Evaluation of the combined antibiotics exposure using the simulator of human intestinal microbial ecosystem (SHIME)

Abstract Background: Antibiotics are emerging toxic contaminant that have potential public health risk worldwide, which also would cause human intestinal microbial disorder and develop multiple human diseases. However, to date, the combination effects of antibiotics on human intestinal microbiota dysbiosis and related health risk are not fully understood. Moreover, there is limited information on using probiotics or synbiotics for restoration of intestinal microbiome affected by antibiotics. Therefore, this study evaluated the in vitro ability of combined effects of amoxicillin (Amx) and gentamycin (Gen), and the restoration effects of probiotics or synbiotics on ARGs as well as human disease-related pathways in the simulated human gut.Results: This study indicated that the combination exposure of Amx and Gen was confirmed to promote the increase of most ARGs and the disease-related pathways, which may be better restored by probiotics treatment. The results of the alpha diversity of the combined antibiotics exposure or the recovery microbial community showed no difference from the control. However, the beta diversity results indicated their differences, and the ascending colon sample recovered better under natural condition while the descending colon sample recovered better after probiotics treatment. Combination effects on the genetic level might attribute to microbiota shift, which were explained well by the phenomenon that Escherichia/Shigella was positively associated with the ARGs, and Klebsiella and Escherichia/Shigella were positively related to the human disease-related pathways.Conclusion: These results might be valuable to direct the future work and opened up new perspectives to address the direct effects of combine antibiotics on the intestinal microbiota and find a promising strategy to restore the antibiotics associated dysbiosis of gut microbiota.

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Human gut microbiota evaluation and comparation after the separate or combined antibiotics exposure using the simulator of human intestinal microbial ecosystem (SHIME)

10.21203/rs.3.rs-34434/v1 ◽

2020 ◽

Author(s):

Lei Liu ◽

Ranjit Das ◽

Pengcheng Suo ◽

Huai Lin ◽

Hongmei Qi ◽

...

Keyword(s):

Gut Microbiota ◽

Health Risk ◽

Intestinal Microbiota ◽

Human Disease ◽

Combined Treatment ◽

Antibiotic Resistance Genes ◽

Human Gut ◽

Combination Effects ◽

Combination Antibiotics

Abstract Background A cocktail of drugs is an emerging toxic contaminant that has potential public health risk worldwide, which also would cause human intestinal microbial disorder and develop multiple human diseases. However, to date, the combination effects of antibiotics cocktail on human intestinal microbiota dysbiosis and related health risk are not fully understood. Therefore, for the first time, this study evaluated and compared the in vitro ability of amoxicillin (AMX) and polymyxin E (POL) used separately or combined on antibiotic resistance genes (ARGs) as well as human disease-related pathways in the simulated human gut. Results This study indicated that the combination exposure of POL with AMX reduced the occurrence of drug resistance in the gut microbiota caused by single antibiotic treatment. However, in comparison with the separate use of AMX and POL, the combined treatment exhibited a significantly higher ability to increase the human disease-related pathways. The combination effects on genetic level might attribute to microbiota shift, as co-occurrence patterns suggested that Bifidobacterium attributed to ARGs increasing in the POL treatment group and Enterobacter played a crucial role in human disease-related pathways enrichment after combination treatment. Conclusion These results may open up new perspectives for assessing the direct effects of combination antibiotics on the intestinal microbiota. These suggested side-effects should be considered for a combination of antibiotics prescription.

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Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome

Microbiome ◽

10.1186/s40168-020-00981-z ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Hannes Petruschke ◽

Christian Schori ◽

Sebastian Canzler ◽

Sarah Riesbeck ◽

Anja Poehlein ◽

...

Keyword(s):

Microbial Communities ◽

Intestinal Microbiota ◽

De Novo ◽

Bacterial Species ◽

Intestinal Microbiome ◽

Single Strain ◽

Small Proteins ◽

Human Intestinal Microbiota ◽

Wide Range

Abstract Background The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. Results We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx. Conclusions We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract.

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Impact of Chronic Tetracycline Exposure on Human Intestinal Microbiota in a Continuous Flow Bioreactor Model

Antibiotics ◽

10.3390/antibiotics10080886 ◽

2021 ◽

Vol 10 (8) ◽

pp. 886

Author(s):

Youngbeom Ahn ◽

Ji Young Jung ◽

Ohgew Kweon ◽

Brian T. Veach ◽

Sangeeta Khare ◽

...

Keyword(s):

Molecular Analysis ◽

Intestinal Microbiota ◽

Continuous Flow ◽

Antimicrobial Drug ◽

Bioreactor Culture ◽

Analysis Techniques ◽

Human Intestinal Microbiota ◽

Traditional Cultures ◽

The Impact

Studying potential dietary exposure to antimicrobial drug residues via meat and dairy products is essential to ensure human health and consumer safety. When studying how antimicrobial residues in food impact the development of antimicrobial drug resistance and disrupt normal bacteria community structure in the intestine, there are diverse methodological challenges to overcome. In this study, traditional cultures and molecular analysis techniques were used to determine the effects of tetracycline at chronic subinhibitory exposure levels on human intestinal microbiota using an in vitro continuous flow bioreactor. Six bioreactor culture vessels containing human fecal suspensions were maintained at 37 °C for 7 days. After a steady state was achieved, the suspensions were dosed with 0, 0.015, 0.15, 1.5, 15, or 150 µg/mL tetracycline, respectively. Exposure to 150 µg/mL tetracycline resulted in a decrease of total anaerobic bacteria from 1.9 × 107 ± 0.3 × 107 down to 2 × 106 ± 0.8 × 106 CFU/mL. Dose-dependent effects of tetracycline were noted for perturbations of tetB and tetD gene expression and changes in acetate and propionate concentrations. Although no-observed-adverse-effect concentrations differed, depending on the traditional cultures and the molecular analysis techniques used, this in vitro continuous flow bioreactor study contributes to the knowledge base regarding the impact of chronic exposure of tetracycline on human intestinal microbiota.

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The Modulatory Effect of Anthocyanins from Purple Sweet Potato on Human Intestinal Microbiota in Vitro

Journal of Agricultural and Food Chemistry ◽

10.1021/acs.jafc.6b00586 ◽

2016 ◽

Vol 64 (12) ◽

pp. 2582-2590 ◽

Cited By ~ 49

Author(s):

Xin Zhang ◽

Yang Yang ◽

Zufang Wu ◽

Peifang Weng

Keyword(s):

Sweet Potato ◽

Intestinal Microbiota ◽

Human Intestinal Microbiota ◽

Purple Sweet Potato

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Fermentation in vitro of EGCG, GCG and EGCG3"Me isolated from Oolong tea by human intestinal microbiota

Food Research International ◽

10.1016/j.foodres.2013.10.005 ◽

2013 ◽

Vol 54 (2) ◽

pp. 1589-1595 ◽

Cited By ~ 57

Author(s):

Xin Zhang ◽

Xiuling Zhu ◽

Yongkang Sun ◽

Bing Hu ◽

Yi Sun ◽

...

Keyword(s):

Intestinal Microbiota ◽

Oolong Tea ◽

Human Intestinal Microbiota

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In vitro extraction and fermentation of polyphenols from grape seeds (Vitis vinifera) by human intestinal microbiota

Food & Function ◽

10.1039/c6fo00032k ◽

2016 ◽

Vol 7 (4) ◽

pp. 1959-1967 ◽

Cited By ~ 26

Author(s):

Li Zhou ◽

Wei Wang ◽

Jun Huang ◽

Yu Ding ◽

Zhouqiang Pan ◽

...

Keyword(s):

Vitis Vinifera ◽

Intestinal Microbiota ◽

Extraction Yield ◽

Liquid Extraction ◽

Pressurized Liquid Extraction ◽

Grape Seeds ◽

Total Polyphenols ◽

Human Intestinal Microbiota

The effects of several parameters on the extraction yield of total polyphenols from grape seeds by pressurized liquid extraction were investigated.

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In Vitro Bioconversion of Polyphenols from Black Tea and Red Wine/Grape Juice by Human Intestinal Microbiota Displays Strong Interindividual Variability

Journal of Agricultural and Food Chemistry ◽

10.1021/jf101475m ◽

2010 ◽

Vol 58 (18) ◽

pp. 10236-10246 ◽

Cited By ~ 113

Author(s):

Gabriele Gross ◽

Doris M. Jacobs ◽

Sonja Peters ◽

Sam Possemiers ◽

John van Duynhoven ◽

...

Keyword(s):

Intestinal Microbiota ◽

Red Wine ◽

Interindividual Variability ◽

Grape Juice ◽

Black Tea ◽

Wine Grape ◽

Human Intestinal Microbiota

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Chemical profiling of root bark extract from Oplopanax elatus and its in vitro biotransformation by human intestinal microbiota

PeerJ ◽

10.7717/peerj.12513 ◽

2021 ◽

Vol 9 ◽

pp. e12513

Author(s):

Jin-Yi Wan ◽

Jing-Xuan Wan ◽

Shilei Wang ◽

Xiaolu Wang ◽

Wenqian Guo ◽

...

Keyword(s):

Intestinal Microbiota ◽

Ultra Performance Liquid Chromatography ◽

Bark Extract ◽

Chemical Components ◽

Root Bark ◽

Chemical Profiling ◽

Human Intestinal Microbiota ◽

Oplopanax Elatus ◽

Main Components

Oplopanax elatus (Nakai) Nakai, in the Araliaceae family, has been used in traditional Chinese medicine (TCM) to treat diseases as an adaptogen for thousands of years. This study established an ultra-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry (UPLC-Q-TOF/MS) method to identify chemical components and biotransformation metabolites of root bark extract from O. elatus. A total of 18 compounds were characterized in O. elatus extract, and 62 metabolites by human intestinal microbiota were detected. Two polyynes, falcarindiol and oplopandiol were recognized as the main components of O. elatus, whose metabolites are further illustrated. Several metabolic pathways were proposed to generate the detected metabolites, including methylation, hydrogenation, demethylation, dehydroxylation, and hydroxylation. These findings indicated that intestinal microbiota might play an essential role in mediating the bioactivity of O. elatus.

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