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

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

10.21203/rs.3.rs-46837/v1 ◽

2020 ◽

Author(s):

Lei Liu ◽

Hongmei Qi ◽

Pengcheng Suo ◽

Huai Lin ◽

Siyi Wang ◽

...

Keyword(s):

Health Risk ◽

Intestinal Microbiota ◽

Human Disease ◽

Alpha Diversity ◽

Intestinal Microbiome ◽

Limited Information ◽

Combination Effects ◽

Human Intestinal Microbiota ◽

Future Work

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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Evaluation of Gentamicin Exposure Effects on Human gut Microbiota using the Simulator of Human Intestinal Microbial Ecosystem (SHIME)

10.21203/rs.3.rs-41489/v1 ◽

2020 ◽

Author(s):

Lei Liu ◽

Hongmei Qi ◽

Pengcheng Suo ◽

Siyi Wang ◽

Huai Lin ◽

...

Keyword(s):

Gut Microbiota ◽

Human Disease ◽

Intestinal Flora ◽

Antibiotic Resistance Genes ◽

Intestinal Bacteria ◽

Resistant Bacteria ◽

Human Gut ◽

Exogenous Bacteria ◽

The Moment

Abstract Background: Antibiotics are emerging toxic contaminant that have potential public health risk worldwide. They may cause the human intestinal microbial disorder, as well as the spreading of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Most of the intestinal bacteria are not cultivable for the moment, tracking the special gene-labeled plasmid from the exogenous bacteria would help obtain the direct evidence of the horizontal transfer of ARGs in the intestinal flora. However, to date, there are only a few research reports applying the exogenous labeled bacteria to study the transfer of ARGs among intestinal bacteria. Therefore, for the first time, this study evaluated the in vitro ability of gentamicin on colonization of exogenous bacteria and plasmid in the simulated human gut. Results: This study indicated that exposure to gentamicin may be conducive to the colonization of exogenous bacteria and plasmid, as well as the conjugation of plasmid to gut microbiota. Gentamicin exposure was also confirmed to reduce the gene numbers of human disease-related pathways and promote the drug resistance in the gut microbiota. The effects on the genetic level might attribute to microbiota shift, as co-occurrence patterns suggested that Bacteroides attributed to the ARGs enrichment and Klebsiella played a crucial role in human disease-related pathways reduction after gentamicin treatment. Conclusion: These results may open up new perspectives for assessing the direct effects of antibiotics on the intestinal microbiota. These suggested side-effects should be considered for antibiotics prescription.

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Intestinal Microbiota Composition Modulates Choline Bioavailability from Diet and Accumulation of the Proatherogenic Metabolite Trimethylamine-N-Oxide

mBio ◽

10.1128/mbio.02481-14 ◽

2015 ◽

Vol 6 (2) ◽

Cited By ~ 254

Author(s):

Kymberleigh A. Romano ◽

Eugenio I. Vivas ◽

Daniel Amador-Noguez ◽

Federico E. Rey

Keyword(s):

Gut Microbiota ◽

Intestinal Microbiota ◽

Human Life ◽

Water Soluble ◽

Human Gut ◽

Choline Intake ◽

Low Levels ◽

And Function ◽

Dietary Choline

ABSTRACT Choline is a water-soluble nutrient essential for human life. Gut microbial metabolism of choline results in the production of trimethylamine (TMA), which upon absorption by the host is converted in the liver to trimethylamine-N-oxide (TMAO). Recent studies revealed that TMAO exacerbates atherosclerosis in mice and positively correlates with the severity of this disease in humans. However, which microbes contribute to TMA production in the human gut, the extent to which host factors (e.g., genotype) and diet affect TMA production and colonization of these microbes, and the effects TMA-producing microbes have on the bioavailability of dietary choline remain largely unknown. We screened a collection of 79 sequenced human intestinal isolates encompassing the major phyla found in the human gut and identified nine strains capable of producing TMA from choline in vitro. Gnotobiotic mouse studies showed that TMAO accumulates in the serum of animals colonized with TMA-producing species, but not in the serum of animals colonized with intestinal isolates that do not generate TMA from choline in vitro. Remarkably, low levels of colonization by TMA-producing bacteria significantly reduced choline levels available to the host. This effect was more pronounced as the abundance of TMA-producing bacteria increased. Our findings provide a framework for designing strategies aimed at changing the representation or activity of TMA-producing bacteria in the human gut and suggest that the TMA-producing status of the gut microbiota should be considered when making recommendations about choline intake requirements for humans. IMPORTANCE Cardiovascular disease (CVD) is the leading cause of death and disability worldwide, and increased trimethylamine N-oxide (TMAO) levels have been causally linked with CVD development. This work identifies members of the human gut microbiota responsible for both the accumulation of trimethylamine (TMA), the precursor of the proatherogenic compound TMAO, and subsequent decreased choline bioavailability to the host. Understanding how to manipulate the representation and function of choline-consuming, TMA-producing species in the intestinal microbiota could potentially lead to novel means for preventing or treating atherosclerosis and choline deficiency-associated diseases.

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I-screen: In Vitro Platform Containing Ex Vivo Human Gut Microbiota to Study Compound Metabolism through Intestinal Microbiota

10.26226/morressier.57d6b2b9d462b8028d88ecd7 ◽

2016 ◽

Author(s):

Evita van de Steeg

Keyword(s):

Gut Microbiota ◽

Intestinal Microbiota ◽

Ex Vivo ◽

Human Gut ◽

Human Gut Microbiota

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Arsenic in Rice Bran Products: In Vitro Oral Bioaccessibility, Arsenic Transformation by Human Gut Microbiota, and Human Health Risk Assessment

Journal of Agricultural and Food Chemistry ◽

10.1021/acs.jafc.9b02008 ◽

2019 ◽

Vol 67 (17) ◽

pp. 4987-4994 ◽

Cited By ~ 10

Author(s):

Naiyi Yin ◽

Pengfei Wang ◽

Yan Li ◽

Huili Du ◽

Xiaochen Chen ◽

...

Keyword(s):

Risk Assessment ◽

Gut Microbiota ◽

Health Risk ◽

Human Health ◽

Rice Bran ◽

Human Health Risk ◽

Human Gut ◽

Oral Bioaccessibility ◽

Arsenic Transformation

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In vitro study of the interaction between human gut microbiota and herbal extracts using willow bark extract as an example

Planta Medica ◽

10.1055/s-0036-1596386 ◽

2016 ◽

Vol 81 (S 01) ◽

pp. S1-S381

Author(s):

EM Pferschy-Wenzig ◽

K Koskinen ◽

C Moissl-Eichinger ◽

R Bauer

Keyword(s):

Gut Microbiota ◽

In Vitro Study ◽

Vitro Study ◽

Bark Extract ◽

Herbal Extracts ◽

Human Gut ◽

Human Gut Microbiota ◽

Willow Bark

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Metabolization of the herbal combination STW-5 by human gut microbiota in vitro

10.1055/s-0037-1608399 ◽

2017 ◽

Author(s):

EM Pferschy-Wenzig ◽

A Roßmann ◽

K Koskinen ◽

H Abdel-Aziz ◽

C Moissl-Eichinger ◽

...

Keyword(s):

Gut Microbiota ◽

Human Gut ◽

Human Gut Microbiota

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Preservation of Human Gut Microbiota Inoculums for In Vitro Fermentations Studies

Fermentation ◽

10.3390/fermentation7010014 ◽

2021 ◽

Vol 7 (1) ◽

pp. 14

Author(s):

Nelson Mota de Carvalho ◽

Diana Luazi Oliveira ◽

Mayra Anton Dib Saleh ◽

Manuela Pintado ◽

Ana Raquel Madureira

Keyword(s):

Gut Microbiota ◽

Metabolic Profile ◽

Bacterial Count ◽

Glycerol Solution ◽

Metabolic Profiles ◽

Human Gut ◽

Colonic Fermentation ◽

In Vitro Fermentation ◽

Fecal Samples

The use of fecal inoculums for in vitro fermentation models requires a viable gut microbiota, capable of fermenting the unabsorbed nutrients. Fresh samples from human donors are used; however, the availability of fresh fecal inoculum and its inherent variability is often a problem. This study aimed to optimize a method of preserving pooled human fecal samples for in vitro fermentation studies. Different conditions and times of storage at −20 °C were tested. In vitro fermentation experiments were carried out for both fresh and frozen inoculums, and the metabolic profile compared. In comparison with the fresh, the inoculum frozen in a PBS and 30% glycerol solution, had a significantly lower (p < 0.05) bacterial count (<1 log CFU/mL). However, no significant differences (p < 0.05) were found between the metabolic profiles after 48 h. Hence, a PBS and 30% glycerol solution can be used to maintain the gut microbiota viability during storage at −20 °C for at least 3 months, without interfering with the normal course of colonic fermentation.

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Wheat cell walls and constituent polysaccharides induce similar microbiota profiles upon in vitro fermentation despite different short chain fatty acid end-product levels.

Food & Function ◽

10.1039/d0fo02509g ◽

2021 ◽

Author(s):

Shiyi Lu ◽

Deirdre Mikkelsen ◽

Hong Yao ◽

Barbara Williams ◽

Bernadine Flanagan ◽

...

Keyword(s):

Fatty Acid ◽

Gut Microbiota ◽

Plant Cell ◽

Cell Walls ◽

Short Chain Fatty Acid ◽

Chain Fatty Acid ◽

Plant Cell Walls ◽

Human Gut ◽

In Vitro Fermentation

Plant cell walls as well as their component polysaccharides in foods can be utilized to alter and maintain a beneficial human gut microbiota, but it is not known whether the...

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