demonstrated shift to reduce metabolic potential and to increased mechanisms, which mediate more survival condition through intraspecies perturbations.ImportanceThe human gut microbiome plays an important role both in health and disease. The use of antibiotics can alter gut microbiota composition, which can cause complications of various kinds. H. pylori eradication therapy causes multiple shifts and alterations (including intraspecies changes) of the intestinal microbiota structure and leads to the accumulation of genes which determine resistance to macrolides. Since these changes are not the same for patients with various diseases, patients with duodenal ulcer may be further paid special attention for reducing side effects, such as antibiotic-induced dysbiosis. Also, study of antibiotic treatment in terms of its impact upon the human gut microbiota allows shedding light on of the complex processes that cause accumulation and spread of antibiotic resistance. An identification and understanding of these complicated processes may help to constrain antibiotic resistance spread, which is of great importance for human health care.

scholarly journals Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model

Nutrients ◽  
2017 ◽  
Vol 9 (6) ◽  
pp. 533 ◽  
Author(s):  
Athanasios Koutsos ◽  
Maria Lima ◽  
Lorenza Conterno ◽  
Mattia Gasperotti ◽  
Martina Bianchi ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbiota Composition ◽  
Human Gut ◽  
Apple Varieties ◽  
Human Gut Microbiota ◽  
Metabolic Output ◽  
Gut Microbiota Composition

scholarly journals A Bayesian Negative Binomial Hierarchical Model for Identifying Diet–Gut Microbiome Associations

2021 ◽  
Vol 12 ◽  
Author(s):  
Alma Revers ◽  
Xiang Zhang ◽  
Aeilko H. Zwinderman
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Phylogenetic Relationships ◽  
Negative Binomial ◽  
Urban Setting ◽  
Microbiota Composition ◽  
Human Gut ◽  
Bayesian Hierarchical ◽  
Gut Microbiota Composition

The human gut microbiota composition plays an important role in human health. Long-term diet intervention may shape human gut microbiome. Therefore, many studies focus on discovering links between long-term diets and gut microbiota composition. This study aimed to incorporate the phylogenetic relationships between the operational taxonomic units (OTUs) into the diet-microbe association analysis, using a Bayesian hierarchical negative binomial (NB) model. We regularized the dispersion parameter of the negative binomial distribution by assuming a mean-dispersion association. A simulation study showed that, if over-dispersion is present in the microbiome data, our approach performed better in terms of mean squared error (MSE) of the slope-estimates compared to the standard NB regression model or a Bayesian hierarchical NB model without including the phylogenetic relationships. Data of the Healthy Life in an Urban Setting (HELIUS) study showed that for some phylogenetic families the (posterior) variances of the slope-estimates were decreasing when including the phylogenetic relationships into the analyses. In contrast, when OTUs of the same family were not similarly affected by the food item, some bias was introduced, leading to larger (posterior) variances of the slope-estimates. Overall, the Bayesian hierarchical NB model, with a dependency between the mean and dispersion parameters, proved to be a robust method for analyzing diet-microbe associations.

The effect of diet on the fluctuations of human gut microbiota

MedPharmRes ◽  
2019 ◽  
Vol 3 (1) ◽  
pp. 22-24
Author(s):  
Binh Nguyen
Keyword(s):  
Individual Differences ◽  
Gut Microbiota ◽  
Microbiota Composition ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
The Individual ◽  
Gut Microbiota Composition

It was previously thought that the establishment of the gut microbiota was completed within the first two years of life, and this community maintains fairly stable throughout the adult lifetime thereafter. However, recent evidence shows that the gut microbiota composition is constantly changing in the gut environment and is heavily influenced by diet. The individual differences responding to diets would root on the fluctuations of gut microbiota if dietary fluctuations affect the composition of gut microbiota so significantly.

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