Vancomycin exposure caused opportunistic pathogens bloom in intestinal microbiome by simulator of the human intestinal microbial ecosystem (SHIME)

Liu, Lei; Wang, Qing; Wu, Xin‐Yan; Qi, Hongmei; Das, Ranjit; Lin, Hongtao; Shi, Jingliang; Wang, Siyi; Yang, Jing; Xue, Yingang; Mao, Daqing; Luo, Yi

doi:10.1016/j.envpol.2020.114399

Cited by 33 publications

(35 citation statements)

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“…Our unpublished data also revealed that inulin could restore the alpha diversity and beta diversity of the intestinal ora well. Our previous research also carried out a comparison of the restoration effects between natural condition with fecal bacteria transplantation [36]. In that study, after vancomycin exposure or restoration, the richness, evenness and diversity of microbial communities were indistinguishable from control, which was similar as this study.…”

Section: The Restoration Effects Of Probiotics and Synbiotics On Micrsupporting

confidence: 82%

“…For in vivo studies, highest percentage of Proteobacteria had also been observed in fecal samples from healthy human and animals [34,35]. Our previous in vitro studies also discovered this phenomenon [36,37]. At the genus level, it has been veri ed in our previous study that after Amx exposure, Bacteroides and Klebsiella were enriched in the intestinal ora, while the abundance of Bi dobacterium was reduced [37].…”

Section: Discussionmentioning

confidence: 73%

“…Our previous study showed that the abundance of Klebsiella in the intestinal ora indeed reduced in natural recovery condition, while compared with initial control group, the decrease of Bi dobacterium and the increase of Klebsiella and Bacteroides caused by Amx exposure were still obvious [37]. Our previous research also compared the recovery effects of natural condition with fecal bacteria transplantation, which indicated that the changes in intestinal ora caused by vancomycin exposure did not recover to the initial state while the recovery effects of fecal bacteria transplantation were obvious [36]. The above studies suggested that prebiotics, probiotics and fecal bacteria were effective in restoring the composition of the intestinal ora affected by antibiotics exposure.…”

Section: Discussionmentioning

confidence: 92%

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

Liu¹,

Qi²,

Suo³

et al. 2020

Preprint

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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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Section: The Restoration Effects Of Probiotics and Synbiotics On Micrsupporting

confidence: 82%

Section: Discussionmentioning

confidence: 73%

Section: Discussionmentioning

confidence: 92%

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

Liu¹,

Qi²,

Suo³

et al. 2020

Preprint

Self Cite

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show abstract

“…The effects of antibiotics on alpha diversity, the taxon richness (Chao1 index), evenness (Simpson index), and diversity (Shannon index) were calculated for all the samples as previous did [91,92]. Linear discriminant analysis effect size (LEfSe) was performed to determine bacterial taxa that were signi cantly differed between the six groups using the Galaxy application tool [93].…”

Section: S Rrna Gene Sequencing and Analysismentioning

confidence: 99%

“…High-throughput-qPCR reactions were performed using the Wafergen SmartChip Real-time PCR system as previous did [91,92]. The reactions were conducted by Anhui MicroAnaly Gene Technologies Co., Ltd (Anhui, China).…”

Section: High-throughput Quantitative Pcr (Ht-qpcr) and Analysismentioning

confidence: 99%

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

Liu¹,

Das²,

Suo³

et al. 2020

Preprint

Self Cite

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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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The role of bacterial metabolism in human gut colonization

Muñoz-Cazalla,

de Quinto,

Álvaro-Llorente

et al. 2024

Int Microbiol

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Can we anticipate the emergence of the next pandemic antibiotic-resistant bacterial clone? Addressing such an ambitious question relies on our ability to comprehensively understand the ecological and epidemiological factors fostering the evolution of high-risk clones. Among these factors, the ability to persistently colonize and thrive in the human gut is crucial for most high-risk clones. Nonetheless, the causes and mechanisms facilitating successful gut colonization remain obscure. Here, we review recent evidence that suggests that bacterial metabolism plays a pivotal role in determining the ability of high-risk clones to colonize the human gut. Subsequently, we outline novel approaches that enable the exploration of microbial metabolism at an unprecedented scale and level of detail. A thorough understanding of the constraints and opportunities of bacterial metabolism in gut colonization will foster our ability to predict the emergence of high-risk clones and take appropriate containment strategies.

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Vancomycin exposure caused opportunistic pathogens bloom in intestinal microbiome by simulator of the human intestinal microbial ecosystem (SHIME)

Cited by 33 publications

References 50 publications

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

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

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

The role of bacterial metabolism in human gut colonization

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